diff --git a/binarycpython/tests/test_grid.py b/binarycpython/tests/test_grid.py
index 2d1d9b0feb323ad6b9ac52db6ade2ded48a05cf1..f5692ea0c463b2d350d71400204b443496ca0471 100644
--- a/binarycpython/tests/test_grid.py
+++ b/binarycpython/tests/test_grid.py
@@ -102,7 +102,7 @@ class test_Population(unittest.TestCase):
"""
test_pop = Population()
- test_pop.set(amt_cores=2, verbosity=TEST_VERBOSITY)
+ test_pop.set(num_cores=2, verbosity=TEST_VERBOSITY)
test_pop.set(M_1=10)
test_pop.set(data_dir="/tmp/binary_c_python")
test_pop.set(ensemble_filter_SUPERNOVAE=1, ensemble_dt=1000)
@@ -115,7 +115,7 @@ class test_Population(unittest.TestCase):
self.assertTrue(test_pop.bse_options["ensemble_filter_SUPERNOVAE"] == 1)
#
- self.assertTrue(test_pop.grid_options["amt_cores"] == 2)
+ self.assertTrue(test_pop.grid_options["num_cores"] == 2)
def test_cmdline(self):
with Capturing() as output:
@@ -132,8 +132,9 @@ class test_Population(unittest.TestCase):
# make a dummy cmdline arg input
sys.argv = [
"script",
- "--cmdline",
- "metallicity=0.0002 amt_cores=2 data_dir=/tmp/binary_c_python",
+ "metallicity=0.0002",
+ "num_cores=2",
+ "data_dir=/tmp/binary_c_python",
]
# Set up population
@@ -148,8 +149,8 @@ class test_Population(unittest.TestCase):
self.assertTrue(test_pop.bse_options["metallicity"] == "0.0002")
# Amt cores
- self.assertTrue(isinstance(test_pop.grid_options["amt_cores"], int))
- self.assertTrue(test_pop.grid_options["amt_cores"] == 2)
+ self.assertTrue(isinstance(test_pop.grid_options["num_cores"], int))
+ self.assertTrue(test_pop.grid_options["num_cores"] == 2)
# datadir
self.assertTrue(isinstance(test_pop.custom_options["data_dir"], str))
@@ -242,7 +243,7 @@ class test_Population(unittest.TestCase):
test_pop = Population()
test_pop.set(metallicity=0.02, verbosity=TEST_VERBOSITY)
test_pop.set(M_1=10)
- test_pop.set(amt_cores=2)
+ test_pop.set(num_cores=2)
test_pop.set(data_dir="/tmp")
population_settings = test_pop.return_population_settings()
@@ -252,7 +253,7 @@ class test_Population(unittest.TestCase):
self.assertTrue(population_settings["bse_options"]["M_1"] == 10)
self.assertIn("grid_options", population_settings)
- self.assertTrue(population_settings["grid_options"]["amt_cores"] == 2)
+ self.assertTrue(population_settings["grid_options"]["num_cores"] == 2)
self.assertIn("custom_options", population_settings)
self.assertTrue(population_settings["custom_options"]["data_dir"] == "/tmp")
@@ -341,7 +342,7 @@ class test_Population(unittest.TestCase):
test_pop.set(metallicity=0.02, verbosity=TEST_VERBOSITY)
test_pop.set(M_1=10)
- test_pop.set(amt_cores=2)
+ test_pop.set(num_cores=2)
test_pop.set(data_dir=TMP_DIR)
# datadir
@@ -469,7 +470,7 @@ class test_Population(unittest.TestCase):
Printf("TEST_CUSTOM_LOGGING_1 %30.12e %g %g %g %g\\n",
//
stardata->model.time, // 1
-
+
// masses
stardata->common.zero_age.mass[0], //
stardata->common.zero_age.mass[1], //
@@ -534,7 +535,7 @@ class test_grid_evolve(unittest.TestCase):
test_pop_evolve_1_thread = Population()
test_pop_evolve_1_thread.set(
- amt_cores=1, M_2=1, orbital_period=100000, verbosity=TEST_VERBOSITY
+ num_cores=1, M_2=1, orbital_period=100000, verbosity=TEST_VERBOSITY
)
resolution = {"M_1": 10}
@@ -573,7 +574,7 @@ class test_grid_evolve(unittest.TestCase):
test_pop = Population()
test_pop.set(
- amt_cores=2, M_2=1, orbital_period=100000, verbosity=TEST_VERBOSITY
+ num_cores=2, M_2=1, orbital_period=100000, verbosity=TEST_VERBOSITY
)
resolution = {"M_1": 10}
@@ -611,13 +612,13 @@ class test_grid_evolve(unittest.TestCase):
"""
data_dir_value = os.path.join(TMP_DIR, "grid_tests")
- amt_cores_value = 2
+ num_cores_value = 2
custom_logging_string = 'Printf("MY_STELLAR_DATA_TEST_EXAMPLE %g %g %g %g\\n",((double)stardata->model.time),((double)stardata->star[0].mass),((double)stardata->model.probability),((double)stardata->model.dt));'
test_pop = Population()
test_pop.set(
- amt_cores=amt_cores_value,
+ num_cores=num_cores_value,
verbosity=TEST_VERBOSITY,
M_2=1,
orbital_period=100000,
@@ -651,7 +652,7 @@ class test_grid_evolve(unittest.TestCase):
analytics["population_name"], thread_id
),
)
- for thread_id in range(amt_cores_value)
+ for thread_id in range(num_cores_value)
]
for output_name in output_names:
@@ -675,7 +676,7 @@ class test_grid_evolve(unittest.TestCase):
test_pop = Population()
test_pop.set(
- amt_cores=2, M_2=1, orbital_period=100000, verbosity=TEST_VERBOSITY
+ num_cores=2, M_2=1, orbital_period=100000, verbosity=TEST_VERBOSITY
)
# Set the amt of failed systems that each thread will log
@@ -686,7 +687,7 @@ Exit_binary_c(BINARY_C_NORMAL_EXIT, "testing exits. This is part of the testing,
Printf("TEST_CUSTOM_LOGGING_1 %30.12e %g %g %g %g\\n",
//
stardata->model.time, // 1
-
+
// masses
stardata->common.zero_age.mass[0], //
stardata->common.zero_age.mass[1], //
@@ -730,7 +731,7 @@ Printf("TEST_CUSTOM_LOGGING_1 %30.12e %g %g %g %g\\n",
test_pop = Population()
test_pop.set(
- amt_cores=2, M_2=1, orbital_period=100000, verbosity=TEST_VERBOSITY
+ num_cores=2, M_2=1, orbital_period=100000, verbosity=TEST_VERBOSITY
)
test_pop.set(failed_systems_threshold=4)
test_pop.set(C_logging_code=CUSTOM_LOGGING_STRING_WITH_EXIT)
@@ -784,7 +785,7 @@ Printf("TEST_CUSTOM_LOGGING_1 %30.12e %g %g %g %g\\n",
test_pop = Population()
test_pop.set(
- amt_cores=1, M_2=1, orbital_period=100000, verbosity=TEST_VERBOSITY
+ num_cores=1, M_2=1, orbital_period=100000, verbosity=TEST_VERBOSITY
)
resolution = {"M_1": 10}
@@ -800,11 +801,11 @@ Printf("TEST_CUSTOM_LOGGING_1 %30.12e %g %g %g %g\\n",
"""
data_dir_value = TMP_DIR
- amt_cores_value = 2
+ num_cores_value = 2
test_pop = Population()
test_pop.set(
- amt_cores=amt_cores_value,
+ num_cores=num_cores_value,
verbosity=TEST_VERBOSITY,
M_2=1,
orbital_period=100000,
@@ -845,7 +846,7 @@ Printf("TEST_CUSTOM_LOGGING_1 %30.12e %g %g %g %g\\n",
analytics["population_name"], thread_id
),
)
- for thread_id in range(amt_cores_value)
+ for thread_id in range(num_cores_value)
]
for output_name in output_names:
@@ -874,11 +875,11 @@ Printf("TEST_CUSTOM_LOGGING_1 %30.12e %g %g %g %g\\n",
"""
data_dir_value = TMP_DIR
- amt_cores_value = 2
+ num_cores_value = 2
test_pop = Population()
test_pop.set(
- amt_cores=amt_cores_value,
+ num_cores=num_cores_value,
verbosity=TEST_VERBOSITY,
M_2=1,
orbital_period=100000,
@@ -931,12 +932,12 @@ Printf("TEST_CUSTOM_LOGGING_1 %30.12e %g %g %g %g\\n",
"""
data_dir_value = TMP_DIR
- amt_cores_value = 2
+ num_cores_value = 2
# First
test_pop_1 = Population()
test_pop_1.set(
- amt_cores=amt_cores_value,
+ num_cores=num_cores_value,
verbosity=TEST_VERBOSITY,
M_2=1,
orbital_period=100000,
@@ -975,7 +976,7 @@ Printf("TEST_CUSTOM_LOGGING_1 %30.12e %g %g %g %g\\n",
# second
test_pop_2 = Population()
test_pop_2.set(
- amt_cores=amt_cores_value,
+ num_cores=num_cores_value,
verbosity=TEST_VERBOSITY,
M_2=1,
orbital_period=100000,
@@ -1016,7 +1017,7 @@ Printf("TEST_CUSTOM_LOGGING_1 %30.12e %g %g %g %g\\n",
analytics_2["population_name"], thread_id
),
)
- for thread_id in range(amt_cores_value)
+ for thread_id in range(num_cores_value)
]
ensemble_output_2 = {}
@@ -1073,7 +1074,7 @@ def parse_function_adding_results(self, output):
#
if not len(parameters) == len(values):
- print("Amount of column names isnt equal to amount of columns")
+ print("Number of column names isnt equal to number of columns")
raise ValueError
# record the probability of this line (Beware, this is meant to only be run once for each system. its a controls quantity)
@@ -1095,7 +1096,7 @@ class test_resultdict(unittest.TestCase):
if (stardata->model.time < stardata->model.max_evolution_time)
{
Printf("EXAMPLE_OUTPUT %30.16e %g %g %30.12e %d\\n",
- //
+ //
stardata->model.time, // 1
stardata->star[0].mass, // 2
stardata->common.zero_age.mass[0], // 3
@@ -1112,7 +1113,7 @@ class test_resultdict(unittest.TestCase):
example_pop.set(
max_evolution_time=15000, # bse_options
# grid_options
- amt_cores=3,
+ num_cores=3,
tmp_dir=TMP_DIR,
# Custom options
data_dir=os.path.join(TMP_DIR, "test_resultdict"), # custom_options
diff --git a/binarycpython/tests/test_grid_options_defaults.py b/binarycpython/tests/test_grid_options_defaults.py
index ce9ad4adf5fe31e9282fd4608182eb063bd26412..18291f2eed88a878fe165e889d8fc42b717e8f15 100644
--- a/binarycpython/tests/test_grid_options_defaults.py
+++ b/binarycpython/tests/test_grid_options_defaults.py
@@ -35,7 +35,7 @@ class test_grid_options_defaults(unittest.TestCase):
result_1 = grid_options_help(input_1)
self.assertEqual(result_1, {}, msg="Dict should be empty")
- input_2 = "amt_cores"
+ input_2 = "num_cores"
result_2 = grid_options_help(input_2)
self.assertIn(
input_2,
diff --git a/binarycpython/utils/distribution_functions.py b/binarycpython/utils/distribution_functions.py
index caf505f5951662ce579fe771e694c48bd3f88dbe..9fbb263cb31b303fd464f41f02686c6e6fa76558 100644
--- a/binarycpython/utils/distribution_functions.py
+++ b/binarycpython/utils/distribution_functions.py
@@ -1132,7 +1132,7 @@ def Moe_di_Stefano_2017_multiplicity_fractions(options, verbosity=0):
Moecache["rinterpolator_multiplicity"] = py_rinterpolate.Rinterpolate(
table=Moecache["multiplicity_table"], # Contains the table of data
nparams=1, # logM1
- ndata=4, # The amount of datapoints (the parameters that we want to interpolate)
+ ndata=4, # The number of datapoints (the parameters that we want to interpolate)
verbosity=verbosity - (_MS_VERBOSITY_INTERPOLATOR_LEVEL - 1),
)
diff --git a/binarycpython/utils/functions.py b/binarycpython/utils/functions.py
index 2db16b859d5c6e7bf87d2b95f0a1a78b3f9eefd2..9ae916850edec972b58c977bcb4c4fd2fd1f1a72 100644
--- a/binarycpython/utils/functions.py
+++ b/binarycpython/utils/functions.py
@@ -1716,7 +1716,7 @@ def inspect_dict(
def count_keys_recursive(input_dict):
"""
- Function to count the total amount of keys in a dictionary
+ Function to count the total number of keys in a dictionary
"""
local_count = 0
diff --git a/binarycpython/utils/grid.py b/binarycpython/utils/grid.py
index 37e0bf0b9bf197e491472883b612fa5030f87a0b..5d096f4f7b3d550c42e31ec2d3e90174690aba25 100644
--- a/binarycpython/utils/grid.py
+++ b/binarycpython/utils/grid.py
@@ -298,8 +298,6 @@ class Population:
# get the cmd-line args in the form x=y
cmdline_args = sys.argv[1:]
- # How its set up now is that as input you need to give --cmdline "metallicity=0.002"
- # Its checked if this exists and handled accordingly.
if cmdline_args:
verbose_print(
"Found cmdline args. Parsing them now",
@@ -515,7 +513,7 @@ class Population:
Examples:
range = [math.log(m_min), math.log(m_max)]
resolution:
- Resolution of the sampled range (amount of samples).
+ Resolution of the sampled range (number of samples).
TODO: check if this is used anywhere
Examples:
@@ -895,7 +893,7 @@ class Population:
# array to store memory use per-thread
mem = 1.0 * mem_use()
self.shared_memory["memory_use_per_thread"] = multiprocessing.Array(
- "d", [mem] * self.grid_options["amt_cores"]
+ "d", [mem] * self.grid_options["num_cores"]
)
def clean(self) -> None:
@@ -1026,7 +1024,7 @@ class Population:
self.grid_options["_end_time_evolution"]
- self.grid_options["_start_time_evolution"],
self.grid_options["_total_starcount"],
- self.grid_options["amt_cores"],
+ self.grid_options["num_cores"],
),
self.grid_options["verbosity"],
0,
@@ -1080,7 +1078,7 @@ class Population:
return stream_logger
- def _system_queue_filler(self, job_queue, amt_cores):
+ def _system_queue_filler(self, job_queue, num_cores):
"""
Function that is responsible for keeping the queue filled.
@@ -1130,7 +1128,7 @@ class Population:
if self.grid_options["verbosity"] >= _LOGGER_VERBOSITY_LEVEL:
stream_logger.debug(f"Signaling stop to processes") # DEBUG
- for _ in range(amt_cores):
+ for _ in range(num_cores):
job_queue.put("STOP")
def _evolve_population_grid(self):
@@ -1139,7 +1137,7 @@ class Population:
First we set up the multiprocessing manager and the job and result queue.
- Then we spawn <self.grid_options["amt_cores"]> amount of process instances,
+ Then we spawn <self.grid_options["num_cores"]> number of process instances,
and signal them to start.
While the processes are waiting for their instructions, we start the queue filler,
@@ -1159,11 +1157,16 @@ class Population:
# Set up the manager object that can share info between processes
manager = multiprocessing.Manager()
job_queue = manager.Queue(maxsize=self.grid_options["max_queue_size"])
- result_queue = manager.Queue(maxsize=self.grid_options["amt_cores"])
+
+ # backwards compatibility
+ if "amt_cores" in self.grid_options:
+ self.grid_options["num_cores"] = self.grid_options["amt_cores"]
+
+ result_queue = manager.Queue(maxsize=self.grid_options["num_cores"])
# Create process instances
processes = []
- for ID in range(self.grid_options["amt_cores"]):
+ for ID in range(self.grid_options["num_cores"]):
processes.append(
multiprocessing.Process(
target=self._process_run_population_grid,
@@ -1176,7 +1179,7 @@ class Population:
p.start()
# Set up the system_queue
- self._system_queue_filler(job_queue, amt_cores=self.grid_options["amt_cores"])
+ self._system_queue_filler(job_queue, num_cores=self.grid_options["num_cores"])
# Join the processes
for p in processes:
@@ -2066,7 +2069,7 @@ class Population:
Function that generates the code from which the population will be made.
dry_run: when True, it will return the starcount at the end so that we know
- what the total amount of systems is.
+ what the total number of systems is.
The phasevol values are handled by generating a second array
@@ -2614,9 +2617,9 @@ class Population:
"# Factor the multiplicity fraction into the probability\n",
"probability = probability * self._calculate_multiplicity_fraction(parameter_dict)"
+ "\n",
- # Add division by amount of repeats
+ # Add division by number of repeats
"\n",
- "# Divide the probability by the amount of repeats\n",
+ "# Divide the probability by the number of repeats\n",
'probability = probability / self.grid_options["repeat"]' + "\n",
# Now we yield the system self.grid_options["repeat"] times.
"\n",
@@ -2702,7 +2705,6 @@ class Population:
print_freq = 10
# Calculate amount of time left
-
# calculate amount of time passed
# time_passed = time.time() - self.grid_options["_start_time_evolution"]
@@ -2735,7 +2737,7 @@ class Population:
###################################################
def _dry_run_source_file(self):
"""
- Function to go through the source_file and count the amount of lines and the total probability
+ Function to go through the source_file and count the number of lines and the total probability
"""
system_generator = self.grid_options["_system_generator"]
@@ -2889,7 +2891,7 @@ class Population:
# python_details = get_python_details()
# scriptname = path_of_calling_script()
# command = "{} {}".format(python_details["executable"], scriptname)
- # command += ' --cmdline "{}"'.format(
+ # command += '{}'.format(
# " ".join(
# [
# "{}".format(self.grid_options["_commandline_input"]),
@@ -3463,7 +3465,7 @@ class Population:
def _increment_count(self):
"""
- Function to add to the total amount of stars. For now not used
+ Function to add to the total number of stars. For now not used
"""
self.grid_options["_count"] += 1
@@ -3520,7 +3522,7 @@ class Population:
0,
)
- # Keep track of the amount of failed systems and their error codes
+ # Keep track of the number of failed systems and their error codes
self.grid_options["_failed_prob"] += system_dict["probability"]
self.grid_options["_failed_count"] += 1
self.grid_options["_errors_found"] = True
@@ -3548,14 +3550,14 @@ class Population:
1,
)
- # Check if we have exceeded the amount of errors
+ # Check if we have exceeded the number of errors
if (
self.grid_options["_failed_count"]
> self.grid_options["failed_systems_threshold"]
):
if not self.grid_options["_errors_exceeded"]:
verbose_print(
- "Process {} exceeded the maximum ({}) amount of failing systems. Stopped logging them to files now".format(
+ "Process {} exceeded the maximum ({}) number of failing systems. Stopped logging them to files now".format(
self.process_ID,
self.grid_options["failed_systems_threshold"],
),
@@ -4471,7 +4473,7 @@ eccentricity3=0
now: the time now as a UNIX-style epoch in seconds (float)
system_number: the system number
- TODO: add information about the amount of cores. the TPR shows the dt/dn but i want to see the amt per core too
+ TODO: add information about the number of cores. the TPR shows the dt/dn but i want to see the number per core too
"""
# calculate estimated time of arrive (eta and eta_secs), time per run (tpr)
@@ -4498,6 +4500,7 @@ eccentricity3=0
eta, units, tpr, eta_secs = trem(
dt, system_number, dn, self.grid_options["_total_starcount"]
)
+ tpr *= self.grid_options['num_cores']
if eta_secs < secs_per_day:
fintime = time.localtime(now + eta_secs)
diff --git a/binarycpython/utils/grid_options_defaults.py b/binarycpython/utils/grid_options_defaults.py
index 065d2412703c3aac854fdecdf6baa20caead6aa9..8e4435201d5d74c85a358fd2384a1a763a4f22db 100644
--- a/binarycpython/utils/grid_options_defaults.py
+++ b/binarycpython/utils/grid_options_defaults.py
@@ -29,7 +29,7 @@ grid_options_defaults_dict = {
##########################
# general (or unordered..)
##########################
- "amt_cores": 1, # total amount of cores used to evolve the population
+ "num_cores": 1, # total number of cores used to evolve the population
"parse_function": None, # Function to parse the output with.
"multiplicity_fraction_function": 0, # Which multiplicity fraction function to use. 0: None, 1: Arenou 2010, 2: Rhagavan 2010, 3: M&S 2017
"tmp_dir": temp_dir(), # Setting the temp dir of the program
@@ -160,7 +160,7 @@ grid_options_defaults_dict = {
# "slurm_jobid": "", # slurm job id (%A)
# "slurm_memory": 512, # in MB, the memory use of the job
# "slurm_warn_max_memory": 1024, # in MB : warn if mem req. > this
- # "slurm_use_all_node_CPUs": 0, # 1 = use all of a node's CPUs. 0 = use a given amount of CPUs
+ # "slurm_use_all_node_CPUs": 0, # 1 = use all of a node's CPUs. 0 = use a given number of CPUs
# "slurm_postpone_join": 0, # if 1 do not join on slurm, join elsewhere. want to do it off the slurm grid (e.g. with more RAM)
# "slurm_jobarrayindex": "", # slurm job array index (%a)
# "slurm_jobname": "binary_grid", # default
@@ -450,17 +450,17 @@ grid_options_descriptions = {
"_binary_c_shared_library": "Full path to the libbinary_c file. This options is not used in the population object",
"verbosity": "Verbosity of the population code. Default is 0, by which only errors will be printed. Higher values will show more output, which is good for debugging.",
"binary": "Set this to 1 if the population contains binaries. Input: int", # TODO: write what effect this has.
- "amt_cores": "The amount of cores that the population grid will use. The multiprocessing is useful but make sure to figure out how many logical cores the machine has. The core is multi processed, not multi threaded, and will gain no extra speed when amt_cores exceeds the amount of logical cores. Input: int",
+ "num_cores": "The number of cores that the population grid will use. The multiprocessing is useful but make sure to figure out how many logical cores the machine has (use e.g. psutil.cpu_count(logical=False) to find the true number of cores, psutil.cpu_count(logical=True) to find the number of logical cores). The core is multi processed, not multi threaded, and will gain no extra speed when num_cores exceeds the number of logical cores. Input: int",
"_start_time_evolution": "Variable storing the start timestamp of the population evolution. Set by the object itself.", # TODO: make sure this is logged to a file
"_end_time_evolution": "Variable storing the end timestamp of the population evolution. Set by the object itself", # TODO: make sure this is logged to a file
- "_total_starcount": "Variable storing the total amount of systems in the generator. Used and set by the population object.",
+ "_total_starcount": "Variable storing the total number of systems in the generator. Used and set by the population object.",
"_custom_logging_shared_library_file": "filename for the custom_logging shared library. Used and set by the population object",
"_errors_found": "Variable storing a Boolean flag whether errors by binary_c are encountered.",
- "_errors_exceeded": "Variable storing a Boolean flag whether the amount of errors was higher than the set threshold (failed_systems_threshold). If True, then the command line arguments of the failing systems will not be stored in the failed_system_log files.",
+ "_errors_exceeded": "Variable storing a Boolean flag whether the number of errors was higher than the set threshold (failed_systems_threshold). If True, then the command line arguments of the failing systems will not be stored in the failed_system_log files.",
"source_file_filename": "Variable containing the source file containing lines of binary_c command line calls. These all have to start with binary_c.", # TODO: Expand
"C_auto_logging": "Dictionary containing parameters to be logged by binary_c. The structure of this dictionary is as follows: the key is used as the headline which the user can then catch. The value at that key is a list of binary_c system parameters (like star[0].mass)",
"C_logging_code": "Variable to store the exact code that is used for the custom_logging. In this way the user can do more complex logging, as well as putting these logging strings in files.",
- "_failed_count": "Variable storing the amount of failed systems.",
+ "_failed_count": "Variable storing the number of failed systems.",
"_evolution_type_options": "List containing the evolution type options.",
"_failed_prob": "Variable storing the total probability of all the failed systems",
"_failed_systems_error_codes": "List storing the unique error codes raised by binary_c of the failed systems",
@@ -477,7 +477,7 @@ grid_options_descriptions = {
"_probtot": "Total probability of the population.", # TODO: check whether this is used properly throughout
"_main_pid": "Main process ID of the master process. Used and set by the population object.",
"_store_memaddr": "Memory address of the store object for binary_c.",
- "failed_systems_threshold": "Variable storing the maximum amount of systems that are allowed to fail before logging their command line arguments to failed_systems log files",
+ "failed_systems_threshold": "Variable storing the maximum number of systems that are allowed to fail before logging their command line arguments to failed_systems log files",
"parse_function": "Function that the user can provide to handle the output the binary_c. This function has to take the arguments (self, output). Its best not to return anything in this function, and just store stuff in the self.grid_results dictionary, or just output results to a file",
"condor": "Int flag whether to use a condor type population evolution. Not implemented yet.", # TODO: describe this in more detail
"slurm": "Int flag whether to use a Slurm type population evolution.", # TODO: describe this in more detail
@@ -716,7 +716,7 @@ def grid_options_description_checker(print_info: bool = True) -> int:
print_info: whether to print out information about which options contain proper descriptions and which do not
Returns:
- the amount of undescribed keys
+ the number of undescribed keys
"""
# Get the keys
diff --git a/binarycpython/utils/spacing_functions.py b/binarycpython/utils/spacing_functions.py
index 4ef7271526c0cd48eecb52ce38e60d5948acd7ac..563ca859e4e373b00f3d54ab1c880bfbceb5f016 100644
--- a/binarycpython/utils/spacing_functions.py
+++ b/binarycpython/utils/spacing_functions.py
@@ -190,7 +190,7 @@ def const_dt(self,
# we want to use the right number of CPU cores
lifetime_population.set(
do_dry_run = False,
- amt_cores = self.grid_options['amt_cores'],
+ num_cores = self.grid_options['num_cores'],
max_stellar_type_1=10
)
diff --git a/docs/Doxygen/Doxyfile b/docs/Doxygen/Doxyfile
index a1933d48d24194103f50f2b463d6f60354784b6f..38a51360cabadb149c105b1e4344d745928e3747 100644
--- a/docs/Doxygen/Doxyfile
+++ b/docs/Doxygen/Doxyfile
@@ -63,7 +63,7 @@ OUTPUT_DIRECTORY =
# If the CREATE_SUBDIRS tag is set to YES then doxygen will create 4096 sub-
# directories (in 2 levels) under the output directory of each output format and
# will distribute the generated files over these directories. Enabling this
-# option can be useful when feeding doxygen a huge amount of source files, where
+# option can be useful when feeding doxygen a huge number of source files, where
# putting all generated files in the same directory would otherwise causes
# performance problems for the file system.
# The default value is: NO.
@@ -1255,7 +1255,7 @@ HTML_DYNAMIC_SECTIONS = NO
# shown in the various tree structured indices initially; the user can expand
# and collapse entries dynamically later on. Doxygen will expand the tree to
# such a level that at most the specified number of entries are visible (unless
-# a fully collapsed tree already exceeds this amount). So setting the number of
+# a fully collapsed tree already exceeds this number). So setting the number of
# entries 1 will produce a full collapsed tree by default. 0 is a special value
# representing an infinite number of entries and will result in a full expanded
# tree by default.
@@ -2288,7 +2288,7 @@ UML_LOOK = NO
# number of items for each type to make the size more manageable. Set this to 0
# for no limit. Note that the threshold may be exceeded by 50% before the limit
# is enforced. So when you set the threshold to 10, up to 15 fields may appear,
-# but if the number exceeds 15, the total amount of fields shown is limited to
+# but if the number exceeds 15, the total number of fields shown is limited to
# 10.
# Minimum value: 0, maximum value: 100, default value: 10.
# This tag requires that the tag HAVE_DOT is set to YES.
diff --git a/docs/build/doctrees/binary_c_parameters.doctree b/docs/build/doctrees/binary_c_parameters.doctree
index 95b8f7090e04fa0459582c8d43f09c730a2d45a3..e1e95ff8ea4c0c1ca1e3701c78918753b3bcb203 100644
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diff --git a/docs/build/doctrees/custom_logging_functions.doctree b/docs/build/doctrees/custom_logging_functions.doctree
index 2baedf88c0674787690b0e452b62a95a58a06441..aca2eeb0dea1f0649562bd61794b8e83c5bada0e 100644
Binary files a/docs/build/doctrees/custom_logging_functions.doctree and b/docs/build/doctrees/custom_logging_functions.doctree differ
diff --git a/docs/build/doctrees/distribution_functions.doctree b/docs/build/doctrees/distribution_functions.doctree
index a5f832e6551b727b5e2b85396944895cb9f40287..2dde764f2f0402f7c12dd8a30f15271ccc7dcaf4 100644
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diff --git a/docs/build/doctrees/environment.pickle b/docs/build/doctrees/environment.pickle
index 61181afdb4f5e62b0fa4b32c33d50998e3a99a0a..89f94bfa08e92f32431ec9aea9092b519515620c 100644
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diff --git a/docs/build/doctrees/example_notebooks.doctree b/docs/build/doctrees/example_notebooks.doctree
index a352e95a0d22a41b8f80e39ff4308c96db027b27..92026e4a035a287faa06fcceec0cc552a0817014 100644
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diff --git a/docs/build/doctrees/functions.doctree b/docs/build/doctrees/functions.doctree
index cd805d6b1cd93d5e9d46d6ef07f6497939a92505..c83b5db2e08accb69c11de36d83177c99f03ce50 100644
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diff --git a/docs/build/doctrees/grid.doctree b/docs/build/doctrees/grid.doctree
index e45c1acb9e1a01e68fe24b85a89f17f67c85a0c8..aa0c85d22105af075276438b0668e17980857622 100644
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diff --git a/docs/build/doctrees/grid_options_defaults.doctree b/docs/build/doctrees/grid_options_defaults.doctree
index a30f5c4df06312a6b3100c35e328ecc52d10ce2b..7eb900ee2c434bca0bd069e7791e48cbfde05489 100644
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diff --git a/docs/build/doctrees/grid_options_descriptions.doctree b/docs/build/doctrees/grid_options_descriptions.doctree
index 1e8841878b5416327ae4627ab83e4c39cc365b98..03c9aee903ed9caa64edd89d6d9257bbe55a4a7c 100644
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diff --git a/docs/build/doctrees/hpc_functions.doctree b/docs/build/doctrees/hpc_functions.doctree
index 4fcafc7f3b5df064761c1d4e79a39e2b745defa0..7fcbe014b6430ac625a8babeafe7280e20d02c61 100644
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diff --git a/docs/build/doctrees/index.doctree b/docs/build/doctrees/index.doctree
index 05f3ff5a58b6c27b26dbd1fa53daec18af13fac6..5a8255bc65869d79a8aa11db2c72e06a5e99bd27 100644
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diff --git a/docs/build/doctrees/modules.doctree b/docs/build/doctrees/modules.doctree
index e39ddcdbc7468db4e520ea49e532ac855e217618..8d5a8bd603d315bbeff31ade64c06a3edc3a0267 100644
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diff --git a/docs/build/doctrees/nbsphinx/notebook_HRD.ipynb b/docs/build/doctrees/nbsphinx/notebook_HRD.ipynb
index 52590f8a2a6abc7245e9ea0c08d274432cd2a1ad..bf95d554d2125de449ec4b8404550132e06091f7 100644
--- a/docs/build/doctrees/nbsphinx/notebook_HRD.ipynb
+++ b/docs/build/doctrees/nbsphinx/notebook_HRD.ipynb
@@ -264,7 +264,7 @@
"## Evolving the grid\n",
"Now that we configured all the main parts of the population object, we can actually run the population! Doing this is straightforward: `population.evolve()`\n",
"\n",
- "This will start up the processing of all the systems. We can control how many cores are used by settings `amt_cores`. By setting the `verbosity` of the population object to a higher value we can get a lot of verbose information about the run, but for now we will set it to 0.\n",
+ "This will start up the processing of all the systems. We can control how many cores are used by settings `num_cores`. By setting the `verbosity` of the population object to a higher value we can get a lot of verbose information about the run, but for now we will set it to 0.\n",
"\n",
"There are many grid_options that can lead to different behaviour of the evolution of the grid. Please do have a look at those: [grid options docs](https://ri0005.pages.surrey.ac.uk/binary_c-python/grid_options_descriptions.html), and try "
]
@@ -300,7 +300,7 @@
" # verbose output is not required \n",
" verbosity=0,\n",
" # set number of threads (i.e. number of CPU cores we use)\n",
- " amt_cores=4,\n",
+ " num_cores=4,\n",
" )\n",
"\n",
"# Evolve the population - this is the slow, number-crunching step\n",
@@ -796,7 +796,7 @@
],
"metadata": {
"kernelspec": {
- "display_name": "Python 3",
+ "display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
@@ -810,7 +810,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
- "version": "3.6.4"
+ "version": "3.9.5"
}
},
"nbformat": 4,
diff --git a/docs/build/doctrees/nbsphinx/notebook_common_envelope_evolution.ipynb b/docs/build/doctrees/nbsphinx/notebook_common_envelope_evolution.ipynb
index 526320ccf954c1ed86c6d5c641204c4a9345bbe5..feb6b18e6a264b08eab1e52d639106123f494cf5 100644
--- a/docs/build/doctrees/nbsphinx/notebook_common_envelope_evolution.ipynb
+++ b/docs/build/doctrees/nbsphinx/notebook_common_envelope_evolution.ipynb
@@ -363,7 +363,7 @@
"metadata": {},
"source": [
"## Evolving the grid\n",
- "Now we actually run the population. This may take a little while. You can set amt_cores higher if you have a powerful machine."
+ "Now we actually run the population. This may take a little while. You can set num_cores higher if you have a powerful machine."
]
},
{
@@ -378,7 +378,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "adding: amt_cores=4 to grid_options\n",
+ "adding: num_cores=4 to grid_options\n",
"Creating and loading custom logging functionality\n",
"Generating grid code\n",
"Generating grid code\n",
@@ -540,7 +540,7 @@
"# set number of threads\n",
"population.set(\n",
" # set number of threads (i.e. number of CPU cores we use)\n",
- " amt_cores=4,\n",
+ " num_cores=4,\n",
" )\n",
"\n",
"# Evolve the population - this is the slow, number-crunching step\n",
@@ -686,7 +686,7 @@
],
"metadata": {
"kernelspec": {
- "display_name": "Python 3",
+ "display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
@@ -700,7 +700,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
- "version": "3.6.4"
+ "version": "3.9.5"
}
},
"nbformat": 4,
diff --git a/docs/build/doctrees/nbsphinx/notebook_individual_systems.ipynb b/docs/build/doctrees/nbsphinx/notebook_individual_systems.ipynb
index 85aef1e3962a1626f37a9ef36bf5e16f479eb68e..50c604385e0365b3404fb8d6427b9b9f0c0f7fbf 100644
--- a/docs/build/doctrees/nbsphinx/notebook_individual_systems.ipynb
+++ b/docs/build/doctrees/nbsphinx/notebook_individual_systems.ipynb
@@ -8,19 +8,22 @@
"# Tutorial: Running individual systems with binary_c-python\n",
"This notebook will show you how to run single systems and analyze their results.\n",
"\n",
- "It can be useful to have some functions to quickly run a single system to e.g. inspect what evolutionary steps a specific system goes through, to plot the mass loss evolution of a single star, etc. "
+ "It can be useful to have some functions to quickly run a single system to, for example, inspect what evolutionary steps a specific system goes through, to plot the mass loss evolution of a single system, etc. "
]
},
{
"cell_type": "markdown",
"id": "dd5d9ec7-5791-45f1-afbd-225947e2a583",
- "metadata": {},
+ "metadata": {
+ "tags": []
+ },
"source": [
- "## Single system with run_wrapper\n",
+ "## Single system with run_system_wrapper\n",
+ "\n",
"The simplest method to run a single system is to use the run_system wrapper. This function deals with setting up the argument string, makes sure all the required parameters are included and handles setting and cleaning up the custom logging functionality (see notebook_custom_logging).\n",
"\n",
"As arguments to this function we can add any of the parameters that binary_c itself actually knows, as well as:\n",
- "- custom_logging_code: string containing a print statement that binary_c can use to print information\n",
+ "- custom_logging_code: string containing a Printf statement that binary_c can use to print information\n",
"- log_filename: path of the logfile that binary_c generates\n",
"- parse_function: function that handles parsing the output of binary-c"
]
@@ -86,7 +89,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- " TIME M1 M2 K1 K2 SEP PER ECC R1/ROL1 R2/ROL2 TYPE RANDOM_SEED=17089 RANDOM_COUNT=0\n",
+ " TIME M1 M2 K1 K2 SEP PER ECC R1/ROL1 R2/ROL2 TYPE RANDOM_SEED=12122 RANDOM_COUNT=0\n",
" 0.0000 1.000 0.000 1 15 -1 -1 -1.00 0.000 0.000 \"INITIAL \"\n",
" 11003.1302 1.000 0.000 2 15 -1 -1 -1.00 0.000 0.000 \"OFF_MS\"\n",
" 11003.1302 1.000 0.000 2 15 -1 -1 -1.00 0.000 0.000 \"TYPE_CHNGE\"\n",
@@ -225,18 +228,18 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "0 time mass initial_mass stellar_type\n",
- "1 0 1 1 1\n",
- "2 0 1 1 1\n",
- "3 1e-06 1 1 1\n",
- "4 2e-06 1 1 1\n",
- "5 3e-06 1 1 1\n",
- "... ... ... ... ...\n",
- "1617 12461.8 0.546683 1 6\n",
- "1618 12461.9 0.517749 1 11\n",
- "1619 13461.9 0.517749 1 11\n",
- "1620 14461.9 0.517749 1 11\n",
- "1621 15000 0.517749 1 11\n",
+ "0 time mass initial_mass stellar_type\n",
+ "1 0.0 1.0 1.0 1.0\n",
+ "2 0.0 1.0 1.0 1.0\n",
+ "3 0.000001 1.0 1.0 1.0\n",
+ "4 0.000002 1.0 1.0 1.0\n",
+ "5 0.000003 1.0 1.0 1.0\n",
+ "... ... ... ... ...\n",
+ "1617 12461.819616 0.546683 1.0 6.0\n",
+ "1618 12461.945773 0.517749 1.0 11.0\n",
+ "1619 13461.945773 0.517749 1.0 11.0\n",
+ "1620 14461.945773 0.517749 1.0 11.0\n",
+ "1621 15000.0 0.517749 1.0 11.0\n",
"\n",
"[1621 rows x 4 columns]\n"
]
@@ -358,7 +361,7 @@
"Creating and loading custom logging functionality\n",
"Running binary_c M_1 10 api_log_filename_prefix /tmp/binary_c_python/notebooks/notebook_individual_systems\n",
"Cleaning up the custom logging stuff. type: single\n",
- "Removed /tmp/binary_c_python/custom_logging/libcustom_logging_8967553693ac4e11a49c42d4eef773e8.so\n",
+ "Removed /tmp/binary_c_python/custom_logging/libcustom_logging_6d4ed30fa6684630885c08523336d45f.so\n",
"EXAMPLE_MASSLOSS 0.000000000000e+00 10 0 10 1\n",
"EXAMPLE_MASSLOSS 0.000000000000e+00 10 10 10 1\n",
"EXAMPLE_MASSLOSS 1.000000000000e-06 10 10 10 1\n",
@@ -460,13 +463,13 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "adding: parse_function=<function object_parse_function at 0x7fb4d41ebbf8> to grid_options\n",
+ "adding: parse_function=<function object_parse_function at 0x14938275de50> to grid_options\n",
"<<<< Warning: Key does not match previously known parameter: adding: output_dir=/tmp/binary_c_python/notebooks/notebook_individual_systems to custom_options >>>>\n",
"adding: api_log_filename_prefix=/tmp/binary_c_python/notebooks/notebook_individual_systems to BSE_options\n",
"Creating and loading custom logging functionality\n",
"Running binary_c M_1 10 api_log_filename_prefix /tmp/binary_c_python/notebooks/notebook_individual_systems\n",
"Cleaning up the custom logging stuff. type: single\n",
- "Removed /tmp/binary_c_python/custom_logging/libcustom_logging_5d7779e8190e4b79b10c7e6a44cb0e7e.so\n",
+ "Removed /tmp/binary_c_python/custom_logging/libcustom_logging_3bc2f679982a4df6a2b83d382e83d724.so\n",
"[['time', 'mass', 'initial_mass', 'stellar_type'], [0.0, 10.0, 0.0, 10.0, 1.0], [0.0, 10.0, 10.0, 10.0, 1.0], [1e-06, 10.0, 10.0, 10.0, 1.0]]\n",
"dict_keys(['time', 'mass', 'initial_mass', 'stellar_type'])\n"
]
@@ -496,7 +499,7 @@
"## Single system via API functionality\n",
"It is possible to construct your own functionality to run a single system by directly calling the API function to run a system. Under the hood all the other functions and wrappers actually use this API.\n",
"\n",
- "There are less failsafes for this method, so this make sure the input is correct and binary_c knows all the arguments you pass in.\n",
+ "There are fewer failsafes for this method, so this make sure the input is correct and binary_c knows all the arguments you pass in.\n",
"\n",
"for more details on this API function see `notebook_api_functions`"
]
@@ -519,7 +522,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "SINGLE_STAR_LIFETIME 15 14.9947\n",
+ "SINGLE_STAR_LIFETIME 15 14.9927\n",
"\n"
]
}
diff --git a/docs/build/doctrees/nbsphinx/notebook_luminosity_function_binaries.ipynb b/docs/build/doctrees/nbsphinx/notebook_luminosity_function_binaries.ipynb
index c6b5f1e64cc36c684fdf5cefe0fae4b450a1c936..f054310a62ea8a37e55df724be75879dababbe38 100644
--- a/docs/build/doctrees/nbsphinx/notebook_luminosity_function_binaries.ipynb
+++ b/docs/build/doctrees/nbsphinx/notebook_luminosity_function_binaries.ipynb
@@ -5,7 +5,7 @@
"id": "bbbaafbb-fd7d-4b73-a970-93506ba35d71",
"metadata": {},
"source": [
- "# Zero-age stellar luminosity function in binaries\n",
+ "# Example use case: Zero-age stellar luminosity function in binaries\n",
"\n",
"In this notebook we compute the luminosity function of the zero-age main-sequence by running a population of binary stars using binary_c. \n",
"\n",
@@ -369,7 +369,7 @@
"## Evolving the grid\n",
"Now that we configured all the main parts of the population object, we can actually run the population! Doing this is straightforward: `population.evolve()`\n",
"\n",
- "This will start up the processing of all the systems. We can control how many cores are used by settings `amt_cores`. By setting the `verbosity` of the population object to a higher value we can get a lot of verbose information about the run, but for now we will set it to 0.\n",
+ "This will start up the processing of all the systems. We can control how many cores are used by settings `num_cores`. By setting the `verbosity` of the population object to a higher value we can get a lot of verbose information about the run, but for now we will set it to 0.\n",
"\n",
"There are many grid_options that can lead to different behaviour of the evolution of the grid. Please do have a look at those: [grid options docs](https://ri0005.pages.surrey.ac.uk/binary_c-python/grid_options_descriptions.html), and try "
]
@@ -386,7 +386,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "adding: amt_cores=4 to grid_options\n",
+ "adding: num_cores=4 to grid_options\n",
"Running the population now, this may take a little while...\n",
"Creating and loading custom logging functionality\n",
"Generating grid code\n",
@@ -547,7 +547,7 @@
" # verbose output is not required \n",
" verbosity=1,\n",
" # set number of threads (i.e. number of CPU cores we use)\n",
- " amt_cores=4,\n",
+ " num_cores=4,\n",
" )\n",
"\n",
"# Evolve the population - this is the slow, number-crunching step\n",
diff --git a/docs/build/doctrees/nbsphinx/notebook_luminosity_function_single.ipynb b/docs/build/doctrees/nbsphinx/notebook_luminosity_function_single.ipynb
index cdae316f90802fe46611ea17732506c0410aef55..09af8acc59f26e909901c0649e02a0d0864b789a 100644
--- a/docs/build/doctrees/nbsphinx/notebook_luminosity_function_single.ipynb
+++ b/docs/build/doctrees/nbsphinx/notebook_luminosity_function_single.ipynb
@@ -297,7 +297,7 @@
"## Evolving the grid\n",
"Now that we configured all the main parts of the population object, we can actually run the population! Doing this is straightforward: `population.evolve()`\n",
"\n",
- "This will start up the processing of all the systems. We can control how many cores are used by settings `amt_cores`. By setting the `verbosity` of the population object to a higher value we can get a lot of verbose information about the run, but for now we will set it to 0.\n",
+ "This will start up the processing of all the systems. We can control how many cores are used by settings `num_cores`. By setting the `verbosity` of the population object to a higher value we can get a lot of verbose information about the run, but for now we will set it to 0.\n",
"\n",
"There are many grid_options that can lead to different behaviour of the evolution of the grid. Please do have a look at those: [grid options docs](https://ri0005.pages.surrey.ac.uk/binary_c-python/grid_options_descriptions.html), and try "
]
@@ -332,7 +332,7 @@
" # verbose output is not required \n",
" verbosity=0,\n",
" # set number of threads (i.e. number of CPU cores we use)\n",
- " amt_cores=2,\n",
+ " num_cores=2,\n",
" )\n",
"\n",
"# Evolve the population - this is the slow, number-crunching step\n",
@@ -703,7 +703,7 @@
],
"metadata": {
"kernelspec": {
- "display_name": "Python 3",
+ "display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
@@ -717,7 +717,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
- "version": "3.6.4"
+ "version": "3.9.5"
}
},
"nbformat": 4,
diff --git a/docs/build/doctrees/nbsphinx/notebook_population.ipynb b/docs/build/doctrees/nbsphinx/notebook_population.ipynb
index a24638c0bd3a15a57bbf611fccb71b2100c75945..1ec2f94d3b03db0bccabe6ea2d2c100946add611 100644
--- a/docs/build/doctrees/nbsphinx/notebook_population.ipynb
+++ b/docs/build/doctrees/nbsphinx/notebook_population.ipynb
@@ -62,7 +62,7 @@
"adding: orbital_period=45000000080 to BSE_options\n",
"adding: max_evolution_time=15000 to BSE_options\n",
"adding: eccentricity=0.02 to BSE_options\n",
- "adding: amt_cores=2 to grid_options\n",
+ "adding: num_cores=2 to grid_options\n",
"adding: tmp_dir=/tmp/binary_c_python/notebooks/notebook_population to grid_options\n",
"<<<< Warning: Key does not match previously known parameter: adding: data_dir=/tmp/binary_c_python/notebooks/notebook_population/example_python_population_result to custom_options >>>>\n",
"<<<< Warning: Key does not match previously known parameter: adding: base_filename=example_pop.dat to custom_options >>>>\n",
@@ -92,7 +92,7 @@
"\n",
"\n",
" # grid_options\n",
- " amt_cores=2,\n",
+ " num_cores=2,\n",
" tmp_dir=TMP_DIR,\n",
" \n",
" # Custom options # TODO: need to be set in grid_options probably\n",
@@ -219,7 +219,7 @@
" Examples:\n",
" range = [math.log(m_min), math.log(m_max)]\n",
" resolution:\n",
- " Resolution of the sampled range (amount of samples).\n",
+ " Resolution of the sampled range (number of samples).\n",
" TODO: check if this is used anywhere\n",
" \n",
" Examples:\n",
@@ -496,7 +496,7 @@
" print(line)\n",
" \n",
" if not len(parameters) == len(values):\n",
- " print(\"Amount of column names isnt equal to amount of columns\")\n",
+ " print(\"Number of column names isnt equal to number of columns\")\n",
" raise ValueError\n",
"\n",
" if not os.path.exists(outfilename):\n",
@@ -520,7 +520,7 @@
"## Evolving the grid\n",
"Now that we configured all the main parts of the population object, we can actually run the population! Doing this is straightforward: `example_pop.evolve()`\n",
"\n",
- "This will start up the processing of all the systems. We can control how many cores are used by settings `amt_cores`. By setting the `verbosity` of the population object to a higher value we can get a lot of verbose information about the run, but for now we will set it to 0.\n",
+ "This will start up the processing of all the systems. We can control how many cores are used by settings `num_cores`. By setting the `verbosity` of the population object to a higher value we can get a lot of verbose information about the run, but for now we will set it to 0.\n",
"\n",
"There are many grid_options that can lead to different behaviour of the evolution of the grid. Please do have a look at those: [grid options docs](https://ri0005.pages.surrey.ac.uk/binary_c-python/grid_options_descriptions.html), and try "
]
@@ -770,7 +770,7 @@
" values = el.split()[1:]\n",
"\n",
" if not len(parameters) == len(values):\n",
- " print(\"Amount of column names isnt equal to amount of columns\")\n",
+ " print(\"Number of column names isnt equal to number of columns\")\n",
" raise ValueError\n",
"\n",
" if not os.path.exists(outfilename):\n",
@@ -797,7 +797,7 @@
" eccentricity=0.02, # bse_options\n",
" \n",
" # grid_options\n",
- " amt_cores=2,\n",
+ " num_cores=2,\n",
" tmp_dir=TMP_DIR,\n",
"\n",
" # Custom options: the data directory and the output filename\n",
@@ -963,7 +963,7 @@
" values = el.split()[1:]\n",
"\n",
" if not len(parameters) == len(values):\n",
- " print(\"Amount of column names isnt equal to amount of columns\")\n",
+ " print(\"Number of column names isnt equal to number of columns\")\n",
" raise ValueError\n",
"\n",
" if not os.path.exists(outfilename):\n",
@@ -990,7 +990,7 @@
" eccentricity=0.02, # bse_options\n",
" \n",
" # grid_options\n",
- " amt_cores=2, # grid_options\n",
+ " num_cores=2, # grid_options\n",
" tmp_dir=TMP_DIR,\n",
"\n",
" # Custom options: the data directory and the output filename\n",
diff --git a/docs/build/doctrees/notebook_HRD.doctree b/docs/build/doctrees/notebook_HRD.doctree
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--- a/docs/build/html/.buildinfo
+++ b/docs/build/html/.buildinfo
@@ -1,4 +1,4 @@
# Sphinx build info version 1
# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 44b2282a912f792069bea03167435e80
+config: e979aa9eb24450dd330ad22ac37f144a
tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/build/html/_modules/binarycpython/utils/custom_logging_functions.html b/docs/build/html/_modules/binarycpython/utils/custom_logging_functions.html
index d22fad99c9b5d87d385672275d93ab7b45a53d3b..d279da69d16df20a814dc67087bf52bdca12a505 100644
--- a/docs/build/html/_modules/binarycpython/utils/custom_logging_functions.html
+++ b/docs/build/html/_modules/binarycpython/utils/custom_logging_functions.html
@@ -1,69 +1,32 @@
-
-
<!DOCTYPE html>
<html class="writer-html5" lang="en" >
<head>
- <meta charset="utf-8">
-
- <meta name="viewport" content="width=device-width, initial-scale=1.0">
-
+ <meta charset="utf-8" />
+ <meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>binarycpython.utils.custom_logging_functions — binary_c-python documentation</title>
-
-
-
- <link rel="stylesheet" href="../../../_static/css/theme.css" type="text/css" />
- <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
-
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+ <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
+ <link rel="stylesheet" href="../../../_static/css/theme.css" type="text/css" />
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<script src="../../../_static/js/html5shiv.min.js"></script>
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-
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+ <script data-url_root="../../../" id="documentation_options" src="../../../_static/documentation_options.js"></script>
<script src="../../../_static/jquery.js"></script>
<script src="../../../_static/underscore.js"></script>
<script src="../../../_static/doctools.js"></script>
- <script src="../../../_static/language_data.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
- <script async="async" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.7/latest.js?config=TeX-AMS-MML_HTMLorMML"></script>
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-
- <script type="text/javascript" src="../../../_static/js/theme.js"></script>
-
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+ <script src="../../../_static/js/theme.js"></script>
<link rel="index" title="Index" href="../../../genindex.html" />
<link rel="search" title="Search" href="../../../search.html" />
</head>
-<body class="wy-body-for-nav">
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+<body class="wy-body-for-nav">
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-
<nav data-toggle="wy-nav-shift" class="wy-nav-side">
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<div class="wy-side-nav-search" >
-
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- <a href="../../../index.html" class="icon icon-home" alt="Documentation Home"> binary_c-python
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+ <a href="../../../index.html" class="icon icon-home"> binary_c-python
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<form id="rtd-search-form" class="wy-form" action="../../../search.html" method="get">
<input type="text" name="q" placeholder="Search docs" />
@@ -71,19 +34,8 @@
<input type="hidden" name="area" value="default" />
</form>
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-
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-
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- <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
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- <p class="caption"><span class="caption-text">Contents:</span></p>
+ </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
+ <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
<ul>
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<li class="toctree-l1"><a class="reference internal" href="../../../modules.html">Binarycpython code</a></li>
@@ -94,67 +46,30 @@
<li class="toctree-l1"><a class="reference external" href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/issues/new">Submit an issue</a></li>
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<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
-
+
<h1>Source code for binarycpython.utils.custom_logging_functions</h1><div class="highlight"><pre>
<span></span><span class="sd">"""</span>
<span class="sd">Module containing functions for the custom logging functionality.</span>
@@ -210,7 +125,7 @@
<span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="n">logging_dict</span><span class="p">:</span>
<span class="n">verbose_print</span><span class="p">(</span>
<span class="s2">"Generating Print statement for custom logging code with </span><span class="si">{}</span><span class="s2"> as a header"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
- <span class="n">key</span>
+ <span class="n">key</span>
<span class="p">),</span>
<span class="n">verbosity</span><span class="p">,</span>
<span class="mi">1</span><span class="p">,</span>
@@ -464,7 +379,7 @@
<span class="c1">#</span>
<span class="n">verbose_print</span><span class="p">(</span>
<span class="s2">"Got options to compile:</span><span class="se">\n\t</span><span class="s2">cc = </span><span class="si">{cc}</span><span class="se">\n\t</span><span class="s2">ccflags = </span><span class="si">{ccflags}</span><span class="se">\n\t</span><span class="s2">ld = </span><span class="si">{ld}</span><span class="se">\n\t</span><span class="s2">libs = </span><span class="si">{libs}</span><span class="se">\n\t</span><span class="s2">inc = </span><span class="si">{inc}</span><span class="se">\n\n</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
- <span class="n">cc</span><span class="o">=</span><span class="n">cc</span><span class="p">,</span> <span class="n">ccflags</span><span class="o">=</span><span class="n">ccflags</span><span class="p">,</span> <span class="n">ld</span><span class="o">=</span><span class="n">ld</span><span class="p">,</span> <span class="n">libs</span><span class="o">=</span><span class="n">libs</span><span class="p">,</span> <span class="n">inc</span><span class="o">=</span><span class="n">inc</span>
+ <span class="n">cc</span><span class="o">=</span><span class="n">cc</span><span class="p">,</span> <span class="n">ccflags</span><span class="o">=</span><span class="n">ccflags</span><span class="p">,</span> <span class="n">ld</span><span class="o">=</span><span class="n">ld</span><span class="p">,</span> <span class="n">libs</span><span class="o">=</span><span class="n">libs</span><span class="p">,</span> <span class="n">inc</span><span class="o">=</span><span class="n">inc</span>
<span class="p">),</span>
<span class="n">verbosity</span><span class="p">,</span>
<span class="mi">1</span><span class="p">,</span>
@@ -516,7 +431,7 @@
<span class="c1"># Execute compilation and create the library</span>
<span class="n">verbose_print</span><span class="p">(</span>
<span class="s2">"Building shared library for custom logging with (binary_c.h) on </span><span class="si">{}</span><span class="se">\n</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
- <span class="n">socket</span><span class="o">.</span><span class="n">gethostname</span><span class="p">()</span>
+ <span class="n">socket</span><span class="o">.</span><span class="n">gethostname</span><span class="p">()</span>
<span class="p">),</span>
<span class="n">verbosity</span><span class="p">,</span>
<span class="mi">1</span><span class="p">,</span>
@@ -538,6 +453,7 @@
<span class="mi">1</span><span class="p">,</span>
<span class="p">)</span></div>
+
<div class="viewcode-block" id="create_and_load_logging_function"><a class="viewcode-back" href="../../../custom_logging_functions.html#binarycpython.utils.custom_logging_functions.create_and_load_logging_function">[docs]</a><span class="k">def</span> <span class="nf">create_and_load_logging_function</span><span class="p">(</span>
<span class="n">custom_logging_code</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">verbosity</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">0</span><span class="p">,</span> <span class="n">custom_tmp_dir</span><span class="o">=</span><span class="kc">None</span>
<span class="p">)</span> <span class="o">-></span> <span class="n">Tuple</span><span class="p">[</span><span class="nb">int</span><span class="p">,</span> <span class="nb">str</span><span class="p">]:</span>
@@ -621,55 +537,36 @@
</pre></div>
</div>
-
</div>
<footer>
-
<hr/>
<div role="contentinfo">
- <p>
-
- © Copyright 2021, David Hendriks, Robert Izzard
-
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+ <p>© Copyright 2021, David Hendriks, Robert Izzard.</p>
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+Generated on binarycpython git branch: auto_resolution git revision be7bd630af892a785312affc34d87c57eb337fd3 url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/tree/auto_resolution">git url</a>.
<br><br>
-Using binary_c with bit branch newmaster: git revision: "6185:20210910:1621c23a5" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/newmaster">git url</a>.
+Using binary_c with bit branch master: git revision: "6209:20211006:c4a4c332e" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/master">git url</a>.
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diff --git a/docs/build/html/_modules/binarycpython/utils/distribution_functions.html b/docs/build/html/_modules/binarycpython/utils/distribution_functions.html
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--- a/docs/build/html/_modules/binarycpython/utils/distribution_functions.html
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<h1>Source code for binarycpython.utils.distribution_functions</h1><div class="highlight"><pre>
<span></span><span class="sd">"""</span>
<span class="sd">Module containing the predefined distribution functions</span>
@@ -178,7 +93,7 @@
<span class="sd"> - TODO: make an n-part power law that's general enough to fix the three part and the 4 part</span>
<span class="sd">"""</span>
-<span class="kn">import</span> <span class="nn">gc</span>
+<span class="kn">import</span> <span class="nn">functools</span>
<span class="kn">import</span> <span class="nn">math</span>
<span class="kn">import</span> <span class="nn">json</span>
@@ -293,8 +208,8 @@
<span class="n">prob</span> <span class="o">=</span> <span class="mf">1.0</span> <span class="o">/</span> <span class="p">(</span><span class="n">max_bound</span> <span class="o">-</span> <span class="n">min_bound</span><span class="p">)</span>
<span class="k">return</span> <span class="n">prob</span></div>
-
-<div class="viewcode-block" id="powerlaw_constant"><a class="viewcode-back" href="../../../distribution_functions.html#binarycpython.utils.distribution_functions.powerlaw_constant">[docs]</a><span class="k">def</span> <span class="nf">powerlaw_constant</span><span class="p">(</span>
+<div class="viewcode-block" id="powerlaw_constant"><a class="viewcode-back" href="../../../distribution_functions.html#binarycpython.utils.distribution_functions.powerlaw_constant">[docs]</a><span class="nd">@functools</span><span class="o">.</span><span class="n">lru_cache</span><span class="p">(</span><span class="n">maxsize</span><span class="o">=</span><span class="mi">16</span><span class="p">)</span>
+<span class="k">def</span> <span class="nf">powerlaw_constant</span><span class="p">(</span>
<span class="n">min_val</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="nb">int</span><span class="p">,</span> <span class="nb">float</span><span class="p">],</span> <span class="n">max_val</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="nb">int</span><span class="p">,</span> <span class="nb">float</span><span class="p">],</span> <span class="n">k</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="nb">int</span><span class="p">,</span> <span class="nb">float</span><span class="p">]</span>
<span class="p">)</span> <span class="o">-></span> <span class="n">Union</span><span class="p">[</span><span class="nb">int</span><span class="p">,</span> <span class="nb">float</span><span class="p">]:</span>
<span class="sd">"""</span>
@@ -361,8 +276,8 @@
<span class="c1"># )</span>
<span class="k">return</span> <span class="n">prob</span></div>
-
-<div class="viewcode-block" id="calculate_constants_three_part_powerlaw"><a class="viewcode-back" href="../../../distribution_functions.html#binarycpython.utils.distribution_functions.calculate_constants_three_part_powerlaw">[docs]</a><span class="k">def</span> <span class="nf">calculate_constants_three_part_powerlaw</span><span class="p">(</span>
+<div class="viewcode-block" id="calculate_constants_three_part_powerlaw"><a class="viewcode-back" href="../../../distribution_functions.html#binarycpython.utils.distribution_functions.calculate_constants_three_part_powerlaw">[docs]</a><span class="nd">@functools</span><span class="o">.</span><span class="n">lru_cache</span><span class="p">(</span><span class="n">maxsize</span><span class="o">=</span><span class="mi">16</span><span class="p">)</span>
+<span class="k">def</span> <span class="nf">calculate_constants_three_part_powerlaw</span><span class="p">(</span>
<span class="n">m0</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="nb">int</span><span class="p">,</span> <span class="nb">float</span><span class="p">],</span>
<span class="n">m1</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="nb">int</span><span class="p">,</span> <span class="nb">float</span><span class="p">],</span>
<span class="n">m2</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="nb">int</span><span class="p">,</span> <span class="nb">float</span><span class="p">],</span>
@@ -481,8 +396,8 @@
<span class="k">return</span> <span class="n">prob</span></div>
-
-<div class="viewcode-block" id="gaussian_normalizing_const"><a class="viewcode-back" href="../../../distribution_functions.html#binarycpython.utils.distribution_functions.gaussian_normalizing_const">[docs]</a><span class="k">def</span> <span class="nf">gaussian_normalizing_const</span><span class="p">(</span>
+<div class="viewcode-block" id="gaussian_normalizing_const"><a class="viewcode-back" href="../../../distribution_functions.html#binarycpython.utils.distribution_functions.gaussian_normalizing_const">[docs]</a><span class="nd">@functools</span><span class="o">.</span><span class="n">lru_cache</span><span class="p">(</span><span class="n">maxsize</span><span class="o">=</span><span class="mi">16</span><span class="p">)</span>
+<span class="k">def</span> <span class="nf">gaussian_normalizing_const</span><span class="p">(</span>
<span class="n">mean</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="nb">int</span><span class="p">,</span> <span class="nb">float</span><span class="p">],</span>
<span class="n">sigma</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="nb">int</span><span class="p">,</span> <span class="nb">float</span><span class="p">],</span>
<span class="n">gmin</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="nb">int</span><span class="p">,</span> <span class="nb">float</span><span class="p">],</span>
@@ -877,7 +792,7 @@
<span class="sd"> """</span>
<span class="n">res</span> <span class="o">=</span> <span class="mi">0</span>
- <span class="k">if</span> <span class="p">(</span><span class="n">M1</span> <span class="o"><</span> <span class="mi">15</span><span class="p">)</span> <span class="ow">or</span> <span class="p">(</span><span class="n">M2</span> <span class="o">/</span> <span class="n">M1</span> <span class="o"><</span> <span class="mf">0.1</span><span class="p">):</span>
+ <span class="k">if</span> <span class="p">(</span><span class="n">M1</span> <span class="o"><</span> <span class="mf">15.0</span><span class="p">)</span> <span class="ow">or</span> <span class="p">(</span><span class="n">M2</span> <span class="o">/</span> <span class="n">M1</span> <span class="o"><</span> <span class="mf">0.1</span><span class="p">):</span>
<span class="n">res</span> <span class="o">=</span> <span class="mf">1.0</span> <span class="o">/</span> <span class="p">(</span><span class="n">math</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="n">amax</span><span class="p">)</span> <span class="o">-</span> <span class="n">math</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="n">amin</span><span class="p">))</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">p1</span> <span class="o">=</span> <span class="mf">1.0</span> <span class="o">+</span> <span class="n">p</span>
@@ -1103,8 +1018,8 @@
<span class="c1"># known value if we try to interpolate outside of the tables.</span>
<span class="c1"># There are still some open tasks and improvements that can be made:</span>
<span class="c1">#</span>
-<span class="c1"># TODO: Solve the memory issues that are present. </span>
-<span class="c1"># Are the interpolators not cleaned? </span>
+<span class="c1"># TODO: Solve the memory issues that are present.</span>
+<span class="c1"># Are the interpolators not cleaned?</span>
<span class="c1"># TODO: Parallelize the setting up of the interpolators</span>
<span class="c1"># TODO: Generalise the code such that we can input other/newer tables</span>
@@ -1115,6 +1030,7 @@
<span class="c1"># Global dictionary to store values in</span>
<span class="n">Moecache</span> <span class="o">=</span> <span class="p">{}</span>
+
<div class="viewcode-block" id="poisson"><a class="viewcode-back" href="../../../distribution_functions.html#binarycpython.utils.distribution_functions.poisson">[docs]</a><span class="k">def</span> <span class="nf">poisson</span><span class="p">(</span><span class="n">lambda_val</span><span class="p">,</span> <span class="n">n</span><span class="p">,</span> <span class="n">nmax</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">verbosity</span><span class="o">=</span><span class="mi">0</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Function that calculates the Poisson value and normalises</span>
@@ -1169,6 +1085,7 @@
<span class="k">return</span> <span class="p">(</span><span class="n">lambda_val</span> <span class="o">**</span> <span class="n">n</span><span class="p">)</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">exp</span><span class="p">(</span><span class="o">-</span><span class="n">lambda_val</span><span class="p">)</span> <span class="o">/</span> <span class="p">(</span><span class="mf">1.0</span> <span class="o">*</span> <span class="n">math</span><span class="o">.</span><span class="n">factorial</span><span class="p">(</span><span class="n">n</span><span class="p">))</span>
+
<div class="viewcode-block" id="get_max_multiplicity"><a class="viewcode-back" href="../../../distribution_functions.html#binarycpython.utils.distribution_functions.get_max_multiplicity">[docs]</a><span class="k">def</span> <span class="nf">get_max_multiplicity</span><span class="p">(</span><span class="n">multiplicity_array</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Function to get the maximum multiplicity</span>
@@ -1180,6 +1097,7 @@
<span class="n">max_multiplicity</span> <span class="o">=</span> <span class="n">n</span> <span class="o">+</span> <span class="mi">1</span>
<span class="k">return</span> <span class="n">max_multiplicity</span></div>
+
<div class="viewcode-block" id="merge_multiplicities"><a class="viewcode-back" href="../../../distribution_functions.html#binarycpython.utils.distribution_functions.merge_multiplicities">[docs]</a><span class="k">def</span> <span class="nf">merge_multiplicities</span><span class="p">(</span><span class="n">result_array</span><span class="p">,</span> <span class="n">max_multiplicity</span><span class="p">,</span> <span class="n">verbosity</span><span class="o">=</span><span class="mi">0</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Function to fold the multiplicities higher than the max_multiplicity onto the max_multiplicity</span>
@@ -1205,21 +1123,26 @@
<span class="c1"># Fold multiplicities:</span>
<span class="n">verbose_print</span><span class="p">(</span>
- <span class="s2">"</span><span class="se">\t</span><span class="s2">M&S: merge_multiplicities: Merging multiplicities with initial array </span><span class="si">{}</span><span class="s2"> and max multiplicity </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">result_array</span><span class="p">,</span> <span class="n">max_multiplicity</span><span class="p">),</span>
+ <span class="s2">"</span><span class="se">\t</span><span class="s2">M&S: merge_multiplicities: Merging multiplicities with initial array </span><span class="si">{}</span><span class="s2"> and max multiplicity </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+ <span class="n">result_array</span><span class="p">,</span> <span class="n">max_multiplicity</span>
+ <span class="p">),</span>
<span class="n">verbosity</span><span class="p">,</span>
<span class="n">_MS_VERBOSITY_LEVEL</span><span class="p">,</span>
<span class="p">)</span>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">max_multiplicity</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">result_array</span><span class="p">))[::</span><span class="o">-</span><span class="mi">1</span><span class="p">]:</span>
- <span class="n">result_array</span><span class="p">[</span><span class="n">i</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span> <span class="o">+=</span> <span class="n">result_array</span><span class="p">[</span><span class="n">i</span><span class="p">]</span>
+ <span class="n">result_array</span><span class="p">[</span><span class="n">i</span> <span class="o">-</span> <span class="mi">1</span><span class="p">]</span> <span class="o">+=</span> <span class="n">result_array</span><span class="p">[</span><span class="n">i</span><span class="p">]</span>
<span class="n">result_array</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">=</span> <span class="mi">0</span>
<span class="n">verbose_print</span><span class="p">(</span>
- <span class="s2">"</span><span class="se">\t</span><span class="s2">M&S: merge_multiplicities: Merging multiplicities to new array </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">result_array</span><span class="p">),</span>
+ <span class="s2">"</span><span class="se">\t</span><span class="s2">M&S: merge_multiplicities: Merging multiplicities to new array </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+ <span class="n">result_array</span>
+ <span class="p">),</span>
<span class="n">verbosity</span><span class="p">,</span>
<span class="n">_MS_VERBOSITY_LEVEL</span><span class="p">,</span>
<span class="p">)</span>
<span class="k">return</span> <span class="n">result_array</span></div>
+
<div class="viewcode-block" id="normalize_dict"><a class="viewcode-back" href="../../../distribution_functions.html#binarycpython.utils.distribution_functions.normalize_dict">[docs]</a><span class="k">def</span> <span class="nf">normalize_dict</span><span class="p">(</span><span class="n">result_dict</span><span class="p">,</span> <span class="n">verbosity</span><span class="o">=</span><span class="mi">0</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Function to normalise a dictionary</span>
@@ -1230,6 +1153,7 @@
<span class="n">result_dict</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">result_dict</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">/</span> <span class="n">sum_result</span>
<span class="k">return</span> <span class="n">result_dict</span></div>
+
<div class="viewcode-block" id="Moe_di_Stefano_2017_multiplicity_fractions"><a class="viewcode-back" href="../../../distribution_functions.html#binarycpython.utils.distribution_functions.Moe_di_Stefano_2017_multiplicity_fractions">[docs]</a><span class="k">def</span> <span class="nf">Moe_di_Stefano_2017_multiplicity_fractions</span><span class="p">(</span><span class="n">options</span><span class="p">,</span> <span class="n">verbosity</span><span class="o">=</span><span class="mi">0</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Function that creates a list of probability fractions and</span>
@@ -1247,11 +1171,15 @@
<span class="c1"># Use the global Moecache</span>
<span class="k">global</span> <span class="n">Moecache</span>
- <span class="n">multiplicity_modulator_array</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">options</span><span class="p">[</span><span class="s2">"multiplicity_modulator"</span><span class="p">])</span> <span class="c1"># Modulator array</span>
+ <span class="n">multiplicity_modulator_array</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span>
+ <span class="n">options</span><span class="p">[</span><span class="s2">"multiplicity_modulator"</span><span class="p">]</span>
+ <span class="p">)</span> <span class="c1"># Modulator array</span>
<span class="c1"># Check for length</span>
- <span class="k">if</span> <span class="ow">not</span> <span class="nb">len</span><span class="p">(</span><span class="n">multiplicity_modulator_array</span><span class="p">)</span><span class="o">==</span><span class="mi">4</span><span class="p">:</span>
- <span class="n">msg</span> <span class="o">=</span> <span class="s2">"Multiplicity modulator has to have 4 elements. Now it is </span><span class="si">{}</span><span class="s2">, len: </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">multiplicity_modulator_array</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">multiplicity_modulator_array</span><span class="p">))</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="nb">len</span><span class="p">(</span><span class="n">multiplicity_modulator_array</span><span class="p">)</span> <span class="o">==</span> <span class="mi">4</span><span class="p">:</span>
+ <span class="n">msg</span> <span class="o">=</span> <span class="s2">"Multiplicity modulator has to have 4 elements. Now it is </span><span class="si">{}</span><span class="s2">, len: </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+ <span class="n">multiplicity_modulator_array</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">multiplicity_modulator_array</span><span class="p">)</span>
+ <span class="p">)</span>
<span class="n">verbose_print</span><span class="p">(</span>
<span class="n">msg</span><span class="p">,</span>
<span class="n">verbosity</span><span class="p">,</span>
@@ -1260,8 +1188,10 @@
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
<span class="c1"># Set up some arrays</span>
- <span class="n">full_fractions_array</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="mi">4</span><span class="p">)</span> <span class="c1"># Meant to contain the real fractions</span>
- <span class="n">weighted_fractions_array</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="mi">4</span><span class="p">)</span> <span class="c1"># Meant to contain the fractions multiplied by the multiplicity modulator</span>
+ <span class="n">full_fractions_array</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="mi">4</span><span class="p">)</span> <span class="c1"># Meant to contain the real fractions</span>
+ <span class="n">weighted_fractions_array</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span>
+ <span class="mi">4</span>
+ <span class="p">)</span> <span class="c1"># Meant to contain the fractions multiplied by the multiplicity modulator</span>
<span class="c1"># Get max multiplicity</span>
<span class="n">max_multiplicity</span> <span class="o">=</span> <span class="n">get_max_multiplicity</span><span class="p">(</span><span class="n">multiplicity_modulator_array</span><span class="p">)</span>
@@ -1275,7 +1205,7 @@
<span class="n">Moecache</span><span class="p">[</span><span class="s2">"rinterpolator_multiplicity"</span><span class="p">]</span> <span class="o">=</span> <span class="n">py_rinterpolate</span><span class="o">.</span><span class="n">Rinterpolate</span><span class="p">(</span>
<span class="n">table</span><span class="o">=</span><span class="n">Moecache</span><span class="p">[</span><span class="s2">"multiplicity_table"</span><span class="p">],</span> <span class="c1"># Contains the table of data</span>
<span class="n">nparams</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="c1"># logM1</span>
- <span class="n">ndata</span><span class="o">=</span><span class="mi">4</span><span class="p">,</span> <span class="c1"># The amount of datapoints (the parameters that we want to interpolate)</span>
+ <span class="n">ndata</span><span class="o">=</span><span class="mi">4</span><span class="p">,</span> <span class="c1"># The number of datapoints (the parameters that we want to interpolate)</span>
<span class="n">verbosity</span><span class="o">=</span><span class="n">verbosity</span> <span class="o">-</span> <span class="p">(</span><span class="n">_MS_VERBOSITY_INTERPOLATOR_LEVEL</span> <span class="o">-</span> <span class="mi">1</span><span class="p">),</span>
<span class="p">)</span>
@@ -1289,10 +1219,12 @@
<span class="n">full_fractions_array</span><span class="p">[</span><span class="n">n</span><span class="p">]</span> <span class="o">=</span> <span class="n">poisson</span><span class="p">(</span><span class="n">multiplicity</span><span class="p">,</span> <span class="n">n</span><span class="p">,</span> <span class="mi">3</span><span class="p">,</span> <span class="n">verbosity</span><span class="p">)</span>
<span class="c1"># Normalize it so it fills to one when taking all the multiplicities:</span>
- <span class="n">full_fractions_array</span> <span class="o">=</span> <span class="n">full_fractions_array</span><span class="o">/</span><span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">full_fractions_array</span><span class="p">)</span>
+ <span class="n">full_fractions_array</span> <span class="o">=</span> <span class="n">full_fractions_array</span> <span class="o">/</span> <span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">full_fractions_array</span><span class="p">)</span>
<span class="n">verbose_print</span><span class="p">(</span>
- <span class="s2">"</span><span class="se">\t</span><span class="s2">M&S: Moe_di_Stefano_2017_multiplicity_fractions: using model </span><span class="si">{}</span><span class="s2">: full_fractions_array: </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="s2">"Poisson"</span><span class="p">,</span> <span class="n">full_fractions_array</span><span class="p">),</span>
+ <span class="s2">"</span><span class="se">\t</span><span class="s2">M&S: Moe_di_Stefano_2017_multiplicity_fractions: using model </span><span class="si">{}</span><span class="s2">: full_fractions_array: </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+ <span class="s2">"Poisson"</span><span class="p">,</span> <span class="n">full_fractions_array</span>
+ <span class="p">),</span>
<span class="n">verbosity</span><span class="p">,</span>
<span class="n">_MS_VERBOSITY_LEVEL</span><span class="p">,</span>
<span class="p">)</span>
@@ -1305,15 +1237,16 @@
<span class="c1"># Fill with the raw values</span>
<span class="k">for</span> <span class="n">n</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">3</span><span class="p">):</span>
- <span class="n">full_fractions_array</span><span class="p">[</span><span class="n">n</span><span class="p">]</span> <span class="o">=</span> <span class="p">(</span>
- <span class="n">Moecache</span><span class="p">[</span><span class="s2">"rinterpolator_multiplicity"</span><span class="p">]</span><span class="o">.</span><span class="n">interpolate</span><span class="p">(</span>
- <span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">log10</span><span class="p">(</span><span class="n">options</span><span class="p">[</span><span class="s2">"M_1"</span><span class="p">])]</span>
- <span class="p">)[</span><span class="n">n</span> <span class="o">+</span> <span class="mi">1</span><span class="p">])</span>
+ <span class="n">full_fractions_array</span><span class="p">[</span><span class="n">n</span><span class="p">]</span> <span class="o">=</span> <span class="n">Moecache</span><span class="p">[</span>
+ <span class="s2">"rinterpolator_multiplicity"</span>
+ <span class="p">]</span><span class="o">.</span><span class="n">interpolate</span><span class="p">([</span><span class="n">np</span><span class="o">.</span><span class="n">log10</span><span class="p">(</span><span class="n">options</span><span class="p">[</span><span class="s2">"M_1"</span><span class="p">])])[</span><span class="n">n</span> <span class="o">+</span> <span class="mi">1</span><span class="p">]</span>
<span class="c1"># Set last value</span>
<span class="n">full_fractions_array</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="o">=</span> <span class="mf">0.0</span> <span class="c1"># no quadruples</span>
<span class="n">verbose_print</span><span class="p">(</span>
- <span class="s2">"</span><span class="se">\t</span><span class="s2">M&S: Moe_di_Stefano_2017_multiplicity_fractions: using model </span><span class="si">{}</span><span class="s2">: full_fractions_array: </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="s2">"data"</span><span class="p">,</span> <span class="n">full_fractions_array</span><span class="p">),</span>
+ <span class="s2">"</span><span class="se">\t</span><span class="s2">M&S: Moe_di_Stefano_2017_multiplicity_fractions: using model </span><span class="si">{}</span><span class="s2">: full_fractions_array: </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+ <span class="s2">"data"</span><span class="p">,</span> <span class="n">full_fractions_array</span>
+ <span class="p">),</span>
<span class="n">verbosity</span><span class="p">,</span>
<span class="n">_MS_VERBOSITY_LEVEL</span><span class="p">,</span>
<span class="p">)</span>
@@ -1322,7 +1255,9 @@
<span class="k">if</span> <span class="n">options</span><span class="p">[</span><span class="s2">"normalize_multiplicities"</span><span class="p">]</span> <span class="o">==</span> <span class="s2">"raw"</span><span class="p">:</span>
<span class="c1"># Don't multiply by the multiplicity_array, but do give a fractions array</span>
<span class="n">verbose_print</span><span class="p">(</span>
- <span class="s2">"</span><span class="se">\t</span><span class="s2">M&S: Moe_di_Stefano_2017_multiplicity_fractions: Not normalising (using raw results): results: </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">full_fractions_array</span><span class="p">),</span>
+ <span class="s2">"</span><span class="se">\t</span><span class="s2">M&S: Moe_di_Stefano_2017_multiplicity_fractions: Not normalising (using raw results): results: </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+ <span class="n">full_fractions_array</span>
+ <span class="p">),</span>
<span class="n">verbosity</span><span class="p">,</span>
<span class="n">_MS_VERBOSITY_LEVEL</span><span class="p">,</span>
<span class="p">)</span>
@@ -1333,10 +1268,12 @@
<span class="n">weighted_fractions_array</span> <span class="o">=</span> <span class="n">full_fractions_array</span> <span class="o">*</span> <span class="n">multiplicity_modulator_array</span>
<span class="c1"># Normalise this so it is in total 1:</span>
- <span class="n">result</span> <span class="o">=</span> <span class="n">weighted_fractions_array</span><span class="o">/</span><span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">weighted_fractions_array</span><span class="p">)</span>
+ <span class="n">result</span> <span class="o">=</span> <span class="n">weighted_fractions_array</span> <span class="o">/</span> <span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">weighted_fractions_array</span><span class="p">)</span>
<span class="n">verbose_print</span><span class="p">(</span>
- <span class="s2">"</span><span class="se">\t</span><span class="s2">M&S: Moe_di_Stefano_2017_multiplicity_fractions: Normalising with </span><span class="si">{}</span><span class="s2">. result: </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="s2">"norm"</span><span class="p">,</span> <span class="n">result</span><span class="p">),</span>
+ <span class="s2">"</span><span class="se">\t</span><span class="s2">M&S: Moe_di_Stefano_2017_multiplicity_fractions: Normalising with </span><span class="si">{}</span><span class="s2">. result: </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+ <span class="s2">"norm"</span><span class="p">,</span> <span class="n">result</span>
+ <span class="p">),</span>
<span class="n">verbosity</span><span class="p">,</span>
<span class="n">_MS_VERBOSITY_LEVEL</span><span class="p">,</span>
<span class="p">)</span>
@@ -1344,13 +1281,17 @@
<span class="k">elif</span> <span class="n">options</span><span class="p">[</span><span class="s2">"normalize_multiplicities"</span><span class="p">]</span> <span class="o">==</span> <span class="s2">"merge"</span><span class="p">:</span>
<span class="c1"># We first take the full multiplicity array</span>
<span class="c1"># (i.e. not multiplied by multiplier) and do the merging</span>
- <span class="n">result</span> <span class="o">=</span> <span class="n">merge_multiplicities</span><span class="p">(</span><span class="n">full_fractions_array</span><span class="p">,</span> <span class="n">max_multiplicity</span><span class="p">,</span> <span class="n">verbosity</span><span class="o">=</span><span class="n">verbosity</span><span class="p">)</span>
+ <span class="n">result</span> <span class="o">=</span> <span class="n">merge_multiplicities</span><span class="p">(</span>
+ <span class="n">full_fractions_array</span><span class="p">,</span> <span class="n">max_multiplicity</span><span class="p">,</span> <span class="n">verbosity</span><span class="o">=</span><span class="n">verbosity</span>
+ <span class="p">)</span>
<span class="c1"># Then normalise to be sure</span>
- <span class="n">result</span> <span class="o">=</span> <span class="n">result</span><span class="o">/</span><span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">result</span><span class="p">)</span>
+ <span class="n">result</span> <span class="o">=</span> <span class="n">result</span> <span class="o">/</span> <span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">result</span><span class="p">)</span>
<span class="n">verbose_print</span><span class="p">(</span>
- <span class="s2">"</span><span class="se">\t</span><span class="s2">M&S: Moe_di_Stefano_2017_multiplicity_fractions: Normalising with </span><span class="si">{}</span><span class="s2">, max_multiplicity=</span><span class="si">{}</span><span class="s2"> result=</span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="s2">"merge"</span><span class="p">,</span> <span class="n">max_multiplicity</span><span class="p">,</span> <span class="n">result</span><span class="p">),</span>
+ <span class="s2">"</span><span class="se">\t</span><span class="s2">M&S: Moe_di_Stefano_2017_multiplicity_fractions: Normalising with </span><span class="si">{}</span><span class="s2">, max_multiplicity=</span><span class="si">{}</span><span class="s2"> result=</span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+ <span class="s2">"merge"</span><span class="p">,</span> <span class="n">max_multiplicity</span><span class="p">,</span> <span class="n">result</span>
+ <span class="p">),</span>
<span class="n">verbosity</span><span class="p">,</span>
<span class="n">_MS_VERBOSITY_LEVEL</span><span class="p">,</span>
<span class="p">)</span>
@@ -1364,6 +1305,7 @@
<span class="c1"># return array reference</span>
<span class="k">return</span> <span class="n">result</span></div>
+
<div class="viewcode-block" id="build_q_table"><a class="viewcode-back" href="../../../distribution_functions.html#binarycpython.utils.distribution_functions.build_q_table">[docs]</a><span class="k">def</span> <span class="nf">build_q_table</span><span class="p">(</span><span class="n">options</span><span class="p">,</span> <span class="n">m</span><span class="p">,</span> <span class="n">p</span><span class="p">,</span> <span class="n">verbosity</span><span class="o">=</span><span class="mi">0</span><span class="p">):</span>
<span class="c1">############################################################</span>
<span class="c1">#</span>
@@ -1428,7 +1370,7 @@
<span class="c1"># 0</span>
<span class="c1"># ] # TODO: this lower range must not be lower than Mmin.</span>
- <span class="n">qmin</span> <span class="o">=</span> <span class="n">options</span><span class="p">[</span><span class="s1">'Mmin'</span><span class="p">]</span><span class="o">/</span><span class="n">options</span><span class="p">[</span><span class="s1">'M_1'</span><span class="p">]</span>
+ <span class="n">qmin</span> <span class="o">=</span> <span class="n">options</span><span class="p">[</span><span class="s2">"Mmin"</span><span class="p">]</span> <span class="o">/</span> <span class="n">options</span><span class="p">[</span><span class="s2">"M_1"</span><span class="p">]</span>
<span class="n">verbose_print</span><span class="p">(</span>
<span class="s2">"</span><span class="se">\t</span><span class="s2">M&S: build_q_table qmin: </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
<span class="n">qmin</span><span class="p">,</span>
@@ -1537,11 +1479,11 @@
<span class="c1"># with a flat distribution up to 1.0.</span>
<span class="k">if</span> <span class="n">qs</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="mf">1.0</span><span class="p">:</span>
<span class="n">qs</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">=</span> <span class="mf">1.0</span> <span class="o">-</span> <span class="mf">1e-6</span>
- <span class="n">qs</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="mi">1</span>
+ <span class="n">qs</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="mi">1</span><span class="p">)</span>
<span class="n">qdata</span><span class="p">[</span><span class="n">qs</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span> <span class="o">=</span> <span class="mi">1</span>
<span class="n">qdata</span><span class="p">[</span><span class="n">qs</span><span class="p">[</span><span class="mi">1</span><span class="p">]]</span> <span class="o">=</span> <span class="mi">1</span>
<span class="k">else</span><span class="p">:</span>
- <span class="n">qs</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="mf">1.0</span>
+ <span class="n">qs</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="mi">1</span><span class="p">)</span>
<span class="n">qdata</span><span class="p">[</span><span class="n">qs</span><span class="p">[</span><span class="mi">1</span><span class="p">]]</span> <span class="o">=</span> <span class="n">qs</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
<span class="c1"># We actually should do the extrapolation now.</span>
@@ -1604,13 +1546,15 @@
<span class="n">verbosity</span><span class="p">,</span>
<span class="n">_MS_VERBOSITY_LEVEL</span><span class="p">,</span>
<span class="p">)</span>
- <span class="k">if</span> <span class="n">pre</span><span class="o">==</span><span class="s1">'low'</span><span class="p">:</span>
- <span class="n">below_qlimit</span> <span class="o">=</span> <span class="n">qlimit</span><span class="o">-</span><span class="n">qeps</span>
+ <span class="k">if</span> <span class="n">pre</span> <span class="o">==</span> <span class="s2">"low"</span><span class="p">:</span>
+ <span class="n">below_qlimit</span> <span class="o">=</span> <span class="n">qlimit</span> <span class="o">-</span> <span class="n">qeps</span>
<span class="k">if</span> <span class="n">below_qlimit</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
<span class="n">qdata</span><span class="p">[</span><span class="n">below_qlimit</span><span class="p">]</span> <span class="o">=</span> <span class="mi">0</span>
<span class="n">qdata</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">=</span> <span class="mi">0</span>
<span class="n">verbose_print</span><span class="p">(</span>
- <span class="s2">"</span><span class="se">\t</span><span class="s2">M&S: build_q_table: using linear extrapolation and setting the points below the lower q bound (</span><span class="si">{}</span><span class="s2">) to 0 "</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">qlimit</span><span class="p">),</span>
+ <span class="s2">"</span><span class="se">\t</span><span class="s2">M&S: build_q_table: using linear extrapolation and setting the points below the lower q bound (</span><span class="si">{}</span><span class="s2">) to 0 "</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+ <span class="n">qlimit</span>
+ <span class="p">),</span>
<span class="n">verbosity</span><span class="p">,</span>
<span class="n">_MS_VERBOSITY_LEVEL</span><span class="p">,</span>
<span class="p">)</span>
@@ -1633,14 +1577,16 @@
<span class="n">verbosity</span><span class="p">,</span>
<span class="n">_MS_VERBOSITY_LEVEL</span><span class="p">,</span>
<span class="p">)</span>
- <span class="k">elif</span> <span class="n">method</span><span class="o">==</span><span class="s2">"poly"</span><span class="p">:</span>
+ <span class="k">elif</span> <span class="n">method</span> <span class="o">==</span> <span class="s2">"poly"</span><span class="p">:</span>
<span class="c1"># TODO: consider implementing the poly method (see Perl version)</span>
- <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">"M&S: build_q_table: Method 'poly' not implemented"</span><span class="p">)</span>
+ <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
+ <span class="s2">"M&S: build_q_table: Method 'poly' not implemented"</span>
+ <span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">msg</span> <span class="o">=</span> <span class="s2">"</span><span class="se">\t</span><span class="s2">M&S: build_q_table: Error no other methods available. The chosen method (</span><span class="si">{}</span><span class="s2">) does not exist!"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
- <span class="n">method</span>
- <span class="p">)</span>
+ <span class="n">method</span>
+ <span class="p">)</span>
<span class="n">verbose_print</span><span class="p">(</span>
<span class="n">msg</span><span class="p">,</span>
<span class="n">verbosity</span><span class="p">,</span>
@@ -1674,14 +1620,18 @@
<span class="p">)</span>
<span class="c1"># now we integrate and renormalise (if the table is not all zero)</span>
- <span class="n">I</span> <span class="o">=</span> <span class="n">get_integration_constant_q</span><span class="p">(</span><span class="n">q_interpolator</span><span class="p">,</span> <span class="n">tmp_table</span><span class="p">,</span> <span class="n">qdata</span><span class="p">,</span> <span class="n">verbosity</span><span class="o">=</span><span class="n">verbosity</span><span class="p">)</span>
+ <span class="n">I</span> <span class="o">=</span> <span class="n">get_integration_constant_q</span><span class="p">(</span>
+ <span class="n">q_interpolator</span><span class="p">,</span> <span class="n">tmp_table</span><span class="p">,</span> <span class="n">qdata</span><span class="p">,</span> <span class="n">verbosity</span><span class="o">=</span><span class="n">verbosity</span>
+ <span class="p">)</span>
<span class="k">if</span> <span class="n">I</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
<span class="c1"># normalise to 1.0 by dividing the data by 1.0/$I</span>
<span class="n">q_interpolator</span><span class="o">.</span><span class="n">multiply_table_column</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mf">1.0</span> <span class="o">/</span> <span class="n">I</span><span class="p">)</span>
<span class="c1"># test this</span>
- <span class="n">new_I</span> <span class="o">=</span> <span class="n">get_integration_constant_q</span><span class="p">(</span><span class="n">q_interpolator</span><span class="p">,</span> <span class="n">tmp_table</span><span class="p">,</span> <span class="n">qdata</span><span class="p">,</span> <span class="n">verbosity</span><span class="o">=</span><span class="n">verbosity</span><span class="p">)</span>
+ <span class="n">new_I</span> <span class="o">=</span> <span class="n">get_integration_constant_q</span><span class="p">(</span>
+ <span class="n">q_interpolator</span><span class="p">,</span> <span class="n">tmp_table</span><span class="p">,</span> <span class="n">qdata</span><span class="p">,</span> <span class="n">verbosity</span><span class="o">=</span><span class="n">verbosity</span>
+ <span class="p">)</span>
<span class="c1"># fail if error in integral > 1e-6 (should be ~ machine precision)</span>
<span class="k">if</span> <span class="nb">abs</span><span class="p">(</span><span class="mf">1.0</span> <span class="o">-</span> <span class="n">new_I</span><span class="p">)</span> <span class="o">></span> <span class="mf">1e-6</span><span class="p">:</span>
@@ -1774,8 +1724,8 @@
<span class="n">x</span> <span class="o">=</span> <span class="n">q_interpolator</span><span class="o">.</span><span class="n">interpolate</span><span class="p">([</span><span class="n">q</span><span class="p">])</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
<span class="n">msg</span> <span class="o">=</span> <span class="s2">"</span><span class="se">\t</span><span class="s2">M&S: build_q_table: Q interpolator table interpolation failed.</span><span class="se">\n\t\t</span><span class="s2">tmp_table = </span><span class="si">{}</span><span class="se">\n\t\t</span><span class="s2">q_data = </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
- <span class="nb">str</span><span class="p">(</span><span class="n">tmp_table</span><span class="p">),</span> <span class="nb">str</span><span class="p">(</span><span class="n">qdata</span><span class="p">)</span>
- <span class="p">)</span>
+ <span class="nb">str</span><span class="p">(</span><span class="n">tmp_table</span><span class="p">),</span> <span class="nb">str</span><span class="p">(</span><span class="n">qdata</span><span class="p">)</span>
+ <span class="p">)</span>
<span class="n">verbose_print</span><span class="p">(</span>
<span class="n">msg</span><span class="p">,</span>
<span class="n">verbosity</span><span class="p">,</span>
@@ -1819,7 +1769,12 @@
<div class="viewcode-block" id="calc_e_integral"><a class="viewcode-back" href="../../../distribution_functions.html#binarycpython.utils.distribution_functions.calc_e_integral">[docs]</a><span class="k">def</span> <span class="nf">calc_e_integral</span><span class="p">(</span>
- <span class="n">options</span><span class="p">,</span> <span class="n">integrals_string</span><span class="p">,</span> <span class="n">interpolator_name</span><span class="p">,</span> <span class="n">mass_string</span><span class="p">,</span> <span class="n">period_string</span><span class="p">,</span> <span class="n">verbosity</span><span class="o">=</span><span class="mi">0</span>
+ <span class="n">options</span><span class="p">,</span>
+ <span class="n">integrals_string</span><span class="p">,</span>
+ <span class="n">interpolator_name</span><span class="p">,</span>
+ <span class="n">mass_string</span><span class="p">,</span>
+ <span class="n">period_string</span><span class="p">,</span>
+ <span class="n">verbosity</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span>
<span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Function to calculate the P integral</span>
@@ -1854,7 +1809,15 @@
<span class="n">Moecache</span><span class="p">[</span><span class="n">integrals_string</span><span class="p">][</span><span class="n">mass_period_string</span><span class="p">]</span> <span class="o">=</span> <span class="n">I</span>
<span class="n">verbose_print</span><span class="p">(</span>
<span class="s2">"</span><span class="se">\t</span><span class="s2">M&S: calc_ecc_integral: min_ecc: </span><span class="si">{}</span><span class="s2"> max ecc: </span><span class="si">{}</span><span class="s2"> integrals_string: </span><span class="si">{}</span><span class="s2"> interpolator_name: </span><span class="si">{}</span><span class="s2"> mass_string: </span><span class="si">{}</span><span class="s2"> period_string: </span><span class="si">{}</span><span class="s2"> mass: </span><span class="si">{}</span><span class="s2"> period: </span><span class="si">{}</span><span class="s2"> I: </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
- <span class="n">min_ecc</span><span class="p">,</span> <span class="n">max_ecc</span><span class="p">,</span> <span class="n">integrals_string</span><span class="p">,</span> <span class="n">interpolator_name</span><span class="p">,</span> <span class="n">mass_string</span><span class="p">,</span> <span class="n">period_string</span><span class="p">,</span> <span class="n">options</span><span class="p">[</span><span class="n">mass_string</span><span class="p">],</span> <span class="n">options</span><span class="p">[</span><span class="n">period_string</span><span class="p">],</span> <span class="n">I</span>
+ <span class="n">min_ecc</span><span class="p">,</span>
+ <span class="n">max_ecc</span><span class="p">,</span>
+ <span class="n">integrals_string</span><span class="p">,</span>
+ <span class="n">interpolator_name</span><span class="p">,</span>
+ <span class="n">mass_string</span><span class="p">,</span>
+ <span class="n">period_string</span><span class="p">,</span>
+ <span class="n">options</span><span class="p">[</span><span class="n">mass_string</span><span class="p">],</span>
+ <span class="n">options</span><span class="p">[</span><span class="n">period_string</span><span class="p">],</span>
+ <span class="n">I</span><span class="p">,</span>
<span class="p">),</span>
<span class="n">verbosity</span><span class="p">,</span>
<span class="n">_MS_VERBOSITY_LEVEL</span><span class="p">,</span>
@@ -1862,7 +1825,15 @@
<span class="k">else</span><span class="p">:</span>
<span class="n">verbose_print</span><span class="p">(</span>
<span class="s2">"</span><span class="se">\t</span><span class="s2">M&S: calc_ecc_integral: Found cached value for min_ecc: </span><span class="si">{}</span><span class="s2"> max ecc: </span><span class="si">{}</span><span class="s2"> integrals_string: </span><span class="si">{}</span><span class="s2"> interpolator_name: </span><span class="si">{}</span><span class="s2"> mass_string: </span><span class="si">{}</span><span class="s2"> period_string: </span><span class="si">{}</span><span class="s2"> mass: </span><span class="si">{}</span><span class="s2"> period: </span><span class="si">{}</span><span class="s2"> I: </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
- <span class="n">min_ecc</span><span class="p">,</span> <span class="n">max_ecc</span><span class="p">,</span> <span class="n">integrals_string</span><span class="p">,</span> <span class="n">interpolator_name</span><span class="p">,</span> <span class="n">mass_string</span><span class="p">,</span> <span class="n">period_string</span><span class="p">,</span> <span class="n">options</span><span class="p">[</span><span class="n">mass_string</span><span class="p">],</span> <span class="n">options</span><span class="p">[</span><span class="n">period_string</span><span class="p">],</span> <span class="n">Moecache</span><span class="p">[</span><span class="n">integrals_string</span><span class="p">][</span><span class="n">mass_period_string</span><span class="p">]</span>
+ <span class="n">min_ecc</span><span class="p">,</span>
+ <span class="n">max_ecc</span><span class="p">,</span>
+ <span class="n">integrals_string</span><span class="p">,</span>
+ <span class="n">interpolator_name</span><span class="p">,</span>
+ <span class="n">mass_string</span><span class="p">,</span>
+ <span class="n">period_string</span><span class="p">,</span>
+ <span class="n">options</span><span class="p">[</span><span class="n">mass_string</span><span class="p">],</span>
+ <span class="n">options</span><span class="p">[</span><span class="n">period_string</span><span class="p">],</span>
+ <span class="n">Moecache</span><span class="p">[</span><span class="n">integrals_string</span><span class="p">][</span><span class="n">mass_period_string</span><span class="p">],</span>
<span class="p">),</span>
<span class="n">verbosity</span><span class="p">,</span>
<span class="n">_MS_VERBOSITY_LEVEL</span><span class="p">,</span>
@@ -1902,7 +1873,12 @@
<span class="n">Moecache</span><span class="p">[</span><span class="n">integrals_string</span><span class="p">][</span><span class="n">options</span><span class="p">[</span><span class="n">mass_string</span><span class="p">]]</span> <span class="o">=</span> <span class="n">I</span>
<span class="n">verbose_print</span><span class="p">(</span>
<span class="s2">"</span><span class="se">\t</span><span class="s2">M&S: calc_P_integral: min_P: </span><span class="si">{}</span><span class="s2"> integrals_string: </span><span class="si">{}</span><span class="s2"> interpolator_name: </span><span class="si">{}</span><span class="s2"> mass_string: </span><span class="si">{}</span><span class="s2"> mass: </span><span class="si">{}</span><span class="s2"> I: </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
- <span class="n">min_P</span><span class="p">,</span> <span class="n">integrals_string</span><span class="p">,</span> <span class="n">interpolator_name</span><span class="p">,</span> <span class="n">mass_string</span><span class="p">,</span> <span class="n">options</span><span class="p">[</span><span class="n">mass_string</span><span class="p">],</span> <span class="n">I</span>
+ <span class="n">min_P</span><span class="p">,</span>
+ <span class="n">integrals_string</span><span class="p">,</span>
+ <span class="n">interpolator_name</span><span class="p">,</span>
+ <span class="n">mass_string</span><span class="p">,</span>
+ <span class="n">options</span><span class="p">[</span><span class="n">mass_string</span><span class="p">],</span>
+ <span class="n">I</span><span class="p">,</span>
<span class="p">),</span>
<span class="n">verbosity</span><span class="p">,</span>
<span class="n">_MS_VERBOSITY_LEVEL</span><span class="p">,</span>
@@ -1910,12 +1886,18 @@
<span class="k">else</span><span class="p">:</span>
<span class="n">verbose_print</span><span class="p">(</span>
<span class="s2">"</span><span class="se">\t</span><span class="s2">M&S: calc_P_integral: Found cached value for min_P: </span><span class="si">{}</span><span class="s2"> integrals_string: </span><span class="si">{}</span><span class="s2"> interpolator_name: </span><span class="si">{}</span><span class="s2"> mass_string: </span><span class="si">{}</span><span class="s2"> mass: </span><span class="si">{}</span><span class="s2"> I: </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
- <span class="n">min_P</span><span class="p">,</span> <span class="n">integrals_string</span><span class="p">,</span> <span class="n">interpolator_name</span><span class="p">,</span> <span class="n">mass_string</span><span class="p">,</span> <span class="n">options</span><span class="p">[</span><span class="n">mass_string</span><span class="p">],</span> <span class="n">Moecache</span><span class="p">[</span><span class="n">integrals_string</span><span class="p">][</span><span class="n">options</span><span class="p">[</span><span class="n">mass_string</span><span class="p">]]</span>
+ <span class="n">min_P</span><span class="p">,</span>
+ <span class="n">integrals_string</span><span class="p">,</span>
+ <span class="n">interpolator_name</span><span class="p">,</span>
+ <span class="n">mass_string</span><span class="p">,</span>
+ <span class="n">options</span><span class="p">[</span><span class="n">mass_string</span><span class="p">],</span>
+ <span class="n">Moecache</span><span class="p">[</span><span class="n">integrals_string</span><span class="p">][</span><span class="n">options</span><span class="p">[</span><span class="n">mass_string</span><span class="p">]],</span>
<span class="p">),</span>
<span class="n">verbosity</span><span class="p">,</span>
<span class="n">_MS_VERBOSITY_LEVEL</span><span class="p">,</span>
<span class="p">)</span></div>
+
<div class="viewcode-block" id="calc_total_probdens"><a class="viewcode-back" href="../../../distribution_functions.html#binarycpython.utils.distribution_functions.calc_total_probdens">[docs]</a><span class="k">def</span> <span class="nf">calc_total_probdens</span><span class="p">(</span><span class="n">prob_dict</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Function to calculate the total probability density</span>
@@ -1924,10 +1906,11 @@
<span class="n">total_probdens</span> <span class="o">=</span> <span class="mi">1</span>
<span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="n">prob_dict</span><span class="p">:</span>
<span class="n">total_probdens</span> <span class="o">*=</span> <span class="n">prob_dict</span><span class="p">[</span><span class="n">key</span><span class="p">]</span>
- <span class="n">prob_dict</span><span class="p">[</span><span class="s1">'total_probdens'</span><span class="p">]</span> <span class="o">=</span> <span class="n">total_probdens</span>
+ <span class="n">prob_dict</span><span class="p">[</span><span class="s2">"total_probdens"</span><span class="p">]</span> <span class="o">=</span> <span class="n">total_probdens</span>
<span class="k">return</span> <span class="n">prob_dict</span></div>
+
<div class="viewcode-block" id="Moe_di_Stefano_2017_pdf"><a class="viewcode-back" href="../../../distribution_functions.html#binarycpython.utils.distribution_functions.Moe_di_Stefano_2017_pdf">[docs]</a><span class="k">def</span> <span class="nf">Moe_di_Stefano_2017_pdf</span><span class="p">(</span><span class="n">options</span><span class="p">,</span> <span class="n">verbosity</span><span class="o">=</span><span class="mi">0</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Moe & diStefano function to calculate the probability density.</span>
@@ -1950,7 +1933,9 @@
<span class="n">_MS_VERBOSITY_LEVEL</span><span class="p">,</span>
<span class="p">)</span>
- <span class="n">prob_dict</span> <span class="o">=</span> <span class="p">{}</span> <span class="c1"># Dictionary containing all the pdf values for the different parameters</span>
+ <span class="n">prob_dict</span> <span class="o">=</span> <span class="p">(</span>
+ <span class="p">{}</span>
+ <span class="p">)</span> <span class="c1"># Dictionary containing all the pdf values for the different parameters</span>
<span class="c1"># Get the multiplicity from the options, and if its not there, calculate it based on the</span>
<span class="c1"># TODO: the function below makes no sense. We NEED to pass the multiplicity in the</span>
@@ -1981,11 +1966,13 @@
<span class="c1"># multiplicity fraction</span>
<span class="c1"># Calculate the probability, or rather, fraction, of stars that belong to this mass</span>
- <span class="n">multiplicity_probability</span> <span class="o">=</span> <span class="n">Moe_di_Stefano_2017_multiplicity_fractions</span><span class="p">(</span><span class="n">options</span><span class="p">,</span> <span class="n">verbosity</span><span class="p">)[</span><span class="n">multiplicity</span> <span class="o">-</span> <span class="mi">1</span><span class="p">]</span>
- <span class="n">prob_dict</span><span class="p">[</span><span class="s1">'multiplicity'</span><span class="p">]</span> <span class="o">=</span> <span class="n">multiplicity_probability</span>
+ <span class="n">multiplicity_probability</span> <span class="o">=</span> <span class="n">Moe_di_Stefano_2017_multiplicity_fractions</span><span class="p">(</span>
+ <span class="n">options</span><span class="p">,</span> <span class="n">verbosity</span>
+ <span class="p">)[</span><span class="n">multiplicity</span> <span class="o">-</span> <span class="mi">1</span><span class="p">]</span>
+ <span class="n">prob_dict</span><span class="p">[</span><span class="s2">"multiplicity"</span><span class="p">]</span> <span class="o">=</span> <span class="n">multiplicity_probability</span>
<span class="n">verbose_print</span><span class="p">(</span>
<span class="s2">"</span><span class="se">\t</span><span class="s2">M&S: Moe_di_Stefano_2017_pdf: Appended multiplicity (mass1 = </span><span class="si">{}</span><span class="s2">) probability (</span><span class="si">{}</span><span class="s2">) to the prob dict (</span><span class="si">{}</span><span class="s2">)"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
- <span class="n">options</span><span class="p">[</span><span class="s2">"M_1"</span><span class="p">],</span> <span class="n">prob_dict</span><span class="p">[</span><span class="s1">'multiplicity'</span><span class="p">],</span> <span class="n">prob_dict</span>
+ <span class="n">options</span><span class="p">[</span><span class="s2">"M_1"</span><span class="p">],</span> <span class="n">prob_dict</span><span class="p">[</span><span class="s2">"multiplicity"</span><span class="p">],</span> <span class="n">prob_dict</span>
<span class="p">),</span>
<span class="n">verbosity</span><span class="p">,</span>
<span class="n">_MS_VERBOSITY_LEVEL</span><span class="p">,</span>
@@ -2000,10 +1987,10 @@
<span class="c1"># TODO: Create an n-part-powerlaw method that can have breakpoints and slopes. I'm using a three-part power law now.</span>
<span class="c1"># TODO: is this actually the correct way? putting the M1 in there? Do we sample in log space?</span>
<span class="n">M1_probability</span> <span class="o">=</span> <span class="n">Kroupa2001</span><span class="p">(</span><span class="n">options</span><span class="p">[</span><span class="s2">"M_1"</span><span class="p">])</span> <span class="o">*</span> <span class="n">options</span><span class="p">[</span><span class="s2">"M_1"</span><span class="p">]</span>
- <span class="n">prob_dict</span><span class="p">[</span><span class="s1">'M_1'</span><span class="p">]</span> <span class="o">=</span> <span class="n">M1_probability</span>
+ <span class="n">prob_dict</span><span class="p">[</span><span class="s2">"M_1"</span><span class="p">]</span> <span class="o">=</span> <span class="n">M1_probability</span>
<span class="n">verbose_print</span><span class="p">(</span>
<span class="s2">"</span><span class="se">\t</span><span class="s2">M&S: Moe_di_Stefano_2017_pdf: Appended Mass (m=</span><span class="si">{}</span><span class="s2">) probability (</span><span class="si">{}</span><span class="s2">) to the prob dict (</span><span class="si">{}</span><span class="s2">)"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
- <span class="n">options</span><span class="p">[</span><span class="s2">"M_1"</span><span class="p">],</span> <span class="n">prob_dict</span><span class="p">[</span><span class="s1">'M_1'</span><span class="p">],</span> <span class="n">prob_dict</span>
+ <span class="n">options</span><span class="p">[</span><span class="s2">"M_1"</span><span class="p">],</span> <span class="n">prob_dict</span><span class="p">[</span><span class="s2">"M_1"</span><span class="p">],</span> <span class="n">prob_dict</span>
<span class="p">),</span>
<span class="n">verbosity</span><span class="p">,</span>
<span class="n">_MS_VERBOSITY_LEVEL</span><span class="p">,</span>
@@ -2038,7 +2025,11 @@
<span class="p">)</span>
<span class="c1"># Make a table storing Moe's data for q distributions</span>
- <span class="k">if</span> <span class="n">options</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"M_2"</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span> <span class="ow">or</span> <span class="n">options</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"M_3"</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span> <span class="ow">or</span> <span class="n">options</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"M_4"</span><span class="p">,</span> <span class="kc">None</span><span class="p">):</span>
+ <span class="k">if</span> <span class="p">(</span>
+ <span class="n">options</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"M_2"</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+ <span class="ow">or</span> <span class="n">options</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"M_3"</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+ <span class="ow">or</span> <span class="n">options</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"M_4"</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+ <span class="p">):</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">Moecache</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"rinterpolator_q"</span><span class="p">,</span> <span class="kc">None</span><span class="p">):</span>
<span class="n">Moecache</span><span class="p">[</span><span class="s2">"rinterpolator_q"</span><span class="p">]</span> <span class="o">=</span> <span class="n">py_rinterpolate</span><span class="o">.</span><span class="n">Rinterpolate</span><span class="p">(</span>
<span class="n">table</span><span class="o">=</span><span class="n">Moecache</span><span class="p">[</span><span class="s2">"q_distributions"</span><span class="p">],</span> <span class="c1"># Contains the table of data</span>
@@ -2056,10 +2047,12 @@
<span class="c1"># Make a table storing Moe's data for q distributions, but only if the ecc is actually sampled</span>
<span class="k">if</span> <span class="s2">"ecc"</span> <span class="ow">in</span> <span class="n">options</span><span class="p">:</span>
- <span class="k">if</span> <span class="ow">not</span> <span class="n">options</span><span class="p">[</span><span class="s1">'ecc'</span><span class="p">]</span><span class="o">==</span><span class="kc">None</span><span class="p">:</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">options</span><span class="p">[</span><span class="s2">"ecc"</span><span class="p">]</span> <span class="o">==</span> <span class="kc">None</span><span class="p">:</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">Moecache</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"rinterpolator_e"</span><span class="p">,</span> <span class="kc">None</span><span class="p">):</span>
<span class="n">Moecache</span><span class="p">[</span><span class="s2">"rinterpolator_e"</span><span class="p">]</span> <span class="o">=</span> <span class="n">py_rinterpolate</span><span class="o">.</span><span class="n">Rinterpolate</span><span class="p">(</span>
- <span class="n">table</span><span class="o">=</span><span class="n">Moecache</span><span class="p">[</span><span class="s2">"ecc_distributions"</span><span class="p">],</span> <span class="c1"># Contains the table of data</span>
+ <span class="n">table</span><span class="o">=</span><span class="n">Moecache</span><span class="p">[</span>
+ <span class="s2">"ecc_distributions"</span>
+ <span class="p">],</span> <span class="c1"># Contains the table of data</span>
<span class="n">nparams</span><span class="o">=</span><span class="mi">3</span><span class="p">,</span> <span class="c1"># log10M, log10P, e</span>
<span class="n">ndata</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="c1">#</span>
<span class="n">verbosity</span><span class="o">=</span><span class="n">verbosity</span> <span class="o">-</span> <span class="p">(</span><span class="n">_MS_VERBOSITY_INTERPOLATOR_LEVEL</span> <span class="o">-</span> <span class="mi">1</span><span class="p">),</span>
@@ -2095,10 +2088,10 @@
<span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">log10</span><span class="p">(</span><span class="n">options</span><span class="p">[</span><span class="s2">"M_1"</span><span class="p">]),</span> <span class="n">np</span><span class="o">.</span><span class="n">log10</span><span class="p">(</span><span class="n">options</span><span class="p">[</span><span class="s2">"P"</span><span class="p">])]</span>
<span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
<span class="n">p_val</span> <span class="o">=</span> <span class="n">p_val</span> <span class="o">/</span> <span class="n">Moecache</span><span class="p">[</span><span class="s2">"P_integrals"</span><span class="p">][</span><span class="n">options</span><span class="p">[</span><span class="s2">"M_1"</span><span class="p">]]</span>
- <span class="n">prob_dict</span><span class="p">[</span><span class="s1">'P'</span><span class="p">]</span> <span class="o">=</span> <span class="n">p_val</span>
+ <span class="n">prob_dict</span><span class="p">[</span><span class="s2">"P"</span><span class="p">]</span> <span class="o">=</span> <span class="n">p_val</span>
<span class="n">verbose_print</span><span class="p">(</span>
<span class="s2">"</span><span class="se">\t</span><span class="s2">M&S: Moe_di_Stefano_2017_pdf: Appended period (m=</span><span class="si">{}</span><span class="s2">, P=</span><span class="si">{}</span><span class="s2">) probability (</span><span class="si">{}</span><span class="s2">) to the prob list (</span><span class="si">{}</span><span class="s2">)"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
- <span class="n">options</span><span class="p">[</span><span class="s2">"M_1"</span><span class="p">],</span> <span class="n">options</span><span class="p">[</span><span class="s2">"P"</span><span class="p">],</span> <span class="n">prob_dict</span><span class="p">[</span><span class="s1">'P'</span><span class="p">],</span> <span class="n">prob_dict</span>
+ <span class="n">options</span><span class="p">[</span><span class="s2">"M_1"</span><span class="p">],</span> <span class="n">options</span><span class="p">[</span><span class="s2">"P"</span><span class="p">],</span> <span class="n">prob_dict</span><span class="p">[</span><span class="s2">"P"</span><span class="p">],</span> <span class="n">prob_dict</span>
<span class="p">),</span>
<span class="n">verbosity</span><span class="p">,</span>
<span class="n">_MS_VERBOSITY_LEVEL</span><span class="p">,</span>
@@ -2123,24 +2116,28 @@
<span class="c1"># Construct the q table</span>
<span class="n">build_q_table</span><span class="p">(</span><span class="n">options</span><span class="p">,</span> <span class="n">m_label</span><span class="p">,</span> <span class="n">p_label</span><span class="p">,</span> <span class="n">verbosity</span><span class="o">=</span><span class="n">verbosity</span><span class="p">)</span>
<span class="n">verbose_print</span><span class="p">(</span>
- <span class="s2">"</span><span class="se">\t</span><span class="s2">M&S: Moe_di_Stefano_2017_pdf: Created q_table (</span><span class="si">{}</span><span class="s2">) for m=</span><span class="si">{}</span><span class="s2"> p=</span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">Moecache</span><span class="p">[</span>
- <span class="s2">"rinterpolator_q_given_</span><span class="si">{}</span><span class="s2">_log10</span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">m_label</span><span class="p">,</span> <span class="n">p_label</span><span class="p">)</span>
- <span class="p">],</span> <span class="n">options</span><span class="p">[</span><span class="n">m_label</span><span class="p">],</span> <span class="n">options</span><span class="p">[</span><span class="n">p_label</span><span class="p">]),</span>
+ <span class="s2">"</span><span class="se">\t</span><span class="s2">M&S: Moe_di_Stefano_2017_pdf: Created q_table (</span><span class="si">{}</span><span class="s2">) for m=</span><span class="si">{}</span><span class="s2"> p=</span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+ <span class="n">Moecache</span><span class="p">[</span>
+ <span class="s2">"rinterpolator_q_given_</span><span class="si">{}</span><span class="s2">_log10</span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">m_label</span><span class="p">,</span> <span class="n">p_label</span><span class="p">)</span>
+ <span class="p">],</span>
+ <span class="n">options</span><span class="p">[</span><span class="n">m_label</span><span class="p">],</span>
+ <span class="n">options</span><span class="p">[</span><span class="n">p_label</span><span class="p">],</span>
+ <span class="p">),</span>
<span class="n">verbosity</span><span class="p">,</span>
<span class="n">_MS_VERBOSITY_LEVEL</span><span class="p">,</span>
<span class="p">)</span>
<span class="c1"># Add probability for the mass ratio</span>
<span class="n">q_prob</span> <span class="o">=</span> <span class="n">Moecache</span><span class="p">[</span>
- <span class="s2">"rinterpolator_q_given_</span><span class="si">{}</span><span class="s2">_log10</span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">m_label</span><span class="p">,</span> <span class="n">p_label</span><span class="p">)</span>
- <span class="p">]</span><span class="o">.</span><span class="n">interpolate</span><span class="p">([</span><span class="n">secondary_mass</span> <span class="o">/</span> <span class="n">primary_mass</span><span class="p">])[</span><span class="mi">0</span><span class="p">]</span>
- <span class="n">prob_dict</span><span class="p">[</span><span class="s1">'q'</span><span class="p">]</span> <span class="o">=</span> <span class="n">q_prob</span>
+ <span class="s2">"rinterpolator_q_given_</span><span class="si">{}</span><span class="s2">_log10</span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">m_label</span><span class="p">,</span> <span class="n">p_label</span><span class="p">)</span>
+ <span class="p">]</span><span class="o">.</span><span class="n">interpolate</span><span class="p">([</span><span class="n">secondary_mass</span> <span class="o">/</span> <span class="n">primary_mass</span><span class="p">])[</span><span class="mi">0</span><span class="p">]</span>
+ <span class="n">prob_dict</span><span class="p">[</span><span class="s2">"q"</span><span class="p">]</span> <span class="o">=</span> <span class="n">q_prob</span>
<span class="n">verbose_print</span><span class="p">(</span>
<span class="s2">"</span><span class="se">\t</span><span class="s2">M&S: Moe_di_Stefano_2017_pdf: appended mass ratio (M=</span><span class="si">{}</span><span class="s2"> P=</span><span class="si">{}</span><span class="s2"> q=</span><span class="si">{}</span><span class="s2">) probability (</span><span class="si">{}</span><span class="s2">) to the prob list (</span><span class="si">{}</span><span class="s2">) "</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
<span class="n">options</span><span class="p">[</span><span class="s2">"M_1"</span><span class="p">],</span>
<span class="n">options</span><span class="p">[</span><span class="s2">"P"</span><span class="p">],</span>
<span class="n">options</span><span class="p">[</span><span class="s2">"M_2"</span><span class="p">]</span> <span class="o">/</span> <span class="n">options</span><span class="p">[</span><span class="s2">"M_1"</span><span class="p">],</span>
- <span class="n">prob_dict</span><span class="p">[</span><span class="s1">'q'</span><span class="p">],</span>
+ <span class="n">prob_dict</span><span class="p">[</span><span class="s2">"q"</span><span class="p">],</span>
<span class="n">prob_dict</span><span class="p">,</span>
<span class="p">),</span>
<span class="n">verbosity</span><span class="p">,</span>
@@ -2156,7 +2153,7 @@
<span class="c1"># Only do this if the eccentricity is sampled</span>
<span class="k">if</span> <span class="s2">"ecc"</span> <span class="ow">in</span> <span class="n">options</span><span class="p">:</span>
- <span class="k">if</span> <span class="ow">not</span> <span class="n">options</span><span class="p">[</span><span class="s1">'ecc'</span><span class="p">]</span><span class="o">==</span><span class="kc">None</span><span class="p">:</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">options</span><span class="p">[</span><span class="s2">"ecc"</span><span class="p">]</span> <span class="o">==</span> <span class="kc">None</span><span class="p">:</span>
<span class="c1"># Calculate ecc integral or use cached value</span>
<span class="n">calc_e_integral</span><span class="p">(</span>
<span class="n">options</span><span class="p">,</span> <span class="s2">"ecc_integrals"</span><span class="p">,</span> <span class="s2">"rinterpolator_e"</span><span class="p">,</span> <span class="s2">"M_1"</span><span class="p">,</span> <span class="s2">"P"</span><span class="p">,</span> <span class="n">verbosity</span>
@@ -2168,10 +2165,14 @@
<span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">log10</span><span class="p">(</span><span class="n">options</span><span class="p">[</span><span class="s2">"M_1"</span><span class="p">]),</span> <span class="n">np</span><span class="o">.</span><span class="n">log10</span><span class="p">(</span><span class="n">options</span><span class="p">[</span><span class="s2">"P"</span><span class="p">]),</span> <span class="n">options</span><span class="p">[</span><span class="s2">"ecc"</span><span class="p">]]</span>
<span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
<span class="n">ecc_val</span> <span class="o">=</span> <span class="n">ecc_val</span> <span class="o">/</span> <span class="n">Moecache</span><span class="p">[</span><span class="s2">"ecc_integrals"</span><span class="p">][</span><span class="n">mass_period_string</span><span class="p">]</span>
- <span class="n">prob_dict</span><span class="p">[</span><span class="s1">'ecc'</span><span class="p">]</span> <span class="o">=</span> <span class="n">ecc_val</span>
+ <span class="n">prob_dict</span><span class="p">[</span><span class="s2">"ecc"</span><span class="p">]</span> <span class="o">=</span> <span class="n">ecc_val</span>
<span class="n">verbose_print</span><span class="p">(</span>
<span class="s2">"</span><span class="se">\t</span><span class="s2">M&S: Moe_di_Stefano_2017_pdf: Appended eccentricity (m=</span><span class="si">{}</span><span class="s2">, P=</span><span class="si">{}</span><span class="s2">, ecc=</span><span class="si">{}</span><span class="s2">) probability (</span><span class="si">{}</span><span class="s2">) to the prob list (</span><span class="si">{}</span><span class="s2">)"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
- <span class="n">options</span><span class="p">[</span><span class="s2">"M_1"</span><span class="p">],</span> <span class="n">options</span><span class="p">[</span><span class="s2">"P"</span><span class="p">],</span> <span class="n">options</span><span class="p">[</span><span class="s2">"ecc"</span><span class="p">],</span> <span class="n">prob_dict</span><span class="p">[</span><span class="s1">'ecc'</span><span class="p">],</span> <span class="n">prob_dict</span>
+ <span class="n">options</span><span class="p">[</span><span class="s2">"M_1"</span><span class="p">],</span>
+ <span class="n">options</span><span class="p">[</span><span class="s2">"P"</span><span class="p">],</span>
+ <span class="n">options</span><span class="p">[</span><span class="s2">"ecc"</span><span class="p">],</span>
+ <span class="n">prob_dict</span><span class="p">[</span><span class="s2">"ecc"</span><span class="p">],</span>
+ <span class="n">prob_dict</span><span class="p">,</span>
<span class="p">),</span>
<span class="n">verbosity</span><span class="p">,</span>
<span class="n">_MS_VERBOSITY_LEVEL</span><span class="p">,</span>
@@ -2201,7 +2202,7 @@
<span class="k">if</span> <span class="n">options</span><span class="p">[</span><span class="s2">"P2"</span><span class="p">]</span> <span class="o"><</span> <span class="n">min_P2</span><span class="p">:</span>
<span class="c1"># period is too short : system is not hierarchical</span>
- <span class="n">prob_dict</span><span class="p">[</span><span class="s1">'P2'</span><span class="p">]</span> <span class="o">=</span> <span class="mi">0</span>
+ <span class="n">prob_dict</span><span class="p">[</span><span class="s2">"P2"</span><span class="p">]</span> <span class="o">=</span> <span class="mi">0</span>
<span class="n">verbose_print</span><span class="p">(</span>
<span class="s2">"</span><span class="se">\t</span><span class="s2">M&S: Moe_di_Stefano_2017_pdf: period2 is too short: </span><span class="si">{}</span><span class="s2"> < </span><span class="si">{}</span><span class="s2">, system is not hierarchical. Added 0 to probability list"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
<span class="n">options</span><span class="p">[</span><span class="s2">"P1"</span><span class="p">],</span> <span class="n">min_P2</span>
@@ -2236,10 +2237,14 @@
<span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">log10</span><span class="p">(</span><span class="n">options</span><span class="p">[</span><span class="s2">"M_1+M_2"</span><span class="p">]),</span> <span class="n">np</span><span class="o">.</span><span class="n">log10</span><span class="p">(</span><span class="n">options</span><span class="p">[</span><span class="s2">"P2"</span><span class="p">])]</span>
<span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
<span class="n">p_val</span> <span class="o">=</span> <span class="n">p_val</span> <span class="o">/</span> <span class="n">Moecache</span><span class="p">[</span><span class="s2">"P2_integrals"</span><span class="p">][</span><span class="n">options</span><span class="p">[</span><span class="s2">"M_1+M_2"</span><span class="p">]]</span>
- <span class="n">prob_dict</span><span class="p">[</span><span class="s1">'P2'</span><span class="p">]</span> <span class="o">=</span> <span class="n">p_val</span>
+ <span class="n">prob_dict</span><span class="p">[</span><span class="s2">"P2"</span><span class="p">]</span> <span class="o">=</span> <span class="n">p_val</span>
<span class="n">verbose_print</span><span class="p">(</span>
<span class="s2">"</span><span class="se">\t</span><span class="s2">M&S: Moe_di_Stefano_2017_pdf: Appended period2 (m1=</span><span class="si">{}</span><span class="s2"> m2=</span><span class="si">{}</span><span class="s2">, P2=</span><span class="si">{}</span><span class="s2">) probability (</span><span class="si">{}</span><span class="s2">) to the prob list (</span><span class="si">{}</span><span class="s2">)"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
- <span class="n">options</span><span class="p">[</span><span class="s2">"M_1"</span><span class="p">],</span> <span class="n">options</span><span class="p">[</span><span class="s2">"M_2"</span><span class="p">],</span> <span class="n">options</span><span class="p">[</span><span class="s2">"P2"</span><span class="p">],</span> <span class="n">prob_dict</span><span class="p">[</span><span class="s1">'P2'</span><span class="p">],</span> <span class="n">prob_dict</span>
+ <span class="n">options</span><span class="p">[</span><span class="s2">"M_1"</span><span class="p">],</span>
+ <span class="n">options</span><span class="p">[</span><span class="s2">"M_2"</span><span class="p">],</span>
+ <span class="n">options</span><span class="p">[</span><span class="s2">"P2"</span><span class="p">],</span>
+ <span class="n">prob_dict</span><span class="p">[</span><span class="s2">"P2"</span><span class="p">],</span>
+ <span class="n">prob_dict</span><span class="p">,</span>
<span class="p">),</span>
<span class="n">verbosity</span><span class="p">,</span>
<span class="n">_MS_VERBOSITY_LEVEL</span><span class="p">,</span>
@@ -2272,14 +2277,14 @@
<span class="n">q2_val</span> <span class="o">=</span> <span class="n">Moecache</span><span class="p">[</span>
<span class="s2">"rinterpolator_q_given_</span><span class="si">{}</span><span class="s2">_log10</span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">m_label</span><span class="p">,</span> <span class="n">p_label</span><span class="p">)</span>
<span class="p">]</span><span class="o">.</span><span class="n">interpolate</span><span class="p">([</span><span class="n">secondary_mass</span> <span class="o">/</span> <span class="n">primary_mass</span><span class="p">])[</span><span class="mi">0</span><span class="p">]</span>
- <span class="n">prob_dict</span><span class="p">[</span><span class="s1">'q2'</span><span class="p">]</span> <span class="o">=</span> <span class="n">q2_val</span>
+ <span class="n">prob_dict</span><span class="p">[</span><span class="s2">"q2"</span><span class="p">]</span> <span class="o">=</span> <span class="n">q2_val</span>
<span class="n">verbose_print</span><span class="p">(</span>
<span class="s2">"</span><span class="se">\t</span><span class="s2">M&S: Moe_di_Stefano_2017_pdf: appended mass ratio (M_1+M_2=</span><span class="si">{}</span><span class="s2"> M_3=</span><span class="si">{}</span><span class="s2"> P=</span><span class="si">{}</span><span class="s2"> q=</span><span class="si">{}</span><span class="s2">) probability (</span><span class="si">{}</span><span class="s2">) to the prob list (</span><span class="si">{}</span><span class="s2">) "</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
<span class="n">options</span><span class="p">[</span><span class="s2">"M_1+M_2"</span><span class="p">],</span>
<span class="n">options</span><span class="p">[</span><span class="s2">"M_3"</span><span class="p">],</span>
<span class="n">options</span><span class="p">[</span><span class="s2">"P"</span><span class="p">],</span>
<span class="n">secondary_mass</span> <span class="o">/</span> <span class="n">primary_mass</span><span class="p">,</span>
- <span class="n">prob_dict</span><span class="p">[</span><span class="s1">'q2'</span><span class="p">],</span>
+ <span class="n">prob_dict</span><span class="p">[</span><span class="s2">"q2"</span><span class="p">],</span>
<span class="n">prob_dict</span><span class="p">,</span>
<span class="p">),</span>
<span class="n">verbosity</span><span class="p">,</span>
@@ -2323,10 +2328,14 @@
<span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">log10</span><span class="p">(</span><span class="n">options</span><span class="p">[</span><span class="s2">"M_1+M_2"</span><span class="p">]),</span> <span class="n">np</span><span class="o">.</span><span class="n">log10</span><span class="p">(</span><span class="n">options</span><span class="p">[</span><span class="s2">"P2"</span><span class="p">])]</span>
<span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
<span class="n">p_val</span> <span class="o">=</span> <span class="n">p_val</span> <span class="o">/</span> <span class="n">Moecache</span><span class="p">[</span><span class="s2">"P2_integrals"</span><span class="p">][</span><span class="n">options</span><span class="p">[</span><span class="s2">"M_1+M_2"</span><span class="p">]]</span>
- <span class="n">prob_dict</span><span class="p">[</span><span class="s1">'P3'</span><span class="p">]</span> <span class="o">=</span> <span class="n">p_val</span>
+ <span class="n">prob_dict</span><span class="p">[</span><span class="s2">"P3"</span><span class="p">]</span> <span class="o">=</span> <span class="n">p_val</span>
<span class="n">verbose_print</span><span class="p">(</span>
<span class="s2">"</span><span class="se">\t</span><span class="s2">M&S: Moe_di_Stefano_2017_pdf: Appended period2 (M=4) (M_1=</span><span class="si">{}</span><span class="s2"> M_2=</span><span class="si">{}</span><span class="s2">, P2=</span><span class="si">{}</span><span class="s2">) probability (</span><span class="si">{}</span><span class="s2">) to the prob list (</span><span class="si">{}</span><span class="s2">)"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
- <span class="n">options</span><span class="p">[</span><span class="s2">"M_1"</span><span class="p">],</span> <span class="n">options</span><span class="p">[</span><span class="s2">"M_2"</span><span class="p">],</span> <span class="n">options</span><span class="p">[</span><span class="s2">"P2"</span><span class="p">],</span> <span class="n">prob_dict</span><span class="p">[</span><span class="s1">'P3'</span><span class="p">],</span> <span class="n">prob_dict</span>
+ <span class="n">options</span><span class="p">[</span><span class="s2">"M_1"</span><span class="p">],</span>
+ <span class="n">options</span><span class="p">[</span><span class="s2">"M_2"</span><span class="p">],</span>
+ <span class="n">options</span><span class="p">[</span><span class="s2">"P2"</span><span class="p">],</span>
+ <span class="n">prob_dict</span><span class="p">[</span><span class="s2">"P3"</span><span class="p">],</span>
+ <span class="n">prob_dict</span><span class="p">,</span>
<span class="p">),</span>
<span class="n">verbosity</span><span class="p">,</span>
<span class="n">_MS_VERBOSITY_LEVEL</span><span class="p">,</span>
@@ -2358,16 +2367,16 @@
<span class="c1"># Add the probability</span>
<span class="n">q3_prob</span> <span class="o">=</span> <span class="n">Moecache</span><span class="p">[</span>
- <span class="s2">"rinterpolator_q_given_</span><span class="si">{}</span><span class="s2">_log10</span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">m_label</span><span class="p">,</span> <span class="n">p_label</span><span class="p">)</span>
+ <span class="s2">"rinterpolator_q_given_</span><span class="si">{}</span><span class="s2">_log10</span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">m_label</span><span class="p">,</span> <span class="n">p_label</span><span class="p">)</span>
<span class="p">]</span><span class="o">.</span><span class="n">interpolate</span><span class="p">([</span><span class="n">secondary_mass</span> <span class="o">/</span> <span class="n">primary_mass</span><span class="p">])[</span><span class="mi">0</span><span class="p">]</span>
- <span class="n">prob_dict</span><span class="p">[</span><span class="s1">'q3'</span><span class="p">]</span> <span class="o">=</span> <span class="n">q3_prob</span>
+ <span class="n">prob_dict</span><span class="p">[</span><span class="s2">"q3"</span><span class="p">]</span> <span class="o">=</span> <span class="n">q3_prob</span>
<span class="n">verbose_print</span><span class="p">(</span>
<span class="s2">"</span><span class="se">\t</span><span class="s2">M&S: Moe_di_Stefano_2017_pdf: appended mass ratio (M_1+M_2=</span><span class="si">{}</span><span class="s2"> M_3=</span><span class="si">{}</span><span class="s2"> P=</span><span class="si">{}</span><span class="s2"> q=</span><span class="si">{}</span><span class="s2">) probability (</span><span class="si">{}</span><span class="s2">) to the prob list (</span><span class="si">{}</span><span class="s2">) "</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
<span class="n">options</span><span class="p">[</span><span class="s2">"M_1+M_2"</span><span class="p">],</span>
<span class="n">options</span><span class="p">[</span><span class="s2">"M_3"</span><span class="p">],</span>
<span class="n">options</span><span class="p">[</span><span class="s2">"P"</span><span class="p">],</span>
<span class="n">secondary_mass</span> <span class="o">/</span> <span class="n">primary_mass</span><span class="p">,</span>
- <span class="n">prob_dict</span><span class="p">[</span><span class="s1">'q3'</span><span class="p">],</span>
+ <span class="n">prob_dict</span><span class="p">[</span><span class="s2">"q3"</span><span class="p">],</span>
<span class="n">prob_dict</span><span class="p">,</span>
<span class="p">),</span>
<span class="n">verbosity</span><span class="p">,</span>
@@ -2382,8 +2391,8 @@
<span class="c1"># check for input of multiplicity</span>
<span class="k">elif</span> <span class="n">multiplicity</span> <span class="ow">not</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">5</span><span class="p">):</span>
<span class="n">msg</span> <span class="o">=</span> <span class="s2">"</span><span class="se">\t</span><span class="s2">M&S: Moe_di_Stefano_2017_pdf: Unknown multiplicity </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
- <span class="n">multiplicity</span>
- <span class="p">)</span>
+ <span class="n">multiplicity</span>
+ <span class="p">)</span>
<span class="n">verbose_print</span><span class="p">(</span>
<span class="n">msg</span><span class="p">,</span>
<span class="n">verbosity</span><span class="p">,</span>
@@ -2401,7 +2410,7 @@
<span class="n">options</span><span class="p">[</span><span class="s2">"M_1"</span><span class="p">],</span>
<span class="nb">len</span><span class="p">(</span><span class="n">prob_dict</span><span class="p">),</span>
<span class="nb">str</span><span class="p">(</span><span class="n">prob_dict</span><span class="p">),</span>
- <span class="n">prob_dict</span><span class="p">[</span><span class="s1">'total_probdens'</span><span class="p">]</span>
+ <span class="n">prob_dict</span><span class="p">[</span><span class="s2">"total_probdens"</span><span class="p">],</span>
<span class="p">),</span>
<span class="n">verbosity</span><span class="p">,</span>
<span class="n">_MS_VERBOSITY_LEVEL</span><span class="p">,</span>
@@ -2412,10 +2421,10 @@
<span class="n">options</span><span class="p">[</span><span class="s2">"M_1"</span><span class="p">],</span>
<span class="n">options</span><span class="p">[</span><span class="s2">"M_2"</span><span class="p">]</span> <span class="o">/</span> <span class="n">options</span><span class="p">[</span><span class="s2">"M_1"</span><span class="p">]</span> <span class="k">if</span> <span class="n">options</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"M_2"</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span> <span class="k">else</span> <span class="s2">"N/A"</span><span class="p">,</span>
<span class="n">np</span><span class="o">.</span><span class="n">log10</span><span class="p">(</span><span class="n">options</span><span class="p">[</span><span class="s2">"P"</span><span class="p">]),</span>
- <span class="n">options</span><span class="p">[</span><span class="s1">'ecc'</span><span class="p">]</span> <span class="k">if</span> <span class="n">options</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"ecc"</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span> <span class="k">else</span> <span class="s2">"N/A"</span><span class="p">,</span>
+ <span class="n">options</span><span class="p">[</span><span class="s2">"ecc"</span><span class="p">]</span> <span class="k">if</span> <span class="n">options</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"ecc"</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span> <span class="k">else</span> <span class="s2">"N/A"</span><span class="p">,</span>
<span class="nb">len</span><span class="p">(</span><span class="n">prob_dict</span><span class="p">),</span>
<span class="nb">str</span><span class="p">(</span><span class="n">prob_dict</span><span class="p">),</span>
- <span class="n">prob_dict</span><span class="p">[</span><span class="s1">'total_probdens'</span><span class="p">]</span>
+ <span class="n">prob_dict</span><span class="p">[</span><span class="s2">"total_probdens"</span><span class="p">],</span>
<span class="p">),</span>
<span class="n">verbosity</span><span class="p">,</span>
<span class="n">_MS_VERBOSITY_LEVEL</span><span class="p">,</span>
@@ -2432,7 +2441,7 @@
<span class="n">options</span><span class="p">[</span><span class="s2">"ecc2"</span><span class="p">]</span> <span class="k">if</span> <span class="n">options</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"ecc2"</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span> <span class="k">else</span> <span class="s2">"N/A"</span><span class="p">,</span>
<span class="nb">len</span><span class="p">(</span><span class="n">prob_dict</span><span class="p">),</span>
<span class="nb">str</span><span class="p">(</span><span class="n">prob_dict</span><span class="p">),</span>
- <span class="n">prob_dict</span><span class="p">[</span><span class="s1">'total_probdens'</span><span class="p">]</span>
+ <span class="n">prob_dict</span><span class="p">[</span><span class="s2">"total_probdens"</span><span class="p">],</span>
<span class="p">),</span>
<span class="n">verbosity</span><span class="p">,</span>
<span class="n">_MS_VERBOSITY_LEVEL</span><span class="p">,</span>
@@ -2443,14 +2452,16 @@
<span class="n">options</span><span class="p">[</span><span class="s2">"M_1"</span><span class="p">],</span>
<span class="n">options</span><span class="p">[</span><span class="s2">"M_2"</span><span class="p">]</span> <span class="o">/</span> <span class="n">options</span><span class="p">[</span><span class="s2">"M_1"</span><span class="p">]</span> <span class="k">if</span> <span class="n">options</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"M_2"</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span> <span class="k">else</span> <span class="s2">"N/A"</span><span class="p">,</span>
<span class="n">np</span><span class="o">.</span><span class="n">log10</span><span class="p">(</span><span class="n">options</span><span class="p">[</span><span class="s2">"P"</span><span class="p">]),</span>
- <span class="n">options</span><span class="p">[</span><span class="s1">'ecc'</span><span class="p">]</span> <span class="k">if</span> <span class="n">options</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"ecc"</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span> <span class="k">else</span> <span class="s2">"N/A"</span><span class="p">,</span>
+ <span class="n">options</span><span class="p">[</span><span class="s2">"ecc"</span><span class="p">]</span> <span class="k">if</span> <span class="n">options</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"ecc"</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span> <span class="k">else</span> <span class="s2">"N/A"</span><span class="p">,</span>
<span class="n">options</span><span class="p">[</span><span class="s2">"M_3"</span><span class="p">],</span>
<span class="n">np</span><span class="o">.</span><span class="n">log10</span><span class="p">(</span><span class="n">options</span><span class="p">[</span><span class="s2">"P2"</span><span class="p">]),</span>
<span class="n">options</span><span class="p">[</span><span class="s2">"ecc2"</span><span class="p">]</span> <span class="k">if</span> <span class="n">options</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"ecc2"</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span> <span class="k">else</span> <span class="s2">"N/A"</span><span class="p">,</span>
<span class="n">options</span><span class="p">[</span><span class="s2">"M_4"</span><span class="p">],</span>
<span class="n">np</span><span class="o">.</span><span class="n">log10</span><span class="p">(</span><span class="n">options</span><span class="p">[</span><span class="s2">"P3"</span><span class="p">]),</span>
<span class="n">options</span><span class="p">[</span><span class="s2">"ecc3"</span><span class="p">]</span> <span class="k">if</span> <span class="n">options</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"ecc3"</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span> <span class="k">else</span> <span class="s2">"N/A"</span><span class="p">,</span>
- <span class="nb">len</span><span class="p">(</span><span class="n">prob_dict</span><span class="p">),</span> <span class="nb">str</span><span class="p">(</span><span class="n">prob_dict</span><span class="p">),</span> <span class="n">prob_dict</span><span class="p">[</span><span class="s1">'total_probdens'</span><span class="p">]</span>
+ <span class="nb">len</span><span class="p">(</span><span class="n">prob_dict</span><span class="p">),</span>
+ <span class="nb">str</span><span class="p">(</span><span class="n">prob_dict</span><span class="p">),</span>
+ <span class="n">prob_dict</span><span class="p">[</span><span class="s2">"total_probdens"</span><span class="p">],</span>
<span class="p">),</span>
<span class="n">verbosity</span><span class="p">,</span>
<span class="n">_MS_VERBOSITY_LEVEL</span><span class="p">,</span>
@@ -2459,55 +2470,36 @@
</pre></div>
</div>
-
</div>
<footer>
-
<hr/>
<div role="contentinfo">
- <p>
-
- © Copyright 2021, David Hendriks, Robert Izzard
-
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+ <p>© Copyright 2021, David Hendriks, Robert Izzard.</p>
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-Using binary_c with bit branch newmaster: git revision: "6185:20210910:1621c23a5" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/newmaster">git url</a>.
+Using binary_c with bit branch master: git revision: "6209:20211006:c4a4c332e" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/master">git url</a>.
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<h1>Source code for binarycpython.utils.functions</h1><div class="highlight"><pre>
<span></span><span class="sd">"""</span>
<span class="sd">Module containing most of the utility functions for the binarycpython package</span>
@@ -176,6 +91,9 @@
<span class="kn">import</span> <span class="nn">subprocess</span>
<span class="kn">import</span> <span class="nn">time</span>
<span class="kn">import</span> <span class="nn">types</span>
+<span class="kn">import</span> <span class="nn">resource</span>
+<span class="kn">import</span> <span class="nn">psutil</span>
+<span class="kn">from</span> <span class="nn">colorama</span> <span class="kn">import</span> <span class="n">Fore</span><span class="p">,</span> <span class="n">Back</span><span class="p">,</span> <span class="n">Style</span>
<span class="kn">from</span> <span class="nn">io</span> <span class="kn">import</span> <span class="n">StringIO</span>
<span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Union</span><span class="p">,</span> <span class="n">Any</span>
@@ -197,6 +115,100 @@
<span class="c1">########################################################</span>
<span class="c1"># Unsorted</span>
<span class="c1">########################################################</span>
+
+
+<div class="viewcode-block" id="format_number"><a class="viewcode-back" href="../../../functions.html#binarycpython.utils.functions.format_number">[docs]</a><span class="k">def</span> <span class="nf">format_number</span><span class="p">(</span><span class="n">number</span><span class="p">):</span>
+ <span class="c1"># compact number formatter</span>
+
+ <span class="n">string</span> <span class="o">=</span> <span class="s2">"</span><span class="si">{number:.2g}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">number</span><span class="o">=</span><span class="n">number</span><span class="p">)</span>
+ <span class="n">string</span> <span class="o">=</span> <span class="n">string</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">"e+0"</span><span class="p">,</span> <span class="s2">"e+"</span><span class="p">)</span>
+ <span class="n">string</span> <span class="o">=</span> <span class="n">string</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">"e-0"</span><span class="p">,</span> <span class="s2">"e-"</span><span class="p">)</span>
+
+ <span class="k">return</span> <span class="n">string</span></div>
+
+
+<div class="viewcode-block" id="check_if_in_shell"><a class="viewcode-back" href="../../../functions.html#binarycpython.utils.functions.check_if_in_shell">[docs]</a><span class="k">def</span> <span class="nf">check_if_in_shell</span><span class="p">():</span>
+ <span class="sd">"""</span>
+<span class="sd"> Function to check whether the script is running from a shell</span>
+<span class="sd"> """</span>
+
+ <span class="k">if</span> <span class="n">sys</span><span class="o">.</span><span class="n">stdin</span> <span class="ow">and</span> <span class="n">sys</span><span class="o">.</span><span class="n">stdin</span><span class="o">.</span><span class="n">isatty</span><span class="p">():</span>
+ <span class="n">in_shell</span> <span class="o">=</span> <span class="kc">True</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">in_shell</span> <span class="o">=</span> <span class="kc">False</span>
+
+ <span class="k">return</span> <span class="n">in_shell</span></div>
+
+
+<div class="viewcode-block" id="ANSI_colours"><a class="viewcode-back" href="../../../functions.html#binarycpython.utils.functions.ANSI_colours">[docs]</a><span class="k">def</span> <span class="nf">ANSI_colours</span><span class="p">():</span>
+ <span class="c1"># ANSI colours dictionary</span>
+ <span class="n">foreground_colours</span> <span class="o">=</span> <span class="p">{</span>
+ <span class="s2">"red"</span><span class="p">:</span> <span class="n">Fore</span><span class="o">.</span><span class="n">RED</span><span class="p">,</span>
+ <span class="s2">"yellow"</span><span class="p">:</span> <span class="n">Fore</span><span class="o">.</span><span class="n">YELLOW</span><span class="p">,</span>
+ <span class="s2">"blue"</span><span class="p">:</span> <span class="n">Fore</span><span class="o">.</span><span class="n">BLUE</span><span class="p">,</span>
+ <span class="s2">"cyan"</span><span class="p">:</span> <span class="n">Fore</span><span class="o">.</span><span class="n">CYAN</span><span class="p">,</span>
+ <span class="s2">"green"</span><span class="p">:</span> <span class="n">Fore</span><span class="o">.</span><span class="n">GREEN</span><span class="p">,</span>
+ <span class="s2">"magenta"</span><span class="p">:</span> <span class="n">Fore</span><span class="o">.</span><span class="n">MAGENTA</span><span class="p">,</span>
+ <span class="s2">"white"</span><span class="p">:</span> <span class="n">Fore</span><span class="o">.</span><span class="n">WHITE</span><span class="p">,</span>
+ <span class="s2">"black"</span><span class="p">:</span> <span class="n">Fore</span><span class="o">.</span><span class="n">BLACK</span><span class="p">,</span>
+ <span class="p">}</span>
+
+ <span class="n">background_colours</span> <span class="o">=</span> <span class="p">{</span>
+ <span class="s2">"red"</span><span class="p">:</span> <span class="n">Back</span><span class="o">.</span><span class="n">RED</span><span class="p">,</span>
+ <span class="s2">"yellow"</span><span class="p">:</span> <span class="n">Back</span><span class="o">.</span><span class="n">YELLOW</span><span class="p">,</span>
+ <span class="s2">"blue"</span><span class="p">:</span> <span class="n">Back</span><span class="o">.</span><span class="n">BLUE</span><span class="p">,</span>
+ <span class="s2">"cyan"</span><span class="p">:</span> <span class="n">Back</span><span class="o">.</span><span class="n">CYAN</span><span class="p">,</span>
+ <span class="s2">"green"</span><span class="p">:</span> <span class="n">Back</span><span class="o">.</span><span class="n">GREEN</span><span class="p">,</span>
+ <span class="s2">"magenta"</span><span class="p">:</span> <span class="n">Back</span><span class="o">.</span><span class="n">MAGENTA</span><span class="p">,</span>
+ <span class="s2">"white"</span><span class="p">:</span> <span class="n">Back</span><span class="o">.</span><span class="n">WHITE</span><span class="p">,</span>
+ <span class="s2">"black"</span><span class="p">:</span> <span class="n">Back</span><span class="o">.</span><span class="n">BLACK</span><span class="p">,</span>
+ <span class="p">}</span>
+
+ <span class="n">default_style</span> <span class="o">=</span> <span class="n">Style</span><span class="o">.</span><span class="n">BRIGHT</span>
+ <span class="n">colours</span> <span class="o">=</span> <span class="p">{}</span>
+
+ <span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="n">foreground_colours</span><span class="p">:</span>
+ <span class="n">colours</span><span class="p">[</span><span class="n">c</span><span class="p">]</span> <span class="o">=</span> <span class="n">default_style</span> <span class="o">+</span> <span class="n">foreground_colours</span><span class="p">[</span><span class="n">c</span><span class="p">]</span>
+ <span class="k">for</span> <span class="n">d</span> <span class="ow">in</span> <span class="n">background_colours</span><span class="p">:</span>
+ <span class="n">colours</span><span class="p">[</span><span class="n">c</span> <span class="o">+</span> <span class="s2">" on "</span> <span class="o">+</span> <span class="n">d</span><span class="p">]</span> <span class="o">=</span> <span class="n">foreground_colours</span><span class="p">[</span><span class="n">c</span><span class="p">]</span> <span class="o">+</span> <span class="n">background_colours</span><span class="p">[</span><span class="n">d</span><span class="p">]</span>
+ <span class="n">colours</span><span class="p">[</span><span class="s2">"reset"</span><span class="p">]</span> <span class="o">=</span> <span class="n">Style</span><span class="o">.</span><span class="n">RESET_ALL</span>
+
+ <span class="k">return</span> <span class="n">colours</span></div>
+
+
+<div class="viewcode-block" id="mem_use"><a class="viewcode-back" href="../../../functions.html#binarycpython.utils.functions.mem_use">[docs]</a><span class="k">def</span> <span class="nf">mem_use</span><span class="p">():</span>
+ <span class="sd">"""</span>
+<span class="sd"> Return current process memory use in MB. (Takes no arguments) Note: this is per-thread only.</span>
+<span class="sd"> """</span>
+
+ <span class="k">return</span> <span class="n">resource</span><span class="o">.</span><span class="n">getrusage</span><span class="p">(</span><span class="n">resource</span><span class="o">.</span><span class="n">RUSAGE_SELF</span><span class="p">)</span><span class="o">.</span><span class="n">ru_maxrss</span> <span class="o">/</span> <span class="mf">1024.0</span></div>
+
+
+<div class="viewcode-block" id="trem"><a class="viewcode-back" href="../../../functions.html#binarycpython.utils.functions.trem">[docs]</a><span class="k">def</span> <span class="nf">trem</span><span class="p">(</span><span class="n">dt</span><span class="p">,</span> <span class="n">count</span><span class="p">,</span> <span class="n">dn</span><span class="p">,</span> <span class="n">n</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Estimate time remaining (seconds) given a differential time and count (i.e. progress = $count/$n). $dt is the time since the last call, $count is the current progress count, $dn is the number run since the last call, and $n is the total number required.</span>
+<span class="sd"> """</span>
+ <span class="n">tpr</span> <span class="o">=</span> <span class="n">dt</span> <span class="o">/</span> <span class="nb">max</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="n">dn</span><span class="p">)</span>
+ <span class="n">etasecs</span> <span class="o">=</span> <span class="n">tpr</span> <span class="o">*</span> <span class="p">(</span><span class="n">n</span> <span class="o">-</span> <span class="n">count</span><span class="p">)</span>
+ <span class="p">(</span><span class="n">eta</span><span class="p">,</span> <span class="n">units</span><span class="p">)</span> <span class="o">=</span> <span class="n">conv_time_units</span><span class="p">(</span><span class="n">etasecs</span><span class="p">)</span>
+ <span class="k">return</span> <span class="p">(</span><span class="n">eta</span><span class="p">,</span> <span class="n">units</span><span class="p">,</span> <span class="n">tpr</span><span class="p">,</span> <span class="n">etasecs</span><span class="p">)</span></div>
+
+
+<div class="viewcode-block" id="conv_time_units"><a class="viewcode-back" href="../../../functions.html#binarycpython.utils.functions.conv_time_units">[docs]</a><span class="k">def</span> <span class="nf">conv_time_units</span><span class="p">(</span><span class="n">t</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Converts time (t, in seconds, passing in as the only argument) to seconds, minutes or hours depending on its magnitude. Returns a tuple (t,units).</span>
+<span class="sd"> """</span>
+ <span class="n">units</span> <span class="o">=</span> <span class="s2">"s"</span>
+ <span class="c1"># default to seconds</span>
+ <span class="k">if</span> <span class="n">t</span> <span class="o">></span> <span class="mi">60</span><span class="p">:</span>
+ <span class="n">t</span> <span class="o">/=</span> <span class="mi">60</span>
+ <span class="n">units</span> <span class="o">=</span> <span class="s2">"m"</span>
+ <span class="k">if</span> <span class="n">t</span> <span class="o">></span> <span class="mi">60</span><span class="p">:</span>
+ <span class="n">t</span> <span class="o">/=</span> <span class="mi">60</span>
+ <span class="n">units</span> <span class="o">=</span> <span class="s2">"h"</span>
+ <span class="k">return</span> <span class="p">(</span><span class="n">t</span><span class="p">,</span> <span class="n">units</span><span class="p">)</span></div>
+
+
<div class="viewcode-block" id="AutoVivificationDict"><a class="viewcode-back" href="../../../functions.html#binarycpython.utils.functions.AutoVivificationDict">[docs]</a><span class="k">class</span> <span class="nc">AutoVivificationDict</span><span class="p">(</span><span class="nb">dict</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Implementation of perl's autovivification feature, by overriding the</span>
@@ -226,6 +238,7 @@
<span class="bp">self</span> <span class="o">=</span> <span class="n">other</span>
<span class="k">return</span> <span class="bp">self</span></div>
+
<div class="viewcode-block" id="bin_data"><a class="viewcode-back" href="../../../functions.html#binarycpython.utils.functions.bin_data">[docs]</a><span class="k">def</span> <span class="nf">bin_data</span><span class="p">(</span><span class="n">value</span><span class="p">,</span> <span class="n">binwidth</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Function that bins the data</span>
@@ -233,20 +246,22 @@
<span class="sd"> Uses the absolute value of binwidth</span>
<span class="sd"> """</span>
- <span class="k">return</span> <span class="p">((</span><span class="mf">0.5</span> <span class="k">if</span> <span class="n">value</span> <span class="o">></span> <span class="mf">0.0</span> <span class="k">else</span> <span class="o">-</span><span class="mf">0.5</span><span class="p">)</span> <span class="o">+</span> <span class="nb">int</span><span class="p">(</span><span class="n">value</span><span class="o">/</span><span class="nb">abs</span><span class="p">(</span><span class="n">binwidth</span><span class="p">)))</span> <span class="o">*</span> <span class="nb">abs</span><span class="p">(</span><span class="n">binwidth</span><span class="p">)</span></div>
+ <span class="k">return</span> <span class="p">((</span><span class="mf">0.5</span> <span class="k">if</span> <span class="n">value</span> <span class="o">></span> <span class="mf">0.0</span> <span class="k">else</span> <span class="o">-</span><span class="mf">0.5</span><span class="p">)</span> <span class="o">+</span> <span class="nb">int</span><span class="p">(</span><span class="n">value</span> <span class="o">/</span> <span class="nb">abs</span><span class="p">(</span><span class="n">binwidth</span><span class="p">)))</span> <span class="o">*</span> <span class="nb">abs</span><span class="p">(</span><span class="n">binwidth</span><span class="p">)</span></div>
+
<div class="viewcode-block" id="convert_bytes"><a class="viewcode-back" href="../../../functions.html#binarycpython.utils.functions.convert_bytes">[docs]</a><span class="k">def</span> <span class="nf">convert_bytes</span><span class="p">(</span><span class="n">size</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Function to return the size + a magnitude string</span>
<span class="sd"> """</span>
- <span class="k">for</span> <span class="n">name</span> <span class="ow">in</span> <span class="p">[</span><span class="s1">'bytes'</span><span class="p">,</span> <span class="s1">'KB'</span><span class="p">,</span> <span class="s1">'MB'</span><span class="p">,</span> <span class="s1">'GB'</span><span class="p">,</span> <span class="s1">'TB'</span><span class="p">]:</span>
+ <span class="k">for</span> <span class="n">name</span> <span class="ow">in</span> <span class="p">[</span><span class="s2">"bytes"</span><span class="p">,</span> <span class="s2">"KB"</span><span class="p">,</span> <span class="s2">"MB"</span><span class="p">,</span> <span class="s2">"GB"</span><span class="p">,</span> <span class="s2">"TB"</span><span class="p">]:</span>
<span class="k">if</span> <span class="n">size</span> <span class="o"><</span> <span class="mf">1024.0</span><span class="p">:</span>
<span class="k">return</span> <span class="s2">"</span><span class="si">%3.1f</span><span class="s2"> </span><span class="si">%s</span><span class="s2">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">size</span><span class="p">,</span> <span class="n">name</span><span class="p">)</span>
<span class="n">size</span> <span class="o">/=</span> <span class="mf">1024.0</span>
<span class="k">return</span> <span class="n">size</span></div>
+
<div class="viewcode-block" id="get_size"><a class="viewcode-back" href="../../../functions.html#binarycpython.utils.functions.get_size">[docs]</a><span class="k">def</span> <span class="nf">get_size</span><span class="p">(</span><span class="n">obj</span><span class="p">,</span> <span class="n">seen</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Recursively finds size of objects</span>
@@ -266,9 +281,9 @@
<span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">obj</span><span class="p">,</span> <span class="nb">dict</span><span class="p">):</span>
<span class="n">size</span> <span class="o">+=</span> <span class="nb">sum</span><span class="p">([</span><span class="n">get_size</span><span class="p">(</span><span class="n">v</span><span class="p">,</span> <span class="n">seen</span><span class="p">)</span> <span class="k">for</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">obj</span><span class="o">.</span><span class="n">values</span><span class="p">()])</span>
<span class="n">size</span> <span class="o">+=</span> <span class="nb">sum</span><span class="p">([</span><span class="n">get_size</span><span class="p">(</span><span class="n">k</span><span class="p">,</span> <span class="n">seen</span><span class="p">)</span> <span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="n">obj</span><span class="o">.</span><span class="n">keys</span><span class="p">()])</span>
- <span class="k">elif</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">obj</span><span class="p">,</span> <span class="s1">'__dict__'</span><span class="p">):</span>
+ <span class="k">elif</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">obj</span><span class="p">,</span> <span class="s2">"__dict__"</span><span class="p">):</span>
<span class="n">size</span> <span class="o">+=</span> <span class="n">get_size</span><span class="p">(</span><span class="n">obj</span><span class="o">.</span><span class="vm">__dict__</span><span class="p">,</span> <span class="n">seen</span><span class="p">)</span>
- <span class="k">elif</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">obj</span><span class="p">,</span> <span class="s1">'__iter__'</span><span class="p">)</span> <span class="ow">and</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">obj</span><span class="p">,</span> <span class="p">(</span><span class="nb">str</span><span class="p">,</span> <span class="nb">bytes</span><span class="p">,</span> <span class="nb">bytearray</span><span class="p">)):</span>
+ <span class="k">elif</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">obj</span><span class="p">,</span> <span class="s2">"__iter__"</span><span class="p">)</span> <span class="ow">and</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">obj</span><span class="p">,</span> <span class="p">(</span><span class="nb">str</span><span class="p">,</span> <span class="nb">bytes</span><span class="p">,</span> <span class="nb">bytearray</span><span class="p">)):</span>
<span class="n">size</span> <span class="o">+=</span> <span class="nb">sum</span><span class="p">([</span><span class="n">get_size</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">seen</span><span class="p">)</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">obj</span><span class="p">])</span>
<span class="k">return</span> <span class="n">size</span></div>
@@ -283,7 +298,9 @@
<span class="n">original_ensemble_results</span> <span class="o">=</span> <span class="n">ensemble_dictionary</span>
- <span class="n">float_format_ensemble_results</span> <span class="o">=</span> <span class="n">recursive_change_key_to_float</span><span class="p">(</span><span class="n">original_ensemble_results</span><span class="p">)</span>
+ <span class="n">float_format_ensemble_results</span> <span class="o">=</span> <span class="n">recursive_change_key_to_float</span><span class="p">(</span>
+ <span class="n">original_ensemble_results</span>
+ <span class="p">)</span>
<span class="k">del</span> <span class="n">original_ensemble_results</span>
<span class="n">gc</span><span class="o">.</span><span class="n">collect</span><span class="p">()</span>
@@ -293,7 +310,9 @@
<span class="n">gc</span><span class="o">.</span><span class="n">collect</span><span class="p">()</span>
<span class="c1"># Then Change the keys back to a string but with a %g format.</span>
- <span class="n">reformatted_ensemble_results</span> <span class="o">=</span> <span class="n">recursive_change_key_to_string</span><span class="p">(</span><span class="n">sorted_ensemble_results</span><span class="p">)</span>
+ <span class="n">reformatted_ensemble_results</span> <span class="o">=</span> <span class="n">recursive_change_key_to_string</span><span class="p">(</span>
+ <span class="n">sorted_ensemble_results</span>
+ <span class="p">)</span>
<span class="k">del</span> <span class="n">sorted_ensemble_results</span>
<span class="n">gc</span><span class="o">.</span><span class="n">collect</span><span class="p">()</span>
@@ -491,7 +510,6 @@
<span class="k">yield</span> <span class="n">val</span><span class="o">.</span><span class="vm">__name__</span></div>
-
<div class="viewcode-block" id="convfloat"><a class="viewcode-back" href="../../../functions.html#binarycpython.utils.functions.convfloat">[docs]</a><span class="k">def</span> <span class="nf">convfloat</span><span class="p">(</span><span class="n">x</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Convert scalar x to a float if we can, in which case return the float, otherwise just return x without changing it. Usually, x is a string, but could be anything that float() can handle without failure.</span>
@@ -502,8 +520,8 @@
<span class="k">except</span> <span class="ne">ValueError</span><span class="p">:</span>
<span class="k">return</span> <span class="n">x</span></div>
-<div class="viewcode-block" id="datalinedict"><a class="viewcode-back" href="../../../functions.html#binarycpython.utils.functions.datalinedict">[docs]</a><span class="k">def</span> <span class="nf">datalinedict</span><span class="p">(</span><span class="n">line</span> <span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
- <span class="n">parameters</span> <span class="p">:</span> <span class="nb">list</span><span class="p">):</span>
+
+<div class="viewcode-block" id="datalinedict"><a class="viewcode-back" href="../../../functions.html#binarycpython.utils.functions.datalinedict">[docs]</a><span class="k">def</span> <span class="nf">datalinedict</span><span class="p">(</span><span class="n">line</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">parameters</span><span class="p">:</span> <span class="nb">list</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Convert a line of data to a more convenient dictionary.</span>
<span class="sd"> Arguments:</span>
@@ -513,29 +531,30 @@
<span class="sd"> Note: if the parameter is a floating point number, it will be converted to Python's float type.</span>
<span class="sd"> """</span>
- <span class="k">return</span> <span class="p">{</span><span class="n">param</span><span class="p">:</span><span class="n">convfloat</span><span class="p">(</span><span class="n">value</span><span class="p">)</span> <span class="k">for</span> <span class="n">param</span><span class="p">,</span> <span class="n">value</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="n">parameters</span><span class="p">,</span> <span class="n">line</span><span class="o">.</span><span class="n">split</span><span class="p">())}</span></div>
+ <span class="k">return</span> <span class="p">{</span><span class="n">param</span><span class="p">:</span> <span class="n">convfloat</span><span class="p">(</span><span class="n">value</span><span class="p">)</span> <span class="k">for</span> <span class="n">param</span><span class="p">,</span> <span class="n">value</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="n">parameters</span><span class="p">,</span> <span class="n">line</span><span class="o">.</span><span class="n">split</span><span class="p">())}</span></div>
+
-<div class="viewcode-block" id="pad_output_distribution"><a class="viewcode-back" href="../../../functions.html#binarycpython.utils.functions.pad_output_distribution">[docs]</a><span class="k">def</span> <span class="nf">pad_output_distribution</span><span class="p">(</span><span class="n">dist</span> <span class="p">:</span> <span class="nb">dict</span><span class="p">,</span>
- <span class="n">binwidth</span> <span class="p">:</span> <span class="nb">float</span><span class="p">):</span>
+<div class="viewcode-block" id="pad_output_distribution"><a class="viewcode-back" href="../../../functions.html#binarycpython.utils.functions.pad_output_distribution">[docs]</a><span class="k">def</span> <span class="nf">pad_output_distribution</span><span class="p">(</span><span class="n">dist</span><span class="p">:</span> <span class="nb">dict</span><span class="p">,</span> <span class="n">binwidth</span><span class="p">:</span> <span class="nb">float</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Given a distribution, dist (a dictionary), which should be binned every binwidth (float), fill the distribution with zeros when there is no data. Note: this changes the data in place.</span>
<span class="sd"> """</span>
<span class="c1"># sorted list of the keys</span>
- <span class="n">skeys</span> <span class="o">=</span> <span class="nb">sorted</span><span class="p">(</span><span class="n">dist</span><span class="o">.</span><span class="n">keys</span><span class="p">(),</span> <span class="n">key</span> <span class="o">=</span> <span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="nb">float</span><span class="p">(</span><span class="n">x</span><span class="p">))</span>
+ <span class="n">skeys</span> <span class="o">=</span> <span class="nb">sorted</span><span class="p">(</span><span class="n">dist</span><span class="o">.</span><span class="n">keys</span><span class="p">(),</span> <span class="n">key</span><span class="o">=</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="nb">float</span><span class="p">(</span><span class="n">x</span><span class="p">))</span>
<span class="c1"># get min and max, offset by the binwidth</span>
- <span class="n">min_val</span> <span class="o">=</span> <span class="n">skeys</span><span class="p">[</span> <span class="mi">0</span><span class="p">]</span> <span class="o">-</span> <span class="n">binwidth</span>
+ <span class="n">min_val</span> <span class="o">=</span> <span class="n">skeys</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">-</span> <span class="n">binwidth</span>
<span class="n">max_val</span> <span class="o">=</span> <span class="n">skeys</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span> <span class="o">+</span> <span class="n">binwidth</span>
<span class="c1"># pad with zeros</span>
<span class="n">x</span> <span class="o">=</span> <span class="n">min_val</span>
<span class="k">while</span> <span class="n">x</span> <span class="o"><=</span> <span class="n">max_val</span><span class="p">:</span>
- <span class="n">dist</span><span class="p">[</span><span class="n">x</span><span class="p">]</span> <span class="o">=</span> <span class="n">dist</span><span class="o">.</span><span class="n">setdefault</span><span class="p">(</span><span class="n">x</span><span class="p">,</span><span class="mf">0.0</span><span class="p">)</span>
+ <span class="n">dist</span><span class="p">[</span><span class="n">x</span><span class="p">]</span> <span class="o">=</span> <span class="n">dist</span><span class="o">.</span><span class="n">setdefault</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="mf">0.0</span><span class="p">)</span>
<span class="n">x</span> <span class="o">+=</span> <span class="n">binwidth</span>
<span class="k">return</span> <span class="n">dist</span></div>
+
<div class="viewcode-block" id="catchtime"><a class="viewcode-back" href="../../../functions.html#binarycpython.utils.functions.catchtime">[docs]</a><span class="k">class</span> <span class="nc">catchtime</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Context manager to calculate time spent</span>
@@ -580,6 +599,7 @@
<span class="k">del</span> <span class="bp">self</span><span class="o">.</span><span class="n">_stringio</span> <span class="c1"># free up some memory</span>
<span class="n">sys</span><span class="o">.</span><span class="n">stdout</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_stdout</span></div></div>
+
<div class="viewcode-block" id="call_binary_c_config"><a class="viewcode-back" href="../../../functions.html#binarycpython.utils.functions.call_binary_c_config">[docs]</a><span class="k">def</span> <span class="nf">call_binary_c_config</span><span class="p">(</span><span class="n">argument</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Function to interface with the binary_c config file</span>
@@ -601,10 +621,9 @@
<span class="n">msg</span> <span class="o">=</span> <span class="s2">"binary_c-config file does not exist. Aborting"</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
- <span class="n">output</span> <span class="o">=</span> <span class="p">(</span>
- <span class="n">subprocess</span><span class="o">.</span><span class="n">run</span><span class="p">([</span><span class="n">BINARY_C_CONFIG</span><span class="p">,</span> <span class="n">argument</span><span class="p">],</span> <span class="n">stdout</span><span class="o">=</span><span class="n">subprocess</span><span class="o">.</span><span class="n">PIPE</span><span class="p">,</span> <span class="n">check</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
- <span class="o">.</span><span class="n">stdout</span><span class="o">.</span><span class="n">decode</span><span class="p">(</span><span class="s2">"utf-8"</span><span class="p">)</span>
- <span class="p">)</span>
+ <span class="n">output</span> <span class="o">=</span> <span class="n">subprocess</span><span class="o">.</span><span class="n">run</span><span class="p">(</span>
+ <span class="p">[</span><span class="n">BINARY_C_CONFIG</span><span class="p">,</span> <span class="n">argument</span><span class="p">],</span> <span class="n">stdout</span><span class="o">=</span><span class="n">subprocess</span><span class="o">.</span><span class="n">PIPE</span><span class="p">,</span> <span class="n">check</span><span class="o">=</span><span class="kc">True</span>
+ <span class="p">)</span><span class="o">.</span><span class="n">stdout</span><span class="o">.</span><span class="n">decode</span><span class="p">(</span><span class="s2">"utf-8"</span><span class="p">)</span>
<span class="k">return</span> <span class="n">output</span></div>
@@ -630,6 +649,7 @@
<span class="k">if</span> <span class="n">verbosity</span> <span class="o">>=</span> <span class="n">minimal_verbosity</span><span class="p">:</span>
<span class="nb">print</span><span class="p">(</span><span class="n">message</span><span class="p">)</span></div>
+
<div class="viewcode-block" id="remove_file"><a class="viewcode-back" href="../../../functions.html#binarycpython.utils.functions.remove_file">[docs]</a><span class="k">def</span> <span class="nf">remove_file</span><span class="p">(</span><span class="n">file</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">verbosity</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">0</span><span class="p">)</span> <span class="o">-></span> <span class="kc">None</span><span class="p">:</span>
<span class="sd">"""</span>
<span class="sd"> Function to remove files but with verbosity</span>
@@ -663,6 +683,10 @@
<span class="p">)</span></div>
+<div class="viewcode-block" id="get_username"><a class="viewcode-back" href="../../../functions.html#binarycpython.utils.functions.get_username">[docs]</a><span class="k">def</span> <span class="nf">get_username</span><span class="p">():</span>
+ <span class="k">return</span> <span class="n">psutil</span><span class="o">.</span><span class="n">Process</span><span class="p">()</span><span class="o">.</span><span class="n">username</span><span class="p">()</span></div>
+
+
<div class="viewcode-block" id="temp_dir"><a class="viewcode-back" href="../../../functions.html#binarycpython.utils.functions.temp_dir">[docs]</a><span class="k">def</span> <span class="nf">temp_dir</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-></span> <span class="nb">str</span><span class="p">:</span>
<span class="sd">"""</span>
<span class="sd"> Function to create directory within the TMP directory of the file system</span>
@@ -677,7 +701,8 @@
<span class="sd"> """</span>
<span class="n">tmp_dir</span> <span class="o">=</span> <span class="n">tempfile</span><span class="o">.</span><span class="n">gettempdir</span><span class="p">()</span>
- <span class="n">path</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">tmp_dir</span><span class="p">,</span> <span class="s2">"binary_c_python"</span><span class="p">)</span>
+ <span class="n">username</span> <span class="o">=</span> <span class="n">get_username</span><span class="p">()</span>
+ <span class="n">path</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">tmp_dir</span><span class="p">,</span> <span class="s2">"binary_c_python-</span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">username</span><span class="p">))</span>
<span class="c1"># loop over the other paths if there are any:</span>
<span class="k">if</span> <span class="n">args</span><span class="p">:</span>
@@ -923,14 +948,16 @@
<span class="n">split_info</span> <span class="o">=</span> <span class="n">el</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">"Ensemble "</span><span class="p">)[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">" is "</span><span class="p">)</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">split_info</span><span class="p">)</span> <span class="o">></span> <span class="mi">1</span><span class="p">:</span>
- <span class="k">if</span> <span class="ow">not</span> <span class="n">split_info</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">'filter'</span><span class="p">):</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">split_info</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s2">"filter"</span><span class="p">):</span>
<span class="n">ensemble_dict</span><span class="p">[</span><span class="nb">int</span><span class="p">(</span><span class="n">split_info</span><span class="p">[</span><span class="mi">0</span><span class="p">])]</span> <span class="o">=</span> <span class="n">split_info</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
<span class="k">else</span><span class="p">:</span>
- <span class="n">filter_no</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">split_info</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">'filter '</span><span class="p">,</span> <span class="s1">''</span><span class="p">))</span>
+ <span class="n">filter_no</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">split_info</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">"filter "</span><span class="p">,</span> <span class="s2">""</span><span class="p">))</span>
<span class="n">ensemble_filter_dict</span><span class="p">[</span><span class="n">filter_no</span><span class="p">]</span> <span class="o">=</span> <span class="n">split_info</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
<span class="n">version_info_dict</span><span class="p">[</span><span class="s2">"ensembles"</span><span class="p">]</span> <span class="o">=</span> <span class="n">ensemble_dict</span> <span class="k">if</span> <span class="n">ensemble_dict</span> <span class="k">else</span> <span class="kc">None</span>
- <span class="n">version_info_dict</span><span class="p">[</span><span class="s2">"ensemble_filters"</span><span class="p">]</span> <span class="o">=</span> <span class="n">ensemble_filter_dict</span> <span class="k">if</span> <span class="n">ensemble_filter_dict</span> <span class="k">else</span> <span class="kc">None</span>
+ <span class="n">version_info_dict</span><span class="p">[</span><span class="s2">"ensemble_filters"</span><span class="p">]</span> <span class="o">=</span> <span class="p">(</span>
+ <span class="n">ensemble_filter_dict</span> <span class="k">if</span> <span class="n">ensemble_filter_dict</span> <span class="k">else</span> <span class="kc">None</span>
+ <span class="p">)</span>
<span class="c1">##########################</span>
<span class="c1"># macros:</span>
@@ -1159,7 +1186,9 @@
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">value_dicts</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
<span class="nb">print</span><span class="p">(</span>
- <span class="s2">"Sorry, didn't find any line matching your header </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">selected_header</span><span class="p">)</span>
+ <span class="s2">"Sorry, didn't find any line matching your header </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+ <span class="n">selected_header</span>
+ <span class="p">)</span>
<span class="p">)</span>
<span class="k">return</span> <span class="kc">None</span>
@@ -1741,7 +1770,7 @@
<span class="sd"> type(input_dict[key]) (except if the value is a dict)</span>
<span class="sd"> """</span>
- <span class="n">structure_dict</span> <span class="o">=</span> <span class="n">OrderedDict</span><span class="p">()</span> <span class="c1"># TODO: check if this still works</span>
+ <span class="n">structure_dict</span> <span class="o">=</span> <span class="n">OrderedDict</span><span class="p">()</span> <span class="c1"># TODO: check if this still works</span>
<span class="c1">#</span>
<span class="k">for</span> <span class="n">key</span><span class="p">,</span> <span class="n">value</span> <span class="ow">in</span> <span class="n">input_dict</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
@@ -1760,7 +1789,7 @@
<div class="viewcode-block" id="count_keys_recursive"><a class="viewcode-back" href="../../../functions.html#binarycpython.utils.functions.count_keys_recursive">[docs]</a><span class="k">def</span> <span class="nf">count_keys_recursive</span><span class="p">(</span><span class="n">input_dict</span><span class="p">):</span>
<span class="sd">"""</span>
-<span class="sd"> Function to count the total amount of keys in a dictionary</span>
+<span class="sd"> Function to count the total number of keys in a dictionary</span>
<span class="sd"> """</span>
<span class="n">local_count</span> <span class="o">=</span> <span class="mi">0</span>
@@ -1796,7 +1825,7 @@
<span class="sd"> """</span>
<span class="c1"># Set up new dict</span>
- <span class="n">new_dict</span> <span class="o">=</span> <span class="n">OrderedDict</span><span class="p">()</span> <span class="c1"># TODO: check if this still necessary</span>
+ <span class="n">new_dict</span> <span class="o">=</span> <span class="n">OrderedDict</span><span class="p">()</span> <span class="c1"># TODO: check if this still necessary</span>
<span class="c1">#</span>
<span class="n">keys_1</span> <span class="o">=</span> <span class="n">dict_1</span><span class="o">.</span><span class="n">keys</span><span class="p">()</span>
@@ -1834,11 +1863,17 @@
<span class="c1"># If they keys are not the same, it depends on their type whether we still deal with them at all, or just raise an error</span>
<span class="k">if</span> <span class="ow">not</span> <span class="nb">type</span><span class="p">(</span><span class="n">dict_1</span><span class="p">[</span><span class="n">key</span><span class="p">])</span> <span class="ow">is</span> <span class="nb">type</span><span class="p">(</span><span class="n">dict_2</span><span class="p">[</span><span class="n">key</span><span class="p">]):</span>
<span class="c1"># Exceptions: numbers can be added</span>
- <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">dict_1</span><span class="p">[</span><span class="n">key</span><span class="p">],</span> <span class="p">(</span><span class="nb">int</span><span class="p">,</span> <span class="nb">float</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">float64</span><span class="p">))</span> <span class="ow">and</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">dict_2</span><span class="p">[</span><span class="n">key</span><span class="p">],</span> <span class="p">(</span><span class="nb">int</span><span class="p">,</span> <span class="nb">float</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">float64</span><span class="p">)):</span>
+ <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">dict_1</span><span class="p">[</span><span class="n">key</span><span class="p">],</span> <span class="p">(</span><span class="nb">int</span><span class="p">,</span> <span class="nb">float</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">float64</span><span class="p">))</span> <span class="ow">and</span> <span class="nb">isinstance</span><span class="p">(</span>
+ <span class="n">dict_2</span><span class="p">[</span><span class="n">key</span><span class="p">],</span> <span class="p">(</span><span class="nb">int</span><span class="p">,</span> <span class="nb">float</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">float64</span><span class="p">)</span>
+ <span class="p">):</span>
<span class="n">new_dict</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">dict_1</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">+</span> <span class="n">dict_2</span><span class="p">[</span><span class="n">key</span><span class="p">]</span>
<span class="c1"># Exceptions: versions of dicts can be merged</span>
- <span class="k">elif</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">dict_1</span><span class="p">[</span><span class="n">key</span><span class="p">],</span> <span class="p">(</span><span class="nb">dict</span><span class="p">,</span> <span class="n">OrderedDict</span><span class="p">,</span> <span class="nb">type</span><span class="p">(</span><span class="n">AutoVivificationDict</span><span class="p">)))</span> <span class="ow">and</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">dict_2</span><span class="p">[</span><span class="n">key</span><span class="p">],</span> <span class="p">(</span><span class="nb">dict</span><span class="p">,</span> <span class="n">OrderedDict</span><span class="p">,</span> <span class="nb">type</span><span class="p">(</span><span class="n">AutoVivificationDict</span><span class="p">))):</span>
+ <span class="k">elif</span> <span class="nb">isinstance</span><span class="p">(</span>
+ <span class="n">dict_1</span><span class="p">[</span><span class="n">key</span><span class="p">],</span> <span class="p">(</span><span class="nb">dict</span><span class="p">,</span> <span class="n">OrderedDict</span><span class="p">,</span> <span class="nb">type</span><span class="p">(</span><span class="n">AutoVivificationDict</span><span class="p">))</span>
+ <span class="p">)</span> <span class="ow">and</span> <span class="nb">isinstance</span><span class="p">(</span>
+ <span class="n">dict_2</span><span class="p">[</span><span class="n">key</span><span class="p">],</span> <span class="p">(</span><span class="nb">dict</span><span class="p">,</span> <span class="n">OrderedDict</span><span class="p">,</span> <span class="nb">type</span><span class="p">(</span><span class="n">AutoVivificationDict</span><span class="p">))</span>
+ <span class="p">):</span>
<span class="n">new_dict</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">merge_dicts</span><span class="p">(</span><span class="n">dict_1</span><span class="p">[</span><span class="n">key</span><span class="p">],</span> <span class="n">dict_2</span><span class="p">[</span><span class="n">key</span><span class="p">])</span>
<span class="c1"># If the above cases have not dealt with it, then we should raise an error</span>
@@ -1876,7 +1911,9 @@
<span class="n">new_dict</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">dict_1</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">+</span> <span class="n">dict_2</span><span class="p">[</span><span class="n">key</span><span class="p">]</span>
<span class="c1"># Astropy quantities (using a dummy type representing the numpy array)</span>
- <span class="k">elif</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">dict_1</span><span class="p">[</span><span class="n">key</span><span class="p">],</span> <span class="nb">type</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="mi">1</span><span class="p">])</span><span class="o">*</span><span class="n">u</span><span class="o">.</span><span class="n">m</span><span class="p">))</span> <span class="ow">and</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">dict_2</span><span class="p">[</span><span class="n">key</span><span class="p">],</span> <span class="nb">type</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="mi">1</span><span class="p">])</span><span class="o">*</span><span class="n">u</span><span class="o">.</span><span class="n">m</span><span class="p">)):</span>
+ <span class="k">elif</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">dict_1</span><span class="p">[</span><span class="n">key</span><span class="p">],</span> <span class="nb">type</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="mi">1</span><span class="p">])</span> <span class="o">*</span> <span class="n">u</span><span class="o">.</span><span class="n">m</span><span class="p">))</span> <span class="ow">and</span> <span class="nb">isinstance</span><span class="p">(</span>
+ <span class="n">dict_2</span><span class="p">[</span><span class="n">key</span><span class="p">],</span> <span class="nb">type</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="mi">1</span><span class="p">])</span> <span class="o">*</span> <span class="n">u</span><span class="o">.</span><span class="n">m</span><span class="p">)</span>
+ <span class="p">):</span>
<span class="n">new_dict</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">dict_1</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">+</span> <span class="n">dict_2</span><span class="p">[</span><span class="n">key</span><span class="p">]</span>
<span class="c1"># dicts</span>
@@ -1921,7 +1958,7 @@
<span class="sd"> """</span>
<span class="c1"># Set up new dict</span>
- <span class="n">new_dict</span> <span class="o">=</span> <span class="n">OrderedDict</span><span class="p">()</span> <span class="c1"># TODO: check if this still works</span>
+ <span class="n">new_dict</span> <span class="o">=</span> <span class="n">OrderedDict</span><span class="p">()</span> <span class="c1"># TODO: check if this still works</span>
<span class="c1">#</span>
<span class="n">keys_1</span> <span class="o">=</span> <span class="n">dict_1</span><span class="o">.</span><span class="n">keys</span><span class="p">()</span>
@@ -1999,7 +2036,7 @@
<span class="sd"> """</span>
<span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="n">input_dict</span><span class="p">:</span>
- <span class="k">if</span> <span class="ow">not</span> <span class="n">key</span> <span class="o">==</span> <span class="s1">'general_info'</span><span class="p">:</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">key</span> <span class="o">==</span> <span class="s2">"general_info"</span><span class="p">:</span>
<span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">input_dict</span><span class="p">[</span><span class="n">key</span><span class="p">],</span> <span class="p">(</span><span class="nb">dict</span><span class="p">,</span> <span class="n">OrderedDict</span><span class="p">)):</span>
<span class="n">input_dict</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">multiply_values_dict</span><span class="p">(</span><span class="n">input_dict</span><span class="p">[</span><span class="n">key</span><span class="p">],</span> <span class="n">factor</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
@@ -2008,6 +2045,7 @@
<span class="k">return</span> <span class="n">input_dict</span></div>
+
<div class="viewcode-block" id="custom_sort_dict"><a class="viewcode-back" href="../../../functions.html#binarycpython.utils.functions.custom_sort_dict">[docs]</a><span class="k">def</span> <span class="nf">custom_sort_dict</span><span class="p">(</span><span class="n">input_dict</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Returns a dictionary that is ordered, but can handle numbers better than normal OrderedDict</span>
@@ -2037,7 +2075,7 @@
<span class="n">msg</span> <span class="o">=</span> <span class="s2">"Different types in the same dictionary key set"</span>
<span class="c1"># Create a string repr of the type name to sort them afterwards</span>
- <span class="n">str_types</span> <span class="o">=</span> <span class="p">{</span><span class="nb">repr</span><span class="p">(</span><span class="n">el</span><span class="p">):</span><span class="n">el</span> <span class="k">for</span> <span class="n">el</span> <span class="ow">in</span> <span class="n">all_types_keys</span><span class="p">}</span>
+ <span class="n">str_types</span> <span class="o">=</span> <span class="p">{</span><span class="nb">repr</span><span class="p">(</span><span class="n">el</span><span class="p">):</span> <span class="n">el</span> <span class="k">for</span> <span class="n">el</span> <span class="ow">in</span> <span class="n">all_types_keys</span><span class="p">}</span>
<span class="c1"># Set up sorted keys list</span>
<span class="n">sorted_keys</span> <span class="o">=</span> <span class="p">[]</span>
@@ -2067,15 +2105,19 @@
<span class="sd"> Does not work with lists as values</span>
<span class="sd"> """</span>
- <span class="n">new_dict</span> <span class="o">=</span> <span class="n">OrderedDict</span><span class="p">()</span> <span class="c1"># TODO: check if this still works</span>
+ <span class="n">new_dict</span> <span class="o">=</span> <span class="n">OrderedDict</span><span class="p">()</span> <span class="c1"># TODO: check if this still works</span>
<span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="n">input_dict</span><span class="p">:</span>
<span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">input_dict</span><span class="p">[</span><span class="n">key</span><span class="p">],</span> <span class="p">(</span><span class="nb">dict</span><span class="p">,</span> <span class="n">OrderedDict</span><span class="p">)):</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">num_key</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">key</span><span class="p">)</span>
- <span class="n">new_dict</span><span class="p">[</span><span class="n">num_key</span><span class="p">]</span> <span class="o">=</span> <span class="n">recursive_change_key_to_float</span><span class="p">(</span><span class="n">copy</span><span class="o">.</span><span class="n">deepcopy</span><span class="p">(</span><span class="n">input_dict</span><span class="p">[</span><span class="n">key</span><span class="p">]))</span>
+ <span class="n">new_dict</span><span class="p">[</span><span class="n">num_key</span><span class="p">]</span> <span class="o">=</span> <span class="n">recursive_change_key_to_float</span><span class="p">(</span>
+ <span class="n">copy</span><span class="o">.</span><span class="n">deepcopy</span><span class="p">(</span><span class="n">input_dict</span><span class="p">[</span><span class="n">key</span><span class="p">])</span>
+ <span class="p">)</span>
<span class="k">except</span> <span class="ne">ValueError</span><span class="p">:</span>
- <span class="n">new_dict</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">recursive_change_key_to_float</span><span class="p">(</span><span class="n">copy</span><span class="o">.</span><span class="n">deepcopy</span><span class="p">(</span><span class="n">input_dict</span><span class="p">[</span><span class="n">key</span><span class="p">]))</span>
+ <span class="n">new_dict</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">recursive_change_key_to_float</span><span class="p">(</span>
+ <span class="n">copy</span><span class="o">.</span><span class="n">deepcopy</span><span class="p">(</span><span class="n">input_dict</span><span class="p">[</span><span class="n">key</span><span class="p">])</span>
+ <span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">num_key</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">key</span><span class="p">)</span>
@@ -2091,15 +2133,19 @@
<span class="sd"> Function to recursively change the key back to a string but this time in a format that we decide</span>
<span class="sd"> """</span>
- <span class="n">new_dict</span> <span class="o">=</span> <span class="n">OrderedDict</span><span class="p">()</span> <span class="c1"># TODO: check if this still works</span>
+ <span class="n">new_dict</span> <span class="o">=</span> <span class="n">OrderedDict</span><span class="p">()</span> <span class="c1"># TODO: check if this still works</span>
<span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="n">input_dict</span><span class="p">:</span>
<span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">input_dict</span><span class="p">[</span><span class="n">key</span><span class="p">],</span> <span class="p">(</span><span class="nb">dict</span><span class="p">,</span> <span class="n">OrderedDict</span><span class="p">)):</span>
<span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">key</span><span class="p">,</span> <span class="p">(</span><span class="nb">int</span><span class="p">,</span> <span class="nb">float</span><span class="p">)):</span>
<span class="n">string_key</span> <span class="o">=</span> <span class="s2">"</span><span class="si">{:g}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">key</span><span class="p">)</span>
- <span class="n">new_dict</span><span class="p">[</span><span class="n">string_key</span><span class="p">]</span> <span class="o">=</span> <span class="n">recursive_change_key_to_string</span><span class="p">(</span><span class="n">copy</span><span class="o">.</span><span class="n">deepcopy</span><span class="p">(</span><span class="n">input_dict</span><span class="p">[</span><span class="n">key</span><span class="p">]))</span>
+ <span class="n">new_dict</span><span class="p">[</span><span class="n">string_key</span><span class="p">]</span> <span class="o">=</span> <span class="n">recursive_change_key_to_string</span><span class="p">(</span>
+ <span class="n">copy</span><span class="o">.</span><span class="n">deepcopy</span><span class="p">(</span><span class="n">input_dict</span><span class="p">[</span><span class="n">key</span><span class="p">])</span>
+ <span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
- <span class="n">new_dict</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">recursive_change_key_to_string</span><span class="p">(</span><span class="n">copy</span><span class="o">.</span><span class="n">deepcopy</span><span class="p">(</span><span class="n">input_dict</span><span class="p">[</span><span class="n">key</span><span class="p">]))</span>
+ <span class="n">new_dict</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">recursive_change_key_to_string</span><span class="p">(</span>
+ <span class="n">copy</span><span class="o">.</span><span class="n">deepcopy</span><span class="p">(</span><span class="n">input_dict</span><span class="p">[</span><span class="n">key</span><span class="p">])</span>
+ <span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">key</span><span class="p">,</span> <span class="p">(</span><span class="nb">int</span><span class="p">,</span> <span class="nb">float</span><span class="p">)):</span>
<span class="n">string_key</span> <span class="o">=</span> <span class="s2">"</span><span class="si">{:g}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">key</span><span class="p">)</span>
@@ -2253,55 +2299,36 @@
</pre></div>
</div>
-
</div>
<footer>
-
<hr/>
<div role="contentinfo">
- <p>
-
- © Copyright 2021, David Hendriks, Robert Izzard
-
- </p>
+ <p>© Copyright 2021, David Hendriks, Robert Izzard.</p>
</div>
-
-
-
- Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a
-
- <a href="https://github.com/rtfd/sphinx_rtd_theme">theme</a>
-
+
+ Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
+ <a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
provided by <a href="https://readthedocs.org">Read the Docs</a>.
+
<br><br>
-Generated on binarycpython git branch: master git revision 0886cd4f1d7f43222aac21d6ed91e917b67b20fc url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/tree/master">git url</a>.
+Generated on binarycpython git branch: auto_resolution git revision be7bd630af892a785312affc34d87c57eb337fd3 url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/tree/auto_resolution">git url</a>.
<br><br>
-Using binary_c with bit branch newmaster: git revision: "6185:20210910:1621c23a5" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/newmaster">git url</a>.
+Using binary_c with bit branch master: git revision: "6209:20211006:c4a4c332e" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/master">git url</a>.
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diff --git a/docs/build/html/_modules/binarycpython/utils/grid.html b/docs/build/html/_modules/binarycpython/utils/grid.html
index 28d95d8881fc89218f0f454a8041f2237a484299..dda5b07a838275a15f00f63ff06801233cfa84ad 100644
--- a/docs/build/html/_modules/binarycpython/utils/grid.html
+++ b/docs/build/html/_modules/binarycpython/utils/grid.html
@@ -1,69 +1,32 @@
-
-
<!DOCTYPE html>
<html class="writer-html5" lang="en" >
<head>
- <meta charset="utf-8">
-
- <meta name="viewport" content="width=device-width, initial-scale=1.0">
-
+ <meta charset="utf-8" />
+ <meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>binarycpython.utils.grid — binary_c-python documentation</title>
-
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- <link rel="stylesheet" href="../../../_static/css/theme.css" type="text/css" />
- <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
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+ <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
+ <link rel="stylesheet" href="../../../_static/css/theme.css" type="text/css" />
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<script src="../../../_static/js/html5shiv.min.js"></script>
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-
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+ <script data-url_root="../../../" id="documentation_options" src="../../../_static/documentation_options.js"></script>
<script src="../../../_static/jquery.js"></script>
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<script src="../../../_static/doctools.js"></script>
- <script src="../../../_static/language_data.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
- <script async="async" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.7/latest.js?config=TeX-AMS-MML_HTMLorMML"></script>
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+ <script src="../../../_static/js/theme.js"></script>
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</head>
-<body class="wy-body-for-nav">
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+<body class="wy-body-for-nav">
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-
<nav data-toggle="wy-nav-shift" class="wy-nav-side">
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-
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- <a href="../../../index.html" class="icon icon-home" alt="Documentation Home"> binary_c-python
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+ <a href="../../../index.html" class="icon icon-home"> binary_c-python
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<input type="text" name="q" placeholder="Search docs" />
@@ -71,19 +34,8 @@
<input type="hidden" name="area" value="default" />
</form>
</div>
-
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+ <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
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<li class="toctree-l1"><a class="reference internal" href="../../../modules.html">Binarycpython code</a></li>
@@ -94,67 +46,30 @@
<li class="toctree-l1"><a class="reference external" href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/issues/new">Submit an issue</a></li>
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-
+
<h1>Source code for binarycpython.utils.grid</h1><div class="highlight"><pre>
<span></span><span class="sd">"""</span>
<span class="sd">Module containing the Population grid class object.</span>
@@ -181,6 +96,7 @@
<span class="kn">import</span> <span class="nn">os</span>
<span class="kn">import</span> <span class="nn">gc</span>
<span class="kn">import</span> <span class="nn">sys</span>
+
<span class="kn">import</span> <span class="nn">copy</span>
<span class="kn">import</span> <span class="nn">json</span>
<span class="kn">import</span> <span class="nn">time</span>
@@ -198,6 +114,10 @@
<span class="kn">import</span> <span class="nn">setproctitle</span>
<span class="kn">import</span> <span class="nn">py_rinterpolate</span>
+<span class="kn">from</span> <span class="nn">colorama</span> <span class="kn">import</span> <span class="n">init</span> <span class="k">as</span> <span class="n">colorama_init</span>
+
+<span class="n">colorama_init</span><span class="p">()</span>
+
<span class="kn">from</span> <span class="nn">binarycpython.utils.grid_options_defaults</span> <span class="kn">import</span> <span class="p">(</span>
<span class="n">grid_options_defaults_dict</span><span class="p">,</span>
<span class="n">moe_di_stefano_default_options</span><span class="p">,</span>
@@ -211,6 +131,7 @@
<span class="n">binary_c_log_code</span><span class="p">,</span>
<span class="n">create_and_load_logging_function</span><span class="p">,</span>
<span class="p">)</span>
+
<span class="kn">from</span> <span class="nn">binarycpython.utils.functions</span> <span class="kn">import</span> <span class="p">(</span>
<span class="n">get_defaults</span><span class="p">,</span>
<span class="n">remove_file</span><span class="p">,</span>
@@ -229,6 +150,12 @@
<span class="n">multiply_values_dict</span><span class="p">,</span>
<span class="n">format_ensemble_results</span><span class="p">,</span>
<span class="n">AutoVivificationDict</span><span class="p">,</span>
+ <span class="n">trem</span><span class="p">,</span>
+ <span class="n">conv_time_units</span><span class="p">,</span>
+ <span class="n">mem_use</span><span class="p">,</span>
+ <span class="n">ANSI_colours</span><span class="p">,</span>
+ <span class="n">check_if_in_shell</span><span class="p">,</span>
+ <span class="n">format_number</span><span class="p">,</span>
<span class="p">)</span>
<span class="c1"># from binarycpython.utils.hpc_functions import (</span>
@@ -248,10 +175,10 @@
<span class="n">raghavan2010_binary_fraction</span><span class="p">,</span>
<span class="n">Moe_di_Stefano_2017_multiplicity_fractions</span><span class="p">,</span>
<span class="p">)</span>
-
<span class="kn">from</span> <span class="nn">binarycpython</span> <span class="kn">import</span> <span class="n">_binary_c_bindings</span>
-<span class="n">secs_per_day</span> <span class="o">=</span> <span class="mi">86400</span> <span class="c1"># probably needs to go somewhere more sensible</span>
+<span class="n">secs_per_day</span> <span class="o">=</span> <span class="mi">86400</span> <span class="c1"># probably needs to go somewhere more sensible</span>
+
<div class="viewcode-block" id="Population"><a class="viewcode-back" href="../../../grid.html#binarycpython.utils.grid.Population">[docs]</a><span class="k">class</span> <span class="nc">Population</span><span class="p">:</span>
<span class="sd">"""</span>
@@ -259,7 +186,7 @@
<span class="sd"> population of systems</span>
<span class="sd"> """</span>
- <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Initialisation function of the population class</span>
<span class="sd"> """</span>
@@ -284,27 +211,52 @@
<span class="c1"># Custom options</span>
<span class="bp">self</span><span class="o">.</span><span class="n">custom_options</span> <span class="o">=</span> <span class="p">{}</span>
- <span class="c1"># shared memory used for logging</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">shared_memory</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="c1"># grid code generation</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">indent_depth</span> <span class="o">=</span> <span class="mi">0</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">indent_string</span> <span class="o">=</span> <span class="s2">" "</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">code_string</span> <span class="o">=</span> <span class="s2">""</span>
+
+ <span class="c1"># Set the options that are passed at creation of the object</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">set</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
<span class="c1"># Load M&s options</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">]</span> <span class="o">=</span> <span class="n">copy</span><span class="o">.</span><span class="n">deepcopy</span><span class="p">(</span><span class="n">moe_di_stefano_default_options</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">]</span> <span class="o">=</span> <span class="n">copy</span><span class="o">.</span><span class="n">deepcopy</span><span class="p">(</span><span class="n">moe_di_stefano_default_options</span><span class="p">)</span>
- <span class="c1"># Write M&S options to a file</span>
- <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"tmp_dir"</span><span class="p">],</span> <span class="s2">"moe_distefano"</span><span class="p">),</span> <span class="n">exist_ok</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
- <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"tmp_dir"</span><span class="p">],</span> <span class="s2">"moe_distefano"</span><span class="p">),</span> <span class="s2">"moeopts.dat"</span><span class="p">),</span> <span class="s2">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
- <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">json</span><span class="o">.</span><span class="n">dumps</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">],</span> <span class="n">indent</span><span class="o">=</span><span class="mi">4</span><span class="p">))</span>
+ <span class="c1"># Write M&S options to a file. NOTE: not sure why i put this here anymore</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"tmp_dir"</span><span class="p">],</span> <span class="s2">"moe_distefano"</span><span class="p">),</span> <span class="n">exist_ok</span><span class="o">=</span><span class="kc">True</span>
+ <span class="p">)</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"tmp_dir"</span><span class="p">],</span> <span class="s2">"moe_distefano"</span><span class="p">),</span>
+ <span class="s2">"moeopts.dat"</span><span class="p">,</span>
+ <span class="p">),</span>
+ <span class="s2">"w"</span><span class="p">,</span>
+ <span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
+ <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">json</span><span class="o">.</span><span class="n">dumps</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">],</span> <span class="n">indent</span><span class="o">=</span><span class="mi">4</span><span class="p">))</span>
<span class="c1"># Argline dict</span>
<span class="bp">self</span><span class="o">.</span><span class="n">argline_dict</span> <span class="o">=</span> <span class="p">{}</span>
- <span class="c1"># Set main process id</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"_main_pid"</span><span class="p">]</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">getpid</span><span class="p">()</span>
-
<span class="c1"># Set some memory dicts</span>
<span class="bp">self</span><span class="o">.</span><span class="n">persistent_data_memory_dict</span> <span class="o">=</span> <span class="p">{}</span>
- <span class="c1">#</span>
+ <span class="c1"># shared memory used for logging</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">shared_memory</span> <span class="o">=</span> <span class="p">{}</span>
+
+ <span class="c1"># variable to test if we're running in a shell</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">in_shell</span> <span class="o">=</span> <span class="n">check_if_in_shell</span><span class="p">()</span>
+
+ <span class="c1"># ANSI colours: use them if in a shell</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">ANSI_colours</span> <span class="o">=</span> <span class="n">ANSI_colours</span><span class="p">()</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">in_shell</span> <span class="o">==</span> <span class="kc">False</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">ANSI_colours</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">ANSI_colours</span><span class="p">[</span><span class="n">c</span><span class="p">]</span> <span class="o">=</span> <span class="s2">""</span>
+
+ <span class="c1"># Set global (OS) process id</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"_main_pid"</span><span class="p">]</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">getpid</span><span class="p">()</span>
+
+ <span class="c1"># local process ID</span>
<span class="bp">self</span><span class="o">.</span><span class="n">process_ID</span> <span class="o">=</span> <span class="mi">0</span>
<span class="c1"># Create location to store results. Users should write to this dictionary.</span>
@@ -326,7 +278,7 @@
<span class="c1"># - For a population the bse_options will get copied to a temp_bse_options dict and updated with</span>
<span class="c1"># all the parameters generated by the grid</span>
- <span class="c1"># I will NOT create the argument line by fully writing ALL the defaults and overriding user</span>
+ <span class="c1"># I will not create the argument line by fully writing all the defaults and overriding user</span>
<span class="c1"># input, that seems not necessary because by using the get_defaults() function we already</span>
<span class="c1"># know for sure which parameter names are valid for the binary_c version</span>
<span class="c1"># And because binary_c uses internal defaults, its not necessary to explicitly pass them.</span>
@@ -350,8 +302,6 @@
<span class="sd"> via kwargs all the arguments are either set to binary_c parameters, grid_options or custom_options (see above)</span>
<span class="sd"> """</span>
- <span class="c1"># Select the params that end with %d</span>
-
<span class="c1"># Go over all the input</span>
<span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span>
<span class="c1"># Filter out keys for the bse_options</span>
@@ -398,13 +348,14 @@
<span class="n">key</span><span class="p">,</span> <span class="n">kwargs</span><span class="p">[</span><span class="n">key</span><span class="p">]</span>
<span class="p">),</span>
<span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"verbosity"</span><span class="p">],</span>
- <span class="mi">1</span><span class="p">,</span>
+ <span class="mi">0</span><span class="p">,</span> <span class="c1"># NOTE: setting this to be 0 prevents mistakes being overlooked.</span>
<span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">custom_options</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">kwargs</span><span class="p">[</span><span class="n">key</span><span class="p">]</span></div>
<div class="viewcode-block" id="Population.parse_cmdline"><a class="viewcode-back" href="../../../grid.html#binarycpython.utils.grid.Population.parse_cmdline">[docs]</a> <span class="k">def</span> <span class="nf">parse_cmdline</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-></span> <span class="kc">None</span><span class="p">:</span>
<span class="sd">"""</span>
-<span class="sd"> Function to handle settings values via the command line.</span>
+<span class="sd"> Function to handle settings values via the command line in the form x=y, w=z, etc.</span>
+
<span class="sd"> Best to be called after all the .set(..) lines, and just before the .evolve() is called</span>
<span class="sd"> If you input any known parameter (i.e. contained in grid_options, defaults/bse_options</span>
@@ -415,21 +366,14 @@
<span class="sd"> can change to ints.</span>
<span class="sd"> The value of any new parameter (which will go to custom_options) will be a string.</span>
-
-<span class="sd"> Tasks:</span>
-<span class="sd"> - TODO: remove the need for --cmdline</span>
<span class="sd"> """</span>
- <span class="n">parser</span> <span class="o">=</span> <span class="n">argparse</span><span class="o">.</span><span class="n">ArgumentParser</span><span class="p">()</span>
- <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
- <span class="s2">"--cmdline"</span><span class="p">,</span>
- <span class="n">help</span><span class="o">=</span><span class="s1">'Setting values via the commandline. Input like --cmdline "metallicity=0.02"'</span><span class="p">,</span>
- <span class="p">)</span>
- <span class="n">args</span> <span class="o">=</span> <span class="n">parser</span><span class="o">.</span><span class="n">parse_args</span><span class="p">()</span>
+ <span class="c1"># get the cmd-line args in the form x=y</span>
+ <span class="n">cmdline_args</span> <span class="o">=</span> <span class="n">sys</span><span class="o">.</span><span class="n">argv</span><span class="p">[</span><span class="mi">1</span><span class="p">:]</span>
<span class="c1"># How its set up now is that as input you need to give --cmdline "metallicity=0.002"</span>
<span class="c1"># Its checked if this exists and handled accordingly.</span>
- <span class="k">if</span> <span class="n">args</span><span class="o">.</span><span class="n">cmdline</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">cmdline_args</span><span class="p">:</span>
<span class="n">verbose_print</span><span class="p">(</span>
<span class="s2">"Found cmdline args. Parsing them now"</span><span class="p">,</span>
<span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"verbosity"</span><span class="p">],</span>
@@ -437,17 +381,12 @@
<span class="p">)</span>
<span class="c1"># Grab the input and split them up, while accepting only non-empty entries</span>
- <span class="n">cmdline_args</span> <span class="o">=</span> <span class="n">args</span><span class="o">.</span><span class="n">cmdline</span>
+ <span class="c1"># cmdline_args = args</span>
<span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"_commandline_input"</span><span class="p">]</span> <span class="o">=</span> <span class="n">cmdline_args</span>
- <span class="n">split_args</span> <span class="o">=</span> <span class="p">[</span>
- <span class="n">cmdline_arg</span>
- <span class="k">for</span> <span class="n">cmdline_arg</span> <span class="ow">in</span> <span class="n">cmdline_args</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">" "</span><span class="p">)</span>
- <span class="k">if</span> <span class="ow">not</span> <span class="n">cmdline_arg</span> <span class="o">==</span> <span class="s2">""</span>
- <span class="p">]</span>
<span class="c1"># Make dict and fill it</span>
<span class="n">cmdline_dict</span> <span class="o">=</span> <span class="p">{}</span>
- <span class="k">for</span> <span class="n">cmdline_arg</span> <span class="ow">in</span> <span class="n">split_args</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">cmdline_arg</span> <span class="ow">in</span> <span class="n">cmdline_args</span><span class="p">:</span>
<span class="n">split</span> <span class="o">=</span> <span class="n">cmdline_arg</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">"="</span><span class="p">)</span>
<span class="n">parameter</span> <span class="o">=</span> <span class="n">split</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
<span class="n">value</span> <span class="o">=</span> <span class="n">split</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
@@ -474,10 +413,10 @@
<span class="n">parameter</span><span class="p">,</span> <span class="nb">type</span><span class="p">(</span><span class="n">value</span><span class="p">),</span> <span class="nb">type</span><span class="p">(</span><span class="n">old_value</span><span class="p">)</span>
<span class="p">),</span>
<span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"verbosity"</span><span class="p">],</span>
- <span class="mi">1</span><span class="p">,</span>
+ <span class="mi">2</span><span class="p">,</span>
<span class="p">)</span>
<span class="n">value</span> <span class="o">=</span> <span class="nb">type</span><span class="p">(</span><span class="n">old_value</span><span class="p">)(</span><span class="n">value</span><span class="p">)</span>
- <span class="n">verbose_print</span><span class="p">(</span><span class="s2">"Success!"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"verbosity"</span><span class="p">],</span> <span class="mi">1</span><span class="p">)</span>
+ <span class="n">verbose_print</span><span class="p">(</span><span class="s2">"Success!"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"verbosity"</span><span class="p">],</span> <span class="mi">2</span><span class="p">)</span>
<span class="k">except</span> <span class="ne">ValueError</span><span class="p">:</span>
<span class="n">verbose_print</span><span class="p">(</span>
@@ -525,11 +464,7 @@
<span class="p">):</span>
<span class="k">return</span> <span class="n">grid_variable</span>
-<div class="viewcode-block" id="Population.update_grid_variable"><a class="viewcode-back" href="../../../grid.html#binarycpython.utils.grid.Population.update_grid_variable">[docs]</a> <span class="k">def</span> <span class="nf">update_grid_variable</span><span class="p">(</span>
- <span class="bp">self</span><span class="p">,</span>
- <span class="n">name</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
- <span class="o">**</span><span class="n">kwargs</span>
- <span class="p">)</span> <span class="o">-></span> <span class="kc">None</span><span class="p">:</span>
+<div class="viewcode-block" id="Population.update_grid_variable"><a class="viewcode-back" href="../../../grid.html#binarycpython.utils.grid.Population.update_grid_variable">[docs]</a> <span class="k">def</span> <span class="nf">update_grid_variable</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span> <span class="o">-></span> <span class="kc">None</span><span class="p">:</span>
<span class="sd">"""</span>
<span class="sd"> Function to update the values of a grid variable.</span>
@@ -544,10 +479,12 @@
<span class="k">try</span><span class="p">:</span>
<span class="n">grid_variable</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"_grid_variables"</span><span class="p">][</span><span class="n">name</span><span class="p">]</span>
<span class="k">except</span> <span class="ne">KeyError</span><span class="p">:</span>
- <span class="n">msg</span> <span class="o">=</span> <span class="s2">"Unknown grid variable </span><span class="si">{}</span><span class="s2"> - please create it with the add_grid_variable() method."</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">name</span><span class="p">)</span>
+ <span class="n">msg</span> <span class="o">=</span> <span class="s2">"Unknown grid variable </span><span class="si">{}</span><span class="s2"> - please create it with the add_grid_variable() method."</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+ <span class="n">name</span>
+ <span class="p">)</span>
<span class="k">raise</span> <span class="ne">KeyError</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
- <span class="k">for</span> <span class="n">key</span><span class="p">,</span><span class="n">value</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
+ <span class="k">for</span> <span class="n">key</span><span class="p">,</span> <span class="n">value</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
<span class="n">grid_variable</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">value</span>
<span class="n">verbose_print</span><span class="p">(</span>
<span class="s2">"Updated grid variable: </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">json</span><span class="o">.</span><span class="n">dumps</span><span class="p">(</span><span class="n">grid_variable</span><span class="p">,</span> <span class="n">indent</span><span class="o">=</span><span class="mi">4</span><span class="p">)),</span>
@@ -555,11 +492,24 @@
<span class="mi">1</span><span class="p">,</span>
<span class="p">)</span></div>
-<div class="viewcode-block" id="Population.rename_grid_variable"><a class="viewcode-back" href="../../../grid.html#binarycpython.utils.grid.Population.rename_grid_variable">[docs]</a> <span class="k">def</span> <span class="nf">rename_grid_variable</span><span class="p">(</span>
+<div class="viewcode-block" id="Population.delete_grid_variable"><a class="viewcode-back" href="../../../grid.html#binarycpython.utils.grid.Population.delete_grid_variable">[docs]</a> <span class="k">def</span> <span class="nf">delete_grid_variable</span><span class="p">(</span>
<span class="bp">self</span><span class="p">,</span>
- <span class="n">oldname</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
- <span class="n">newname</span><span class="p">:</span> <span class="nb">str</span>
+ <span class="n">name</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
<span class="p">)</span> <span class="o">-></span> <span class="kc">None</span><span class="p">:</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="k">del</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"_grid_variables"</span><span class="p">][</span><span class="n">name</span><span class="p">]</span>
+ <span class="n">verbose_print</span><span class="p">(</span>
+ <span class="s2">"Deleted grid variable: </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">name</span><span class="p">),</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"verbosity"</span><span class="p">],</span>
+ <span class="mi">1</span><span class="p">,</span>
+ <span class="p">)</span>
+ <span class="k">except</span><span class="p">:</span>
+ <span class="n">msg</span> <span class="o">=</span> <span class="s2">"Failed to remove grid variable </span><span class="si">{}</span><span class="s2"> : please check it exists."</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+ <span class="n">name</span>
+ <span class="p">)</span>
+ <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span></div>
+
+<div class="viewcode-block" id="Population.rename_grid_variable"><a class="viewcode-back" href="../../../grid.html#binarycpython.utils.grid.Population.rename_grid_variable">[docs]</a> <span class="k">def</span> <span class="nf">rename_grid_variable</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">oldname</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">newname</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-></span> <span class="kc">None</span><span class="p">:</span>
<span class="sd">"""</span>
<span class="sd"> Function to rename a grid variable.</span>
@@ -577,10 +527,17 @@
<span class="sd"> """</span>
<span class="k">try</span><span class="p">:</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"_grid_variables"</span><span class="p">][</span><span class="n">newname</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"_grid_variables"</span><span class="p">]</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="n">oldname</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"_grid_variables"</span><span class="p">][</span><span class="n">newname</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span>
+ <span class="s2">"_grid_variables"</span>
+ <span class="p">]</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="n">oldname</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"_grid_variables"</span><span class="p">][</span><span class="n">newname</span><span class="p">][</span><span class="s2">"name"</span><span class="p">]</span> <span class="o">=</span> <span class="n">newname</span>
+ <span class="n">verbose_print</span><span class="p">(</span>
+ <span class="s2">"Rename grid variable: </span><span class="si">{}</span><span class="s2"> to </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">oldname</span><span class="p">,</span> <span class="n">newname</span><span class="p">),</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"verbosity"</span><span class="p">],</span>
+ <span class="mi">1</span><span class="p">,</span>
+ <span class="p">)</span>
<span class="k">except</span><span class="p">:</span>
- <span class="n">msg</span> <span class="o">=</span> <span class="s2">"Failed to rename grid variable </span><span class="si">{}</span><span class="s2"> to </span><span class="si">{}</span><span class="s2">."</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">oldname</span><span class="p">,</span><span class="n">newname</span><span class="p">)</span>
+ <span class="n">msg</span> <span class="o">=</span> <span class="s2">"Failed to rename grid variable </span><span class="si">{}</span><span class="s2"> to </span><span class="si">{}</span><span class="s2">."</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">oldname</span><span class="p">,</span> <span class="n">newname</span><span class="p">)</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span></div>
<div class="viewcode-block" id="Population.add_grid_variable"><a class="viewcode-back" href="../../../grid.html#binarycpython.utils.grid.Population.add_grid_variable">[docs]</a> <span class="k">def</span> <span class="nf">add_grid_variable</span><span class="p">(</span>
@@ -625,24 +582,24 @@
<span class="sd"> Examples:</span>
<span class="sd"> longname = 'Primary mass'</span>
<span class="sd"> range:</span>
-<span class="sd"> Range of values to take. Does not get used really, the spacingfunction is used to</span>
+<span class="sd"> Range of values to take. Does not get used really, the spacingfunc is used to</span>
<span class="sd"> get the values from</span>
<span class="sd"> Examples:</span>
<span class="sd"> range = [math.log(m_min), math.log(m_max)]</span>
<span class="sd"> resolution:</span>
-<span class="sd"> Resolution of the sampled range (amount of samples).</span>
+<span class="sd"> Resolution of the sampled range (number of samples).</span>
<span class="sd"> TODO: check if this is used anywhere</span>
<span class="sd"> Examples:</span>
<span class="sd"> resolution = resolution["M_1"]</span>
-<span class="sd"> spacingfunction:</span>
+<span class="sd"> spacingfunc:</span>
<span class="sd"> Function determining how the range is sampled. You can either use a real function,</span>
<span class="sd"> or a string representation of a function call. Will get written to a file and</span>
<span class="sd"> then evaluated.</span>
<span class="sd"> Examples:</span>
-<span class="sd"> spacingfunction = "const(math.log(m_min), math.log(m_max), {})".format(resolution['M_1'])</span>
+<span class="sd"> spacingfunc = "const(math.log(m_min), math.log(m_max), {})".format(resolution['M_1'])</span>
<span class="sd"> precode:</span>
<span class="sd"> Extra room for some code. This code will be evaluated within the loop of the</span>
@@ -688,7 +645,7 @@
<span class="p">}</span>
<span class="c1"># Check for gridtype input</span>
- <span class="k">if</span> <span class="ow">not</span> <span class="n">gridtype</span> <span class="ow">in</span> <span class="p">[</span><span class="s1">'edge'</span><span class="p">,</span> <span class="s1">'centred'</span><span class="p">]:</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">gridtype</span> <span class="ow">in</span> <span class="p">[</span><span class="s2">"edge"</span><span class="p">,</span> <span class="s2">"centred"</span><span class="p">]:</span>
<span class="n">msg</span> <span class="o">=</span> <span class="s2">"Unknown gridtype value. Please start another one"</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
@@ -837,10 +794,14 @@
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">custom_options</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"data_dir"</span><span class="p">,</span> <span class="kc">None</span><span class="p">):</span>
<span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">custom_options</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"base_filename"</span><span class="p">,</span> <span class="kc">None</span><span class="p">):</span>
<span class="n">base_name</span> <span class="o">=</span> <span class="s2">"simulation_</span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
- <span class="n">datetime</span><span class="o">.</span><span class="n">datetime</span><span class="o">.</span><span class="n">strftime</span><span class="p">(</span><span class="n">datetime</span><span class="o">.</span><span class="n">datetime</span><span class="o">.</span><span class="n">now</span><span class="p">(),</span> <span class="s2">"%Y%m</span><span class="si">%d</span><span class="s2">_%H%M%S"</span><span class="p">)</span>
+ <span class="n">datetime</span><span class="o">.</span><span class="n">datetime</span><span class="o">.</span><span class="n">strftime</span><span class="p">(</span>
+ <span class="n">datetime</span><span class="o">.</span><span class="n">datetime</span><span class="o">.</span><span class="n">now</span><span class="p">(),</span> <span class="s2">"%Y%m</span><span class="si">%d</span><span class="s2">_%H%M%S"</span>
+ <span class="p">)</span>
<span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
- <span class="n">base_name</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">splitext</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">custom_options</span><span class="p">[</span><span class="s2">"base_filename"</span><span class="p">])[</span><span class="mi">0</span><span class="p">]</span>
+ <span class="n">base_name</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">splitext</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">custom_options</span><span class="p">[</span><span class="s2">"base_filename"</span><span class="p">])[</span>
+ <span class="mi">0</span>
+ <span class="p">]</span>
<span class="n">settings_name</span> <span class="o">=</span> <span class="n">base_name</span> <span class="o">+</span> <span class="s2">"_settings.json"</span>
@@ -901,7 +862,10 @@
<span class="sd"> """</span>
<span class="c1"># Only if the values are the 'default' unset values</span>
- <span class="k">if</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"custom_logging_func_memaddr"</span><span class="p">]</span> <span class="o">==</span> <span class="o">-</span><span class="mi">1</span> <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"_custom_logging_shared_library_file"</span><span class="p">]</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">):</span>
+ <span class="k">if</span> <span class="p">(</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"custom_logging_func_memaddr"</span><span class="p">]</span> <span class="o">==</span> <span class="o">-</span><span class="mi">1</span>
+ <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"_custom_logging_shared_library_file"</span><span class="p">]</span> <span class="ow">is</span> <span class="kc">None</span>
+ <span class="p">):</span>
<span class="n">verbose_print</span><span class="p">(</span>
<span class="s2">"Creating and loading custom logging functionality"</span><span class="p">,</span>
<span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"verbosity"</span><span class="p">],</span>
@@ -912,7 +876,8 @@
<span class="c1"># Generate entire shared lib code around logging lines</span>
<span class="n">custom_logging_code</span> <span class="o">=</span> <span class="n">binary_c_log_code</span><span class="p">(</span>
<span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"C_logging_code"</span><span class="p">],</span>
- <span class="n">verbosity</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"verbosity"</span><span class="p">]</span><span class="o">-</span><span class="p">(</span><span class="n">_CUSTOM_LOGGING_VERBOSITY_LEVEL</span><span class="o">-</span><span class="mi">1</span><span class="p">),</span>
+ <span class="n">verbosity</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"verbosity"</span><span class="p">]</span>
+ <span class="o">-</span> <span class="p">(</span><span class="n">_CUSTOM_LOGGING_VERBOSITY_LEVEL</span> <span class="o">-</span> <span class="mi">1</span><span class="p">),</span>
<span class="p">)</span>
<span class="c1"># Load memory address</span>
@@ -921,7 +886,8 @@
<span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"_custom_logging_shared_library_file"</span><span class="p">],</span>
<span class="p">)</span> <span class="o">=</span> <span class="n">create_and_load_logging_function</span><span class="p">(</span>
<span class="n">custom_logging_code</span><span class="p">,</span>
- <span class="n">verbosity</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"verbosity"</span><span class="p">]</span><span class="o">-</span><span class="p">(</span><span class="n">_CUSTOM_LOGGING_VERBOSITY_LEVEL</span><span class="o">-</span><span class="mi">1</span><span class="p">),</span>
+ <span class="n">verbosity</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"verbosity"</span><span class="p">]</span>
+ <span class="o">-</span> <span class="p">(</span><span class="n">_CUSTOM_LOGGING_VERBOSITY_LEVEL</span> <span class="o">-</span> <span class="mi">1</span><span class="p">),</span>
<span class="n">custom_tmp_dir</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"tmp_dir"</span><span class="p">],</span>
<span class="p">)</span>
@@ -929,12 +895,15 @@
<span class="c1"># Generate real logging code</span>
<span class="n">logging_line</span> <span class="o">=</span> <span class="n">autogen_C_logging_code</span><span class="p">(</span>
<span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"C_auto_logging"</span><span class="p">],</span>
- <span class="n">verbosity</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"verbosity"</span><span class="p">]</span><span class="o">-</span><span class="p">(</span><span class="n">_CUSTOM_LOGGING_VERBOSITY_LEVEL</span><span class="o">-</span><span class="mi">1</span><span class="p">),</span>
+ <span class="n">verbosity</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"verbosity"</span><span class="p">]</span>
+ <span class="o">-</span> <span class="p">(</span><span class="n">_CUSTOM_LOGGING_VERBOSITY_LEVEL</span> <span class="o">-</span> <span class="mi">1</span><span class="p">),</span>
<span class="p">)</span>
<span class="c1"># Generate entire shared lib code around logging lines</span>
<span class="n">custom_logging_code</span> <span class="o">=</span> <span class="n">binary_c_log_code</span><span class="p">(</span>
- <span class="n">logging_line</span><span class="p">,</span> <span class="n">verbosity</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"verbosity"</span><span class="p">]</span><span class="o">-</span><span class="p">(</span><span class="n">_CUSTOM_LOGGING_VERBOSITY_LEVEL</span><span class="o">-</span><span class="mi">1</span><span class="p">)</span>
+ <span class="n">logging_line</span><span class="p">,</span>
+ <span class="n">verbosity</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"verbosity"</span><span class="p">]</span>
+ <span class="o">-</span> <span class="p">(</span><span class="n">_CUSTOM_LOGGING_VERBOSITY_LEVEL</span> <span class="o">-</span> <span class="mi">1</span><span class="p">),</span>
<span class="p">)</span>
<span class="c1"># Load memory address</span>
@@ -943,7 +912,8 @@
<span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"_custom_logging_shared_library_file"</span><span class="p">],</span>
<span class="p">)</span> <span class="o">=</span> <span class="n">create_and_load_logging_function</span><span class="p">(</span>
<span class="n">custom_logging_code</span><span class="p">,</span>
- <span class="n">verbosity</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"verbosity"</span><span class="p">]</span><span class="o">-</span><span class="p">(</span><span class="n">_CUSTOM_LOGGING_VERBOSITY_LEVEL</span><span class="o">-</span><span class="mi">1</span><span class="p">),</span>
+ <span class="n">verbosity</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"verbosity"</span><span class="p">]</span>
+ <span class="o">-</span> <span class="p">(</span><span class="n">_CUSTOM_LOGGING_VERBOSITY_LEVEL</span> <span class="o">-</span> <span class="mi">1</span><span class="p">),</span>
<span class="n">custom_tmp_dir</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"tmp_dir"</span><span class="p">],</span>
<span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
@@ -980,17 +950,28 @@
<span class="c1"># Reset population ID:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"_population_id"</span><span class="p">]</span> <span class="o">=</span> <span class="n">uuid</span><span class="o">.</span><span class="n">uuid4</span><span class="p">()</span><span class="o">.</span><span class="n">hex</span>
+ <span class="c1"># save number of stored log stats</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">shared_memory</span><span class="p">[</span><span class="s2">"n_saved_log_stats"</span><span class="p">]</span> <span class="o">=</span> <span class="n">multiprocessing</span><span class="o">.</span><span class="n">Value</span><span class="p">(</span><span class="s2">"i"</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span>
+
<span class="c1"># set previous logging time</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">shared_memory</span><span class="p">[</span><span class="s2">"prev_log_time"</span><span class="p">]</span> <span class="o">=</span> <span class="n">multiprocessing</span><span class="o">.</span><span class="n">Value</span><span class="p">(</span><span class="s1">'d'</span><span class="p">,</span><span class="n">time</span><span class="o">.</span><span class="n">time</span><span class="p">())</span>
+ <span class="n">_t</span> <span class="o">=</span> <span class="n">time</span><span class="o">.</span><span class="n">time</span><span class="p">()</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">shared_memory</span><span class="p">[</span><span class="s2">"prev_log_time"</span><span class="p">]</span> <span class="o">=</span> <span class="n">multiprocessing</span><span class="o">.</span><span class="n">Array</span><span class="p">(</span>
+ <span class="s2">"d"</span><span class="p">,</span> <span class="p">[</span><span class="n">_t</span><span class="p">]</span> <span class="o">*</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"n_logging_stats"</span><span class="p">]</span>
+ <span class="p">)</span>
+
<span class="c1"># set previous logging system number to 0</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">shared_memory</span><span class="p">[</span><span class="s2">"prev_log_system_number"</span><span class="p">]</span> <span class="o">=</span> <span class="n">multiprocessing</span><span class="o">.</span><span class="n">Value</span><span class="p">(</span><span class="s1">'i'</span><span class="p">,</span><span class="mi">0</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">shared_memory</span><span class="p">[</span><span class="s2">"prev_log_system_number"</span><span class="p">]</span> <span class="o">=</span> <span class="n">multiprocessing</span><span class="o">.</span><span class="n">Array</span><span class="p">(</span>
+ <span class="s2">"i"</span><span class="p">,</span> <span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">*</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"n_logging_stats"</span><span class="p">]</span>
+ <span class="p">)</span>
+
<span class="c1"># array to store memory use per-thread</span>
- <span class="n">mem</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_mem_use</span><span class="p">()</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">shared_memory</span><span class="p">[</span><span class="s2">"memory_use_per_thread"</span><span class="p">]</span> <span class="o">=</span> <span class="n">multiprocessing</span><span class="o">.</span><span class="n">Array</span><span class="p">(</span><span class="s1">'d'</span><span class="p">,[</span><span class="mf">1.0</span><span class="o">*</span><span class="n">mem</span><span class="p">]</span><span class="o">*</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"amt_cores"</span><span class="p">])</span>
+ <span class="n">mem</span> <span class="o">=</span> <span class="mf">1.0</span> <span class="o">*</span> <span class="n">mem_use</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">shared_memory</span><span class="p">[</span><span class="s2">"memory_use_per_thread"</span><span class="p">]</span> <span class="o">=</span> <span class="n">multiprocessing</span><span class="o">.</span><span class="n">Array</span><span class="p">(</span>
+ <span class="s2">"d"</span><span class="p">,</span> <span class="p">[</span><span class="n">mem</span><span class="p">]</span> <span class="o">*</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"num_cores"</span><span class="p">]</span>
+ <span class="p">)</span>
-<div class="viewcode-block" id="Population.clean"><a class="viewcode-back" href="../../../grid.html#binarycpython.utils.grid.Population.clean">[docs]</a> <span class="k">def</span> <span class="nf">clean</span><span class="p">(</span>
- <span class="bp">self</span>
- <span class="p">)</span> <span class="o">-></span> <span class="kc">None</span><span class="p">:</span>
+<div class="viewcode-block" id="Population.clean"><a class="viewcode-back" href="../../../grid.html#binarycpython.utils.grid.Population.clean">[docs]</a> <span class="k">def</span> <span class="nf">clean</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-></span> <span class="kc">None</span><span class="p">:</span>
<span class="sd">"""</span>
<span class="sd"> Clean the contents of the population object so it can be reused.</span>
@@ -1016,7 +997,7 @@
<span class="sd"> Returns an dictionary containing the analytics of the run</span>
-<span class="sd"> TODO: change the way this is done. Slurm & CONDOR should probably do this different</span>
+<span class="sd"> TODO: change the way this is done. Slurm & CONDOR should probably do this differently</span>
<span class="sd"> NOTE: SLURM and CONDOR options are not working properly yet</span>
<span class="sd"> """</span>
@@ -1026,11 +1007,14 @@
<span class="c1"># Check which type:</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"slurm"</span><span class="p">]</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
<span class="c1"># Execute Slurm subroutines</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">_slurm_grid</span><span class="p">()</span>
+ <span class="c1"># self._slurm_grid()</span>
+ <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">"Slurm evolution not available at this moment"</span><span class="p">)</span>
<span class="k">elif</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"condor"</span><span class="p">]</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
<span class="c1"># Execute condor subroutines</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">_condor_grid</span><span class="p">()</span>
+ <span class="c1"># self._condor_grid()</span>
+ <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">"Condor evolution not available at this moment"</span><span class="p">)</span>
+
<span class="k">else</span><span class="p">:</span>
<span class="c1"># Execute population evolution subroutines</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_evolve_population</span><span class="p">()</span>
@@ -1054,11 +1038,11 @@
<span class="s2">"total_probability_weighted_mass_run"</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span>
<span class="s2">"_total_probability_weighted_mass_run"</span>
<span class="p">],</span>
- <span class="s2">"zero_prob_stars_skipped"</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'_zero_prob_stars_skipped'</span><span class="p">]</span>
+ <span class="s2">"zero_prob_stars_skipped"</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"_zero_prob_stars_skipped"</span><span class="p">],</span>
<span class="p">}</span>
<span class="c1"># Add analytics dict to the metadata too:</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_ensemble_results</span><span class="p">[</span><span class="s1">'metadata'</span><span class="p">]</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">analytics_dict</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_ensemble_results</span><span class="p">[</span><span class="s2">"metadata"</span><span class="p">]</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">analytics_dict</span><span class="p">)</span>
<span class="c1">##</span>
<span class="c1"># Clean up code: remove files, unset values, unload interpolators etc. This is placed in the general evolve function,</span>
@@ -1115,7 +1099,7 @@
<span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"_end_time_evolution"</span><span class="p">]</span>
<span class="o">-</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"_start_time_evolution"</span><span class="p">],</span>
<span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"_total_starcount"</span><span class="p">],</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"amt_cores"</span><span class="p">],</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"num_cores"</span><span class="p">],</span>
<span class="p">),</span>
<span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"verbosity"</span><span class="p">],</span>
<span class="mi">0</span><span class="p">,</span>
@@ -1169,7 +1153,7 @@
<span class="k">return</span> <span class="n">stream_logger</span>
- <span class="k">def</span> <span class="nf">_system_queue_filler</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">job_queue</span><span class="p">,</span> <span class="n">amt_cores</span><span class="p">):</span>
+ <span class="k">def</span> <span class="nf">_system_queue_filler</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">job_queue</span><span class="p">,</span> <span class="n">num_cores</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Function that is responsible for keeping the queue filled.</span>
@@ -1178,7 +1162,7 @@
<span class="sd"> """</span>
<span class="n">stream_logger</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_get_stream_logger</span><span class="p">()</span>
- <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'verbosity'</span><span class="p">]</span> <span class="o">>=</span> <span class="n">_LOGGER_VERBOSITY_LEVEL</span><span class="p">:</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"verbosity"</span><span class="p">]</span> <span class="o">>=</span> <span class="n">_LOGGER_VERBOSITY_LEVEL</span><span class="p">:</span>
<span class="n">stream_logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"setting up the system_queue_filler now"</span><span class="p">)</span>
<span class="c1"># Setup of the generator</span>
@@ -1198,7 +1182,7 @@
<span class="n">verbose_print</span><span class="p">(</span>
<span class="s2">"Queue produced system </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">system_number</span><span class="p">),</span>
<span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"verbosity"</span><span class="p">],</span>
- <span class="mi">2</span><span class="p">,</span>
+ <span class="mi">3</span><span class="p">,</span>
<span class="p">)</span>
<span class="c1"># Print current size</span>
@@ -1216,10 +1200,10 @@
<span class="c1"># print("\tsystem_queue_filler: Size dir(self): {}".format(convert_bytes(bytes_size_self)))</span>
<span class="c1"># Send closing signal to workers. When they receive this they will terminate</span>
- <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'verbosity'</span><span class="p">]</span> <span class="o">>=</span> <span class="n">_LOGGER_VERBOSITY_LEVEL</span><span class="p">:</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"verbosity"</span><span class="p">]</span> <span class="o">>=</span> <span class="n">_LOGGER_VERBOSITY_LEVEL</span><span class="p">:</span>
<span class="n">stream_logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Signaling stop to processes"</span><span class="p">)</span> <span class="c1"># DEBUG</span>
- <span class="k">for</span> <span class="n">_</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">amt_cores</span><span class="p">):</span>
+ <span class="k">for</span> <span class="n">_</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">num_cores</span><span class="p">):</span>
<span class="n">job_queue</span><span class="o">.</span><span class="n">put</span><span class="p">(</span><span class="s2">"STOP"</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">_evolve_population_grid</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
@@ -1228,7 +1212,7 @@
<span class="sd"> First we set up the multiprocessing manager and the job and result queue.</span>
-<span class="sd"> Then we spawn <self.grid_options["amt_cores"]> amount of process instances,</span>
+<span class="sd"> Then we spawn <self.grid_options["num_cores"]> number of process instances,</span>
<span class="sd"> and signal them to start.</span>
<span class="sd"> While the processes are waiting for their instructions, we start the queue filler,</span>
@@ -1243,17 +1227,21 @@
<span class="sd"> """</span>
<span class="c1"># Set process name</span>
- <span class="n">setproctitle</span><span class="o">.</span><span class="n">setproctitle</span><span class="p">(</span><span class="s1">'binarycpython parent process'</span><span class="p">)</span>
- <span class="n">setproctitle</span><span class="o">.</span><span class="n">setthreadtitle</span><span class="p">(</span><span class="s2">"binarycpython parent thread"</span><span class="p">)</span>
+ <span class="n">setproctitle</span><span class="o">.</span><span class="n">setproctitle</span><span class="p">(</span><span class="s2">"binarycpython parent process"</span><span class="p">)</span>
<span class="c1"># Set up the manager object that can share info between processes</span>
<span class="n">manager</span> <span class="o">=</span> <span class="n">multiprocessing</span><span class="o">.</span><span class="n">Manager</span><span class="p">()</span>
<span class="n">job_queue</span> <span class="o">=</span> <span class="n">manager</span><span class="o">.</span><span class="n">Queue</span><span class="p">(</span><span class="n">maxsize</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"max_queue_size"</span><span class="p">])</span>
- <span class="n">result_queue</span> <span class="o">=</span> <span class="n">manager</span><span class="o">.</span><span class="n">Queue</span><span class="p">(</span><span class="n">maxsize</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"amt_cores"</span><span class="p">])</span>
+
+ <span class="c1"># backwards compatibility</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"num_cores"</span><span class="p">]</span> <span class="ow">and</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"num_cores"</span><span class="p">]:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"num_cores"</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"num_cores"</span><span class="p">]</span>
+
+ <span class="n">result_queue</span> <span class="o">=</span> <span class="n">manager</span><span class="o">.</span><span class="n">Queue</span><span class="p">(</span><span class="n">maxsize</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"num_cores"</span><span class="p">])</span>
<span class="c1"># Create process instances</span>
<span class="n">processes</span> <span class="o">=</span> <span class="p">[]</span>
- <span class="k">for</span> <span class="n">ID</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"amt_cores"</span><span class="p">]):</span>
+ <span class="k">for</span> <span class="n">ID</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"num_cores"</span><span class="p">]):</span>
<span class="n">processes</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
<span class="n">multiprocessing</span><span class="o">.</span><span class="n">Process</span><span class="p">(</span>
<span class="n">target</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">_process_run_population_grid</span><span class="p">,</span>
@@ -1266,7 +1254,7 @@
<span class="n">p</span><span class="o">.</span><span class="n">start</span><span class="p">()</span>
<span class="c1"># Set up the system_queue</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">_system_queue_filler</span><span class="p">(</span><span class="n">job_queue</span><span class="p">,</span> <span class="n">amt_cores</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"amt_cores"</span><span class="p">])</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_system_queue_filler</span><span class="p">(</span><span class="n">job_queue</span><span class="p">,</span> <span class="n">num_cores</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"num_cores"</span><span class="p">])</span>
<span class="c1"># Join the processes</span>
<span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">processes</span><span class="p">:</span>
@@ -1283,11 +1271,15 @@
<span class="k">break</span>
<span class="c1"># Extra ensemble result manipulation:</span>
- <span class="n">combined_output_dict</span><span class="p">[</span><span class="s1">'ensemble_results'</span><span class="p">][</span><span class="s1">'ensemble'</span><span class="p">]</span> <span class="o">=</span> <span class="n">format_ensemble_results</span><span class="p">(</span><span class="n">combined_output_dict</span><span class="p">[</span><span class="s1">'ensemble_results'</span><span class="p">]</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">'ensemble'</span><span class="p">,</span> <span class="p">{}))</span>
+ <span class="n">combined_output_dict</span><span class="p">[</span><span class="s2">"ensemble_results"</span><span class="p">][</span><span class="s2">"ensemble"</span><span class="p">]</span> <span class="o">=</span> <span class="n">format_ensemble_results</span><span class="p">(</span>
+ <span class="n">combined_output_dict</span><span class="p">[</span><span class="s2">"ensemble_results"</span><span class="p">]</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"ensemble"</span><span class="p">,</span> <span class="p">{})</span>
+ <span class="p">)</span>
<span class="n">gc</span><span class="o">.</span><span class="n">collect</span><span class="p">()</span>
<span class="c1"># Take into account that we run this on multiple cores</span>
- <span class="n">combined_output_dict</span><span class="p">[</span><span class="s2">"_total_probability_weighted_mass_run"</span><span class="p">]</span> <span class="o">=</span> <span class="n">combined_output_dict</span><span class="p">[</span><span class="s2">"_total_probability_weighted_mass_run"</span><span class="p">]</span>
+ <span class="n">combined_output_dict</span><span class="p">[</span>
+ <span class="s2">"_total_probability_weighted_mass_run"</span>
+ <span class="p">]</span> <span class="o">=</span> <span class="n">combined_output_dict</span><span class="p">[</span><span class="s2">"_total_probability_weighted_mass_run"</span><span class="p">]</span>
<span class="c1"># Put the values back as object properties</span>
<span class="bp">self</span><span class="o">.</span><span class="n">grid_results</span> <span class="o">=</span> <span class="n">combined_output_dict</span><span class="p">[</span><span class="s2">"results"</span><span class="p">]</span>
@@ -1306,10 +1298,20 @@
<span class="bp">self</span><span class="o">.</span><span class="n">grid_ensemble_results</span><span class="p">[</span><span class="s2">"metadata"</span><span class="p">][</span>
<span class="s2">"total_probability_weighted_mass"</span>
<span class="p">]</span> <span class="o">=</span> <span class="n">combined_output_dict</span><span class="p">[</span><span class="s2">"_total_probability_weighted_mass_run"</span><span class="p">]</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_ensemble_results</span><span class="p">[</span><span class="s2">"metadata"</span><span class="p">][</span><span class="s2">"factored_in_probability_weighted_mass"</span><span class="p">]</span> <span class="o">=</span> <span class="kc">False</span>
- <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'ensemble_factor_in_probability_weighted_mass'</span><span class="p">]:</span>
- <span class="n">multiply_values_dict</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_ensemble_results</span><span class="p">[</span><span class="s1">'ensemble'</span><span class="p">],</span> <span class="mi">1</span><span class="o">/</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_ensemble_results</span><span class="p">[</span><span class="s2">"metadata"</span><span class="p">][</span><span class="s1">'total_probability_weighted_mass'</span><span class="p">])</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_ensemble_results</span><span class="p">[</span><span class="s2">"metadata"</span><span class="p">][</span><span class="s2">"factored_in_probability_weighted_mass"</span><span class="p">]</span> <span class="o">=</span> <span class="kc">True</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_ensemble_results</span><span class="p">[</span><span class="s2">"metadata"</span><span class="p">][</span>
+ <span class="s2">"factored_in_probability_weighted_mass"</span>
+ <span class="p">]</span> <span class="o">=</span> <span class="kc">False</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"ensemble_factor_in_probability_weighted_mass"</span><span class="p">]:</span>
+ <span class="n">multiply_values_dict</span><span class="p">(</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_ensemble_results</span><span class="p">[</span><span class="s2">"ensemble"</span><span class="p">],</span>
+ <span class="mi">1</span>
+ <span class="o">/</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_ensemble_results</span><span class="p">[</span><span class="s2">"metadata"</span><span class="p">][</span>
+ <span class="s2">"total_probability_weighted_mass"</span>
+ <span class="p">],</span>
+ <span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_ensemble_results</span><span class="p">[</span><span class="s2">"metadata"</span><span class="p">][</span>
+ <span class="s2">"factored_in_probability_weighted_mass"</span>
+ <span class="p">]</span> <span class="o">=</span> <span class="kc">True</span>
<span class="c1"># Add settings of the populations</span>
<span class="n">all_info</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">return_all_info</span><span class="p">(</span>
@@ -1318,7 +1320,9 @@
<span class="n">include_binary_c_version_info</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
<span class="n">include_binary_c_help_all</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
<span class="p">)</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_ensemble_results</span><span class="p">[</span><span class="s2">"metadata"</span><span class="p">][</span><span class="s2">"settings"</span><span class="p">]</span> <span class="o">=</span> <span class="n">json</span><span class="o">.</span><span class="n">loads</span><span class="p">(</span><span class="n">json</span><span class="o">.</span><span class="n">dumps</span><span class="p">(</span><span class="n">all_info</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="n">binaryc_json_serializer</span><span class="p">))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_ensemble_results</span><span class="p">[</span><span class="s2">"metadata"</span><span class="p">][</span><span class="s2">"settings"</span><span class="p">]</span> <span class="o">=</span> <span class="n">json</span><span class="o">.</span><span class="n">loads</span><span class="p">(</span>
+ <span class="n">json</span><span class="o">.</span><span class="n">dumps</span><span class="p">(</span><span class="n">all_info</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="n">binaryc_json_serializer</span><span class="p">)</span>
+ <span class="p">)</span>
<span class="c1">##############################</span>
<span class="c1"># Update grid options</span>
@@ -1335,7 +1339,9 @@
<span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span>
<span class="s2">"_total_probability_weighted_mass_run"</span>
<span class="p">]</span> <span class="o">=</span> <span class="n">combined_output_dict</span><span class="p">[</span><span class="s2">"_total_probability_weighted_mass_run"</span><span class="p">]</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'_zero_prob_stars_skipped'</span><span class="p">]</span> <span class="o">=</span> <span class="n">combined_output_dict</span><span class="p">[</span><span class="s1">'_zero_prob_stars_skipped'</span><span class="p">]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"_zero_prob_stars_skipped"</span><span class="p">]</span> <span class="o">=</span> <span class="n">combined_output_dict</span><span class="p">[</span>
+ <span class="s2">"_zero_prob_stars_skipped"</span>
+ <span class="p">]</span>
<span class="k">def</span> <span class="nf">_evolve_system_mp</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">full_system_dict</span><span class="p">):</span>
<span class="sd">"""</span>
@@ -1351,6 +1357,10 @@
<span class="n">persistent_data_memaddr</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">persistent_data_memory_dict</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">process_ID</span><span class="p">]</span>
<span class="c1"># print("thread {}: persistent_data_memaddr: ".format(self.process_ID), persistent_data_memaddr)</span>
+ <span class="c1"># vb2 logging</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'verbosity'</span><span class="p">]</span> <span class="o">>=</span> <span class="mi">2</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">vb2print</span><span class="p">(</span><span class="n">full_system_dict</span><span class="p">,</span><span class="n">binary_cmdline_string</span><span class="p">)</span>
+
<span class="c1"># Get results binary_c</span>
<span class="c1"># print("running: {}".format(binary_cmdline_string))</span>
<span class="n">out</span> <span class="o">=</span> <span class="n">_binary_c_bindings</span><span class="o">.</span><span class="n">run_system</span><span class="p">(</span>
@@ -1391,14 +1401,14 @@
<span class="p">)</span>
<span class="n">stream_logger</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_get_stream_logger</span><span class="p">()</span>
- <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'verbosity'</span><span class="p">]</span> <span class="o">>=</span> <span class="n">_LOGGER_VERBOSITY_LEVEL</span><span class="p">:</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"verbosity"</span><span class="p">]</span> <span class="o">>=</span> <span class="n">_LOGGER_VERBOSITY_LEVEL</span><span class="p">:</span>
<span class="n">stream_logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Setting up processor: process-</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">process_ID</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
<span class="c1"># Set the process names</span>
- <span class="n">name</span> <span class="o">=</span> <span class="s1">'binarycpython population thread </span><span class="si">{}</span><span class="s1">'</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">ID</span><span class="p">)</span>
- <span class="n">name_proc</span> <span class="o">=</span> <span class="s1">'binarycpython population process </span><span class="si">{}</span><span class="s1">'</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">ID</span><span class="p">)</span>
+ <span class="n">name</span> <span class="o">=</span> <span class="s2">"binarycpython population thread </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">ID</span><span class="p">)</span>
+ <span class="n">name_proc</span> <span class="o">=</span> <span class="s2">"binarycpython population process </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">ID</span><span class="p">)</span>
<span class="n">setproctitle</span><span class="o">.</span><span class="n">setproctitle</span><span class="p">(</span><span class="n">name_proc</span><span class="p">)</span>
- <span class="n">setproctitle</span><span class="o">.</span><span class="n">setthreadtitle</span><span class="p">(</span><span class="n">name</span><span class="p">)</span>
+ <span class="c1"># setproctitle.setthreadtitle(name)</span>
<span class="c1"># Set to starting up</span>
<span class="k">with</span> <span class="nb">open</span><span class="p">(</span>
@@ -1454,15 +1464,21 @@
<span class="n">zero_prob_stars_skipped</span> <span class="o">=</span> <span class="mi">0</span>
<span class="n">total_time_calling_binary_c</span> <span class="o">=</span> <span class="mi">0</span>
- <span class="n">start_grid_time</span> <span class="o">=</span> <span class="n">time</span><span class="o">.</span><span class="n">time</span><span class="p">()</span>
- <span class="n">next_log_time</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">shared_memory</span><span class="p">[</span><span class="s2">"prev_log_time"</span><span class="p">]</span><span class="o">.</span><span class="n">value</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"log_dt"</span><span class="p">]</span>
- <span class="n">next_mem_update_time</span> <span class="o">=</span> <span class="n">start_grid_time</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"log_dt"</span><span class="p">]</span>
<span class="n">total_mass_run</span> <span class="o">=</span> <span class="mi">0</span>
<span class="n">total_probability_weighted_mass_run</span> <span class="o">=</span> <span class="mi">0</span>
+ <span class="c1"># variables for the statu bar prints</span>
+ <span class="n">start_grid_time</span> <span class="o">=</span> <span class="n">time</span><span class="o">.</span><span class="n">time</span><span class="p">()</span>
+ <span class="n">next_log_time</span> <span class="o">=</span> <span class="p">(</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">shared_memory</span><span class="p">[</span><span class="s2">"prev_log_time"</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"log_dt"</span><span class="p">]</span>
+ <span class="p">)</span>
+ <span class="n">next_mem_update_time</span> <span class="o">=</span> <span class="n">start_grid_time</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"log_dt"</span><span class="p">]</span>
+
+ <span class="c1">############################################################</span>
<span class="c1"># Go over the queue</span>
<span class="k">for</span> <span class="n">system_number</span><span class="p">,</span> <span class="n">system_dict</span> <span class="ow">in</span> <span class="nb">iter</span><span class="p">(</span><span class="n">job_queue</span><span class="o">.</span><span class="n">get</span><span class="p">,</span> <span class="s2">"STOP"</span><span class="p">):</span>
+ <span class="c1"># At the first system set the status of the thread to running</span>
<span class="k">if</span> <span class="n">localcounter</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
<span class="c1"># Set status to running</span>
@@ -1476,18 +1492,6 @@
<span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
<span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"RUNNING"</span><span class="p">)</span>
- <span class="c1"># if system_number%10==0:</span>
- <span class="c1"># print("_process_run_population_grid: system_number: {}".format(system_number))</span>
- <span class="c1"># bytes_size_Moecache = get_size(Moecache)</span>
- <span class="c1"># print("\t_process_run_population_grid: Size moecache: {}".format(convert_bytes(bytes_size_Moecache)))</span>
-
- <span class="c1"># bytes_size_distribution_constants = get_size(distribution_constants)</span>
- <span class="c1"># print("\t_process_run_population_grid: Size distribution_constants: {}".format(convert_bytes(bytes_size_distribution_constants)))</span>
-
- <span class="c1"># bytes_size_self = get_size(dir(self))</span>
- <span class="c1"># print("\t_process_run_population_grid: Size dir(self): {}".format(convert_bytes(bytes_size_self)))</span>
-
-
<span class="c1"># Combine that with the other settings</span>
<span class="n">full_system_dict</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">bse_options</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
<span class="n">full_system_dict</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">system_dict</span><span class="p">)</span>
@@ -1495,6 +1499,7 @@
<span class="c1"># In the first system, explicitly check all the keys that are passed to see if</span>
<span class="c1"># they match the keys known to binary_c.</span>
<span class="c1"># Won't do that every system cause that is a bit of a waste of computing time.</span>
+ <span class="c1"># TODO: check if we can rename the below var</span>
<span class="k">if</span> <span class="n">number_of_systems_run</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
<span class="c1"># TODO: Put this someplace else and wrap in a function call</span>
<span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="n">full_system_dict</span><span class="o">.</span><span class="n">keys</span><span class="p">():</span>
@@ -1520,47 +1525,88 @@
<span class="c1"># i + 1, self.grid_options["_total_starcount"], full_system_dict</span>
<span class="c1"># )</span>
- <span class="c1">#</span>
-
-<span class="c1"># verbose_print(</span>
-<span class="c1"># "Process {} is handling system {}".format(ID, system_number),</span>
-<span class="c1"># self.grid_options["verbosity"],</span>
-<span class="c1"># 1,</span>
-<span class="c1"># )</span>
+ <span class="c1"># verbose_print(</span>
+ <span class="c1"># "Process {} is handling system {}".format(ID, system_number),</span>
+ <span class="c1"># self.grid_options["verbosity"],</span>
+ <span class="c1"># 1,</span>
+ <span class="c1"># )</span>
+ <span class="c1">######################</span>
+ <span class="c1"># Print status of runs</span>
<span class="c1"># save the current time (used often)</span>
<span class="n">now</span> <span class="o">=</span> <span class="n">time</span><span class="o">.</span><span class="n">time</span><span class="p">()</span>
<span class="c1"># update memory use stats every log_dt seconds (not every time, this is likely a bit expensive)</span>
<span class="k">if</span> <span class="n">now</span> <span class="o">></span> <span class="n">next_mem_update_time</span><span class="p">:</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">shared_memory</span><span class="p">[</span><span class="s2">"memory_use_per_thread"</span><span class="p">][</span><span class="n">ID</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_mem_use</span><span class="p">()</span>
- <span class="n">next_mem_update</span> <span class="o">=</span> <span class="n">now</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"log_dt"</span><span class="p">]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">shared_memory</span><span class="p">[</span><span class="s2">"memory_use_per_thread"</span><span class="p">][</span><span class="n">ID</span><span class="p">]</span> <span class="o">=</span> <span class="n">mem_use</span><span class="p">()</span>
+ <span class="n">next_mem_update_time</span> <span class="o">=</span> <span class="n">now</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"log_dt"</span><span class="p">]</span>
<span class="c1"># calculate the next logging time</span>
- <span class="n">next_log_time</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">shared_memory</span><span class="p">[</span><span class="s2">"prev_log_time"</span><span class="p">]</span><span class="o">.</span><span class="n">value</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"log_dt"</span><span class="p">]</span>
+ <span class="n">next_log_time</span> <span class="o">=</span> <span class="p">(</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">shared_memory</span><span class="p">[</span><span class="s2">"prev_log_time"</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"log_dt"</span><span class="p">]</span>
+ <span class="p">)</span>
+ <span class="c1"># Check if we need to log info again</span>
+ <span class="c1"># TODO: Check if we can put this functionality elsewhere</span>
<span class="k">if</span> <span class="n">now</span> <span class="o">></span> <span class="n">next_log_time</span><span class="p">:</span>
<span class="c1"># we have exceeded the next log time : output and update timers</span>
+ <span class="c1"># Lock the threads. TODO: Do we need to release this?</span>
<span class="n">lock</span> <span class="o">=</span> <span class="n">multiprocessing</span><span class="o">.</span><span class="n">Lock</span><span class="p">()</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">vb1print</span><span class="p">(</span><span class="n">ID</span><span class="p">,</span><span class="n">now</span><span class="p">,</span><span class="n">system_number</span><span class="p">)</span>
+
+ <span class="c1"># Do the printing itself</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">vb1print</span><span class="p">(</span><span class="n">ID</span><span class="p">,</span> <span class="n">now</span><span class="p">,</span> <span class="n">system_number</span><span class="p">,</span> <span class="n">system_dict</span><span class="p">)</span>
+
+ <span class="c1"># Set some values for next time</span>
<span class="n">next_log_time</span> <span class="o">=</span> <span class="n">now</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"log_dt"</span><span class="p">]</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">shared_memory</span><span class="p">[</span><span class="s2">"prev_log_time"</span><span class="p">]</span><span class="o">.</span><span class="n">value</span> <span class="o">=</span> <span class="n">now</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">shared_memory</span><span class="p">[</span><span class="s2">"prev_log_system_number"</span><span class="p">]</span><span class="o">.</span><span class="n">value</span> <span class="o">=</span> <span class="n">system_number</span>
+
+ <span class="c1"># print("PREV ",self.shared_memory["prev_log_time"])</span>
+ <span class="c1"># print("N LOG STATS",self.shared_memory["n_saved_log_stats"].value)</span>
+
+ <span class="c1"># shift the arrays</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">shared_memory</span><span class="p">[</span><span class="s2">"prev_log_time"</span><span class="p">][</span>
+ <span class="o">-</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"n_logging_stats"</span><span class="p">]</span> <span class="o">-</span> <span class="mi">1</span><span class="p">)</span> <span class="p">:</span>
+ <span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">shared_memory</span><span class="p">[</span><span class="s2">"prev_log_time"</span><span class="p">][</span>
+ <span class="p">:</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"n_logging_stats"</span><span class="p">]</span> <span class="o">-</span> <span class="mi">1</span><span class="p">)</span>
+ <span class="p">]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">shared_memory</span><span class="p">[</span><span class="s2">"prev_log_system_number"</span><span class="p">][</span>
+ <span class="o">-</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"n_logging_stats"</span><span class="p">]</span> <span class="o">-</span> <span class="mi">1</span><span class="p">)</span> <span class="p">:</span>
+ <span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">shared_memory</span><span class="p">[</span><span class="s2">"prev_log_system_number"</span><span class="p">][</span>
+ <span class="p">:</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"n_logging_stats"</span><span class="p">]</span> <span class="o">-</span> <span class="mi">1</span><span class="p">)</span>
+ <span class="p">]</span>
+
+ <span class="c1"># set the current time and system number</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">shared_memory</span><span class="p">[</span><span class="s2">"prev_log_time"</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span> <span class="o">=</span> <span class="n">now</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">shared_memory</span><span class="p">[</span><span class="s2">"prev_log_system_number"</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span> <span class="o">=</span> <span class="n">system_number</span>
+
+ <span class="c1"># increase the number of stats</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">shared_memory</span><span class="p">[</span><span class="s2">"n_saved_log_stats"</span><span class="p">]</span><span class="o">.</span><span class="n">value</span> <span class="o">=</span> <span class="nb">min</span><span class="p">(</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">shared_memory</span><span class="p">[</span><span class="s2">"n_saved_log_stats"</span><span class="p">]</span><span class="o">.</span><span class="n">value</span> <span class="o">+</span> <span class="mi">1</span><span class="p">,</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"n_logging_stats"</span><span class="p">],</span>
+ <span class="p">)</span>
+
+ <span class="c1"># print("FIRST (0) ",self.shared_memory["prev_log_time"][0])</span>
+ <span class="c1"># print("LAST (",self.shared_memory["n_saved_log_stats"].value-1,")",self.shared_memory["prev_log_time"][self.shared_memory["n_saved_log_stats"].value-1])</span>
+
+ <span class="c1">###############</span>
+ <span class="c1"># Log current system info</span>
<span class="c1"># In some cases, the whole run crashes. To be able to figure out which system</span>
<span class="c1"># that was on, we log each current system to a file (each thread has one).</span>
<span class="c1"># Each new system overrides the previous</span>
- <span class="k">with</span> <span class="nb">open</span><span class="p">(</span>
- <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"tmp_dir"</span><span class="p">],</span>
- <span class="s2">"current_system"</span><span class="p">,</span>
- <span class="s2">"process_</span><span class="si">{}</span><span class="s2">.txt"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">process_ID</span><span class="p">),</span>
- <span class="p">),</span>
- <span class="s2">"w"</span><span class="p">,</span>
- <span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
- <span class="n">binary_cmdline_string</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_return_argline</span><span class="p">(</span><span class="n">full_system_dict</span><span class="p">)</span>
- <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">binary_cmdline_string</span><span class="p">)</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"log_args"</span><span class="p">]:</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"log_args_dir"</span><span class="p">],</span>
+ <span class="s2">"current_system"</span><span class="p">,</span>
+ <span class="s2">"process_</span><span class="si">{}</span><span class="s2">.txt"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">process_ID</span><span class="p">),</span>
+ <span class="p">),</span>
+ <span class="s2">"w"</span><span class="p">,</span>
+ <span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
+ <span class="n">binary_cmdline_string</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_return_argline</span><span class="p">(</span><span class="n">full_system_dict</span><span class="p">)</span>
+ <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">binary_cmdline_string</span><span class="p">)</span>
+ <span class="c1">##############</span>
+ <span class="c1"># Running the system</span>
<span class="n">start_runtime_binary_c</span> <span class="o">=</span> <span class="n">time</span><span class="o">.</span><span class="n">time</span><span class="p">()</span>
<span class="c1"># If we want to actually evolve the systems</span>
@@ -1569,7 +1615,7 @@
<span class="c1"># Check option to ignore 0 probability systems</span>
<span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"run_zero_probability_system"</span><span class="p">]:</span>
- <span class="k">if</span> <span class="n">full_system_dict</span><span class="p">[</span><span class="s1">'probability'</span><span class="p">]</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">full_system_dict</span><span class="p">[</span><span class="s2">"probability"</span><span class="p">]</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
<span class="n">run_system</span> <span class="o">=</span> <span class="kc">False</span>
<span class="n">zero_prob_stars_skipped</span> <span class="o">+=</span> <span class="mi">1</span>
@@ -1583,6 +1629,9 @@
<span class="n">end_runtime_binary_c</span> <span class="o">-</span> <span class="n">start_runtime_binary_c</span>
<span class="p">)</span> <span class="c1"># keep track of total binary_c call time</span>
+ <span class="c1">############</span>
+ <span class="c1"># Logging runtime</span>
+
<span class="c1"># Debug line: logging all the lines</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"log_runtime_systems"</span><span class="p">]</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
<span class="k">with</span> <span class="nb">open</span><span class="p">(</span>
@@ -1602,6 +1651,9 @@
<span class="p">)</span>
<span class="p">)</span>
+ <span class="c1">####################</span>
+ <span class="c1"># Tallying system information</span>
+
<span class="c1"># Keep track of systems:</span>
<span class="n">probability_of_systems_run</span> <span class="o">+=</span> <span class="n">full_system_dict</span><span class="p">[</span><span class="s2">"probability"</span><span class="p">]</span>
<span class="n">number_of_systems_run</span> <span class="o">+=</span> <span class="mi">1</span>
@@ -1630,10 +1682,13 @@
<span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
<span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"FINISHING"</span><span class="p">)</span>
- <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'verbosity'</span><span class="p">]</span> <span class="o">>=</span> <span class="n">_LOGGER_VERBOSITY_LEVEL</span><span class="p">:</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"verbosity"</span><span class="p">]</span> <span class="o">>=</span> <span class="n">_LOGGER_VERBOSITY_LEVEL</span><span class="p">:</span>
<span class="n">stream_logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Process-</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">process_ID</span><span class="si">}</span><span class="s2"> is finishing."</span><span class="p">)</span>
- <span class="c1"># Handle ensemble output: is ensemble==1, then either directly write that data to a file, or combine everything into 1 file.</span>
+ <span class="c1">####################</span>
+ <span class="c1"># Handle ensemble outut</span>
+
+ <span class="c1"># if ensemble==1, then either directly write that data to a file, or combine everything into 1 file.</span>
<span class="n">ensemble_json</span> <span class="o">=</span> <span class="p">{}</span> <span class="c1"># Make sure it exists already</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">bse_options</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"ensemble"</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
<span class="n">verbose_print</span><span class="p">(</span>
@@ -1641,7 +1696,7 @@
<span class="n">ID</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">persistent_data_memory_dict</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">process_ID</span><span class="p">]</span>
<span class="p">),</span>
<span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"verbosity"</span><span class="p">],</span>
- <span class="mi">2</span><span class="p">,</span>
+ <span class="mi">3</span><span class="p">,</span>
<span class="p">)</span>
<span class="n">ensemble_raw_output</span> <span class="o">=</span> <span class="p">(</span>
@@ -1661,7 +1716,7 @@
<span class="n">verbose_print</span><span class="p">(</span>
<span class="s2">"Process </span><span class="si">{}</span><span class="s2">: Extracting ensemble info from raw string"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">ID</span><span class="p">),</span>
<span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"verbosity"</span><span class="p">],</span>
- <span class="mi">2</span><span class="p">,</span>
+ <span class="mi">3</span><span class="p">,</span>
<span class="p">)</span>
<span class="n">ensemble_json</span><span class="p">[</span><span class="s2">"ensemble"</span><span class="p">]</span> <span class="o">=</span> <span class="n">extract_ensemble_json_from_string</span><span class="p">(</span>
@@ -1689,6 +1744,9 @@
<span class="p">)</span>
<span class="p">)</span>
+ <span class="c1">########</span>
+ <span class="c1"># Clean up and return</span>
+
<span class="c1"># free store memory:</span>
<span class="n">_binary_c_bindings</span><span class="o">.</span><span class="n">free_store_memaddr</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"_store_memaddr"</span><span class="p">])</span>
@@ -1724,7 +1782,6 @@
<span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"_failed_count"</span><span class="p">],</span>
<span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"_failed_prob"</span><span class="p">],</span>
<span class="n">zero_prob_stars_skipped</span><span class="p">,</span>
-
<span class="p">),</span>
<span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"verbosity"</span><span class="p">],</span>
<span class="mi">1</span><span class="p">,</span>
@@ -1769,7 +1826,7 @@
<span class="n">result_queue</span><span class="o">.</span><span class="n">put</span><span class="p">(</span><span class="n">output_dict</span><span class="p">)</span>
- <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'verbosity'</span><span class="p">]</span> <span class="o">>=</span> <span class="n">_LOGGER_VERBOSITY_LEVEL</span><span class="p">:</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"verbosity"</span><span class="p">]</span> <span class="o">>=</span> <span class="n">_LOGGER_VERBOSITY_LEVEL</span><span class="p">:</span>
<span class="n">stream_logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Process-</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">process_ID</span><span class="si">}</span><span class="s2"> is finished."</span><span class="p">)</span>
<span class="c1"># Clean up the interpolators if they exist</span>
@@ -1796,14 +1853,15 @@
<span class="c1">### Custom logging code:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_set_custom_logging</span><span class="p">()</span>
-
<span class="c1"># Check if there are actually arguments passed:</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">bse_options</span><span class="p">:</span>
<span class="c1"># Get argument line and</span>
<span class="n">argline</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_return_argline</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bse_options</span><span class="p">)</span>
- <span class="n">verbose_print</span><span class="p">(</span><span class="s2">"Running </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">argline</span><span class="p">),</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"verbosity"</span><span class="p">],</span> <span class="mi">1</span><span class="p">)</span>
+ <span class="n">verbose_print</span><span class="p">(</span>
+ <span class="s2">"Running </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">argline</span><span class="p">),</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"verbosity"</span><span class="p">],</span> <span class="mi">1</span>
+ <span class="p">)</span>
<span class="c1"># Run system</span>
<span class="n">out</span> <span class="o">=</span> <span class="n">_binary_c_bindings</span><span class="o">.</span><span class="n">run_system</span><span class="p">(</span>
@@ -1830,9 +1888,6 @@
<span class="n">msg</span> <span class="o">=</span> <span class="s2">"No actual evolution options passed to the evolve call. Aborting"</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span></div>
-
-
-
<span class="k">def</span> <span class="nf">_setup</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Function to set up the necessary stuff for the population evolution.</span>
@@ -1923,7 +1978,8 @@
<span class="k">raise</span> <span class="ne">ValueError</span>
<span class="c1"># Set up the grid code with a dry run option to see total probability</span>
- <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'do_dry_run'</span><span class="p">]:</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"do_dry_run"</span><span class="p">]:</span>
+ <span class="nb">print</span><span class="p">(</span><span class="s2">"Doing dry run to calculate total starcount and probability"</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_generate_grid_code</span><span class="p">(</span><span class="n">dry_run</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="c1"># Load the grid code</span>
@@ -1933,11 +1989,15 @@
<span class="bp">self</span><span class="o">.</span><span class="n">_dry_run</span><span class="p">()</span>
<span class="nb">print</span><span class="p">(</span>
- <span class="s2">"Total starcount for this run will be: </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"_total_starcount"</span><span class="p">]</span>
+ <span class="s2">"Total starcount for this run will be: </span><span class="si">{}</span><span class="s2"> with a total probability of </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"_total_starcount"</span><span class="p">],</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"_probtot"</span><span class="p">],</span>
<span class="p">)</span>
<span class="p">)</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"exit_after_dry_run"</span><span class="p">]:</span>
+ <span class="n">exit</span><span class="p">()</span>
+
<span class="c1">#######################</span>
<span class="c1"># Reset values and prepare the grid function</span>
<span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span>
@@ -1966,7 +2026,7 @@
<span class="c1"># TODO: fix this function</span>
<span class="c1"># self._load_source_file_function()</span>
- <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'do_dry_run'</span><span class="p">]:</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"do_dry_run"</span><span class="p">]:</span>
<span class="c1"># Do a dry run</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_dry_run_source_file</span><span class="p">()</span>
@@ -2037,12 +2097,54 @@
<span class="c1"># a variable grid</span>
<span class="c1">###################################################</span>
+ <span class="k">def</span> <span class="nf">_add_code</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="n">indent</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">mindent</span><span class="o">=-</span><span class="mi">1</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Function to add code to the grid code string</span>
+
+<span class="sd"> add code to the code_string</span>
+
+<span class="sd"> indent (=0) is added once at the beginning</span>
+<span class="sd"> mindent (=0) is added for every line</span>
+
+<span class="sd"> don't use both!</span>
+<span class="sd"> """</span>
+
+ <span class="c1"># if we have multiple arguments and have forgotten</span>
+ <span class="c1"># to set mindent = 0, do it here</span>
+ <span class="k">if</span> <span class="n">indent</span> <span class="o">==</span> <span class="mi">0</span> <span class="ow">and</span> <span class="n">mindent</span> <span class="o">==</span> <span class="o">-</span><span class="mi">1</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="n">args</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
+ <span class="n">mindent</span> <span class="o">=</span> <span class="mi">0</span>
+
+ <span class="c1"># if mindent isn't set, use indent</span>
+ <span class="k">if</span> <span class="n">mindent</span> <span class="o">==</span> <span class="o">-</span><span class="mi">1</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">code_string</span> <span class="o">+=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_indent_block</span><span class="p">(</span><span class="n">indent</span><span class="p">)</span>
+
+ <span class="c1"># put everything in the code_string, indenting</span>
+ <span class="c1"># each line if required</span>
+ <span class="k">for</span> <span class="n">thing</span> <span class="ow">in</span> <span class="n">args</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">mindent</span> <span class="o">!=</span> <span class="o">-</span><span class="mi">1</span> <span class="ow">or</span> <span class="nb">len</span><span class="p">(</span><span class="n">args</span><span class="p">)</span> <span class="o">></span> <span class="mi">1</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">code_string</span> <span class="o">+=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_indent_block</span><span class="p">(</span><span class="n">mindent</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">code_string</span> <span class="o">+=</span> <span class="n">thing</span>
+
+ <span class="k">def</span> <span class="nf">_indent_block</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">n</span><span class="o">=</span><span class="mi">0</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> return an indent block, with n extra blocks in it</span>
+<span class="sd"> """</span>
+
+ <span class="k">return</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">indent_depth</span> <span class="o">+</span> <span class="n">n</span><span class="p">)</span> <span class="o">*</span> <span class="bp">self</span><span class="o">.</span><span class="n">indent_string</span>
+
+ <span class="k">def</span> <span class="nf">_increment_indent_depth</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">delta</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> increment the indent indent_depth by delta</span>
+<span class="sd"> """</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">indent_depth</span> <span class="o">+=</span> <span class="n">delta</span>
+
<span class="k">def</span> <span class="nf">_generate_grid_code</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">dry_run</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Function that generates the code from which the population will be made.</span>
<span class="sd"> dry_run: when True, it will return the starcount at the end so that we know</span>
-<span class="sd"> what the total amount of systems is.</span>
+<span class="sd"> what the total number of systems is.</span>
<span class="sd"> The phasevol values are handled by generating a second array</span>
@@ -2062,91 +2164,77 @@
<span class="n">verbose_print</span><span class="p">(</span><span class="s2">"Generating grid code"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"verbosity"</span><span class="p">],</span> <span class="mi">1</span><span class="p">)</span>
- <span class="c1"># Some local values</span>
- <span class="n">code_string</span> <span class="o">=</span> <span class="s2">""</span>
- <span class="n">depth</span> <span class="o">=</span> <span class="mi">0</span>
- <span class="n">indent</span> <span class="o">=</span> <span class="s2">" "</span>
<span class="n">total_grid_variables</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"_grid_variables"</span><span class="p">])</span>
- <span class="c1"># Import packages</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="s2">"import math</span><span class="se">\n</span><span class="s2">"</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="s2">"import numpy as np</span><span class="se">\n</span><span class="s2">"</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="s2">"from collections import OrderedDict</span><span class="se">\n</span><span class="s2">"</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="s2">"from binarycpython.utils.distribution_functions import *</span><span class="se">\n</span><span class="s2">"</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="s2">"from binarycpython.utils.spacing_functions import *</span><span class="se">\n</span><span class="s2">"</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="s2">"from binarycpython.utils.useful_funcs import *</span><span class="se">\n</span><span class="s2">"</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="s2">"</span><span class="se">\n\n</span><span class="s2">"</span>
-
- <span class="c1"># Make the function</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="s2">"def grid_code(self, print_results=True):</span><span class="se">\n</span><span class="s2">"</span>
-
- <span class="c1"># Increase depth</span>
- <span class="n">depth</span> <span class="o">+=</span> <span class="mi">1</span>
-
- <span class="c1"># Write some info in the function</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="p">(</span>
- <span class="n">indent</span> <span class="o">*</span> <span class="n">depth</span>
- <span class="o">+</span> <span class="s2">"# Grid code generated on </span><span class="si">{}</span><span class="se">\n</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
- <span class="n">datetime</span><span class="o">.</span><span class="n">datetime</span><span class="o">.</span><span class="n">now</span><span class="p">()</span><span class="o">.</span><span class="n">isoformat</span><span class="p">()</span>
- <span class="p">)</span>
- <span class="o">+</span> <span class="n">indent</span> <span class="o">*</span> <span class="n">depth</span>
- <span class="o">+</span> <span class="s2">"# This function generates the systems that will be evolved with binary_c</span><span class="se">\n\n</span><span class="s2">"</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_add_code</span><span class="p">(</span>
+ <span class="c1"># Import packages</span>
+ <span class="s2">"import math</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span>
+ <span class="s2">"import numpy as np</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span>
+ <span class="s2">"from collections import OrderedDict</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span>
+ <span class="s2">"from binarycpython.utils.distribution_functions import *</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span>
+ <span class="s2">"from binarycpython.utils.spacing_functions import *</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span>
+ <span class="s2">"from binarycpython.utils.useful_funcs import *</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span>
+ <span class="s2">"</span><span class="se">\n\n</span><span class="s2">"</span><span class="p">,</span>
+ <span class="c1"># Make the function</span>
+ <span class="s2">"def grid_code(self, print_results=True):</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span>
<span class="p">)</span>
- <span class="c1"># Set some values in the generated code:</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="n">indent</span> <span class="o">*</span> <span class="n">depth</span> <span class="o">+</span> <span class="s2">"# Setting initial values</span><span class="se">\n</span><span class="s2">"</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="n">indent</span> <span class="o">*</span> <span class="n">depth</span> <span class="o">+</span> <span class="s2">"_total_starcount = 0</span><span class="se">\n</span><span class="s2">"</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="n">indent</span> <span class="o">*</span> <span class="n">depth</span> <span class="o">+</span> <span class="s2">"starcounts = [0 for i in range(</span><span class="si">{}</span><span class="s2">)]</span><span class="se">\n</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
- <span class="n">total_grid_variables</span>
- <span class="p">)</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="n">indent</span> <span class="o">*</span> <span class="n">depth</span> <span class="o">+</span> <span class="s2">"probabilities = </span><span class="si">{}</span><span class="se">\n</span><span class="s2">"</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="p">(</span>
- <span class="n">indent</span> <span class="o">*</span> <span class="n">depth</span>
- <span class="o">+</span> <span class="s2">"probabilities_list = [0 for i in range(</span><span class="si">{}</span><span class="s2">)]</span><span class="se">\n</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+ <span class="c1"># Increase indent_depth</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_increment_indent_depth</span><span class="p">(</span><span class="o">+</span><span class="mi">1</span><span class="p">)</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">_add_code</span><span class="p">(</span>
+ <span class="c1"># Write some info in the function</span>
+ <span class="s2">"# Grid code generated on </span><span class="si">{}</span><span class="se">\n</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">datetime</span><span class="o">.</span><span class="n">datetime</span><span class="o">.</span><span class="n">now</span><span class="p">()</span><span class="o">.</span><span class="n">isoformat</span><span class="p">()),</span>
+ <span class="s2">"# This function generates the systems that will be evolved with binary_c</span><span class="se">\n\n</span><span class="s2">"</span>
+ <span class="c1"># Set some values in the generated code:</span>
+ <span class="s2">"# Setting initial values</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span>
+ <span class="s2">"_total_starcount = 0</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span>
+ <span class="s2">"starcounts = [0 for i in range(</span><span class="si">{}</span><span class="s2">)]</span><span class="se">\n</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">total_grid_variables</span><span class="p">),</span>
+ <span class="s2">"probabilities = </span><span class="si">{}</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span>
+ <span class="s2">"probabilities_list = [0 for i in range(</span><span class="si">{}</span><span class="s2">)]</span><span class="se">\n</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
<span class="n">total_grid_variables</span>
- <span class="p">)</span>
+ <span class="p">),</span>
+ <span class="s2">"probabilities_sum = [0 for i in range(</span><span class="si">{}</span><span class="s2">)]</span><span class="se">\n</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">total_grid_variables</span><span class="p">),</span>
+ <span class="s2">"parameter_dict = </span><span class="si">{}</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span>
+ <span class="s2">"phasevol = 1</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span>
+ <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span>
<span class="p">)</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="p">(</span>
- <span class="n">indent</span> <span class="o">*</span> <span class="n">depth</span>
- <span class="o">+</span> <span class="s2">"probabilities_sum = [0 for i in range(</span><span class="si">{}</span><span class="s2">)]</span><span class="se">\n</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
- <span class="n">total_grid_variables</span>
- <span class="p">)</span>
+
+ <span class="c1"># Set up the system parameters</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_add_code</span><span class="p">(</span>
+ <span class="s2">"M_1 = None</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span>
+ <span class="s2">"M_2 = None</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span>
+ <span class="s2">"M_3 = None</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span>
+ <span class="s2">"M_4 = None</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span>
+ <span class="s2">"orbital_period = None</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span>
+ <span class="s2">"orbital_period_triple = None</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span>
+ <span class="s2">"orbital_period_quadruple = None</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span>
+ <span class="s2">"eccentricity = None</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span>
+ <span class="s2">"eccentricity2 = None</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span>
+ <span class="s2">"eccentricity3 = None</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span>
+ <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span>
+ <span class="c1"># Prepare the probability</span>
+ <span class="s2">"# setting probability lists</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span>
<span class="p">)</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="n">indent</span> <span class="o">*</span> <span class="n">depth</span> <span class="o">+</span> <span class="s2">"parameter_dict = </span><span class="si">{}</span><span class="se">\n</span><span class="s2">"</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="n">indent</span> <span class="o">*</span> <span class="n">depth</span> <span class="o">+</span> <span class="s2">"phasevol = 1</span><span class="se">\n</span><span class="s2">"</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="n">indent</span> <span class="o">*</span> <span class="n">depth</span> <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span>
-
- <span class="c1"># Setting up the system parameters</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="n">indent</span> <span class="o">*</span> <span class="n">depth</span> <span class="o">+</span> <span class="s2">"M_1 = None</span><span class="se">\n</span><span class="s2">"</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="n">indent</span> <span class="o">*</span> <span class="n">depth</span> <span class="o">+</span> <span class="s2">"M_2 = None</span><span class="se">\n</span><span class="s2">"</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="n">indent</span> <span class="o">*</span> <span class="n">depth</span> <span class="o">+</span> <span class="s2">"M_3 = None</span><span class="se">\n</span><span class="s2">"</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="n">indent</span> <span class="o">*</span> <span class="n">depth</span> <span class="o">+</span> <span class="s2">"M_4 = None</span><span class="se">\n</span><span class="s2">"</span>
-
- <span class="n">code_string</span> <span class="o">+=</span> <span class="n">indent</span> <span class="o">*</span> <span class="n">depth</span> <span class="o">+</span> <span class="s2">"orbital_period = None</span><span class="se">\n</span><span class="s2">"</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="n">indent</span> <span class="o">*</span> <span class="n">depth</span> <span class="o">+</span> <span class="s2">"orbital_period_triple = None</span><span class="se">\n</span><span class="s2">"</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="n">indent</span> <span class="o">*</span> <span class="n">depth</span> <span class="o">+</span> <span class="s2">"orbital_period_quadruple = None</span><span class="se">\n</span><span class="s2">"</span>
-
- <span class="n">code_string</span> <span class="o">+=</span> <span class="n">indent</span> <span class="o">*</span> <span class="n">depth</span> <span class="o">+</span> <span class="s2">"eccentricity = None</span><span class="se">\n</span><span class="s2">"</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="n">indent</span> <span class="o">*</span> <span class="n">depth</span> <span class="o">+</span> <span class="s2">"eccentricity2 = None</span><span class="se">\n</span><span class="s2">"</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="n">indent</span> <span class="o">*</span> <span class="n">depth</span> <span class="o">+</span> <span class="s2">"eccentricity3 = None</span><span class="se">\n</span><span class="s2">"</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="n">indent</span> <span class="o">*</span> <span class="n">depth</span> <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span>
-
- <span class="c1"># Prepare the probability</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="n">indent</span> <span class="o">*</span> <span class="n">depth</span> <span class="o">+</span> <span class="s2">"# setting probability lists</span><span class="se">\n</span><span class="s2">"</span>
+
<span class="k">for</span> <span class="n">grid_variable_el</span> <span class="ow">in</span> <span class="nb">sorted</span><span class="p">(</span>
<span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"_grid_variables"</span><span class="p">]</span><span class="o">.</span><span class="n">items</span><span class="p">(),</span>
<span class="n">key</span><span class="o">=</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="s2">"grid_variable_number"</span><span class="p">],</span>
<span class="p">):</span>
<span class="c1"># Make probabilities dict</span>
<span class="n">grid_variable</span> <span class="o">=</span> <span class="n">grid_variable_el</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="n">indent</span> <span class="o">*</span> <span class="n">depth</span> <span class="o">+</span> <span class="s1">'probabilities["</span><span class="si">{}</span><span class="s1">"] = 0</span><span class="se">\n</span><span class="s1">'</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
- <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"parameter_name"</span><span class="p">]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_add_code</span><span class="p">(</span>
+ <span class="s1">'probabilities["</span><span class="si">{}</span><span class="s1">"] = 0</span><span class="se">\n</span><span class="s1">'</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">grid_variable</span><span class="p">[</span><span class="s2">"parameter_name"</span><span class="p">])</span>
<span class="p">)</span>
<span class="c1">#################################################################################</span>
<span class="c1"># Start of code generation</span>
<span class="c1">#################################################################################</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="n">indent</span> <span class="o">*</span> <span class="n">depth</span> <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_add_code</span><span class="p">(</span><span class="s2">"</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span>
+
+ <span class="c1"># turn vb to True to have debugging output</span>
+ <span class="n">vb</span> <span class="o">=</span> <span class="kc">False</span>
+
<span class="c1"># Generate code</span>
<span class="nb">print</span><span class="p">(</span><span class="s2">"Generating grid code"</span><span class="p">)</span>
<span class="k">for</span> <span class="n">loopnr</span><span class="p">,</span> <span class="n">grid_variable_el</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span>
@@ -2155,24 +2243,90 @@
<span class="n">key</span><span class="o">=</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="s2">"grid_variable_number"</span><span class="p">],</span>
<span class="p">)</span>
<span class="p">):</span>
- <span class="nb">print</span><span class="p">(</span><span class="s2">"Constructing/adding: </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">grid_variable_el</span><span class="p">[</span><span class="mi">0</span><span class="p">]))</span>
+ <span class="n">verbose_print</span><span class="p">(</span>
+ <span class="s2">"Constructing/adding: </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">grid_variable_el</span><span class="p">[</span><span class="mi">0</span><span class="p">]),</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'verbosity'</span><span class="p">],</span>
+ <span class="mi">2</span><span class="p">)</span>
<span class="n">grid_variable</span> <span class="o">=</span> <span class="n">grid_variable_el</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
<span class="c1">#########################</span>
<span class="c1"># Setting up the for loop</span>
<span class="c1"># Add comment for for loop</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="p">(</span>
- <span class="n">indent</span> <span class="o">*</span> <span class="n">depth</span>
- <span class="o">+</span> <span class="s2">"# for loop for </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">grid_variable</span><span class="p">[</span><span class="s2">"parameter_name"</span><span class="p">])</span>
- <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_add_code</span><span class="p">(</span>
+ <span class="s2">"# for loop for </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">grid_variable</span><span class="p">[</span><span class="s2">"parameter_name"</span><span class="p">])</span> <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span>
+ <span class="s2">"sampled_values_</span><span class="si">{}</span><span class="s2"> = </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+ <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">],</span> <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"spacingfunc"</span><span class="p">]</span>
+ <span class="p">)</span>
+ <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span>
<span class="p">)</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="p">(</span>
- <span class="n">indent</span> <span class="o">*</span> <span class="n">depth</span>
- <span class="o">+</span> <span class="s2">"sampled_values_</span><span class="si">{}</span><span class="s2"> = </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
- <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">],</span> <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"spacingfunc"</span><span class="p">]</span>
+ <span class="k">if</span> <span class="n">vb</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_add_code</span><span class="p">(</span>
+ <span class="s2">"print('samples','</span><span class="si">{}</span><span class="s2">',':',sampled_values_</span><span class="si">{}</span><span class="s2">)</span><span class="se">\n</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+ <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">],</span> <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">]</span>
+ <span class="p">)</span>
+ <span class="p">)</span>
+
+ <span class="c1"># # Some print statement</span>
+ <span class="c1"># self._add_code((</span>
+ <span class="c1"># "print('phasevol_{}:', phasevol_{})".format(grid_variable["name"],</span>
+ <span class="c1"># grid_variable["name"])</span>
+ <span class="c1"># + "\n"</span>
+ <span class="c1"># )</span>
+
+ <span class="c1"># TODO: make sure this works</span>
+ <span class="c1"># Adding for loop structure</span>
+ <span class="c1"># self._add_code((</span>
+ <span class="c1"># "for {} in sampled_values_{}:".format(</span>
+ <span class="c1"># grid_variable["name"], grid_variable["name"]</span>
+ <span class="c1"># )</span>
+ <span class="c1"># + "\n"</span>
+ <span class="c1"># )</span>
+
+ <span class="k">if</span> <span class="n">vb</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_add_code</span><span class="p">(</span>
+ <span class="s2">"print('sample </span><span class="si">{}</span><span class="s2"> from',sampled_values_</span><span class="si">{}</span><span class="s2">)"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+ <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">],</span> <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">]</span>
+ <span class="p">)</span>
+ <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span>
<span class="p">)</span>
- <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span>
+
+ <span class="k">if</span> <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"resolution"</span><span class="p">]</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
+ <span class="c1"># generate resolution automatically</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_add_code</span><span class="p">(</span>
+ <span class="s2">"for </span><span class="si">{}</span><span class="s2">_sample_number in range(max(0,len(sampled_values_</span><span class="si">{}</span><span class="s2">)-1)):"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+ <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">],</span> <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">]</span>
+ <span class="p">)</span>
+ <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span>
+ <span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="c1"># use resolution passed in</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_add_code</span><span class="p">(</span>
+ <span class="s2">"for </span><span class="si">{}</span><span class="s2">_sample_number in range(</span><span class="si">{}</span><span class="s2">):"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+ <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">],</span> <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"resolution"</span><span class="p">]</span>
+ <span class="p">)</span>
+ <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span>
+ <span class="p">)</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">_increment_indent_depth</span><span class="p">(</span><span class="o">+</span><span class="mi">1</span><span class="p">)</span>
+
+ <span class="c1"># {}_this and {}_next are this grid point's index and the next</span>
+ <span class="c1"># grid point's index, used in many calculations below</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_add_code</span><span class="p">(</span><span class="s2">"if </span><span class="si">{}</span><span class="s2">_sample_number == 0:</span><span class="se">\n</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">]))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_add_code</span><span class="p">(</span><span class="s2">"</span><span class="si">{}</span><span class="s2">_this = 0;</span><span class="se">\n</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">]),</span> <span class="n">indent</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_add_code</span><span class="p">(</span><span class="s2">"else:</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_add_code</span><span class="p">(</span>
+ <span class="s2">"</span><span class="si">{}</span><span class="s2">_this = </span><span class="si">{}</span><span class="s2">_sample_number; "</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+ <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">],</span> <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">]</span>
+ <span class="p">),</span>
+ <span class="n">indent</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span>
+ <span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_add_code</span><span class="p">(</span>
+ <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span>
+ <span class="s2">"</span><span class="si">{}</span><span class="s2">_next = </span><span class="si">{}</span><span class="s2">_this + 1"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+ <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">],</span> <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">]</span>
+ <span class="p">),</span>
+ <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span>
<span class="p">)</span>
<span class="c1"># TODO: Make clear that the phasevol only works good</span>
@@ -2182,9 +2336,10 @@
<span class="k">if</span> <span class="p">(</span>
<span class="ow">not</span> <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"dphasevol"</span><span class="p">]</span> <span class="o">==</span> <span class="o">-</span><span class="mi">1</span>
<span class="p">):</span> <span class="c1"># A method to turn off this calculation and allow a phasevol = 1</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="p">(</span>
- <span class="n">indent</span> <span class="o">*</span> <span class="n">depth</span>
- <span class="o">+</span> <span class="s2">"phasevol_</span><span class="si">{}</span><span class="s2"> = sampled_values_</span><span class="si">{}</span><span class="s2">[1]-sampled_values_</span><span class="si">{}</span><span class="s2">[0]"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_add_code</span><span class="p">(</span>
+ <span class="s2">"phasevol_</span><span class="si">{}</span><span class="s2"> = sampled_values_</span><span class="si">{}</span><span class="s2">[</span><span class="si">{}</span><span class="s2">_next]-sampled_values_</span><span class="si">{}</span><span class="s2">[</span><span class="si">{}</span><span class="s2">_this]"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+ <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">],</span>
+ <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">],</span>
<span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">],</span>
<span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">],</span>
<span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">],</span>
@@ -2192,48 +2347,73 @@
<span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span>
<span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="n">indent</span> <span class="o">*</span> <span class="n">depth</span> <span class="o">+</span> <span class="s2">"phasevol_</span><span class="si">{}</span><span class="s2"> = 1</span><span class="se">\n</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
- <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">]</span>
- <span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_add_code</span><span class="p">(</span><span class="s2">"phasevol_</span><span class="si">{}</span><span class="s2"> = 1</span><span class="se">\n</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">]))</span>
- <span class="c1"># # Some print statement</span>
- <span class="c1"># code_string += (</span>
- <span class="c1"># indent * depth</span>
- <span class="c1"># + "print('phasevol_{}:', phasevol_{})".format(grid_variable["name"],</span>
- <span class="c1"># grid_variable["name"])</span>
- <span class="c1"># + "\n"</span>
- <span class="c1"># )</span>
-
- <span class="c1"># TODO: make sure this works</span>
- <span class="c1"># Adding for loop structure</span>
- <span class="c1"># code_string += (</span>
- <span class="c1"># indent * depth</span>
- <span class="c1"># + "for {} in sampled_values_{}:".format(</span>
- <span class="c1"># grid_variable["name"], grid_variable["name"]</span>
- <span class="c1"># )</span>
- <span class="c1"># + "\n"</span>
- <span class="c1"># )</span>
+ <span class="c1">##############</span>
+ <span class="c1"># Add phasevol check:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_add_code</span><span class="p">(</span><span class="s2">"if phasevol_</span><span class="si">{}</span><span class="s2"> <= 0:</span><span class="se">\n</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">]))</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="p">(</span>
- <span class="n">indent</span> <span class="o">*</span> <span class="n">depth</span>
- <span class="o">+</span> <span class="s2">"for </span><span class="si">{}</span><span class="s2">_sample_number in range(</span><span class="si">{}</span><span class="s2">):"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
- <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">],</span> <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"resolution"</span><span class="p">]</span>
+ <span class="c1"># TODO: We might actually want to add the starcount and probability to the totals regardless.</span>
+ <span class="c1"># n that case we need another local variable which will prevent it from being run but will track those parameters</span>
+ <span class="c1"># Add phasevol check action:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_add_code</span><span class="p">(</span>
+ <span class="s1">'print("Grid generator: phasevol_</span><span class="si">{}</span><span class="s1"> <= 0! (this=",</span><span class="si">{}</span><span class="s1">_this,", next=",</span><span class="si">{}</span><span class="s1">_next,") Skipping current sample.")'</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+ <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">],</span> <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">],</span> <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">]</span>
<span class="p">)</span>
- <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span>
+ <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span>
+ <span class="s2">"continue"</span> <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span>
+ <span class="n">mindent</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span>
<span class="p">)</span>
- <span class="k">if</span> <span class="n">grid_variable</span><span class="p">[</span><span class="s1">'gridtype'</span><span class="p">]</span> <span class="o">==</span> <span class="s1">'edge'</span><span class="p">:</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="p">(</span>
- <span class="n">indent</span> <span class="o">*</span> <span class="p">(</span><span class="n">depth</span><span class="o">+</span><span class="mi">1</span><span class="p">)</span>
- <span class="o">+</span> <span class="s2">"</span><span class="si">{}</span><span class="s2"> = sampled_values_</span><span class="si">{}</span><span class="s2">[0] + (sampled_values_</span><span class="si">{}</span><span class="s2">[1]-sampled_values_</span><span class="si">{}</span><span class="s2">[0]) * </span><span class="si">{}</span><span class="s2">_sample_number"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
- <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">],</span> <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">],</span> <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">],</span> <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">],</span> <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">]</span>
+
+ <span class="k">if</span> <span class="n">vb</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_add_code</span><span class="p">(</span>
+ <span class="s2">"print('sample </span><span class="si">{}</span><span class="s2"> from ',sampled_values_</span><span class="si">{}</span><span class="s2">,' at this=',</span><span class="si">{}</span><span class="s2">_this,', next=',</span><span class="si">{}</span><span class="s2">_next)"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+ <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">],</span>
+ <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">],</span>
+ <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">],</span>
+ <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">],</span>
<span class="p">)</span>
<span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span>
<span class="p">)</span>
- <span class="k">elif</span> <span class="n">grid_variable</span><span class="p">[</span><span class="s1">'gridtype'</span><span class="p">]</span> <span class="o">==</span> <span class="s1">'centred'</span><span class="p">:</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="p">(</span>
- <span class="n">indent</span> <span class="o">*</span> <span class="p">(</span><span class="n">depth</span><span class="o">+</span><span class="mi">1</span><span class="p">)</span>
- <span class="o">+</span> <span class="s2">"</span><span class="si">{}</span><span class="s2"> = sampled_values_</span><span class="si">{}</span><span class="s2">[0] + 0.5 * (sampled_values_</span><span class="si">{}</span><span class="s2">[1]-sampled_values_</span><span class="si">{}</span><span class="s2">[0]) + (sampled_values_</span><span class="si">{}</span><span class="s2">[1]-sampled_values_</span><span class="si">{}</span><span class="s2">[0]) * </span><span class="si">{}</span><span class="s2">_sample_number"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
- <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">],</span> <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">],</span> <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">],</span> <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">],</span> <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">],</span> <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">],</span> <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">]</span>
+
+ <span class="c1"># select point location based on gridtype (left, centre or right)</span>
+ <span class="k">if</span> <span class="p">(</span>
+ <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"gridtype"</span><span class="p">]</span> <span class="o">==</span> <span class="s2">"edge"</span>
+ <span class="ow">or</span> <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"gridtype"</span><span class="p">]</span> <span class="o">==</span> <span class="s2">"left"</span>
+ <span class="ow">or</span> <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"gridtype"</span><span class="p">]</span> <span class="o">==</span> <span class="s2">"left edge"</span>
+ <span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_add_code</span><span class="p">(</span>
+ <span class="s2">"</span><span class="si">{}</span><span class="s2"> = sampled_values_</span><span class="si">{}</span><span class="s2">[</span><span class="si">{}</span><span class="s2">_this]"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+ <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">],</span>
+ <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">],</span>
+ <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">],</span>
+ <span class="p">)</span>
+ <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span>
+ <span class="p">)</span>
+ <span class="k">elif</span> <span class="p">(</span>
+ <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"gridtype"</span><span class="p">]</span> <span class="o">==</span> <span class="s2">"right"</span>
+ <span class="ow">or</span> <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"gridtype"</span><span class="p">]</span> <span class="o">==</span> <span class="s2">"right edge"</span>
+ <span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_add_code</span><span class="p">(</span>
+ <span class="o">+</span><span class="s2">"</span><span class="si">{}</span><span class="s2"> = sampled_values_</span><span class="si">{}</span><span class="s2">[</span><span class="si">{}</span><span class="s2">_next]"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+ <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">],</span>
+ <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">],</span>
+ <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">],</span>
+ <span class="p">)</span>
+ <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span>
+ <span class="p">)</span>
+ <span class="k">elif</span> <span class="p">(</span>
+ <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"gridtype"</span><span class="p">]</span> <span class="o">==</span> <span class="s2">"centred"</span>
+ <span class="ow">or</span> <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"gridtype"</span><span class="p">]</span> <span class="o">==</span> <span class="s2">"centre"</span>
+ <span class="ow">or</span> <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"gridtype"</span><span class="p">]</span> <span class="o">==</span> <span class="s2">"center"</span>
+ <span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_add_code</span><span class="p">(</span>
+ <span class="s2">"</span><span class="si">{}</span><span class="s2"> = 0.5 * (sampled_values_</span><span class="si">{}</span><span class="s2">[</span><span class="si">{}</span><span class="s2">_next] + sampled_values_</span><span class="si">{}</span><span class="s2">[</span><span class="si">{}</span><span class="s2">_this])"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+ <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">],</span>
+ <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">],</span>
+ <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">],</span>
+ <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">],</span>
+ <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">],</span>
<span class="p">)</span>
<span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span>
<span class="p">)</span>
@@ -2241,112 +2421,104 @@
<span class="n">msg</span> <span class="o">=</span> <span class="s2">"Unknown gridtype value. PLease choose a different one"</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">vb</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_add_code</span><span class="p">(</span>
+ <span class="s2">"print('hence </span><span class="si">{}</span><span class="s2"> = ',</span><span class="si">{}</span><span class="s2">)</span><span class="se">\n</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+ <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">],</span> <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">]</span>
+ <span class="p">)</span>
+ <span class="p">)</span>
+
<span class="c1">#################################################################################</span>
<span class="c1"># Check condition and generate for loop</span>
<span class="c1"># If the grid variable has a condition, write the check and the action</span>
<span class="k">if</span> <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"condition"</span><span class="p">]:</span>
- <span class="c1"># Add comment</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="p">(</span>
- <span class="n">indent</span> <span class="o">*</span> <span class="p">(</span><span class="n">depth</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span>
- <span class="o">+</span> <span class="s2">"# Condition for </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">grid_variable</span><span class="p">[</span><span class="s2">"parameter_name"</span><span class="p">])</span>
- <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span>
- <span class="p">)</span>
- <span class="c1"># Add condition check</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="p">(</span>
- <span class="n">indent</span> <span class="o">*</span> <span class="p">(</span><span class="n">depth</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span>
- <span class="o">+</span> <span class="s2">"if not </span><span class="si">{}</span><span class="s2">:"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">grid_variable</span><span class="p">[</span><span class="s2">"condition"</span><span class="p">])</span>
- <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_add_code</span><span class="p">(</span>
+ <span class="c1"># Add comment</span>
+ <span class="s2">"# Condition for </span><span class="si">{}</span><span class="se">\n</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">grid_variable</span><span class="p">[</span><span class="s2">"parameter_name"</span><span class="p">]),</span>
+ <span class="c1"># Add condition check</span>
+ <span class="s2">"if not </span><span class="si">{}</span><span class="s2">:</span><span class="se">\n</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">grid_variable</span><span class="p">[</span><span class="s2">"condition"</span><span class="p">]),</span>
+ <span class="n">mindent</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span>
<span class="p">)</span>
<span class="c1"># Add condition failed action:</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="p">(</span>
- <span class="n">indent</span> <span class="o">*</span> <span class="p">(</span><span class="n">depth</span> <span class="o">+</span> <span class="mi">2</span><span class="p">)</span>
- <span class="o">+</span> <span class="s1">'print("Grid generator: Condition for </span><span class="si">{}</span><span class="s1"> not met!")'</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
- <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"parameter_name"</span><span class="p">]</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'verbosity'</span><span class="p">]</span> <span class="o">>=</span> <span class="mi">3</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_add_code</span><span class="p">(</span>
+ <span class="s1">'print("Grid generator: Condition for </span><span class="si">{}</span><span class="s1"> not met!")'</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+ <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"parameter_name"</span><span class="p">]</span>
+ <span class="p">)</span>
+ <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span>
+ <span class="s2">"continue"</span> <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span>
+ <span class="n">mindent</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span>
<span class="p">)</span>
- <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span>
- <span class="p">)</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="n">indent</span> <span class="o">*</span> <span class="p">(</span><span class="n">depth</span> <span class="o">+</span> <span class="mi">2</span><span class="p">)</span> <span class="o">+</span> <span class="s2">"continue"</span> <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span>
-
- <span class="c1"># Add some white line</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="n">indent</span> <span class="o">*</span> <span class="p">(</span><span class="n">depth</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span> <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span>
-
- <span class="c1">##############3</span>
- <span class="c1"># Add phasevol check:</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="p">(</span>
- <span class="n">indent</span> <span class="o">*</span> <span class="p">(</span><span class="n">depth</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span>
- <span class="o">+</span> <span class="s2">"if phasevol_</span><span class="si">{}</span><span class="s2"> <= 0:"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">])</span>
- <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span>
- <span class="p">)</span>
-
- <span class="c1"># Add phasevol check action:</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="p">(</span>
- <span class="n">indent</span> <span class="o">*</span> <span class="p">(</span><span class="n">depth</span> <span class="o">+</span> <span class="mi">2</span><span class="p">)</span>
- <span class="o">+</span> <span class="s1">'print("Grid generator: phasevol_</span><span class="si">{}</span><span class="s1"> <= 0!")'</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
- <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">]</span>
- <span class="p">)</span>
- <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span>
- <span class="p">)</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="n">indent</span> <span class="o">*</span> <span class="p">(</span><span class="n">depth</span> <span class="o">+</span> <span class="mi">2</span><span class="p">)</span> <span class="o">+</span> <span class="s2">"continue"</span> <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_add_code</span><span class="p">(</span>
+ <span class="s2">"continue"</span> <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span>
+ <span class="n">mindent</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span>
+ <span class="p">)</span>
+ <span class="c1"># Add some whitespace</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_add_code</span><span class="p">(</span><span class="s2">"</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span>
+
+ <span class="c1"># # Add debugging:</span>
+ <span class="c1"># if grid_variable['name']=='q':</span>
+ <span class="c1"># self._add_code((</span>
+ <span class="c1"># indent=1,</span>
+ <span class="c1"># 'print("sampling:", sampled_values_{}, M_1)'.format(</span>
+ <span class="c1"># grid_variable["name"], grid_variable["name"]</span>
+ <span class="c1"># )</span>
+ <span class="c1"># + "\n"</span>
+ <span class="c1"># )</span>
- <span class="c1"># Add some white line</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="n">indent</span> <span class="o">*</span> <span class="p">(</span><span class="n">depth</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span> <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span>
+ <span class="c1"># Add some whitespace</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_add_code</span><span class="p">(</span><span class="s2">"</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span>
<span class="c1">#########################</span>
<span class="c1"># Setting up pre-code and value in some cases</span>
<span class="c1"># Add pre-code</span>
<span class="k">if</span> <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"precode"</span><span class="p">]:</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="p">(</span>
- <span class="n">indent</span> <span class="o">*</span> <span class="p">(</span><span class="n">depth</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span>
- <span class="o">+</span> <span class="s2">"</span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_add_code</span><span class="p">(</span>
+ <span class="s2">"</span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
<span class="n">grid_variable</span><span class="p">[</span><span class="s2">"precode"</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span>
- <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span> <span class="o">+</span> <span class="n">indent</span> <span class="o">*</span> <span class="p">(</span><span class="n">depth</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span>
+ <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">_indent_block</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>
<span class="p">)</span>
<span class="p">)</span>
<span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span>
<span class="p">)</span>
<span class="c1"># Set phasevol</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="n">indent</span> <span class="o">*</span> <span class="p">(</span><span class="n">depth</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span> <span class="o">+</span> <span class="s2">"phasevol *= phasevol_</span><span class="si">{}</span><span class="se">\n</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
- <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">],</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_add_code</span><span class="p">(</span>
+ <span class="s2">"phasevol *= phasevol_</span><span class="si">{}</span><span class="se">\n</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+ <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">],</span>
+ <span class="p">)</span>
<span class="p">)</span>
<span class="c1">#######################</span>
<span class="c1"># Probabilities</span>
<span class="c1"># Calculate probability</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="n">indent</span> <span class="o">*</span> <span class="p">(</span><span class="n">depth</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span> <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="n">indent</span> <span class="o">*</span> <span class="p">(</span><span class="n">depth</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span> <span class="o">+</span> <span class="s2">"# Setting probabilities</span><span class="se">\n</span><span class="s2">"</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="p">(</span>
- <span class="n">indent</span> <span class="o">*</span> <span class="p">(</span><span class="n">depth</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span>
- <span class="o">+</span> <span class="s2">"d</span><span class="si">{}</span><span class="s2"> = phasevol_</span><span class="si">{}</span><span class="s2"> * (</span><span class="si">{}</span><span class="s2">)"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_add_code</span><span class="p">(</span>
+ <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span>
+ <span class="s2">"# Setting probabilities</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span>
+ <span class="s2">"d</span><span class="si">{}</span><span class="s2"> = phasevol_</span><span class="si">{}</span><span class="s2"> * (</span><span class="si">{}</span><span class="s2">)"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
<span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">],</span>
<span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">],</span>
<span class="n">grid_variable</span><span class="p">[</span><span class="s2">"probdist"</span><span class="p">],</span>
<span class="p">)</span>
- <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span>
- <span class="p">)</span>
-
- <span class="c1"># Saving probability sum</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="p">(</span>
- <span class="n">indent</span> <span class="o">*</span> <span class="p">(</span><span class="n">depth</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span>
- <span class="o">+</span> <span class="s2">"probabilities_sum[</span><span class="si">{}</span><span class="s2">] += d</span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+ <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span>
+ <span class="c1"># Save probability sum</span>
+ <span class="s2">"probabilities_sum[</span><span class="si">{}</span><span class="s2">] += d</span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
<span class="n">grid_variable</span><span class="p">[</span><span class="s2">"grid_variable_number"</span><span class="p">],</span> <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">]</span>
<span class="p">)</span>
- <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span>
+ <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span>
<span class="p">)</span>
<span class="k">if</span> <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"grid_variable_number"</span><span class="p">]</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="p">(</span>
- <span class="n">indent</span> <span class="o">*</span> <span class="p">(</span><span class="n">depth</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span>
- <span class="o">+</span> <span class="s2">"probabilities_list[0] = d</span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">])</span>
- <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_add_code</span><span class="p">(</span>
+ <span class="s2">"probabilities_list[0] = d</span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">])</span> <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span>
<span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="p">(</span>
- <span class="n">indent</span> <span class="o">*</span> <span class="p">(</span><span class="n">depth</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span>
- <span class="o">+</span> <span class="s2">"probabilities_list[</span><span class="si">{}</span><span class="s2">] = probabilities_list[</span><span class="si">{}</span><span class="s2">] * d</span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_add_code</span><span class="p">(</span>
+ <span class="s2">"probabilities_list[</span><span class="si">{}</span><span class="s2">] = probabilities_list[</span><span class="si">{}</span><span class="s2">] * d</span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
<span class="n">grid_variable</span><span class="p">[</span><span class="s2">"grid_variable_number"</span><span class="p">],</span>
<span class="n">grid_variable</span><span class="p">[</span><span class="s2">"grid_variable_number"</span><span class="p">]</span> <span class="o">-</span> <span class="mi">1</span><span class="p">,</span>
<span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">],</span>
@@ -2356,51 +2528,41 @@
<span class="c1">#######################</span>
<span class="c1"># Increment starcount for this parameter</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="n">indent</span> <span class="o">*</span> <span class="p">(</span>
- <span class="n">depth</span> <span class="o">+</span> <span class="mi">1</span>
- <span class="p">)</span> <span class="o">+</span> <span class="s2">"# Increment starcount for </span><span class="si">{}</span><span class="se">\n</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">grid_variable</span><span class="p">[</span><span class="s2">"parameter_name"</span><span class="p">])</span>
-
- <span class="n">code_string</span> <span class="o">+=</span> <span class="p">(</span>
- <span class="n">indent</span> <span class="o">*</span> <span class="p">(</span><span class="n">depth</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span>
- <span class="o">+</span> <span class="s2">"starcounts[</span><span class="si">{}</span><span class="s2">] += 1"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_add_code</span><span class="p">(</span>
+ <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span>
+ <span class="s2">"# Increment starcount for </span><span class="si">{}</span><span class="se">\n</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+ <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"parameter_name"</span><span class="p">]</span>
+ <span class="p">),</span>
+ <span class="s2">"starcounts[</span><span class="si">{}</span><span class="s2">] += 1"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
<span class="n">grid_variable</span><span class="p">[</span><span class="s2">"grid_variable_number"</span><span class="p">],</span>
<span class="p">)</span>
- <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span>
- <span class="p">)</span>
-
- <span class="c1"># Add value to dict</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="p">(</span>
- <span class="n">indent</span> <span class="o">*</span> <span class="p">(</span><span class="n">depth</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span>
- <span class="o">+</span> <span class="s1">'parameter_dict["</span><span class="si">{}</span><span class="s1">"] = </span><span class="si">{}</span><span class="s1">'</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+ <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span>
+ <span class="c1"># Add value to dict</span>
+ <span class="s1">'parameter_dict["</span><span class="si">{}</span><span class="s1">"] = </span><span class="si">{}</span><span class="s1">'</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
<span class="n">grid_variable</span><span class="p">[</span><span class="s2">"parameter_name"</span><span class="p">],</span> <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"parameter_name"</span><span class="p">]</span>
<span class="p">)</span>
- <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span>
+ <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span>
+ <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span>
<span class="p">)</span>
- <span class="c1"># Add some space</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_increment_indent_depth</span><span class="p">(</span><span class="o">-</span><span class="mi">1</span><span class="p">)</span>
<span class="c1"># The final parts of the code, where things are returned, are within the deepest loop,</span>
<span class="c1"># but in some cases code from a higher loop needs to go under it again</span>
<span class="c1"># SO I think its better to put an if statement here that checks</span>
<span class="c1"># whether this is the last loop.</span>
<span class="k">if</span> <span class="n">loopnr</span> <span class="o">==</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"_grid_variables"</span><span class="p">])</span> <span class="o">-</span> <span class="mi">1</span><span class="p">:</span>
-
- <span class="n">code_string</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_write_gridcode_system_call</span><span class="p">(</span>
- <span class="n">code_string</span><span class="p">,</span>
- <span class="n">indent</span><span class="p">,</span>
- <span class="n">depth</span><span class="p">,</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_write_gridcode_system_call</span><span class="p">(</span>
<span class="n">grid_variable</span><span class="p">,</span>
<span class="n">dry_run</span><span class="p">,</span>
<span class="n">grid_variable</span><span class="p">[</span><span class="s2">"branchpoint"</span><span class="p">],</span>
<span class="p">)</span>
- <span class="c1"># increment depth</span>
- <span class="n">depth</span> <span class="o">+=</span> <span class="mi">1</span>
+ <span class="c1"># increment indent_depth</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_increment_indent_depth</span><span class="p">(</span><span class="o">+</span><span class="mi">1</span><span class="p">)</span>
- <span class="n">depth</span> <span class="o">-=</span> <span class="mi">1</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_increment_indent_depth</span><span class="p">(</span><span class="o">-</span><span class="mi">1</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_add_code</span><span class="p">(</span><span class="s2">"</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span>
<span class="c1"># Write parts to write below the part that yield the results.</span>
<span class="c1"># this has to go in a reverse order:</span>
@@ -2414,80 +2576,65 @@
<span class="k">for</span> <span class="n">loopnr</span><span class="p">,</span> <span class="n">grid_variable_el</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">reverse_sorted_grid_variables</span><span class="p">):</span>
<span class="n">grid_variable</span> <span class="o">=</span> <span class="n">grid_variable_el</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="n">indent</span> <span class="o">*</span> <span class="p">(</span><span class="n">depth</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span> <span class="o">+</span> <span class="s2">"#"</span> <span class="o">*</span> <span class="mi">40</span> <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="p">(</span>
- <span class="n">indent</span> <span class="o">*</span> <span class="p">(</span><span class="n">depth</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span>
- <span class="o">+</span> <span class="s2">"# Code below is for finalising the handling of this iteration of the parameter </span><span class="si">{}</span><span class="se">\n</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">])</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_increment_indent_depth</span><span class="p">(</span><span class="o">+</span><span class="mi">1</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_add_code</span><span class="p">(</span>
+ <span class="s2">"#"</span> <span class="o">*</span> <span class="mi">40</span> <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span>
+ <span class="s2">"# Code below is for finalising the handling of this iteration of the parameter </span><span class="si">{}</span><span class="se">\n</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+ <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">]</span>
+ <span class="p">),</span>
<span class="p">)</span>
<span class="c1"># Set phasevol</span>
<span class="c1"># TODO: fix. this isn't supposed to be the value that we give it here. discuss</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="n">indent</span> <span class="o">*</span> <span class="p">(</span><span class="n">depth</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span> <span class="o">+</span> <span class="s2">"phasevol /= phasevol_</span><span class="si">{}</span><span class="se">\n</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
- <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">]</span>
- <span class="p">)</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="n">indent</span> <span class="o">*</span> <span class="p">(</span><span class="n">depth</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span> <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_add_code</span><span class="p">(</span><span class="s2">"phasevol /= phasevol_</span><span class="si">{}</span><span class="se">\n\n</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">]))</span>
- <span class="n">depth</span> <span class="o">-=</span> <span class="mi">1</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_increment_indent_depth</span><span class="p">(</span><span class="o">-</span><span class="mi">2</span><span class="p">)</span>
<span class="c1"># Check the branchpoint part here. The branchpoint makes sure that we can construct</span>
<span class="c1"># a grid with several multiplicities and still can make the system calls for each</span>
<span class="c1"># multiplicity without reconstructing the grid each time</span>
<span class="k">if</span> <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"branchpoint"</span><span class="p">]</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
- <span class="c1"># Add comment</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="p">(</span>
- <span class="n">indent</span> <span class="o">*</span> <span class="p">(</span><span class="n">depth</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span>
- <span class="o">+</span> <span class="s2">"# Condition for branchpoint at </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_increment_indent_depth</span><span class="p">(</span><span class="o">+</span><span class="mi">1</span><span class="p">)</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">_add_code</span><span class="p">(</span>
+ <span class="c1"># Add comment</span>
+ <span class="s2">"# Condition for branchpoint at </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
<span class="n">reverse_sorted_grid_variables</span><span class="p">[</span><span class="n">loopnr</span> <span class="o">+</span> <span class="mi">1</span><span class="p">][</span><span class="mi">1</span><span class="p">][</span><span class="s2">"parameter_name"</span><span class="p">]</span>
<span class="p">)</span>
- <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span>
+ <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span>
+ <span class="c1"># # Add condition check</span>
+ <span class="c1"># "if not {}:".format(grid_variable["condition"])</span>
+ <span class="c1"># + "\n"</span>
+ <span class="c1"># Add branchpoint</span>
+ <span class="s2">"if multiplicity==</span><span class="si">{}</span><span class="s2">:"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">grid_variable</span><span class="p">[</span><span class="s2">"branchpoint"</span><span class="p">])</span> <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span>
<span class="p">)</span>
- <span class="c1"># # Add condition check</span>
- <span class="c1"># code_string += (</span>
- <span class="c1"># indent * (depth + 1)</span>
- <span class="c1"># + "if not {}:".format(grid_variable["condition"])</span>
- <span class="c1"># + "\n"</span>
- <span class="c1"># )</span>
-
- <span class="c1"># Add branchpoint</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="p">(</span>
- <span class="n">indent</span> <span class="o">*</span> <span class="p">(</span><span class="n">depth</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span>
- <span class="o">+</span> <span class="s2">"if multiplicity==</span><span class="si">{}</span><span class="s2">:"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">grid_variable</span><span class="p">[</span><span class="s2">"branchpoint"</span><span class="p">])</span>
- <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span>
- <span class="p">)</span>
-
- <span class="n">code_string</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_write_gridcode_system_call</span><span class="p">(</span>
- <span class="n">code_string</span><span class="p">,</span>
- <span class="n">indent</span><span class="p">,</span>
- <span class="n">depth</span> <span class="o">+</span> <span class="mi">1</span><span class="p">,</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_write_gridcode_system_call</span><span class="p">(</span>
<span class="n">reverse_sorted_grid_variables</span><span class="p">[</span><span class="n">loopnr</span> <span class="o">+</span> <span class="mi">1</span><span class="p">][</span><span class="mi">1</span><span class="p">],</span>
<span class="n">dry_run</span><span class="p">,</span>
<span class="n">grid_variable</span><span class="p">[</span><span class="s2">"branchpoint"</span><span class="p">],</span>
<span class="p">)</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_increment_indent_depth</span><span class="p">(</span><span class="o">-</span><span class="mi">1</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_add_code</span><span class="p">(</span><span class="s2">"</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span>
- <span class="c1">################</span>
+ <span class="c1">###############################</span>
<span class="c1"># Finalising print statements</span>
<span class="c1">#</span>
- <span class="c1"># code_string += indent * (depth + 1) + "\n"</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="n">indent</span> <span class="o">*</span> <span class="p">(</span><span class="n">depth</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span> <span class="o">+</span> <span class="s2">"#"</span> <span class="o">*</span> <span class="mi">40</span> <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="n">indent</span> <span class="o">*</span> <span class="p">(</span><span class="n">depth</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span> <span class="o">+</span> <span class="s2">"if print_results:</span><span class="se">\n</span><span class="s2">"</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="p">(</span>
- <span class="n">indent</span> <span class="o">*</span> <span class="p">(</span><span class="n">depth</span> <span class="o">+</span> <span class="mi">2</span><span class="p">)</span>
- <span class="o">+</span> <span class="s2">"print('Grid has handled </span><span class="si">{}</span><span class="s2"> stars'.format(_total_starcount))</span><span class="se">\n</span><span class="s2">"</span>
- <span class="p">)</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="p">(</span>
- <span class="n">indent</span> <span class="o">*</span> <span class="p">(</span><span class="n">depth</span> <span class="o">+</span> <span class="mi">2</span><span class="p">)</span>
- <span class="o">+</span> <span class="s2">"print('with a total probability of </span><span class="si">{}</span><span class="s2">'.format(self.grid_options['_probtot']))</span><span class="se">\n</span><span class="s2">"</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_increment_indent_depth</span><span class="p">(</span><span class="o">+</span><span class="mi">1</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_add_code</span><span class="p">(</span><span class="s2">"</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span> <span class="s2">"#"</span> <span class="o">*</span> <span class="mi">40</span> <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span> <span class="s2">"if print_results:</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_add_code</span><span class="p">(</span>
+ <span class="s2">"print('Grid has handled </span><span class="si">{}</span><span class="s2"> stars with a total probability of </span><span class="si">{}</span><span class="s2">'.format(_total_starcount,self.grid_options['_probtot']))</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span>
+ <span class="n">mindent</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span>
<span class="p">)</span>
<span class="c1">################</span>
<span class="c1"># Finalising return statement for dry run.</span>
<span class="c1">#</span>
<span class="k">if</span> <span class="n">dry_run</span><span class="p">:</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="n">indent</span> <span class="o">*</span> <span class="p">(</span><span class="n">depth</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span> <span class="o">+</span> <span class="s2">"return _total_starcount</span><span class="se">\n</span><span class="s2">"</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_add_code</span><span class="p">(</span><span class="s2">"return _total_starcount</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_increment_indent_depth</span><span class="p">(</span><span class="o">-</span><span class="mi">1</span><span class="p">)</span>
<span class="c1">#################################################################################</span>
<span class="c1"># Stop of code generation. Here the code is saved and written</span>
@@ -2496,7 +2643,7 @@
<span class="s2">"Saving grid code to grid_options"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"verbosity"</span><span class="p">],</span> <span class="mi">1</span>
<span class="p">)</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"code_string"</span><span class="p">]</span> <span class="o">=</span> <span class="n">code_string</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"code_string"</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">code_string</span>
<span class="c1"># Write to file</span>
<span class="n">gridcode_filename</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
@@ -2512,125 +2659,71 @@
<span class="p">)</span>
<span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">gridcode_filename</span><span class="p">,</span> <span class="s2">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">file</span><span class="p">:</span>
- <span class="n">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">code_string</span><span class="p">)</span>
-
+ <span class="n">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">code_string</span><span class="p">)</span>
- <span class="k">def</span> <span class="nf">_write_gridcode_system_call</span><span class="p">(</span>
- <span class="bp">self</span><span class="p">,</span> <span class="n">code_string</span><span class="p">,</span> <span class="n">indent</span><span class="p">,</span> <span class="n">depth</span><span class="p">,</span> <span class="n">grid_variable</span><span class="p">,</span> <span class="n">dry_run</span><span class="p">,</span> <span class="n">branchpoint</span>
- <span class="p">):</span>
+ <span class="k">def</span> <span class="nf">_write_gridcode_system_call</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">grid_variable</span><span class="p">,</span> <span class="n">dry_run</span><span class="p">,</span> <span class="n">branchpoint</span><span class="p">):</span>
<span class="c1">#################################################################################</span>
<span class="c1"># Here are the calls to the queuing or other solution. this part is for every system</span>
<span class="c1"># Add comment</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="n">indent</span> <span class="o">*</span> <span class="p">(</span><span class="n">depth</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span> <span class="o">+</span> <span class="s2">"#"</span> <span class="o">*</span> <span class="mi">40</span> <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_increment_indent_depth</span><span class="p">(</span><span class="o">+</span><span class="mi">1</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_add_code</span><span class="p">(</span><span class="s2">"#"</span> <span class="o">*</span> <span class="mi">40</span> <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span>
<span class="k">if</span> <span class="n">branchpoint</span><span class="p">:</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="p">(</span>
- <span class="n">indent</span> <span class="o">*</span> <span class="p">(</span><span class="n">depth</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span>
- <span class="o">+</span> <span class="s2">"# Code below will get evaluated for every system at this level of multiplicity (last one of that being </span><span class="si">{}</span><span class="s2">)</span><span class="se">\n</span><span class="s2">"</span>
- <span class="p">)</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">])</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_add_code</span><span class="p">(</span>
+ <span class="s2">"# Code below will get evaluated for every system at this level of multiplicity (last one of that being </span><span class="si">{}</span><span class="s2">)</span><span class="se">\n</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+ <span class="n">grid_variable</span><span class="p">[</span><span class="s2">"name"</span><span class="p">]</span>
+ <span class="p">)</span>
+ <span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="p">(</span>
- <span class="n">indent</span> <span class="o">*</span> <span class="p">(</span><span class="n">depth</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span>
- <span class="o">+</span> <span class="s2">"# Code below will get evaluated for every generated system</span><span class="se">\n</span><span class="s2">"</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_add_code</span><span class="p">(</span>
+ <span class="s2">"# Code below will get evaluated for every generated system</span><span class="se">\n</span><span class="s2">"</span>
<span class="p">)</span>
<span class="c1"># Factor in the custom weight input</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="p">(</span>
- <span class="n">indent</span> <span class="o">*</span> <span class="p">(</span><span class="n">depth</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span>
- <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span>
- <span class="p">)</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="p">(</span>
- <span class="n">indent</span> <span class="o">*</span> <span class="p">(</span><span class="n">depth</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span>
- <span class="o">+</span> <span class="s2">"# Weigh the probability by a custom weighting factor</span><span class="se">\n</span><span class="s2">"</span>
- <span class="p">)</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="p">(</span>
- <span class="n">indent</span> <span class="o">*</span> <span class="p">(</span><span class="n">depth</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span>
- <span class="o">+</span> <span class="s1">'probability = self.grid_options["weight"] * probabilities_list[</span><span class="si">{}</span><span class="s1">]'</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_add_code</span><span class="p">(</span>
+ <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span>
+ <span class="s2">"# Weigh the probability by a custom weighting factor</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span>
+ <span class="s1">'probability = self.grid_options["weight"] * probabilities_list[</span><span class="si">{}</span><span class="s1">]'</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
<span class="n">grid_variable</span><span class="p">[</span><span class="s2">"grid_variable_number"</span><span class="p">]</span>
<span class="p">)</span>
- <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span>
- <span class="p">)</span>
-
- <span class="c1"># Take into account the multiplicity fraction:</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="p">(</span>
- <span class="n">indent</span> <span class="o">*</span> <span class="p">(</span><span class="n">depth</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span>
- <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span>
- <span class="p">)</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="p">(</span>
- <span class="n">indent</span> <span class="o">*</span> <span class="p">(</span><span class="n">depth</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span>
- <span class="o">+</span> <span class="s2">"# Factor the multiplicity fraction into the probability</span><span class="se">\n</span><span class="s2">"</span>
- <span class="p">)</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="p">(</span>
- <span class="n">indent</span> <span class="o">*</span> <span class="p">(</span><span class="n">depth</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span>
- <span class="o">+</span> <span class="s1">'probability = probability * self._calculate_multiplicity_fraction(parameter_dict)'</span>
- <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span>
- <span class="p">)</span>
-
- <span class="c1"># Add division by amount of repeats</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="p">(</span>
- <span class="n">indent</span> <span class="o">*</span> <span class="p">(</span><span class="n">depth</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span>
- <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span>
- <span class="p">)</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="p">(</span>
- <span class="n">indent</span> <span class="o">*</span> <span class="p">(</span><span class="n">depth</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span>
- <span class="o">+</span> <span class="s2">"# Divide the probability by the amount of repeats</span><span class="se">\n</span><span class="s2">"</span>
- <span class="p">)</span>
-
- <span class="n">code_string</span> <span class="o">+=</span> <span class="p">(</span>
- <span class="n">indent</span> <span class="o">*</span> <span class="p">(</span><span class="n">depth</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span>
- <span class="o">+</span> <span class="s1">'probability = probability / self.grid_options["repeat"]'</span>
- <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span>
- <span class="p">)</span>
-
- <span class="c1"># Now we yield the system self.grid_options["repeat"] times.</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="p">(</span>
- <span class="n">indent</span> <span class="o">*</span> <span class="p">(</span><span class="n">depth</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span>
- <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span>
- <span class="p">)</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="p">(</span>
- <span class="n">indent</span> <span class="o">*</span> <span class="p">(</span><span class="n">depth</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span>
- <span class="o">+</span> <span class="s2">"# Loop over the repeats</span><span class="se">\n</span><span class="s2">"</span>
+ <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span>
+ <span class="c1"># Take into account the multiplicity fraction:</span>
+ <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span>
+ <span class="s2">"# Factor the multiplicity fraction into the probability</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span>
+ <span class="s2">"probability = probability * self._calculate_multiplicity_fraction(parameter_dict)"</span>
+ <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span>
+ <span class="c1"># Add division by number of repeats</span>
+ <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span>
+ <span class="s2">"# Divide the probability by the number of repeats</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span>
+ <span class="s1">'probability = probability / self.grid_options["repeat"]'</span> <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span>
+ <span class="c1"># Now we yield the system self.grid_options["repeat"] times.</span>
+ <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span>
+ <span class="s2">"# Loop over the repeats</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span>
+ <span class="s1">'for _ in range(self.grid_options["repeat"]):'</span> <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span>
<span class="p">)</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="p">(</span>
- <span class="n">indent</span> <span class="o">*</span> <span class="p">(</span><span class="n">depth</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span> <span class="o">+</span> <span class="s1">'for _ in range(self.grid_options["repeat"]):'</span> <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_add_code</span><span class="p">(</span>
+ <span class="s2">"_total_starcount += 1</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span>
+ <span class="c1"># set probability and phasevol values into the system dict</span>
+ <span class="s1">'parameter_dict["</span><span class="si">{}</span><span class="s1">"] = </span><span class="si">{}</span><span class="s1">'</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="s2">"probability"</span><span class="p">,</span> <span class="s2">"probability"</span><span class="p">)</span> <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span>
+ <span class="s1">'parameter_dict["</span><span class="si">{}</span><span class="s1">"] = </span><span class="si">{}</span><span class="s1">'</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="s2">"phasevol"</span><span class="p">,</span> <span class="s2">"phasevol"</span><span class="p">)</span> <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span>
+ <span class="c1"># Increment total probability</span>
+ <span class="s2">"self._increment_probtot(probability)</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span>
+ <span class="n">mindent</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span>
<span class="p">)</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="n">indent</span> <span class="o">*</span> <span class="p">(</span><span class="n">depth</span> <span class="o">+</span> <span class="mi">2</span><span class="p">)</span> <span class="o">+</span> <span class="s2">"_total_starcount += 1</span><span class="se">\n</span><span class="s2">"</span>
-
- <span class="c1"># set probability and phasevol values into the system dict</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="p">(</span>
- <span class="n">indent</span> <span class="o">*</span> <span class="p">(</span><span class="n">depth</span> <span class="o">+</span> <span class="mi">2</span><span class="p">)</span>
- <span class="o">+</span> <span class="s1">'parameter_dict["</span><span class="si">{}</span><span class="s1">"] = </span><span class="si">{}</span><span class="s1">'</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="s2">"probability"</span><span class="p">,</span> <span class="s2">"probability"</span><span class="p">)</span>
- <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span>
- <span class="p">)</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="p">(</span>
- <span class="n">indent</span> <span class="o">*</span> <span class="p">(</span><span class="n">depth</span> <span class="o">+</span> <span class="mi">2</span><span class="p">)</span>
- <span class="o">+</span> <span class="s1">'parameter_dict["</span><span class="si">{}</span><span class="s1">"] = </span><span class="si">{}</span><span class="s1">'</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="s2">"phasevol"</span><span class="p">,</span> <span class="s2">"phasevol"</span><span class="p">)</span>
- <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span>
- <span class="p">)</span>
-
- <span class="c1"># Some prints. will be removed</span>
- <span class="c1"># code_string += indent * (depth + 1) + "print(probabilities)\n"</span>
- <span class="c1"># code_string += (</span>
- <span class="c1"># indent * (depth + 1) + 'print("_total_starcount: ", _total_starcount)\n'</span>
- <span class="c1"># )</span>
-
- <span class="c1"># code_string += indent * (depth + 1) + "print(probability)\n"</span>
-
- <span class="c1"># Increment total probability</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="n">indent</span> <span class="o">*</span> <span class="p">(</span><span class="n">depth</span> <span class="o">+</span> <span class="mi">2</span><span class="p">)</span> <span class="o">+</span> <span class="s2">"self._increment_probtot(probability)</span><span class="se">\n</span><span class="s2">"</span>
-
<span class="k">if</span> <span class="ow">not</span> <span class="n">dry_run</span><span class="p">:</span>
<span class="c1"># Handling of what is returned, or what is not.</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="n">indent</span> <span class="o">*</span> <span class="p">(</span><span class="n">depth</span> <span class="o">+</span> <span class="mi">2</span><span class="p">)</span> <span class="o">+</span> <span class="s2">"yield(parameter_dict)</span><span class="se">\n</span><span class="s2">"</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_add_code</span><span class="p">(</span><span class="s2">"yield(parameter_dict)</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span> <span class="n">indent</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
<span class="c1"># If its a dry run, dont do anything with it</span>
<span class="k">else</span><span class="p">:</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="n">indent</span> <span class="o">*</span> <span class="p">(</span><span class="n">depth</span> <span class="o">+</span> <span class="mi">2</span><span class="p">)</span> <span class="o">+</span> <span class="s2">"pass</span><span class="se">\n</span><span class="s2">"</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_add_code</span><span class="p">(</span><span class="s2">"pass</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span> <span class="n">indent</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
- <span class="n">code_string</span> <span class="o">+=</span> <span class="n">indent</span> <span class="o">*</span> <span class="p">(</span><span class="n">depth</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span> <span class="o">+</span> <span class="s2">"#"</span> <span class="o">*</span> <span class="mi">40</span> <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_add_code</span><span class="p">(</span><span class="s2">"#"</span> <span class="o">*</span> <span class="mi">40</span> <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span>
- <span class="k">return</span> <span class="n">code_string</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_increment_indent_depth</span><span class="p">(</span><span class="o">-</span><span class="mi">1</span><span class="p">)</span>
+
+ <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">code_string</span>
<span class="k">def</span> <span class="nf">_load_grid_function</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""</span>
@@ -2667,7 +2760,7 @@
<span class="sd"> Requires the grid to be built as a dry run grid</span>
<span class="sd"> """</span>
-
+ <span class="n">verbose_print</span><span class="p">(</span><span class="s2">"Dry run of the grid"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"verbosity"</span><span class="p">],</span> <span class="mi">1</span><span class="p">)</span>
<span class="n">system_generator</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"_system_generator"</span><span class="p">]</span>
<span class="n">total_starcount</span> <span class="o">=</span> <span class="n">system_generator</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"_total_starcount"</span><span class="p">]</span> <span class="o">=</span> <span class="n">total_starcount</span>
@@ -2687,7 +2780,6 @@
<span class="n">print_freq</span> <span class="o">=</span> <span class="mi">10</span>
<span class="c1"># Calculate amount of time left</span>
-
<span class="c1"># calculate amount of time passed</span>
<span class="c1"># time_passed = time.time() - self.grid_options["_start_time_evolution"]</span>
@@ -2720,7 +2812,7 @@
<span class="c1">###################################################</span>
<span class="k">def</span> <span class="nf">_dry_run_source_file</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""</span>
-<span class="sd"> Function to go through the source_file and count the amount of lines and the total probability</span>
+<span class="sd"> Function to go through the source_file and count the number of lines and the total probability</span>
<span class="sd"> """</span>
<span class="n">system_generator</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"_system_generator"</span><span class="p">]</span>
@@ -3371,10 +3463,8 @@
<span class="nb">print</span><span class="p">(</span><span class="s2">"Error. No grid function found!"</span><span class="p">)</span>
<span class="k">raise</span> <span class="ne">ValueError</span>
-
<span class="k">return</span> <span class="n">binary_c_calls_full_filename</span></div>
-
<span class="k">def</span> <span class="nf">_cleanup_defaults</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Function to clean up the default values:</span>
@@ -3450,7 +3540,7 @@
<span class="k">def</span> <span class="nf">_increment_count</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""</span>
-<span class="sd"> Function to add to the total amount of stars. For now not used</span>
+<span class="sd"> Function to add to the total number of stars. For now not used</span>
<span class="sd"> """</span>
<span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"_count"</span><span class="p">]</span> <span class="o">+=</span> <span class="mi">1</span>
@@ -3507,7 +3597,7 @@
<span class="mi">0</span><span class="p">,</span>
<span class="p">)</span>
- <span class="c1"># Keep track of the amount of failed systems and their error codes</span>
+ <span class="c1"># Keep track of the number of failed systems and their error codes</span>
<span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"_failed_prob"</span><span class="p">]</span> <span class="o">+=</span> <span class="n">system_dict</span><span class="p">[</span><span class="s2">"probability"</span><span class="p">]</span>
<span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"_failed_count"</span><span class="p">]</span> <span class="o">+=</span> <span class="mi">1</span>
<span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"_errors_found"</span><span class="p">]</span> <span class="o">=</span> <span class="kc">True</span>
@@ -3535,14 +3625,14 @@
<span class="mi">1</span><span class="p">,</span>
<span class="p">)</span>
- <span class="c1"># Check if we have exceeded the amount of errors</span>
+ <span class="c1"># Check if we have exceeded the number of errors</span>
<span class="k">if</span> <span class="p">(</span>
<span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"_failed_count"</span><span class="p">]</span>
<span class="o">></span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"failed_systems_threshold"</span><span class="p">]</span>
<span class="p">):</span>
<span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"_errors_exceeded"</span><span class="p">]:</span>
<span class="n">verbose_print</span><span class="p">(</span>
- <span class="s2">"Process </span><span class="si">{}</span><span class="s2"> exceeded the maximum (</span><span class="si">{}</span><span class="s2">) amount of failing systems. Stopped logging them to files now"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+ <span class="s2">"Process </span><span class="si">{}</span><span class="s2"> exceeded the maximum (</span><span class="si">{}</span><span class="s2">) number of failing systems. Stopped logging them to files now"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
<span class="bp">self</span><span class="o">.</span><span class="n">process_ID</span><span class="p">,</span>
<span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"failed_systems_threshold"</span><span class="p">],</span>
<span class="p">),</span>
@@ -3566,9 +3656,9 @@
<span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">argstring</span> <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">verbose_print</span><span class="p">(</span>
- <span class="s2">"binary_c had 0 output. Which is strange. Make sure you mean to do this. If there is actually ensemble output being generated then its fine."</span><span class="p">,</span>
+ <span class="s2">"binary_c output nothing - this is strange. If there is ensemble output being generated then this is fine."</span><span class="p">,</span>
<span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"verbosity"</span><span class="p">],</span>
- <span class="mi">2</span><span class="p">,</span>
+ <span class="mi">3</span><span class="p">,</span>
<span class="p">)</span>
<div class="viewcode-block" id="Population.set_moe_di_stefano_settings"><a class="viewcode-back" href="../../../grid.html#binarycpython.utils.grid.Population.set_moe_di_stefano_settings">[docs]</a> <span class="k">def</span> <span class="nf">set_moe_di_stefano_settings</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">options</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
@@ -3580,13 +3670,22 @@
<span class="k">if</span> <span class="n">options</span><span class="p">:</span>
<span class="c1"># Take the option dictionary that was given and override.</span>
- <span class="n">options</span> <span class="o">=</span> <span class="n">update_dicts</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">],</span> <span class="n">options</span><span class="p">)</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">]</span> <span class="o">=</span> <span class="n">copy</span><span class="o">.</span><span class="n">deepcopy</span><span class="p">(</span><span class="nb">dict</span><span class="p">(</span><span class="n">options</span><span class="p">))</span>
+ <span class="n">options</span> <span class="o">=</span> <span class="n">update_dicts</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">],</span> <span class="n">options</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">]</span> <span class="o">=</span> <span class="n">copy</span><span class="o">.</span><span class="n">deepcopy</span><span class="p">(</span><span class="nb">dict</span><span class="p">(</span><span class="n">options</span><span class="p">))</span>
<span class="c1"># Write options to a file</span>
- <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"tmp_dir"</span><span class="p">],</span> <span class="s2">"moe_distefano"</span><span class="p">),</span> <span class="n">exist_ok</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
- <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"tmp_dir"</span><span class="p">],</span> <span class="s2">"moe_distefano"</span><span class="p">),</span> <span class="s2">"moeopts.dat"</span><span class="p">),</span> <span class="s2">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
- <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">json</span><span class="o">.</span><span class="n">dumps</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">],</span> <span class="n">indent</span><span class="o">=</span><span class="mi">4</span><span class="p">))</span></div>
+ <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"tmp_dir"</span><span class="p">],</span> <span class="s2">"moe_distefano"</span><span class="p">),</span>
+ <span class="n">exist_ok</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
+ <span class="p">)</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"tmp_dir"</span><span class="p">],</span> <span class="s2">"moe_distefano"</span><span class="p">),</span>
+ <span class="s2">"moeopts.dat"</span><span class="p">,</span>
+ <span class="p">),</span>
+ <span class="s2">"w"</span><span class="p">,</span>
+ <span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
+ <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">json</span><span class="o">.</span><span class="n">dumps</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">],</span> <span class="n">indent</span><span class="o">=</span><span class="mi">4</span><span class="p">))</span></div>
<span class="k">def</span> <span class="nf">_load_moe_di_stefano_data</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""</span>
@@ -3594,9 +3693,12 @@
<span class="sd"> """</span>
<span class="c1"># Only if the grid is loaded and Moecache contains information</span>
- <span class="k">if</span> <span class="p">(</span><span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'_loaded_ms_data'</span><span class="p">])</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">Moecache</span><span class="p">:</span>
+ <span class="k">if</span> <span class="p">(</span><span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"_loaded_ms_data"</span><span class="p">])</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">Moecache</span><span class="p">:</span>
<span class="c1"># Load the JSON data</span>
- <span class="n">json_data</span> <span class="o">=</span> <span class="n">get_moe_di_stefano_dataset</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">],</span> <span class="n">verbosity</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'verbosity'</span><span class="p">])</span>
+ <span class="n">json_data</span> <span class="o">=</span> <span class="n">get_moe_di_stefano_dataset</span><span class="p">(</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">],</span>
+ <span class="n">verbosity</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"verbosity"</span><span class="p">],</span>
+ <span class="p">)</span>
<span class="c1"># entry of log10M1 is a list containing 1 dict. We can take the dict out of the list</span>
<span class="n">json_data</span><span class="p">[</span><span class="s2">"log10M1"</span><span class="p">]</span> <span class="o">=</span> <span class="n">json_data</span><span class="p">[</span><span class="s2">"log10M1"</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span>
@@ -3613,8 +3715,17 @@
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
<span class="c1"># Write to file</span>
- <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"tmp_dir"</span><span class="p">],</span> <span class="s2">"moe_distefano"</span><span class="p">),</span> <span class="n">exist_ok</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
- <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"tmp_dir"</span><span class="p">],</span> <span class="s2">"moe_distefano"</span><span class="p">),</span> <span class="s2">"moe.log"</span><span class="p">),</span> <span class="s2">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">logfile</span><span class="p">:</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"tmp_dir"</span><span class="p">],</span> <span class="s2">"moe_distefano"</span><span class="p">),</span>
+ <span class="n">exist_ok</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
+ <span class="p">)</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"tmp_dir"</span><span class="p">],</span> <span class="s2">"moe_distefano"</span><span class="p">),</span>
+ <span class="s2">"moe.log"</span><span class="p">,</span>
+ <span class="p">),</span>
+ <span class="s2">"w"</span><span class="p">,</span>
+ <span class="p">)</span> <span class="k">as</span> <span class="n">logfile</span><span class="p">:</span>
<span class="n">logfile</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"logâ‚â‚€Masses(M☉) </span><span class="si">{}</span><span class="se">\n</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">logmasses</span><span class="p">))</span>
<span class="c1"># Get all the periods and see if they are all consistently present</span>
@@ -3652,9 +3763,13 @@
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
<span class="c1"># Write to file</span>
- <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"tmp_dir"</span><span class="p">],</span> <span class="s2">"moe_distefano"</span><span class="p">),</span> <span class="n">exist_ok</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"tmp_dir"</span><span class="p">],</span> <span class="s2">"moe_distefano"</span><span class="p">),</span>
+ <span class="n">exist_ok</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
+ <span class="p">)</span>
<span class="k">with</span> <span class="nb">open</span><span class="p">(</span>
- <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"tmp_dir"</span><span class="p">],</span> <span class="s2">"moe_distefano"</span><span class="p">,</span> <span class="s2">"moe.log"</span><span class="p">),</span> <span class="s2">"a"</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"tmp_dir"</span><span class="p">],</span> <span class="s2">"moe_distefano"</span><span class="p">,</span> <span class="s2">"moe.log"</span><span class="p">),</span>
+ <span class="s2">"a"</span><span class="p">,</span>
<span class="p">)</span> <span class="k">as</span> <span class="n">logfile</span><span class="p">:</span>
<span class="n">logfile</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"logâ‚â‚€Periods(days) </span><span class="si">{}</span><span class="se">\n</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">logperiods</span><span class="p">))</span>
@@ -3776,7 +3891,12 @@
<span class="k">for</span> <span class="n">ecc</span> <span class="ow">in</span> <span class="n">eccs</span><span class="p">:</span>
<span class="n">Moecache</span><span class="p">[</span><span class="s2">"ecc_distributions"</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
- <span class="p">[</span><span class="nb">float</span><span class="p">(</span><span class="n">logmass</span><span class="p">),</span> <span class="nb">float</span><span class="p">(</span><span class="n">logperiod</span><span class="p">),</span> <span class="nb">float</span><span class="p">(</span><span class="n">ecc</span><span class="p">),</span> <span class="n">ecc_data</span><span class="p">[</span><span class="n">ecc</span><span class="p">]]</span>
+ <span class="p">[</span>
+ <span class="nb">float</span><span class="p">(</span><span class="n">logmass</span><span class="p">),</span>
+ <span class="nb">float</span><span class="p">(</span><span class="n">logperiod</span><span class="p">),</span>
+ <span class="nb">float</span><span class="p">(</span><span class="n">ecc</span><span class="p">),</span>
+ <span class="n">ecc_data</span><span class="p">[</span><span class="n">ecc</span><span class="p">],</span>
+ <span class="p">]</span>
<span class="p">)</span>
<span class="c1">############################################################</span>
@@ -3834,12 +3954,21 @@
<span class="p">)</span>
<span class="c1"># Write to log file</span>
- <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"tmp_dir"</span><span class="p">],</span> <span class="s2">"moe_distefano"</span><span class="p">),</span> <span class="n">exist_ok</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
- <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"tmp_dir"</span><span class="p">],</span> <span class="s2">"moe_distefano"</span><span class="p">),</span> <span class="s2">"moecache.json"</span><span class="p">),</span> <span class="s2">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">cache_filehandle</span><span class="p">:</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"tmp_dir"</span><span class="p">],</span> <span class="s2">"moe_distefano"</span><span class="p">),</span>
+ <span class="n">exist_ok</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
+ <span class="p">)</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"tmp_dir"</span><span class="p">],</span> <span class="s2">"moe_distefano"</span><span class="p">),</span>
+ <span class="s2">"moecache.json"</span><span class="p">,</span>
+ <span class="p">),</span>
+ <span class="s2">"w"</span><span class="p">,</span>
+ <span class="p">)</span> <span class="k">as</span> <span class="n">cache_filehandle</span><span class="p">:</span>
<span class="n">cache_filehandle</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">json</span><span class="o">.</span><span class="n">dumps</span><span class="p">(</span><span class="n">Moecache</span><span class="p">,</span> <span class="n">indent</span><span class="o">=</span><span class="mi">4</span><span class="p">))</span>
<span class="c1"># Signal that the data has been loaded</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'_loaded_ms_data'</span><span class="p">]</span> <span class="o">=</span> <span class="kc">True</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"_loaded_ms_data"</span><span class="p">]</span> <span class="o">=</span> <span class="kc">True</span>
<span class="k">def</span> <span class="nf">_set_moe_di_stefano_distributions</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""</span>
@@ -3850,7 +3979,9 @@
<span class="c1"># first, the multiplicity, this is 1,2,3,4, ...</span>
<span class="c1"># for singles, binaries, triples, quadruples, ...</span>
- <span class="n">max_multiplicity</span> <span class="o">=</span> <span class="n">get_max_multiplicity</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">][</span><span class="s2">"multiplicity_modulator"</span><span class="p">])</span>
+ <span class="n">max_multiplicity</span> <span class="o">=</span> <span class="n">get_max_multiplicity</span><span class="p">(</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"multiplicity_modulator"</span><span class="p">]</span>
+ <span class="p">)</span>
<span class="n">verbose_print</span><span class="p">(</span>
<span class="s2">"</span><span class="se">\t</span><span class="s2">Moe_di_Stefano_2017: Max multiplicity = </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">max_multiplicity</span><span class="p">),</span>
<span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"verbosity"</span><span class="p">],</span>
@@ -3868,10 +3999,10 @@
<span class="n">resolution</span><span class="o">=</span><span class="mi">4</span><span class="p">,</span>
<span class="n">spacingfunc</span><span class="o">=</span><span class="s2">"range(1, 5)"</span><span class="p">,</span>
<span class="n">precode</span><span class="o">=</span><span class="s1">'self.grid_options["multiplicity"] = multiplicity; self.bse_options["multiplicity"] = multiplicity; options=</span><span class="si">{}</span><span class="s1">'</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">]</span>
<span class="p">),</span>
<span class="n">condition</span><span class="o">=</span><span class="s2">"(</span><span class="si">{}</span><span class="s2">[multiplicity-1] > 0)"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
- <span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">][</span><span class="s2">"multiplicity_modulator"</span><span class="p">])</span>
+ <span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"multiplicity_modulator"</span><span class="p">])</span>
<span class="p">),</span>
<span class="n">gridtype</span><span class="o">=</span><span class="s2">"edge"</span><span class="p">,</span>
<span class="n">dphasevol</span><span class="o">=-</span><span class="mi">1</span><span class="p">,</span>
@@ -3891,19 +4022,21 @@
<span class="n">longname</span><span class="o">=</span><span class="s2">"Primary mass"</span><span class="p">,</span>
<span class="n">resolution</span><span class="o">=</span><span class="s2">"options['resolutions']['M'][0]"</span><span class="p">,</span>
<span class="n">spacingfunc</span><span class="o">=</span><span class="s2">"const(np.log(</span><span class="si">{}</span><span class="s2">), np.log(</span><span class="si">{}</span><span class="s2">), </span><span class="si">{}</span><span class="s2">)"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"M"</span><span class="p">][</span><span class="mi">0</span><span class="p">],</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"M"</span><span class="p">][</span><span class="mi">1</span><span class="p">],</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">][</span><span class="s2">"resolutions"</span><span class="p">][</span><span class="s2">"M"</span><span class="p">][</span><span class="mi">0</span><span class="p">],</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"M"</span><span class="p">][</span><span class="mi">0</span><span class="p">],</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"M"</span><span class="p">][</span><span class="mi">1</span><span class="p">],</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"resolutions"</span><span class="p">][</span><span class="s2">"M"</span><span class="p">][</span><span class="mi">0</span><span class="p">],</span>
<span class="p">),</span>
<span class="n">valuerange</span><span class="o">=</span><span class="p">[</span>
- <span class="s2">"np.log(</span><span class="si">{}</span><span class="s2">)"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"M"</span><span class="p">][</span><span class="mi">0</span><span class="p">]),</span>
- <span class="s2">"np.log(</span><span class="si">{}</span><span class="s2">)"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"M"</span><span class="p">][</span><span class="mi">1</span><span class="p">]),</span>
+ <span class="s2">"np.log(</span><span class="si">{}</span><span class="s2">)"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"M"</span><span class="p">][</span><span class="mi">0</span><span class="p">]),</span>
+ <span class="s2">"np.log(</span><span class="si">{}</span><span class="s2">)"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"M"</span><span class="p">][</span><span class="mi">1</span><span class="p">]),</span>
<span class="p">],</span>
<span class="n">gridtype</span><span class="o">=</span><span class="s2">"centred"</span><span class="p">,</span>
<span class="n">dphasevol</span><span class="o">=</span><span class="s2">"dlnm1"</span><span class="p">,</span>
<span class="n">precode</span><span class="o">=</span><span class="s1">'M_1 = np.exp(lnm1); options["M_1"]=M_1'</span><span class="p">,</span>
<span class="n">probdist</span><span class="o">=</span><span class="s2">"Moe_di_Stefano_2017_pdf({{</span><span class="si">{}</span><span class="s2">, </span><span class="si">{}</span><span class="s2">, </span><span class="si">{}</span><span class="s2">}}, verbosity=self.grid_options['verbosity'])['total_probdens'] if multiplicity == 1 else 1"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
- <span class="nb">str</span><span class="p">(</span><span class="nb">dict</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">]))[</span><span class="mi">1</span><span class="p">:</span><span class="o">-</span><span class="mi">1</span><span class="p">],</span> <span class="s2">"'multiplicity': multiplicity"</span><span class="p">,</span> <span class="s2">"'M_1': M_1"</span>
+ <span class="nb">str</span><span class="p">(</span><span class="nb">dict</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">]))[</span><span class="mi">1</span><span class="p">:</span><span class="o">-</span><span class="mi">1</span><span class="p">],</span>
+ <span class="s2">"'multiplicity': multiplicity"</span><span class="p">,</span>
+ <span class="s2">"'M_1': M_1"</span><span class="p">,</span>
<span class="p">),</span>
<span class="p">)</span>
@@ -3914,25 +4047,30 @@
<span class="n">name</span><span class="o">=</span><span class="s2">"log10per"</span><span class="p">,</span>
<span class="n">parameter_name</span><span class="o">=</span><span class="s2">"orbital_period"</span><span class="p">,</span>
<span class="n">longname</span><span class="o">=</span><span class="s2">"log10(Orbital_Period)"</span><span class="p">,</span>
- <span class="n">resolution</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">][</span><span class="s2">"resolutions"</span><span class="p">][</span><span class="s2">"logP"</span><span class="p">][</span><span class="mi">0</span><span class="p">],</span>
+ <span class="n">resolution</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"resolutions"</span><span class="p">][</span><span class="s2">"logP"</span><span class="p">][</span><span class="mi">0</span><span class="p">],</span>
<span class="n">probdist</span><span class="o">=</span><span class="mf">1.0</span><span class="p">,</span>
<span class="n">condition</span><span class="o">=</span><span class="s1">'(self.grid_options["multiplicity"] >= 2)'</span><span class="p">,</span>
- <span class="n">branchpoint</span><span class="o">=</span><span class="mi">1</span> <span class="k">if</span> <span class="n">max_multiplicity</span> <span class="o">></span> <span class="mi">1</span> <span class="k">else</span> <span class="mi">0</span><span class="p">,</span> <span class="c1"># Signal here to put a branchpoint if we have a max multiplicity higher than 1.</span>
+ <span class="n">branchpoint</span><span class="o">=</span><span class="mi">1</span>
+ <span class="k">if</span> <span class="n">max_multiplicity</span> <span class="o">></span> <span class="mi">1</span>
+ <span class="k">else</span> <span class="mi">0</span><span class="p">,</span> <span class="c1"># Signal here to put a branchpoint if we have a max multiplicity higher than 1.</span>
<span class="n">gridtype</span><span class="o">=</span><span class="s2">"centred"</span><span class="p">,</span>
<span class="n">dphasevol</span><span class="o">=</span><span class="s2">"(</span><span class="si">{}</span><span class="s2"> * dlog10per)"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">LOG_LN_CONVERTER</span><span class="p">),</span>
- <span class="n">valuerange</span><span class="o">=</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"logP"</span><span class="p">][</span><span class="mi">0</span><span class="p">],</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"logP"</span><span class="p">][</span><span class="mi">1</span><span class="p">]],</span>
+ <span class="n">valuerange</span><span class="o">=</span><span class="p">[</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"logP"</span><span class="p">][</span><span class="mi">0</span><span class="p">],</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"logP"</span><span class="p">][</span><span class="mi">1</span><span class="p">],</span>
+ <span class="p">],</span>
<span class="n">spacingfunc</span><span class="o">=</span><span class="s2">"const(</span><span class="si">{}</span><span class="s2">, </span><span class="si">{}</span><span class="s2">, </span><span class="si">{}</span><span class="s2">)"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"logP"</span><span class="p">][</span><span class="mi">0</span><span class="p">],</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"logP"</span><span class="p">][</span><span class="mi">1</span><span class="p">],</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">][</span><span class="s2">"resolutions"</span><span class="p">][</span><span class="s2">"logP"</span><span class="p">][</span><span class="mi">0</span><span class="p">],</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"logP"</span><span class="p">][</span><span class="mi">0</span><span class="p">],</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"logP"</span><span class="p">][</span><span class="mi">1</span><span class="p">],</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"resolutions"</span><span class="p">][</span><span class="s2">"logP"</span><span class="p">][</span><span class="mi">0</span><span class="p">],</span>
<span class="p">),</span>
<span class="n">precode</span><span class="o">=</span><span class="s2">"""orbital_period = 10.0**log10per</span>
<span class="s2">qmin=</span><span class="si">{}</span><span class="s2">/M_1</span>
<span class="s2">qmax=maximum_mass_ratio_for_RLOF(M_1, orbital_period)</span>
<span class="s2">"""</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">]</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"Mmin"</span><span class="p">,</span> <span class="mf">0.07</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"Mmin"</span><span class="p">]</span>
<span class="p">),</span>
- <span class="p">)</span> <span class="c1"># TODO: change the maximum_mass_ratio_for_RLOF</span>
+ <span class="p">)</span> <span class="c1"># TODO: change the maximum_mass_ratio_for_RLOF</span>
<span class="c1"># binaries: mass ratio</span>
<span class="bp">self</span><span class="o">.</span><span class="n">add_grid_variable</span><span class="p">(</span>
@@ -3940,14 +4078,14 @@
<span class="n">parameter_name</span><span class="o">=</span><span class="s2">"M_2"</span><span class="p">,</span>
<span class="n">longname</span><span class="o">=</span><span class="s2">"Mass ratio"</span><span class="p">,</span>
<span class="n">valuerange</span><span class="o">=</span><span class="p">[</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"q"</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span>
- <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">]</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"ranges"</span><span class="p">,</span> <span class="p">{})</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"q"</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
- <span class="k">else</span> <span class="s2">"options.get('Mmin', 0.07)/M_1"</span><span class="p">,</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"q"</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span>
- <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">]</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"ranges"</span><span class="p">,</span> <span class="p">{})</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"q"</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"q"</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">]</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"ranges"</span><span class="p">,</span> <span class="p">{})</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"q"</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+ <span class="k">else</span> <span class="s2">"options['Mmin']/M_1"</span><span class="p">,</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"q"</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">]</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"ranges"</span><span class="p">,</span> <span class="p">{})</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"q"</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
<span class="k">else</span> <span class="s2">"qmax"</span><span class="p">,</span>
<span class="p">],</span>
- <span class="n">resolution</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">][</span><span class="s2">"resolutions"</span><span class="p">][</span><span class="s2">"M"</span><span class="p">][</span><span class="mi">1</span><span class="p">],</span>
+ <span class="n">resolution</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"resolutions"</span><span class="p">][</span><span class="s2">"M"</span><span class="p">][</span><span class="mi">1</span><span class="p">],</span>
<span class="n">probdist</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span>
<span class="n">gridtype</span><span class="o">=</span><span class="s2">"centred"</span><span class="p">,</span>
<span class="n">dphasevol</span><span class="o">=</span><span class="s2">"dq"</span><span class="p">,</span>
@@ -3956,35 +4094,45 @@
<span class="s2">sep = calc_sep_from_period(M_1, M_2, orbital_period)</span>
<span class="s2"> """</span><span class="p">,</span>
<span class="n">spacingfunc</span><span class="o">=</span><span class="s2">"const(</span><span class="si">{}</span><span class="s2">, </span><span class="si">{}</span><span class="s2">, </span><span class="si">{}</span><span class="s2">)"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"q"</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span>
- <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">]</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"ranges"</span><span class="p">,</span> <span class="p">{})</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"q"</span><span class="p">,</span> <span class="p">[</span><span class="kc">None</span><span class="p">,</span> <span class="kc">None</span><span class="p">])[</span><span class="mi">0</span><span class="p">]</span>
- <span class="k">else</span> <span class="s2">"</span><span class="si">{}</span><span class="s2">/M_1"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">]</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"Mmin"</span><span class="p">,</span> <span class="mf">0.07</span><span class="p">)),</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"q"</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span>
- <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">]</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"ranges"</span><span class="p">,</span> <span class="p">{})</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"q"</span><span class="p">,</span> <span class="p">[</span><span class="kc">None</span><span class="p">,</span> <span class="kc">None</span><span class="p">])[</span><span class="mi">1</span><span class="p">]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"q"</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">]</span>
+ <span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"ranges"</span><span class="p">,</span> <span class="p">{})</span>
+ <span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"q"</span><span class="p">,</span> <span class="p">[</span><span class="kc">None</span><span class="p">,</span> <span class="kc">None</span><span class="p">])[</span><span class="mi">0</span><span class="p">]</span>
+ <span class="k">else</span> <span class="s2">"</span><span class="si">{}</span><span class="s2">/M_1"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"Mmin"</span><span class="p">]),</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"q"</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">]</span>
+ <span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"ranges"</span><span class="p">,</span> <span class="p">{})</span>
+ <span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"q"</span><span class="p">,</span> <span class="p">[</span><span class="kc">None</span><span class="p">,</span> <span class="kc">None</span><span class="p">])[</span><span class="mi">1</span><span class="p">]</span>
<span class="k">else</span> <span class="s2">"qmax"</span><span class="p">,</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">][</span><span class="s2">"resolutions"</span><span class="p">][</span><span class="s2">"M"</span><span class="p">][</span><span class="mi">1</span><span class="p">],</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"resolutions"</span><span class="p">][</span><span class="s2">"M"</span><span class="p">][</span><span class="mi">1</span><span class="p">],</span>
<span class="p">),</span>
<span class="p">)</span>
<span class="c1"># (optional) binaries: eccentricity</span>
- <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">][</span><span class="s2">"resolutions"</span><span class="p">][</span><span class="s2">"ecc"</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"resolutions"</span><span class="p">][</span><span class="s2">"ecc"</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">add_grid_variable</span><span class="p">(</span>
<span class="n">name</span><span class="o">=</span><span class="s2">"ecc"</span><span class="p">,</span>
<span class="n">parameter_name</span><span class="o">=</span><span class="s2">"eccentricity"</span><span class="p">,</span>
<span class="n">longname</span><span class="o">=</span><span class="s2">"Eccentricity"</span><span class="p">,</span>
- <span class="n">resolution</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">][</span><span class="s2">"resolutions"</span><span class="p">][</span><span class="s2">"ecc"</span><span class="p">][</span><span class="mi">0</span><span class="p">],</span>
+ <span class="n">resolution</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"resolutions"</span><span class="p">][</span><span class="s2">"ecc"</span><span class="p">][</span>
+ <span class="mi">0</span>
+ <span class="p">],</span>
<span class="n">probdist</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span>
<span class="n">gridtype</span><span class="o">=</span><span class="s2">"centred"</span><span class="p">,</span>
<span class="n">dphasevol</span><span class="o">=</span><span class="s2">"decc"</span><span class="p">,</span>
<span class="n">precode</span><span class="o">=</span><span class="s2">"eccentricity=ecc"</span><span class="p">,</span>
<span class="n">valuerange</span><span class="o">=</span><span class="p">[</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"ecc"</span><span class="p">][</span><span class="mi">0</span><span class="p">],</span> <span class="c1"># Just fail if not defined.</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"ecc"</span><span class="p">][</span><span class="mi">1</span><span class="p">],</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"ecc"</span><span class="p">][</span>
+ <span class="mi">0</span>
+ <span class="p">],</span> <span class="c1"># Just fail if not defined.</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"ecc"</span><span class="p">][</span><span class="mi">1</span><span class="p">],</span>
<span class="p">],</span>
<span class="n">spacingfunc</span><span class="o">=</span><span class="s2">"const(</span><span class="si">{}</span><span class="s2">, </span><span class="si">{}</span><span class="s2">, </span><span class="si">{}</span><span class="s2">)"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"ecc"</span><span class="p">][</span><span class="mi">0</span><span class="p">],</span> <span class="c1"># Just fail if not defined.</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"ecc"</span><span class="p">][</span><span class="mi">1</span><span class="p">],</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">][</span><span class="s2">"resolutions"</span><span class="p">][</span><span class="s2">"ecc"</span><span class="p">][</span><span class="mi">0</span><span class="p">],</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"ecc"</span><span class="p">][</span>
+ <span class="mi">0</span>
+ <span class="p">],</span> <span class="c1"># Just fail if not defined.</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"ecc"</span><span class="p">][</span><span class="mi">1</span><span class="p">],</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"resolutions"</span><span class="p">][</span><span class="s2">"ecc"</span><span class="p">][</span><span class="mi">0</span><span class="p">],</span>
<span class="p">),</span>
<span class="p">)</span>
@@ -3995,26 +4143,30 @@
<span class="n">name</span><span class="o">=</span><span class="s2">"log10per2"</span><span class="p">,</span>
<span class="n">parameter_name</span><span class="o">=</span><span class="s2">"orbital_period_triple"</span><span class="p">,</span>
<span class="n">longname</span><span class="o">=</span><span class="s2">"log10(Orbital_Period2)"</span><span class="p">,</span>
- <span class="n">resolution</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">][</span><span class="s2">"resolutions"</span><span class="p">][</span><span class="s2">"logP"</span><span class="p">][</span><span class="mi">1</span><span class="p">],</span>
+ <span class="n">resolution</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"resolutions"</span><span class="p">][</span><span class="s2">"logP"</span><span class="p">][</span>
+ <span class="mi">1</span>
+ <span class="p">],</span>
<span class="n">probdist</span><span class="o">=</span><span class="mf">1.0</span><span class="p">,</span>
<span class="n">condition</span><span class="o">=</span><span class="s1">'(self.grid_options["multiplicity"] >= 3)'</span><span class="p">,</span>
- <span class="n">branchpoint</span><span class="o">=</span><span class="mi">2</span> <span class="k">if</span> <span class="n">max_multiplicity</span> <span class="o">></span> <span class="mi">2</span> <span class="k">else</span> <span class="mi">0</span><span class="p">,</span> <span class="c1"># Signal here to put a branchpoint if we have a max multiplicity higher than 1.</span>
+ <span class="n">branchpoint</span><span class="o">=</span><span class="mi">2</span>
+ <span class="k">if</span> <span class="n">max_multiplicity</span> <span class="o">></span> <span class="mi">2</span>
+ <span class="k">else</span> <span class="mi">0</span><span class="p">,</span> <span class="c1"># Signal here to put a branchpoint if we have a max multiplicity higher than 1.</span>
<span class="n">gridtype</span><span class="o">=</span><span class="s2">"centred"</span><span class="p">,</span>
<span class="n">dphasevol</span><span class="o">=</span><span class="s2">"(</span><span class="si">{}</span><span class="s2"> * dlog10per2)"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">LOG_LN_CONVERTER</span><span class="p">),</span>
<span class="n">valuerange</span><span class="o">=</span><span class="p">[</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"logP"</span><span class="p">][</span><span class="mi">0</span><span class="p">],</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"logP"</span><span class="p">][</span><span class="mi">1</span><span class="p">],</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"logP"</span><span class="p">][</span><span class="mi">0</span><span class="p">],</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"logP"</span><span class="p">][</span><span class="mi">1</span><span class="p">],</span>
<span class="p">],</span>
<span class="n">spacingfunc</span><span class="o">=</span><span class="s2">"const(</span><span class="si">{}</span><span class="s2">, </span><span class="si">{}</span><span class="s2">, </span><span class="si">{}</span><span class="s2">)"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"logP"</span><span class="p">][</span><span class="mi">0</span><span class="p">],</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"logP"</span><span class="p">][</span><span class="mi">1</span><span class="p">],</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">][</span><span class="s2">"resolutions"</span><span class="p">][</span><span class="s2">"logP"</span><span class="p">][</span><span class="mi">1</span><span class="p">],</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"logP"</span><span class="p">][</span><span class="mi">0</span><span class="p">],</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"logP"</span><span class="p">][</span><span class="mi">1</span><span class="p">],</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"resolutions"</span><span class="p">][</span><span class="s2">"logP"</span><span class="p">][</span><span class="mi">1</span><span class="p">],</span>
<span class="p">),</span>
<span class="n">precode</span><span class="o">=</span><span class="s2">"""orbital_period_triple = 10.0**log10per2</span>
<span class="s2">q2min=</span><span class="si">{}</span><span class="s2">/(M_1+M_2)</span>
<span class="s2">q2max=maximum_mass_ratio_for_RLOF(M_1+M_2, orbital_period_triple)</span>
<span class="s2"> """</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">]</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"Mmin"</span><span class="p">,</span> <span class="mf">0.07</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"Mmin"</span><span class="p">]</span>
<span class="p">),</span>
<span class="p">)</span>
@@ -4025,14 +4177,18 @@
<span class="n">parameter_name</span><span class="o">=</span><span class="s2">"M_3"</span><span class="p">,</span>
<span class="n">longname</span><span class="o">=</span><span class="s2">"Mass ratio outer/inner"</span><span class="p">,</span>
<span class="n">valuerange</span><span class="o">=</span><span class="p">[</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"q"</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span>
- <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">]</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"ranges"</span><span class="p">,</span> <span class="p">{})</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"q"</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
- <span class="k">else</span> <span class="s2">"options.get('Mmin', 0.07)/(M_1+M_2)"</span><span class="p">,</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"q"</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span>
- <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">]</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"ranges"</span><span class="p">,</span> <span class="p">{})</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"q"</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"q"</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">]</span>
+ <span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"ranges"</span><span class="p">,</span> <span class="p">{})</span>
+ <span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"q"</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+ <span class="k">else</span> <span class="s2">"options['Mmin']/(M_1+M_2)"</span><span class="p">,</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"q"</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">]</span>
+ <span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"ranges"</span><span class="p">,</span> <span class="p">{})</span>
+ <span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"q"</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
<span class="k">else</span> <span class="s2">"q2max"</span><span class="p">,</span>
<span class="p">],</span>
- <span class="n">resolution</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">][</span><span class="s2">"resolutions"</span><span class="p">][</span><span class="s2">"M"</span><span class="p">][</span><span class="mi">2</span><span class="p">],</span>
+ <span class="n">resolution</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"resolutions"</span><span class="p">][</span><span class="s2">"M"</span><span class="p">][</span><span class="mi">2</span><span class="p">],</span>
<span class="n">probdist</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span>
<span class="n">gridtype</span><span class="o">=</span><span class="s2">"centred"</span><span class="p">,</span>
<span class="n">dphasevol</span><span class="o">=</span><span class="s2">"dq2"</span><span class="p">,</span>
@@ -4042,35 +4198,45 @@
<span class="s2">eccentricity2=0</span>
<span class="s2">"""</span><span class="p">,</span>
<span class="n">spacingfunc</span><span class="o">=</span><span class="s2">"const(</span><span class="si">{}</span><span class="s2">, </span><span class="si">{}</span><span class="s2">, </span><span class="si">{}</span><span class="s2">)"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"q"</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span>
- <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">]</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"ranges"</span><span class="p">,</span> <span class="p">{})</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"q"</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
- <span class="k">else</span> <span class="s2">"options.get('Mmin', 0.07)/(M_1+M_2)"</span><span class="p">,</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"q"</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span>
- <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">]</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"ranges"</span><span class="p">,</span> <span class="p">{})</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"q"</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"q"</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">]</span>
+ <span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"ranges"</span><span class="p">,</span> <span class="p">{})</span>
+ <span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"q"</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+ <span class="k">else</span> <span class="s2">"options['Mmin']/(M_1+M_2)"</span><span class="p">,</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"q"</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">]</span>
+ <span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"ranges"</span><span class="p">,</span> <span class="p">{})</span>
+ <span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"q"</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
<span class="k">else</span> <span class="s2">"q2max"</span><span class="p">,</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">][</span><span class="s2">"resolutions"</span><span class="p">][</span><span class="s2">"M"</span><span class="p">][</span><span class="mi">2</span><span class="p">],</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"resolutions"</span><span class="p">][</span><span class="s2">"M"</span><span class="p">][</span><span class="mi">2</span><span class="p">],</span>
<span class="p">),</span>
<span class="p">)</span>
<span class="c1"># (optional) triples: eccentricity</span>
- <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">][</span><span class="s2">"resolutions"</span><span class="p">][</span><span class="s2">"ecc"</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"resolutions"</span><span class="p">][</span><span class="s2">"ecc"</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">add_grid_variable</span><span class="p">(</span>
<span class="n">name</span><span class="o">=</span><span class="s2">"ecc2"</span><span class="p">,</span>
<span class="n">parameter_name</span><span class="o">=</span><span class="s2">"eccentricity2"</span><span class="p">,</span>
<span class="n">longname</span><span class="o">=</span><span class="s2">"Eccentricity of the triple"</span><span class="p">,</span>
- <span class="n">resolution</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">][</span><span class="s2">"resolutions"</span><span class="p">][</span><span class="s2">"ecc"</span><span class="p">][</span><span class="mi">1</span><span class="p">],</span>
+ <span class="n">resolution</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"resolutions"</span><span class="p">][</span>
+ <span class="s2">"ecc"</span>
+ <span class="p">][</span><span class="mi">1</span><span class="p">],</span>
<span class="n">probdist</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span>
<span class="n">gridtype</span><span class="o">=</span><span class="s2">"centred"</span><span class="p">,</span>
<span class="n">dphasevol</span><span class="o">=</span><span class="s2">"decc2"</span><span class="p">,</span>
<span class="n">precode</span><span class="o">=</span><span class="s2">"eccentricity2=ecc2"</span><span class="p">,</span>
<span class="n">valuerange</span><span class="o">=</span><span class="p">[</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"ecc"</span><span class="p">][</span><span class="mi">0</span><span class="p">],</span> <span class="c1"># Just fail if not defined.</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"ecc"</span><span class="p">][</span><span class="mi">1</span><span class="p">],</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"ecc"</span><span class="p">][</span>
+ <span class="mi">0</span>
+ <span class="p">],</span> <span class="c1"># Just fail if not defined.</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"ecc"</span><span class="p">][</span><span class="mi">1</span><span class="p">],</span>
<span class="p">],</span>
<span class="n">spacingfunc</span><span class="o">=</span><span class="s2">"const(</span><span class="si">{}</span><span class="s2">, </span><span class="si">{}</span><span class="s2">, </span><span class="si">{}</span><span class="s2">)"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"ecc"</span><span class="p">][</span><span class="mi">0</span><span class="p">],</span> <span class="c1"># Just fail if not defined.</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"ecc"</span><span class="p">][</span><span class="mi">1</span><span class="p">],</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">][</span><span class="s2">"resolutions"</span><span class="p">][</span><span class="s2">"ecc"</span><span class="p">][</span><span class="mi">1</span><span class="p">],</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"ecc"</span><span class="p">][</span>
+ <span class="mi">0</span>
+ <span class="p">],</span> <span class="c1"># Just fail if not defined.</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"ecc"</span><span class="p">][</span><span class="mi">1</span><span class="p">],</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"resolutions"</span><span class="p">][</span><span class="s2">"ecc"</span><span class="p">][</span><span class="mi">1</span><span class="p">],</span>
<span class="p">),</span>
<span class="p">)</span>
@@ -4080,26 +4246,30 @@
<span class="n">name</span><span class="o">=</span><span class="s2">"log10per3"</span><span class="p">,</span>
<span class="n">parameter_name</span><span class="o">=</span><span class="s2">"orbital_period_quadruple"</span><span class="p">,</span>
<span class="n">longname</span><span class="o">=</span><span class="s2">"log10(Orbital_Period3)"</span><span class="p">,</span>
- <span class="n">resolution</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">][</span><span class="s2">"resolutions"</span><span class="p">][</span><span class="s2">"logP"</span><span class="p">][</span><span class="mi">2</span><span class="p">],</span>
+ <span class="n">resolution</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"resolutions"</span><span class="p">][</span>
+ <span class="s2">"logP"</span>
+ <span class="p">][</span><span class="mi">2</span><span class="p">],</span>
<span class="n">probdist</span><span class="o">=</span><span class="mf">1.0</span><span class="p">,</span>
<span class="n">condition</span><span class="o">=</span><span class="s1">'(self.grid_options["multiplicity"] >= 4)'</span><span class="p">,</span>
- <span class="n">branchpoint</span><span class="o">=</span><span class="mi">3</span> <span class="k">if</span> <span class="n">max_multiplicity</span> <span class="o">></span> <span class="mi">3</span> <span class="k">else</span> <span class="mi">0</span><span class="p">,</span> <span class="c1"># Signal here to put a branchpoint if we have a max multiplicity higher than 1.</span>
+ <span class="n">branchpoint</span><span class="o">=</span><span class="mi">3</span>
+ <span class="k">if</span> <span class="n">max_multiplicity</span> <span class="o">></span> <span class="mi">3</span>
+ <span class="k">else</span> <span class="mi">0</span><span class="p">,</span> <span class="c1"># Signal here to put a branchpoint if we have a max multiplicity higher than 1.</span>
<span class="n">gridtype</span><span class="o">=</span><span class="s2">"centred"</span><span class="p">,</span>
<span class="n">dphasevol</span><span class="o">=</span><span class="s2">"(</span><span class="si">{}</span><span class="s2"> * dlog10per3)"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">LOG_LN_CONVERTER</span><span class="p">),</span>
<span class="n">valuerange</span><span class="o">=</span><span class="p">[</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"logP"</span><span class="p">][</span><span class="mi">0</span><span class="p">],</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"logP"</span><span class="p">][</span><span class="mi">1</span><span class="p">],</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"logP"</span><span class="p">][</span><span class="mi">0</span><span class="p">],</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"logP"</span><span class="p">][</span><span class="mi">1</span><span class="p">],</span>
<span class="p">],</span>
<span class="n">spacingfunc</span><span class="o">=</span><span class="s2">"const(</span><span class="si">{}</span><span class="s2">, </span><span class="si">{}</span><span class="s2">, </span><span class="si">{}</span><span class="s2">)"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"logP"</span><span class="p">][</span><span class="mi">0</span><span class="p">],</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"logP"</span><span class="p">][</span><span class="mi">1</span><span class="p">],</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">][</span><span class="s2">"resolutions"</span><span class="p">][</span><span class="s2">"logP"</span><span class="p">][</span><span class="mi">2</span><span class="p">],</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"logP"</span><span class="p">][</span><span class="mi">0</span><span class="p">],</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"logP"</span><span class="p">][</span><span class="mi">1</span><span class="p">],</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"resolutions"</span><span class="p">][</span><span class="s2">"logP"</span><span class="p">][</span><span class="mi">2</span><span class="p">],</span>
<span class="p">),</span>
<span class="n">precode</span><span class="o">=</span><span class="s2">"""orbital_period_quadruple = 10.0**log10per3</span>
<span class="s2">q3min=</span><span class="si">{}</span><span class="s2">/(M_3)</span>
<span class="s2">q3max=maximum_mass_ratio_for_RLOF(M_3, orbital_period_quadruple)</span>
<span class="s2"> """</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">]</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"Mmin"</span><span class="p">,</span> <span class="mf">0.07</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"Mmin"</span><span class="p">]</span>
<span class="p">),</span>
<span class="p">)</span>
@@ -4109,14 +4279,20 @@
<span class="n">parameter_name</span><span class="o">=</span><span class="s2">"M_4"</span><span class="p">,</span>
<span class="n">longname</span><span class="o">=</span><span class="s2">"Mass ratio outer low/outer high"</span><span class="p">,</span>
<span class="n">valuerange</span><span class="o">=</span><span class="p">[</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"q"</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span>
- <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">]</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"ranges"</span><span class="p">,</span> <span class="p">{})</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"q"</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
- <span class="k">else</span> <span class="s2">"options.get('Mmin', 0.07)/(M_3)"</span><span class="p">,</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"q"</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span>
- <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">]</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"ranges"</span><span class="p">,</span> <span class="p">{})</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"q"</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"q"</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">]</span>
+ <span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"ranges"</span><span class="p">,</span> <span class="p">{})</span>
+ <span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"q"</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+ <span class="k">else</span> <span class="s2">"options['Mmin']/(M_3)"</span><span class="p">,</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"q"</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">]</span>
+ <span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"ranges"</span><span class="p">,</span> <span class="p">{})</span>
+ <span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"q"</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
<span class="k">else</span> <span class="s2">"q3max"</span><span class="p">,</span>
<span class="p">],</span>
- <span class="n">resolution</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">][</span><span class="s2">"resolutions"</span><span class="p">][</span><span class="s2">"M"</span><span class="p">][</span><span class="mi">3</span><span class="p">],</span>
+ <span class="n">resolution</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"resolutions"</span><span class="p">][</span><span class="s2">"M"</span><span class="p">][</span>
+ <span class="mi">3</span>
+ <span class="p">],</span>
<span class="n">probdist</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span>
<span class="n">gridtype</span><span class="o">=</span><span class="s2">"centred"</span><span class="p">,</span>
<span class="n">dphasevol</span><span class="o">=</span><span class="s2">"dq3"</span><span class="p">,</span>
@@ -4126,39 +4302,47 @@
<span class="s2">eccentricity3=0</span>
<span class="s2">"""</span><span class="p">,</span>
<span class="n">spacingfunc</span><span class="o">=</span><span class="s2">"const(</span><span class="si">{}</span><span class="s2">, </span><span class="si">{}</span><span class="s2">, </span><span class="si">{}</span><span class="s2">)"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"q"</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span>
- <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">]</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"ranges"</span><span class="p">,</span> <span class="p">{})</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"q"</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
- <span class="k">else</span> <span class="s2">"options.get('Mmin', 0.07)/(M_3)"</span><span class="p">,</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"q"</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span>
- <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">]</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"ranges"</span><span class="p">,</span> <span class="p">{})</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"q"</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"q"</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">]</span>
+ <span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"ranges"</span><span class="p">,</span> <span class="p">{})</span>
+ <span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"q"</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+ <span class="k">else</span> <span class="s2">"options['Mmin']/(M_3)"</span><span class="p">,</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"q"</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">]</span>
+ <span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"ranges"</span><span class="p">,</span> <span class="p">{})</span>
+ <span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"q"</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
<span class="k">else</span> <span class="s2">"q3max"</span><span class="p">,</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">][</span><span class="s2">"resolutions"</span><span class="p">][</span><span class="s2">"M"</span><span class="p">][</span><span class="mi">2</span><span class="p">],</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"resolutions"</span><span class="p">][</span><span class="s2">"M"</span><span class="p">][</span><span class="mi">2</span><span class="p">],</span>
<span class="p">),</span>
<span class="p">)</span>
<span class="c1"># (optional) triples: eccentricity</span>
- <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">][</span><span class="s2">"resolutions"</span><span class="p">][</span><span class="s2">"ecc"</span><span class="p">][</span><span class="mi">2</span><span class="p">]</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"resolutions"</span><span class="p">][</span><span class="s2">"ecc"</span><span class="p">][</span><span class="mi">2</span><span class="p">]</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">add_grid_variable</span><span class="p">(</span>
<span class="n">name</span><span class="o">=</span><span class="s2">"ecc3"</span><span class="p">,</span>
<span class="n">parameter_name</span><span class="o">=</span><span class="s2">"eccentricity3"</span><span class="p">,</span>
<span class="n">longname</span><span class="o">=</span><span class="s2">"Eccentricity of the triple+quadruple/outer binary"</span><span class="p">,</span>
- <span class="n">resolution</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">][</span><span class="s2">"resolutions"</span><span class="p">][</span><span class="s2">"ecc"</span><span class="p">][</span><span class="mi">2</span><span class="p">],</span>
+ <span class="n">resolution</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"resolutions"</span><span class="p">][</span>
+ <span class="s2">"ecc"</span>
+ <span class="p">][</span><span class="mi">2</span><span class="p">],</span>
<span class="n">probdist</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span>
<span class="n">gridtype</span><span class="o">=</span><span class="s2">"centred"</span><span class="p">,</span>
<span class="n">dphasevol</span><span class="o">=</span><span class="s2">"decc3"</span><span class="p">,</span>
<span class="n">precode</span><span class="o">=</span><span class="s2">"eccentricity3=ecc3"</span><span class="p">,</span>
<span class="n">valuerange</span><span class="o">=</span><span class="p">[</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"ecc"</span><span class="p">][</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"ecc"</span><span class="p">][</span>
<span class="mi">0</span>
<span class="p">],</span> <span class="c1"># Just fail if not defined.</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"ecc"</span><span class="p">][</span><span class="mi">1</span><span class="p">],</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"ecc"</span><span class="p">][</span><span class="mi">1</span><span class="p">],</span>
<span class="p">],</span>
<span class="n">spacingfunc</span><span class="o">=</span><span class="s2">"const(</span><span class="si">{}</span><span class="s2">, </span><span class="si">{}</span><span class="s2">, </span><span class="si">{}</span><span class="s2">)"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"ecc"</span><span class="p">][</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"ecc"</span><span class="p">][</span>
<span class="mi">0</span>
<span class="p">],</span> <span class="c1"># Just fail if not defined.</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"ecc"</span><span class="p">][</span><span class="mi">1</span><span class="p">],</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">][</span><span class="s2">"resolutions"</span><span class="p">][</span><span class="s2">"ecc"</span><span class="p">][</span><span class="mi">2</span><span class="p">],</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"ranges"</span><span class="p">][</span><span class="s2">"ecc"</span><span class="p">][</span><span class="mi">1</span><span class="p">],</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"resolutions"</span><span class="p">][</span><span class="s2">"ecc"</span><span class="p">][</span>
+ <span class="mi">2</span>
+ <span class="p">],</span>
<span class="p">),</span>
<span class="p">)</span>
@@ -4169,7 +4353,7 @@
<span class="c1"># and add some keys to it:</span>
<span class="n">updated_options</span> <span class="o">=</span> <span class="s2">"{{</span><span class="si">{}</span><span class="s2">, </span><span class="si">{}</span><span class="s2">, </span><span class="si">{}</span><span class="s2">, </span><span class="si">{}</span><span class="s2">, </span><span class="si">{}</span><span class="s2">, </span><span class="si">{}</span><span class="s2">, </span><span class="si">{}</span><span class="s2">, </span><span class="si">{}</span><span class="s2">, </span><span class="si">{}</span><span class="s2">, </span><span class="si">{}</span><span class="s2">, </span><span class="si">{}</span><span class="s2">, </span><span class="si">{}</span><span class="s2">}}"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
- <span class="nb">str</span><span class="p">(</span><span class="nb">dict</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">]))[</span><span class="mi">1</span><span class="p">:</span><span class="o">-</span><span class="mi">1</span><span class="p">],</span>
+ <span class="nb">str</span><span class="p">(</span><span class="nb">dict</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">]))[</span><span class="mi">1</span><span class="p">:</span><span class="o">-</span><span class="mi">1</span><span class="p">],</span>
<span class="s1">'"multiplicity": multiplicity'</span><span class="p">,</span>
<span class="s1">'"M_1": M_1'</span><span class="p">,</span>
<span class="s1">'"M_2": M_2'</span><span class="p">,</span>
@@ -4199,7 +4383,7 @@
<span class="p">)</span>
<span class="c1"># Signal that the M&S grid has been set</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'_set_ms_grid'</span><span class="p">]</span> <span class="o">=</span> <span class="kc">True</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"_set_ms_grid"</span><span class="p">]</span> <span class="o">=</span> <span class="kc">True</span>
<span class="c1">################################################################################################</span>
<div class="viewcode-block" id="Population.Moe_di_Stefano_2017"><a class="viewcode-back" href="../../../grid.html#binarycpython.utils.grid.Population.Moe_di_Stefano_2017">[docs]</a> <span class="k">def</span> <span class="nf">Moe_di_Stefano_2017</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">options</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
@@ -4249,49 +4433,61 @@
<span class="sd"> """</span>
<span class="c1"># Just return 1 if no option has been chosen</span>
- <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'multiplicity_fraction_function'</span><span class="p">]</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"multiplicity_fraction_function"</span><span class="p">]</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
<span class="n">verbose_print</span><span class="p">(</span>
<span class="s2">"_calculate_multiplicity_fraction: Chosen not to use any multiplicity fraction."</span><span class="p">,</span>
<span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"verbosity"</span><span class="p">],</span>
- <span class="mi">2</span><span class="p">,</span>
+ <span class="mi">3</span><span class="p">,</span>
<span class="p">)</span>
<span class="k">return</span> <span class="mi">1</span>
<span class="c1"># Raise an error if the multiplicity is not set</span>
- <span class="k">if</span> <span class="ow">not</span> <span class="n">system_dict</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">'multiplicity'</span><span class="p">,</span> <span class="kc">None</span><span class="p">):</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">system_dict</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"multiplicity"</span><span class="p">,</span> <span class="kc">None</span><span class="p">):</span>
<span class="n">msg</span> <span class="o">=</span> <span class="s2">"Multiplicity value has not been set. When using a specific multiplicity fraction function please set the multiplicity"</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
<span class="c1"># Go over the chosen options</span>
- <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'multiplicity_fraction_function'</span><span class="p">]</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"multiplicity_fraction_function"</span><span class="p">]</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
<span class="c1"># Arenou 2010 will be used</span>
<span class="n">verbose_print</span><span class="p">(</span>
<span class="s2">"_calculate_multiplicity_fraction: Using Arenou 2010 to calculate multiplicity fractions"</span><span class="p">,</span>
<span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"verbosity"</span><span class="p">],</span>
- <span class="mi">2</span><span class="p">,</span>
+ <span class="mi">3</span><span class="p">,</span>
<span class="p">)</span>
- <span class="n">binary_fraction</span> <span class="o">=</span> <span class="n">Arenou2010_binary_fraction</span><span class="p">(</span><span class="n">system_dict</span><span class="p">[</span><span class="s1">'M_1'</span><span class="p">])</span>
- <span class="n">multiplicity_fraction_dict</span> <span class="o">=</span> <span class="p">{</span><span class="mi">1</span><span class="p">:</span> <span class="mi">1</span><span class="o">-</span><span class="n">binary_fraction</span><span class="p">,</span> <span class="mi">2</span><span class="p">:</span> <span class="n">binary_fraction</span><span class="p">,</span> <span class="mi">3</span><span class="p">:</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">4</span><span class="p">:</span> <span class="mi">0</span><span class="p">}</span>
+ <span class="n">binary_fraction</span> <span class="o">=</span> <span class="n">Arenou2010_binary_fraction</span><span class="p">(</span><span class="n">system_dict</span><span class="p">[</span><span class="s2">"M_1"</span><span class="p">])</span>
+ <span class="n">multiplicity_fraction_dict</span> <span class="o">=</span> <span class="p">{</span>
+ <span class="mi">1</span><span class="p">:</span> <span class="mi">1</span> <span class="o">-</span> <span class="n">binary_fraction</span><span class="p">,</span>
+ <span class="mi">2</span><span class="p">:</span> <span class="n">binary_fraction</span><span class="p">,</span>
+ <span class="mi">3</span><span class="p">:</span> <span class="mi">0</span><span class="p">,</span>
+ <span class="mi">4</span><span class="p">:</span> <span class="mi">0</span><span class="p">,</span>
+ <span class="p">}</span>
- <span class="k">elif</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'multiplicity_fraction_function'</span><span class="p">]</span> <span class="o">==</span> <span class="mi">2</span><span class="p">:</span>
+ <span class="k">elif</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"multiplicity_fraction_function"</span><span class="p">]</span> <span class="o">==</span> <span class="mi">2</span><span class="p">:</span>
<span class="c1"># Raghavan 2010 will be used</span>
<span class="n">verbose_print</span><span class="p">(</span>
<span class="s2">"_calculate_multiplicity_fraction: Using Rhagavan 2010 to calculate multiplicity fractions"</span><span class="p">,</span>
<span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"verbosity"</span><span class="p">],</span>
- <span class="mi">2</span><span class="p">,</span>
+ <span class="mi">3</span><span class="p">,</span>
<span class="p">)</span>
- <span class="n">binary_fraction</span> <span class="o">=</span> <span class="n">raghavan2010_binary_fraction</span><span class="p">(</span><span class="n">system_dict</span><span class="p">[</span><span class="s1">'M_1'</span><span class="p">])</span>
- <span class="n">multiplicity_fraction_dict</span> <span class="o">=</span> <span class="p">{</span><span class="mi">1</span><span class="p">:</span> <span class="mi">1</span><span class="o">-</span><span class="n">binary_fraction</span><span class="p">,</span> <span class="mi">2</span><span class="p">:</span> <span class="n">binary_fraction</span><span class="p">,</span> <span class="mi">3</span><span class="p">:</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">4</span><span class="p">:</span> <span class="mi">0</span><span class="p">}</span>
+ <span class="n">binary_fraction</span> <span class="o">=</span> <span class="n">raghavan2010_binary_fraction</span><span class="p">(</span><span class="n">system_dict</span><span class="p">[</span><span class="s2">"M_1"</span><span class="p">])</span>
+ <span class="n">multiplicity_fraction_dict</span> <span class="o">=</span> <span class="p">{</span>
+ <span class="mi">1</span><span class="p">:</span> <span class="mi">1</span> <span class="o">-</span> <span class="n">binary_fraction</span><span class="p">,</span>
+ <span class="mi">2</span><span class="p">:</span> <span class="n">binary_fraction</span><span class="p">,</span>
+ <span class="mi">3</span><span class="p">:</span> <span class="mi">0</span><span class="p">,</span>
+ <span class="mi">4</span><span class="p">:</span> <span class="mi">0</span><span class="p">,</span>
+ <span class="p">}</span>
- <span class="k">elif</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'multiplicity_fraction_function'</span><span class="p">]</span> <span class="o">==</span> <span class="mi">3</span><span class="p">:</span>
+ <span class="k">elif</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"multiplicity_fraction_function"</span><span class="p">]</span> <span class="o">==</span> <span class="mi">3</span><span class="p">:</span>
<span class="c1"># We need to check several things now here:</span>
<span class="c1"># First, are the options for the M&S grid set? On start it is filled with the default settings</span>
- <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">]:</span>
- <span class="n">msg</span> <span class="o">=</span> <span class="s2">"The M&S options do not seem to be set properly. The value is </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">])</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">]:</span>
+ <span class="n">msg</span> <span class="o">=</span> <span class="s2">"The M&S options do not seem to be set properly. The value is </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">]</span>
+ <span class="p">)</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
<span class="c1"># Second: is the Moecache filled.</span>
@@ -4299,26 +4495,31 @@
<span class="n">verbose_print</span><span class="p">(</span>
<span class="s2">"_calculate_multiplicity_fraction: Moecache is empty. It needs to be filled with the data for the interpolators. Loading the data now"</span><span class="p">,</span>
<span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"verbosity"</span><span class="p">],</span>
- <span class="mi">2</span><span class="p">,</span>
+ <span class="mi">3</span><span class="p">,</span>
<span class="p">)</span>
<span class="c1"># Load the data</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_load_moe_di_stefano_data</span><span class="p">()</span>
<span class="c1"># record the prev value</span>
- <span class="n">prev_M1_value_ms</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">]</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">'M_1'</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+ <span class="n">prev_M1_value_ms</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">]</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"M_1"</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
<span class="c1"># Set value of M1 of the current system</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">][</span><span class="s1">'M_1'</span><span class="p">]</span> <span class="o">=</span> <span class="n">system_dict</span><span class="p">[</span><span class="s1">'M_1'</span><span class="p">]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"M_1"</span><span class="p">]</span> <span class="o">=</span> <span class="n">system_dict</span><span class="p">[</span><span class="s2">"M_1"</span><span class="p">]</span>
<span class="c1"># Calculate the multiplicity fraction</span>
- <span class="n">multiplicity_fraction_list</span> <span class="o">=</span> <span class="n">Moe_di_Stefano_2017_multiplicity_fractions</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">],</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"verbosity"</span><span class="p">])</span>
+ <span class="n">multiplicity_fraction_list</span> <span class="o">=</span> <span class="n">Moe_di_Stefano_2017_multiplicity_fractions</span><span class="p">(</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">],</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"verbosity"</span><span class="p">]</span>
+ <span class="p">)</span>
<span class="c1"># Turn into dict</span>
- <span class="n">multiplicity_fraction_dict</span> <span class="o">=</span> <span class="p">{</span><span class="n">el</span><span class="o">+</span><span class="mi">1</span><span class="p">:</span><span class="n">multiplicity_fraction_list</span><span class="p">[</span><span class="n">el</span><span class="p">]</span> <span class="k">for</span> <span class="n">el</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">multiplicity_fraction_list</span><span class="p">))}</span>
+ <span class="n">multiplicity_fraction_dict</span> <span class="o">=</span> <span class="p">{</span>
+ <span class="n">el</span> <span class="o">+</span> <span class="mi">1</span><span class="p">:</span> <span class="n">multiplicity_fraction_list</span><span class="p">[</span><span class="n">el</span><span class="p">]</span>
+ <span class="k">for</span> <span class="n">el</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">multiplicity_fraction_list</span><span class="p">))</span>
+ <span class="p">}</span>
<span class="c1"># Set the prev value back</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'m&s_options'</span><span class="p">][</span><span class="s1">'M_1'</span><span class="p">]</span> <span class="o">=</span> <span class="n">prev_M1_value_ms</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"m&s_options"</span><span class="p">][</span><span class="s2">"M_1"</span><span class="p">]</span> <span class="o">=</span> <span class="n">prev_M1_value_ms</span>
<span class="c1"># we don't know what to do next</span>
<span class="k">else</span><span class="p">:</span>
@@ -4326,148 +4527,162 @@
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
<span class="n">verbose_print</span><span class="p">(</span>
- <span class="s2">"Multiplicity: </span><span class="si">{}</span><span class="s2"> multiplicity_fraction: </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">system_dict</span><span class="p">[</span><span class="s1">'multiplicity'</span><span class="p">],</span> <span class="n">multiplicity_fraction_dict</span><span class="p">[</span><span class="n">system_dict</span><span class="p">[</span><span class="s1">'multiplicity'</span><span class="p">]]),</span>
+ <span class="s2">"Multiplicity: </span><span class="si">{}</span><span class="s2"> multiplicity_fraction: </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+ <span class="n">system_dict</span><span class="p">[</span><span class="s2">"multiplicity"</span><span class="p">],</span>
+ <span class="n">multiplicity_fraction_dict</span><span class="p">[</span><span class="n">system_dict</span><span class="p">[</span><span class="s2">"multiplicity"</span><span class="p">]],</span>
+ <span class="p">),</span>
<span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"verbosity"</span><span class="p">],</span>
- <span class="mi">2</span><span class="p">,</span>
+ <span class="mi">3</span><span class="p">,</span>
<span class="p">)</span>
- <span class="k">return</span> <span class="n">multiplicity_fraction_dict</span><span class="p">[</span><span class="n">system_dict</span><span class="p">[</span><span class="s1">'multiplicity'</span><span class="p">]]</span>
+ <span class="k">return</span> <span class="n">multiplicity_fraction_dict</span><span class="p">[</span><span class="n">system_dict</span><span class="p">[</span><span class="s2">"multiplicity"</span><span class="p">]]</span>
- <span class="k">def</span> <span class="nf">_trem</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span><span class="n">dt</span><span class="p">,</span><span class="n">count</span><span class="p">,</span><span class="n">dn</span><span class="p">,</span><span class="n">n</span><span class="p">):</span>
- <span class="sd">"""</span>
-<span class="sd"> Estimate time remaining (seconds) given a differential time and count (i.e. progress = $count/$n). $dt is the time since the last call, $count is the current progress count, $dn is the number run since the last call, and $n is the total number required.</span>
-<span class="sd"> """</span>
- <span class="n">tpr</span> <span class="o">=</span> <span class="n">dt</span> <span class="o">/</span> <span class="nb">max</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span><span class="n">dn</span><span class="p">)</span>
- <span class="n">etasecs</span> <span class="o">=</span> <span class="n">tpr</span> <span class="o">*</span> <span class="p">(</span><span class="n">n</span> <span class="o">-</span> <span class="n">count</span><span class="p">)</span>
- <span class="p">(</span><span class="n">eta</span><span class="p">,</span><span class="n">units</span><span class="p">)</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_conv_time_units</span><span class="p">(</span><span class="n">etasecs</span><span class="p">)</span>
- <span class="k">return</span> <span class="p">(</span><span class="n">eta</span><span class="p">,</span><span class="n">units</span><span class="p">,</span><span class="n">tpr</span><span class="p">,</span><span class="n">etasecs</span><span class="p">)</span>
+ <span class="c1">######################</span>
+ <span class="c1"># Status logging</span>
- <span class="k">def</span> <span class="nf">_conv_time_units</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span><span class="n">t</span><span class="p">):</span>
- <span class="sd">"""</span>
-<span class="sd"> Converts time (t, in seconds, passing in as the only argument) to seconds, minutes or hours depending on its magnitude. Returns a tuple (t,units).</span>
-<span class="sd"> """</span>
- <span class="n">units</span><span class="o">=</span><span class="s1">'s'</span><span class="p">;</span> <span class="c1"># default to seconds</span>
- <span class="k">if</span> <span class="n">t</span> <span class="o">></span> <span class="mi">60</span><span class="p">:</span>
- <span class="n">t</span> <span class="o">/=</span> <span class="mi">60</span><span class="p">;</span>
- <span class="n">units</span><span class="o">=</span><span class="s1">'m'</span><span class="p">;</span>
- <span class="k">if</span> <span class="n">t</span> <span class="o">></span> <span class="mi">60</span><span class="p">:</span>
- <span class="n">t</span> <span class="o">/=</span><span class="mi">60</span><span class="p">;</span>
- <span class="n">units</span><span class="o">=</span><span class="s1">'h'</span><span class="p">;</span>
- <span class="k">return</span> <span class="p">(</span><span class="n">t</span><span class="p">,</span><span class="n">units</span><span class="p">)</span>
-
-<div class="viewcode-block" id="Population.vb1print"><a class="viewcode-back" href="../../../grid.html#binarycpython.utils.grid.Population.vb1print">[docs]</a> <span class="k">def</span> <span class="nf">vb1print</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span><span class="n">ID</span><span class="p">,</span><span class="n">now</span><span class="p">,</span><span class="n">system_number</span><span class="p">):</span>
+<div class="viewcode-block" id="Population.vb1print"><a class="viewcode-back" href="../../../grid.html#binarycpython.utils.grid.Population.vb1print">[docs]</a> <span class="k">def</span> <span class="nf">vb1print</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ID</span><span class="p">,</span> <span class="n">now</span><span class="p">,</span> <span class="n">system_number</span><span class="p">,</span> <span class="n">system_dict</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Verbosity-level 1 printing, to keep an eye on a grid.</span>
<span class="sd"> Arguments:</span>
-<span class="sd"> ID : thread ID for debugging (int)</span>
-<span class="sd"> now : the time now as a UNIX-style epoch in seconds (float)</span>
-<span class="sd"> system_number : the system number</span>
+<span class="sd"> ID: thread ID for debugging (int)</span>
+<span class="sd"> now: the time now as a UNIX-style epoch in seconds (float)</span>
+<span class="sd"> system_number: the system number</span>
+
+<span class="sd"> TODO: add information about the number of cores. the TPR shows the dt/dn but i want to see the number per core too</span>
<span class="sd"> """</span>
+
<span class="c1"># calculate estimated time of arrive (eta and eta_secs), time per run (tpr)</span>
<span class="n">localtime</span> <span class="o">=</span> <span class="n">time</span><span class="o">.</span><span class="n">localtime</span><span class="p">(</span><span class="n">now</span><span class="p">)</span>
- <span class="n">dt</span> <span class="o">=</span> <span class="n">now</span> <span class="o">-</span> <span class="bp">self</span><span class="o">.</span><span class="n">shared_memory</span><span class="p">[</span><span class="s2">"prev_log_time"</span><span class="p">]</span><span class="o">.</span><span class="n">value</span>
- <span class="n">dn</span> <span class="o">=</span> <span class="n">system_number</span> <span class="o">-</span> <span class="bp">self</span><span class="o">.</span><span class="n">shared_memory</span><span class="p">[</span><span class="s2">"prev_log_system_number"</span><span class="p">]</span><span class="o">.</span><span class="n">value</span>
- <span class="p">(</span><span class="n">eta</span><span class="p">,</span><span class="n">units</span><span class="p">,</span><span class="n">tpr</span><span class="p">,</span><span class="n">eta_secs</span><span class="p">)</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_trem</span><span class="p">(</span><span class="n">dt</span><span class="p">,</span>
- <span class="n">system_number</span><span class="p">,</span>
- <span class="n">dn</span><span class="p">,</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"_total_starcount"</span><span class="p">])</span>
+
+ <span class="c1"># calculate stats</span>
+ <span class="n">n</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">shared_memory</span><span class="p">[</span><span class="s2">"n_saved_log_stats"</span><span class="p">]</span><span class="o">.</span><span class="n">value</span>
+ <span class="k">if</span> <span class="n">n</span> <span class="o"><</span> <span class="mi">2</span><span class="p">:</span>
+ <span class="c1"># simple 1-system calculation: inaccurate</span>
+ <span class="c1"># but best for small n</span>
+ <span class="n">dt</span> <span class="o">=</span> <span class="n">now</span> <span class="o">-</span> <span class="bp">self</span><span class="o">.</span><span class="n">shared_memory</span><span class="p">[</span><span class="s2">"prev_log_time"</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span>
+ <span class="n">dn</span> <span class="o">=</span> <span class="n">system_number</span> <span class="o">-</span> <span class="bp">self</span><span class="o">.</span><span class="n">shared_memory</span><span class="p">[</span><span class="s2">"prev_log_system_number"</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="c1"># average over n_saved_log_stats</span>
+ <span class="n">dt</span> <span class="o">=</span> <span class="p">(</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">shared_memory</span><span class="p">[</span><span class="s2">"prev_log_time"</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span>
+ <span class="o">-</span> <span class="bp">self</span><span class="o">.</span><span class="n">shared_memory</span><span class="p">[</span><span class="s2">"prev_log_time"</span><span class="p">][</span><span class="n">n</span> <span class="o">-</span> <span class="mi">1</span><span class="p">]</span>
+ <span class="p">)</span>
+ <span class="n">dn</span> <span class="o">=</span> <span class="p">(</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">shared_memory</span><span class="p">[</span><span class="s2">"prev_log_system_number"</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span>
+ <span class="o">-</span> <span class="bp">self</span><span class="o">.</span><span class="n">shared_memory</span><span class="p">[</span><span class="s2">"prev_log_system_number"</span><span class="p">][</span><span class="n">n</span> <span class="o">-</span> <span class="mi">1</span><span class="p">]</span>
+ <span class="p">)</span>
+
+ <span class="n">eta</span><span class="p">,</span> <span class="n">units</span><span class="p">,</span> <span class="n">tpr</span><span class="p">,</span> <span class="n">eta_secs</span> <span class="o">=</span> <span class="n">trem</span><span class="p">(</span>
+ <span class="n">dt</span><span class="p">,</span> <span class="n">system_number</span><span class="p">,</span> <span class="n">dn</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"_total_starcount"</span><span class="p">]</span>
+ <span class="p">)</span>
+ <span class="n">tpr</span> <span class="o">*=</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'num_cores'</span><span class="p">]</span>
+
<span class="k">if</span> <span class="n">eta_secs</span> <span class="o"><</span> <span class="n">secs_per_day</span><span class="p">:</span>
<span class="n">fintime</span> <span class="o">=</span> <span class="n">time</span><span class="o">.</span><span class="n">localtime</span><span class="p">(</span><span class="n">now</span> <span class="o">+</span> <span class="n">eta_secs</span><span class="p">)</span>
- <span class="n">etf</span> <span class="o">=</span> <span class="s2">"</span><span class="si">{hours:02d}</span><span class="s2">:</span><span class="si">{minutes:02d}</span><span class="s2">:</span><span class="si">{seconds:02d}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">hours</span> <span class="o">=</span> <span class="n">fintime</span><span class="o">.</span><span class="n">tm_hour</span><span class="p">,</span>
- <span class="n">minutes</span> <span class="o">=</span> <span class="n">fintime</span><span class="o">.</span><span class="n">tm_min</span><span class="p">,</span>
- <span class="n">seconds</span> <span class="o">=</span> <span class="n">fintime</span><span class="o">.</span><span class="n">tm_sec</span><span class="p">)</span>
+ <span class="n">etf</span> <span class="o">=</span> <span class="s2">"</span><span class="si">{hours:02d}</span><span class="s2">:</span><span class="si">{minutes:02d}</span><span class="s2">:</span><span class="si">{seconds:02d}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+ <span class="n">hours</span><span class="o">=</span><span class="n">fintime</span><span class="o">.</span><span class="n">tm_hour</span><span class="p">,</span> <span class="n">minutes</span><span class="o">=</span><span class="n">fintime</span><span class="o">.</span><span class="n">tm_min</span><span class="p">,</span> <span class="n">seconds</span><span class="o">=</span><span class="n">fintime</span><span class="o">.</span><span class="n">tm_sec</span>
+ <span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
- <span class="n">d</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">eta_secs</span><span class="o">/</span><span class="n">secs_per_day</span><span class="p">)</span>
+ <span class="n">d</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">eta_secs</span> <span class="o">/</span> <span class="n">secs_per_day</span><span class="p">)</span>
<span class="k">if</span> <span class="n">d</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
<span class="n">etf</span> <span class="o">=</span> <span class="s2">"Tomorrow"</span>
<span class="k">else</span><span class="p">:</span>
- <span class="n">etf</span> <span class="o">=</span> <span class="s2">"In "</span> <span class="o">+</span> <span class="n">d</span> <span class="o">+</span> <span class="s2">" days"</span>
+ <span class="n">etf</span> <span class="o">=</span> <span class="s2">"In </span><span class="si">{}</span><span class="s2"> days"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">d</span><span class="p">)</span>
<span class="c1"># modulo information</span>
- <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'modulo'</span><span class="p">]</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
- <span class="n">modulo</span> <span class="o">=</span> <span class="s1">''</span> <span class="c1"># usual case</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"modulo"</span><span class="p">]</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
+ <span class="n">modulo</span> <span class="o">=</span> <span class="s2">""</span> <span class="c1"># usual case</span>
<span class="k">else</span><span class="p">:</span>
- <span class="n">modulo</span> <span class="o">=</span> <span class="s1">'%'</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'modulo'</span><span class="p">])</span>
+ <span class="n">modulo</span> <span class="o">=</span> <span class="s2">"%"</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"modulo"</span><span class="p">])</span>
<span class="c1"># add up memory use from each thread</span>
- <span class="n">mem_use</span> <span class="o">=</span> <span class="nb">sum</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">shared_memory</span><span class="p">[</span><span class="s2">"memory_use_per_thread"</span><span class="p">])</span>
+ <span class="n">total_mem_use</span> <span class="o">=</span> <span class="nb">sum</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">shared_memory</span><span class="p">[</span><span class="s2">"memory_use_per_thread"</span><span class="p">])</span>
+
+ <span class="c1"># make a string to describe the system e.g. M1, M2, etc.</span>
+ <span class="n">system_string</span> <span class="o">=</span> <span class="s2">""</span>
+ <span class="k">if</span> <span class="s2">"multiplicity"</span> <span class="ow">in</span> <span class="n">system_dict</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">system_dict</span><span class="p">[</span><span class="s2">"multiplicity"</span><span class="p">]):</span>
+ <span class="n">i1</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="n">i</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span>
+ <span class="n">system_string</span> <span class="o">+=</span> <span class="p">(</span>
+ <span class="s2">"M</span><span class="si">{}</span><span class="s2">="</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">i1</span><span class="p">)</span> <span class="o">+</span> <span class="n">format_number</span><span class="p">(</span><span class="n">system_dict</span><span class="p">[</span><span class="s2">"M_"</span> <span class="o">+</span> <span class="n">i1</span><span class="p">])</span> <span class="o">+</span> <span class="s2">" "</span>
+ <span class="p">)</span>
+ <span class="k">if</span> <span class="s2">"separation"</span> <span class="ow">in</span> <span class="n">system_dict</span><span class="p">:</span>
+ <span class="n">system_string</span> <span class="o">+=</span> <span class="s2">"a="</span> <span class="o">+</span> <span class="n">format_number</span><span class="p">(</span><span class="n">system_dict</span><span class="p">[</span><span class="s2">"separation"</span><span class="p">])</span>
+ <span class="k">if</span> <span class="s2">"orbital_period"</span> <span class="ow">in</span> <span class="n">system_dict</span><span class="p">:</span>
+ <span class="n">system_string</span> <span class="o">+=</span> <span class="s2">"P="</span> <span class="o">+</span> <span class="n">format_number</span><span class="p">(</span><span class="n">system_dict</span><span class="p">[</span><span class="s2">"orbital_period"</span><span class="p">])</span>
+ <span class="c1"># do the print</span>
<span class="n">verbose_print</span><span class="p">(</span>
- <span class="s2">"</span><span class="si">{system_number}</span><span class="s2">/</span><span class="si">{total_starcount}{modulo}</span><span class="s2"> </span><span class="si">{complete:5.1f}% c</span><span class="s2">omplete </span><span class="si">{hours:02d}</span><span class="s2">:</span><span class="si">{minutes:02d}</span><span class="s2">:</span><span class="si">{seconds:02d}</span><span class="s2"> ETA=</span><span class="si">{eta:7.1f}{units}</span><span class="s2"> tpr=</span><span class="si">{tpr:2.2e}</span><span class="s2"> ETF=</span><span class="si">{etf}</span><span class="s2"> mem:</span><span class="si">{mem_use:.1f}</span><span class="s2">MB"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
- <span class="n">system_number</span> <span class="o">=</span> <span class="n">system_number</span><span class="p">,</span>
- <span class="n">total_starcount</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"_total_starcount"</span><span class="p">],</span>
- <span class="n">complete</span><span class="o">=</span><span class="p">(</span><span class="mf">100.0</span><span class="o">*</span><span class="n">system_number</span><span class="p">)</span><span class="o">/</span><span class="p">(</span><span class="mf">1.0</span><span class="o">*</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"_total_starcount"</span><span class="p">]),</span>
- <span class="n">modulo</span> <span class="o">=</span> <span class="n">modulo</span><span class="p">,</span>
- <span class="n">hours</span> <span class="o">=</span> <span class="n">localtime</span><span class="o">.</span><span class="n">tm_hour</span><span class="p">,</span>
- <span class="n">minutes</span> <span class="o">=</span> <span class="n">localtime</span><span class="o">.</span><span class="n">tm_min</span><span class="p">,</span>
- <span class="n">seconds</span> <span class="o">=</span> <span class="n">localtime</span><span class="o">.</span><span class="n">tm_sec</span><span class="p">,</span>
- <span class="n">eta</span> <span class="o">=</span> <span class="n">eta</span><span class="p">,</span>
- <span class="n">units</span> <span class="o">=</span> <span class="n">units</span><span class="p">,</span>
- <span class="n">tpr</span> <span class="o">=</span> <span class="n">tpr</span><span class="p">,</span>
- <span class="n">etf</span> <span class="o">=</span> <span class="n">etf</span><span class="p">,</span>
- <span class="n">mem_use</span> <span class="o">=</span> <span class="n">mem_use</span>
+ <span class="s2">"</span><span class="si">{opening_colour}{system_number}</span><span class="s2">/</span><span class="si">{total_starcount}{modulo}</span><span class="s2"> </span><span class="si">{pc_colour}{pc_complete:5.1f}% c</span><span class="s2">omplete </span><span class="si">{time_colour}{hours:02d}</span><span class="s2">:</span><span class="si">{minutes:02d}</span><span class="s2">:</span><span class="si">{seconds:02d}</span><span class="s2"> </span><span class="si">{ETA_colour}</span><span class="s2">ETA=</span><span class="si">{ETA:7.1f}{units}</span><span class="s2"> tpr=</span><span class="si">{tpr:2.2e}</span><span class="s2"> </span><span class="si">{ETF_colour}</span><span class="s2">ETF=</span><span class="si">{ETF}</span><span class="s2"> </span><span class="si">{mem_use_colour}</span><span class="s2">mem:</span><span class="si">{mem_use:.1f}</span><span class="s2">MB </span><span class="si">{system_string_colour}{system_string}{closing_colour}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+ <span class="n">opening_colour</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">ANSI_colours</span><span class="p">[</span><span class="s2">"reset"</span><span class="p">]</span>
+ <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">ANSI_colours</span><span class="p">[</span><span class="s2">"yellow on black"</span><span class="p">],</span>
+ <span class="n">system_number</span><span class="o">=</span><span class="n">system_number</span><span class="p">,</span>
+ <span class="n">total_starcount</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"_total_starcount"</span><span class="p">],</span>
+ <span class="n">modulo</span><span class="o">=</span><span class="n">modulo</span><span class="p">,</span>
+ <span class="n">pc_colour</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">ANSI_colours</span><span class="p">[</span><span class="s2">"blue on black"</span><span class="p">],</span>
+ <span class="n">pc_complete</span><span class="o">=</span><span class="p">(</span><span class="mf">100.0</span> <span class="o">*</span> <span class="n">system_number</span><span class="p">)</span>
+ <span class="o">/</span> <span class="p">(</span><span class="mf">1.0</span> <span class="o">*</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"_total_starcount"</span><span class="p">])</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"_total_starcount"</span><span class="p">]</span>
+ <span class="k">else</span> <span class="o">-</span><span class="mi">1</span><span class="p">,</span>
+ <span class="n">time_colour</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">ANSI_colours</span><span class="p">[</span><span class="s2">"green on black"</span><span class="p">],</span>
+ <span class="n">hours</span><span class="o">=</span><span class="n">localtime</span><span class="o">.</span><span class="n">tm_hour</span><span class="p">,</span>
+ <span class="n">minutes</span><span class="o">=</span><span class="n">localtime</span><span class="o">.</span><span class="n">tm_min</span><span class="p">,</span>
+ <span class="n">seconds</span><span class="o">=</span><span class="n">localtime</span><span class="o">.</span><span class="n">tm_sec</span><span class="p">,</span>
+ <span class="n">ETA_colour</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">ANSI_colours</span><span class="p">[</span><span class="s2">"red on black"</span><span class="p">],</span>
+ <span class="n">ETA</span><span class="o">=</span><span class="n">eta</span><span class="p">,</span>
+ <span class="n">units</span><span class="o">=</span><span class="n">units</span><span class="p">,</span>
+ <span class="n">tpr</span><span class="o">=</span><span class="n">tpr</span><span class="p">,</span>
+ <span class="n">ETF_colour</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">ANSI_colours</span><span class="p">[</span><span class="s2">"blue"</span><span class="p">],</span>
+ <span class="n">ETF</span><span class="o">=</span><span class="n">etf</span><span class="p">,</span>
+ <span class="n">mem_use_colour</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">ANSI_colours</span><span class="p">[</span><span class="s2">"magenta"</span><span class="p">],</span>
+ <span class="n">mem_use</span><span class="o">=</span><span class="n">total_mem_use</span><span class="p">,</span>
+ <span class="n">system_string_colour</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">ANSI_colours</span><span class="p">[</span><span class="s2">"yellow"</span><span class="p">],</span>
+ <span class="n">system_string</span><span class="o">=</span><span class="n">system_string</span><span class="p">,</span>
+ <span class="n">closing_colour</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">ANSI_colours</span><span class="p">[</span><span class="s2">"reset"</span><span class="p">],</span>
<span class="p">),</span>
<span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"verbosity"</span><span class="p">],</span>
- <span class="mi">1</span>
+ <span class="mi">1</span><span class="p">,</span>
<span class="p">)</span></div>
- <span class="k">def</span> <span class="nf">_mem_use</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
- <span class="sd">"""</span>
-<span class="sd"> Return current process memory use in MB. (Takes no arguments) Note: this is per-thread only.</span>
-<span class="sd"> """</span>
- <span class="k">return</span> <span class="n">resource</span><span class="o">.</span><span class="n">getrusage</span><span class="p">(</span><span class="n">resource</span><span class="o">.</span><span class="n">RUSAGE_SELF</span><span class="p">)</span><span class="o">.</span><span class="n">ru_maxrss</span> <span class="o">/</span> <span class="mf">1024.0</span></div>
+<div class="viewcode-block" id="Population.vb2print"><a class="viewcode-back" href="../../../grid.html#binarycpython.utils.grid.Population.vb2print">[docs]</a> <span class="k">def</span> <span class="nf">vb2print</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">system_dict</span><span class="p">,</span> <span class="n">cmdline_string</span><span class="p">):</span>
+ <span class="nb">print</span><span class="p">(</span><span class="s2">"Running this system now on thread </span><span class="si">{ID}</span><span class="se">\n</span><span class="si">{blue}{cmdline}{reset}</span><span class="se">\n</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+ <span class="n">ID</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">process_ID</span><span class="p">,</span>
+ <span class="n">blue</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">ANSI_colours</span><span class="p">[</span><span class="s2">"blue"</span><span class="p">],</span>
+ <span class="n">cmdline</span><span class="o">=</span><span class="n">cmdline_string</span><span class="p">,</span>
+ <span class="n">reset</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">ANSI_colours</span><span class="p">[</span><span class="s2">"reset"</span><span class="p">]))</span></div></div>
</pre></div>
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- <p>
-
- © Copyright 2021, David Hendriks, Robert Izzard
-
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-Using binary_c with bit branch newmaster: git revision: "6185:20210910:1621c23a5" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/newmaster">git url</a>.
+Using binary_c with bit branch master: git revision: "6209:20211006:c4a4c332e" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/master">git url</a>.
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index d727ebca9d1cc066504565325691482cc0e30eef..f38ca95996d45fa51a5a58605b45cd5813dd27a6 100644
--- a/docs/build/html/_modules/binarycpython/utils/grid_options_defaults.html
+++ b/docs/build/html/_modules/binarycpython/utils/grid_options_defaults.html
@@ -1,69 +1,32 @@
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+ <script data-url_root="../../../" id="documentation_options" src="../../../_static/documentation_options.js"></script>
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@@ -94,67 +46,30 @@
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<h1>Source code for binarycpython.utils.grid_options_defaults</h1><div class="highlight"><pre>
<span></span><span class="sd">"""</span>
<span class="sd">Module that contains the default options for the population grid code along with the description for these options, in the form of dictionaries:</span>
@@ -187,9 +102,9 @@
<span class="c1">##########################</span>
<span class="c1"># general (or unordered..)</span>
<span class="c1">##########################</span>
- <span class="s2">"amt_cores"</span><span class="p">:</span> <span class="mi">1</span><span class="p">,</span> <span class="c1"># total amount of cores used to evolve the population</span>
+ <span class="s2">"num_cores"</span><span class="p">:</span> <span class="mi">1</span><span class="p">,</span> <span class="c1"># total number of cores used to evolve the population</span>
<span class="s2">"parse_function"</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span> <span class="c1"># Function to parse the output with.</span>
- <span class="s2">"multiplicity_fraction_function"</span><span class="p">:</span> <span class="mi">0</span><span class="p">,</span> <span class="c1"># Which multiplicity fraction function to use. 0: None, 1: Arenou 2010, 2: Rhagavan 2010, 3: M&S 2017</span>
+ <span class="s2">"multiplicity_fraction_function"</span><span class="p">:</span> <span class="mi">0</span><span class="p">,</span> <span class="c1"># Which multiplicity fraction function to use. 0: None, 1: Arenou 2010, 2: Rhagavan 2010, 3: M&S 2017</span>
<span class="s2">"tmp_dir"</span><span class="p">:</span> <span class="n">temp_dir</span><span class="p">(),</span> <span class="c1"># Setting the temp dir of the program</span>
<span class="s2">"_main_pid"</span><span class="p">:</span> <span class="o">-</span><span class="mi">1</span><span class="p">,</span> <span class="c1"># Placeholder for the main process id of the run.</span>
<span class="s2">"combine_ensemble_with_thread_joining"</span><span class="p">:</span> <span class="kc">True</span><span class="p">,</span> <span class="c1"># Flag on whether to combine everything and return it to the user or if false: write it to data_dir/ensemble_output_{population_id}_{thread_id}.json</span>
@@ -197,10 +112,11 @@
<span class="s2">"log_runtime_systems"</span><span class="p">:</span> <span class="mi">0</span><span class="p">,</span> <span class="c1"># whether to log the runtime of the systems (1 file per thread. stored in the tmp_dir)</span>
<span class="s2">"_actually_evolve_system"</span><span class="p">:</span> <span class="kc">True</span><span class="p">,</span> <span class="c1"># Whether to actually evolve the systems of just act as if. for testing. used in _process_run_population_grid</span>
<span class="s2">"max_queue_size"</span><span class="p">:</span> <span class="mi">1000</span><span class="p">,</span> <span class="c1"># Maximum size of the system call queue.</span>
- <span class="s2">"run_zero_probability_system"</span><span class="p">:</span> <span class="kc">True</span><span class="p">,</span> <span class="c1"># Whether to run the zero probability systems</span>
+ <span class="s2">"run_zero_probability_system"</span><span class="p">:</span> <span class="kc">True</span><span class="p">,</span> <span class="c1"># Whether to run the zero probability systems</span>
<span class="s2">"_zero_prob_stars_skipped"</span><span class="p">:</span> <span class="mi">0</span><span class="p">,</span>
- <span class="s2">"ensemble_factor_in_probability_weighted_mass"</span><span class="p">:</span> <span class="kc">False</span><span class="p">,</span> <span class="c1"># Whether to multiply the ensemble results by 1/probability_weighted_mass</span>
- <span class="s2">"do_dry_run"</span><span class="p">:</span> <span class="kc">True</span><span class="p">,</span> <span class="c1"># Whether to do a dry run to calculate the total probability for this run</span>
+ <span class="s2">"ensemble_factor_in_probability_weighted_mass"</span><span class="p">:</span> <span class="kc">False</span><span class="p">,</span> <span class="c1"># Whether to multiply the ensemble results by 1/probability_weighted_mass</span>
+ <span class="s2">"do_dry_run"</span><span class="p">:</span> <span class="kc">True</span><span class="p">,</span> <span class="c1"># Whether to do a dry run to calculate the total probability for this run</span>
+ <span class="s2">"exit_after_dry_run"</span><span class="p">:</span> <span class="kc">False</span><span class="p">,</span> <span class="c1"># Exit after dry run?</span>
<span class="c1">##########################</span>
<span class="c1"># Execution log:</span>
<span class="c1">##########################</span>
@@ -208,7 +124,8 @@
<span class="s2">"log_file"</span><span class="p">:</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
<span class="n">temp_dir</span><span class="p">(),</span> <span class="s2">"binary_c_python.log"</span>
<span class="p">),</span> <span class="c1"># Set to None to not log to file. The directory will be created</span>
- <span class="s2">"log_dt"</span> <span class="p">:</span> <span class="mi">5</span><span class="p">,</span> <span class="c1"># time between vb=1 logging outputs</span>
+ <span class="s2">"log_dt"</span><span class="p">:</span> <span class="mi">5</span><span class="p">,</span> <span class="c1"># time between vb=1 logging outputs</span>
+ <span class="s2">"n_logging_stats"</span><span class="p">:</span> <span class="mi">50</span><span class="p">,</span> <span class="c1"># number of logging stats used to calculate time remaining (etc.) default = 50</span>
<span class="c1">##########################</span>
<span class="c1"># binary_c files</span>
<span class="c1">##########################</span>
@@ -225,9 +142,9 @@
<span class="c1">##########################</span>
<span class="c1"># M&S internal settings</span>
<span class="c1">##########################</span>
- <span class="s2">"_loaded_ms_data"</span><span class="p">:</span> <span class="kc">False</span><span class="p">,</span> <span class="c1"># Holds flag whether the M&S data is loaded into memory</span>
- <span class="s2">"_set_ms_grid"</span><span class="p">:</span> <span class="kc">False</span><span class="p">,</span> <span class="c1"># Whether the M&S grid has been loaded</span>
- <span class="s2">"m&s_options"</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span> <span class="c1"># Holds the M&S options.</span>
+ <span class="s2">"_loaded_ms_data"</span><span class="p">:</span> <span class="kc">False</span><span class="p">,</span> <span class="c1"># Holds flag whether the M&S data is loaded into memory</span>
+ <span class="s2">"_set_ms_grid"</span><span class="p">:</span> <span class="kc">False</span><span class="p">,</span> <span class="c1"># Whether the M&S grid has been loaded</span>
+ <span class="s2">"m&s_options"</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span> <span class="c1"># Holds the M&S options.</span>
<span class="c1">##########################</span>
<span class="c1"># Custom logging</span>
<span class="c1">##########################</span>
@@ -316,7 +233,7 @@
<span class="c1"># "slurm_jobid": "", # slurm job id (%A)</span>
<span class="c1"># "slurm_memory": 512, # in MB, the memory use of the job</span>
<span class="c1"># "slurm_warn_max_memory": 1024, # in MB : warn if mem req. > this</span>
- <span class="c1"># "slurm_use_all_node_CPUs": 0, # 1 = use all of a node's CPUs. 0 = use a given amount of CPUs</span>
+ <span class="c1"># "slurm_use_all_node_CPUs": 0, # 1 = use all of a node's CPUs. 0 = use a given number of CPUs</span>
<span class="c1"># "slurm_postpone_join": 0, # if 1 do not join on slurm, join elsewhere. want to do it off the slurm grid (e.g. with more RAM)</span>
<span class="c1"># "slurm_jobarrayindex": "", # slurm job array index (%a)</span>
<span class="c1"># "slurm_jobname": "binary_grid", # default</span>
@@ -606,17 +523,17 @@
<span class="s2">"_binary_c_shared_library"</span><span class="p">:</span> <span class="s2">"Full path to the libbinary_c file. This options is not used in the population object"</span><span class="p">,</span>
<span class="s2">"verbosity"</span><span class="p">:</span> <span class="s2">"Verbosity of the population code. Default is 0, by which only errors will be printed. Higher values will show more output, which is good for debugging."</span><span class="p">,</span>
<span class="s2">"binary"</span><span class="p">:</span> <span class="s2">"Set this to 1 if the population contains binaries. Input: int"</span><span class="p">,</span> <span class="c1"># TODO: write what effect this has.</span>
- <span class="s2">"amt_cores"</span><span class="p">:</span> <span class="s2">"The amount of cores that the population grid will use. The multiprocessing is useful but make sure to figure out how many logical cores the machine has. The core is multi processed, not multi threaded, and will gain no extra speed when amt_cores exceeds the amount of logical cores. Input: int"</span><span class="p">,</span>
+ <span class="s2">"num_cores"</span><span class="p">:</span> <span class="s2">"The number of cores that the population grid will use. The multiprocessing is useful but make sure to figure out how many logical cores the machine has (use e.g. psutil.cpu_count(logical=False) to find the true number of cores, psutil.cpu_count(logical=True) to find the number of logical cores). The core is multi processed, not multi threaded, and will gain no extra speed when num_cores exceeds the number of logical cores. Input: int"</span><span class="p">,</span>
<span class="s2">"_start_time_evolution"</span><span class="p">:</span> <span class="s2">"Variable storing the start timestamp of the population evolution. Set by the object itself."</span><span class="p">,</span> <span class="c1"># TODO: make sure this is logged to a file</span>
<span class="s2">"_end_time_evolution"</span><span class="p">:</span> <span class="s2">"Variable storing the end timestamp of the population evolution. Set by the object itself"</span><span class="p">,</span> <span class="c1"># TODO: make sure this is logged to a file</span>
- <span class="s2">"_total_starcount"</span><span class="p">:</span> <span class="s2">"Variable storing the total amount of systems in the generator. Used and set by the population object."</span><span class="p">,</span>
+ <span class="s2">"_total_starcount"</span><span class="p">:</span> <span class="s2">"Variable storing the total number of systems in the generator. Used and set by the population object."</span><span class="p">,</span>
<span class="s2">"_custom_logging_shared_library_file"</span><span class="p">:</span> <span class="s2">"filename for the custom_logging shared library. Used and set by the population object"</span><span class="p">,</span>
<span class="s2">"_errors_found"</span><span class="p">:</span> <span class="s2">"Variable storing a Boolean flag whether errors by binary_c are encountered."</span><span class="p">,</span>
- <span class="s2">"_errors_exceeded"</span><span class="p">:</span> <span class="s2">"Variable storing a Boolean flag whether the amount of errors was higher than the set threshold (failed_systems_threshold). If True, then the command line arguments of the failing systems will not be stored in the failed_system_log files."</span><span class="p">,</span>
+ <span class="s2">"_errors_exceeded"</span><span class="p">:</span> <span class="s2">"Variable storing a Boolean flag whether the number of errors was higher than the set threshold (failed_systems_threshold). If True, then the command line arguments of the failing systems will not be stored in the failed_system_log files."</span><span class="p">,</span>
<span class="s2">"source_file_filename"</span><span class="p">:</span> <span class="s2">"Variable containing the source file containing lines of binary_c command line calls. These all have to start with binary_c."</span><span class="p">,</span> <span class="c1"># TODO: Expand</span>
<span class="s2">"C_auto_logging"</span><span class="p">:</span> <span class="s2">"Dictionary containing parameters to be logged by binary_c. The structure of this dictionary is as follows: the key is used as the headline which the user can then catch. The value at that key is a list of binary_c system parameters (like star[0].mass)"</span><span class="p">,</span>
<span class="s2">"C_logging_code"</span><span class="p">:</span> <span class="s2">"Variable to store the exact code that is used for the custom_logging. In this way the user can do more complex logging, as well as putting these logging strings in files."</span><span class="p">,</span>
- <span class="s2">"_failed_count"</span><span class="p">:</span> <span class="s2">"Variable storing the amount of failed systems."</span><span class="p">,</span>
+ <span class="s2">"_failed_count"</span><span class="p">:</span> <span class="s2">"Variable storing the number of failed systems."</span><span class="p">,</span>
<span class="s2">"_evolution_type_options"</span><span class="p">:</span> <span class="s2">"List containing the evolution type options."</span><span class="p">,</span>
<span class="s2">"_failed_prob"</span><span class="p">:</span> <span class="s2">"Variable storing the total probability of all the failed systems"</span><span class="p">,</span>
<span class="s2">"_failed_systems_error_codes"</span><span class="p">:</span> <span class="s2">"List storing the unique error codes raised by binary_c of the failed systems"</span><span class="p">,</span>
@@ -633,7 +550,7 @@
<span class="s2">"_probtot"</span><span class="p">:</span> <span class="s2">"Total probability of the population."</span><span class="p">,</span> <span class="c1"># TODO: check whether this is used properly throughout</span>
<span class="s2">"_main_pid"</span><span class="p">:</span> <span class="s2">"Main process ID of the master process. Used and set by the population object."</span><span class="p">,</span>
<span class="s2">"_store_memaddr"</span><span class="p">:</span> <span class="s2">"Memory address of the store object for binary_c."</span><span class="p">,</span>
- <span class="s2">"failed_systems_threshold"</span><span class="p">:</span> <span class="s2">"Variable storing the maximum amount of systems that are allowed to fail before logging their command line arguments to failed_systems log files"</span><span class="p">,</span>
+ <span class="s2">"failed_systems_threshold"</span><span class="p">:</span> <span class="s2">"Variable storing the maximum number of systems that are allowed to fail before logging their command line arguments to failed_systems log files"</span><span class="p">,</span>
<span class="s2">"parse_function"</span><span class="p">:</span> <span class="s2">"Function that the user can provide to handle the output the binary_c. This function has to take the arguments (self, output). Its best not to return anything in this function, and just store stuff in the self.grid_results dictionary, or just output results to a file"</span><span class="p">,</span>
<span class="s2">"condor"</span><span class="p">:</span> <span class="s2">"Int flag whether to use a condor type population evolution. Not implemented yet."</span><span class="p">,</span> <span class="c1"># TODO: describe this in more detail</span>
<span class="s2">"slurm"</span><span class="p">:</span> <span class="s2">"Int flag whether to use a Slurm type population evolution."</span><span class="p">,</span> <span class="c1"># TODO: describe this in more detail</span>
@@ -659,6 +576,11 @@
<span class="c1">###</span>
<span class="c1">#</span>
+<span class="n">MIN_MASS_BINARY_C</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span>
+ <span class="n">return_binary_c_version_info</span><span class="p">(</span><span class="n">parsed</span><span class="o">=</span><span class="kc">True</span><span class="p">)[</span><span class="s2">"macros"</span><span class="p">][</span><span class="s2">"BINARY_C_MINIMUM_STELLAR_MASS"</span><span class="p">]</span>
+<span class="p">)</span>
+
+
<span class="c1"># Default options for the Moe & di Stefano grid</span>
<span class="n">moe_di_stefano_default_options</span> <span class="o">=</span> <span class="p">{</span>
<span class="s2">"resolutions"</span><span class="p">:</span> <span class="p">{</span>
@@ -682,7 +604,8 @@
<span class="s2">"ranges"</span><span class="p">:</span> <span class="p">{</span>
<span class="c1"># stellar masses (Msun)</span>
<span class="s2">"M"</span><span class="p">:</span> <span class="p">[</span>
- <span class="mf">0.08</span><span class="p">,</span> <span class="c1"># 0.08 is a tad bit above the minimum mass. Don't sample at 0.07, otherwise the first row of q values will have a phasevol of 0. Anything higher is fine.</span>
+ <span class="n">MIN_MASS_BINARY_C</span>
+ <span class="o">*</span> <span class="mf">1.05</span><span class="p">,</span> <span class="c1"># 0.08 is a tad bit above the minimum mass. Don't sample at 0.07, otherwise the first row of q values will have a phasevol of 0. Anything higher is fine.</span>
<span class="mf">80.0</span><span class="p">,</span> <span class="c1"># (rather arbitrary) upper mass cutoff</span>
<span class="p">],</span>
<span class="s2">"q"</span><span class="p">:</span> <span class="p">[</span>
@@ -693,8 +616,7 @@
<span class="s2">"ecc"</span><span class="p">:</span> <span class="p">[</span><span class="mf">0.0</span><span class="p">,</span> <span class="mf">0.99</span><span class="p">],</span>
<span class="p">},</span>
<span class="c1"># minimum stellar mass</span>
- <span class="s2">"Mmin"</span><span class="p">:</span> <span class="nb">float</span><span class="p">(</span><span class="n">return_binary_c_version_info</span><span class="p">(</span><span class="n">parsed</span><span class="o">=</span><span class="kc">True</span><span class="p">)[</span><span class="s1">'macros'</span><span class="p">][</span><span class="s1">'BINARY_C_MINIMUM_STELLAR_MASS'</span><span class="p">]),</span> <span class="c1"># We take the value that binary_c has set as the default</span>
-
+ <span class="s2">"Mmin"</span><span class="p">:</span> <span class="n">MIN_MASS_BINARY_C</span><span class="p">,</span> <span class="c1"># We take the value that binary_c has set as the default</span>
<span class="c1"># multiplicity model (as a function of log10M1)</span>
<span class="c1">#</span>
<span class="c1"># You can use 'Poisson' which uses the system multiplicity</span>
@@ -705,7 +627,6 @@
<span class="c1"># from the data, but then triples and quadruples are</span>
<span class="c1"># combined (and there are NO quadruples).</span>
<span class="s2">"multiplicity_model"</span><span class="p">:</span> <span class="s2">"Poisson"</span><span class="p">,</span>
-
<span class="c1"># multiplicity modulator:</span>
<span class="c1"># [single, binary, triple, quadruple]</span>
<span class="c1">#</span>
@@ -868,7 +789,7 @@
<span class="sd"> print_info: whether to print out information about which options contain proper descriptions and which do not</span>
<span class="sd"> Returns:</span>
-<span class="sd"> the amount of undescribed keys</span>
+<span class="sd"> the number of undescribed keys</span>
<span class="sd"> """</span>
<span class="c1"># Get the keys</span>
@@ -973,7 +894,9 @@
<span class="k">for</span> <span class="n">option</span> <span class="ow">in</span> <span class="nb">sorted</span><span class="p">(</span><span class="n">options</span><span class="p">):</span>
<span class="k">if</span> <span class="n">option</span> <span class="ow">in</span> <span class="n">descriptions</span><span class="p">:</span>
<span class="nb">print</span><span class="p">(</span>
- <span class="s2">"| **</span><span class="si">{}</span><span class="s2">**: </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">option</span><span class="p">,</span> <span class="n">descriptions</span><span class="p">[</span><span class="n">option</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">"</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span> <span class="s2">"</span><span class="se">\n\t</span><span class="s2">"</span><span class="p">)),</span>
+ <span class="s2">"| **</span><span class="si">{}</span><span class="s2">**: </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+ <span class="n">option</span><span class="p">,</span> <span class="n">descriptions</span><span class="p">[</span><span class="n">option</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">"</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span> <span class="s2">"</span><span class="se">\n\t</span><span class="s2">"</span><span class="p">)</span>
+ <span class="p">),</span>
<span class="n">file</span><span class="o">=</span><span class="n">filehandle</span><span class="p">,</span>
<span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
@@ -985,55 +908,36 @@
</pre></div>
</div>
-
</div>
<footer>
-
<hr/>
<div role="contentinfo">
- <p>
-
- © Copyright 2021, David Hendriks, Robert Izzard
-
- </p>
+ <p>© Copyright 2021, David Hendriks, Robert Izzard.</p>
</div>
-
-
-
- Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a
-
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-
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+ Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
+ <a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
provided by <a href="https://readthedocs.org">Read the Docs</a>.
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-Generated on binarycpython git branch: master git revision 0886cd4f1d7f43222aac21d6ed91e917b67b20fc url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/tree/master">git url</a>.
+Generated on binarycpython git branch: auto_resolution git revision be7bd630af892a785312affc34d87c57eb337fd3 url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/tree/auto_resolution">git url</a>.
<br><br>
-Using binary_c with bit branch newmaster: git revision: "6185:20210910:1621c23a5" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/newmaster">git url</a>.
+Using binary_c with bit branch master: git revision: "6209:20211006:c4a4c332e" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/master">git url</a>.
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diff --git a/docs/build/html/_modules/binarycpython/utils/plot_functions.html b/docs/build/html/_modules/binarycpython/utils/plot_functions.html
index 75f0703e970a81c2f120fc19c7e3c16acbf4aa6c..b090ada525d7671b1b0ff4201e25599ca5e9ccf6 100644
--- a/docs/build/html/_modules/binarycpython/utils/plot_functions.html
+++ b/docs/build/html/_modules/binarycpython/utils/plot_functions.html
@@ -1,69 +1,32 @@
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+ <a href="../../../index.html" class="icon icon-home"> binary_c-python
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@@ -71,19 +34,8 @@
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<li class="toctree-l1"><a class="reference internal" href="../../../modules.html">Binarycpython code</a></li>
@@ -94,67 +46,30 @@
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<h1>Source code for binarycpython.utils.plot_functions</h1><div class="highlight"><pre>
<span></span><span class="sd">"""</span>
<span class="sd">Module that contains functionality to plot some properties of (binary) systems. </span>
@@ -502,7 +417,7 @@
<span class="p">)</span>
<span class="c1"># Mass 1</span>
- <span class="n">fig</span><span class="o">.</span><span class="n">axes</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="n">df</span><span class="p">[</span><span class="s2">"time"</span><span class="p">],</span> <span class="n">df</span><span class="p">[</span><span class="s2">"mass_1"</span><span class="p">],</span> <span class="n">label</span><span class="o">=</span><span class="s2">"star 1"</span><span class="p">,</span> <span class="n">color</span><span class="o">=</span><span class="s1">'red'</span><span class="p">)</span>
+ <span class="n">fig</span><span class="o">.</span><span class="n">axes</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="n">df</span><span class="p">[</span><span class="s2">"time"</span><span class="p">],</span> <span class="n">df</span><span class="p">[</span><span class="s2">"mass_1"</span><span class="p">],</span> <span class="n">label</span><span class="o">=</span><span class="s2">"star 1"</span><span class="p">,</span> <span class="n">color</span><span class="o">=</span><span class="s2">"red"</span><span class="p">)</span>
<span class="n">fig</span><span class="o">.</span><span class="n">axes</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">axhline</span><span class="p">(</span>
<span class="n">df</span><span class="p">[</span><span class="s2">"pms_mass_1"</span><span class="p">]</span><span class="o">.</span><span class="n">values</span><span class="o">.</span><span class="n">tolist</span><span class="p">()[</span><span class="mi">0</span><span class="p">],</span>
<span class="n">color</span><span class="o">=</span><span class="s2">"red"</span><span class="p">,</span>
@@ -512,7 +427,8 @@
<span class="n">alpha</span><span class="o">=</span><span class="mf">0.5</span><span class="p">,</span>
<span class="p">)</span>
<span class="n">fig</span><span class="o">.</span><span class="n">axes</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span>
- <span class="n">df</span><span class="p">[</span><span class="s2">"time"</span><span class="p">],</span> <span class="n">df</span><span class="p">[</span><span class="s2">"core_mass_1"</span><span class="p">],</span>
+ <span class="n">df</span><span class="p">[</span><span class="s2">"time"</span><span class="p">],</span>
+ <span class="n">df</span><span class="p">[</span><span class="s2">"core_mass_1"</span><span class="p">],</span>
<span class="n">color</span><span class="o">=</span><span class="s2">"red"</span><span class="p">,</span>
<span class="n">linestyle</span><span class="o">=</span><span class="s2">"-."</span><span class="p">,</span>
<span class="n">linewidth</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span>
@@ -531,7 +447,8 @@
<span class="n">alpha</span><span class="o">=</span><span class="mf">0.5</span><span class="p">,</span>
<span class="p">)</span>
<span class="n">fig</span><span class="o">.</span><span class="n">axes</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span>
- <span class="n">df</span><span class="p">[</span><span class="s2">"time"</span><span class="p">],</span> <span class="n">df</span><span class="p">[</span><span class="s2">"core_mass_2"</span><span class="p">],</span>
+ <span class="n">df</span><span class="p">[</span><span class="s2">"time"</span><span class="p">],</span>
+ <span class="n">df</span><span class="p">[</span><span class="s2">"core_mass_2"</span><span class="p">],</span>
<span class="n">color</span><span class="o">=</span><span class="s2">"orange"</span><span class="p">,</span>
<span class="n">linestyle</span><span class="o">=</span><span class="s2">"-."</span><span class="p">,</span>
<span class="n">linewidth</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span>
@@ -806,55 +723,36 @@
</pre></div>
</div>
-
</div>
<footer>
-
<hr/>
<div role="contentinfo">
- <p>
-
- © Copyright 2021, David Hendriks, Robert Izzard
-
- </p>
+ <p>© Copyright 2021, David Hendriks, Robert Izzard.</p>
</div>
-
-
-
- Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a
-
- <a href="https://github.com/rtfd/sphinx_rtd_theme">theme</a>
-
+
+ Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
+ <a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
provided by <a href="https://readthedocs.org">Read the Docs</a>.
+
<br><br>
-Generated on binarycpython git branch: master git revision 0886cd4f1d7f43222aac21d6ed91e917b67b20fc url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/tree/master">git url</a>.
+Generated on binarycpython git branch: auto_resolution git revision be7bd630af892a785312affc34d87c57eb337fd3 url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/tree/auto_resolution">git url</a>.
<br><br>
-Using binary_c with bit branch newmaster: git revision: "6185:20210910:1621c23a5" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/newmaster">git url</a>.
+Using binary_c with bit branch master: git revision: "6209:20211006:c4a4c332e" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/master">git url</a>.
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+ <script>
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diff --git a/docs/build/html/_modules/binarycpython/utils/run_system_wrapper.html b/docs/build/html/_modules/binarycpython/utils/run_system_wrapper.html
index 7b8a8cdb04a54b765a6e5da1aa93e963bf78660f..a5889e61107eccff5e122bd72fddc9c565b5ed31 100644
--- a/docs/build/html/_modules/binarycpython/utils/run_system_wrapper.html
+++ b/docs/build/html/_modules/binarycpython/utils/run_system_wrapper.html
@@ -1,69 +1,32 @@
-
-
<!DOCTYPE html>
<html class="writer-html5" lang="en" >
<head>
- <meta charset="utf-8">
-
- <meta name="viewport" content="width=device-width, initial-scale=1.0">
-
+ <meta charset="utf-8" />
+ <meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>binarycpython.utils.run_system_wrapper — binary_c-python documentation</title>
-
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- <link rel="stylesheet" href="../../../_static/css/theme.css" type="text/css" />
- <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
-
-
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+ <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
+ <link rel="stylesheet" href="../../../_static/css/theme.css" type="text/css" />
<!--[if lt IE 9]>
<script src="../../../_static/js/html5shiv.min.js"></script>
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-
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+ <script data-url_root="../../../" id="documentation_options" src="../../../_static/documentation_options.js"></script>
<script src="../../../_static/jquery.js"></script>
<script src="../../../_static/underscore.js"></script>
<script src="../../../_static/doctools.js"></script>
- <script src="../../../_static/language_data.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
- <script async="async" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.7/latest.js?config=TeX-AMS-MML_HTMLorMML"></script>
- <script type="text/x-mathjax-config">MathJax.Hub.Config({"tex2jax": {"inlineMath": [["$", "$"], ["\\(", "\\)"]], "processEscapes": true, "ignoreClass": "document", "processClass": "math|output_area"}})</script>
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+ <script src="../../../_static/js/theme.js"></script>
<link rel="index" title="Index" href="../../../genindex.html" />
<link rel="search" title="Search" href="../../../search.html" />
</head>
-<body class="wy-body-for-nav">
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+<body class="wy-body-for-nav">
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<nav data-toggle="wy-nav-shift" class="wy-nav-side">
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<div class="wy-side-nav-search" >
-
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- <a href="../../../index.html" class="icon icon-home" alt="Documentation Home"> binary_c-python
-
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+ <a href="../../../index.html" class="icon icon-home"> binary_c-python
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<input type="text" name="q" placeholder="Search docs" />
@@ -71,19 +34,8 @@
<input type="hidden" name="area" value="default" />
</form>
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-
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- <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
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+ </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
+ <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="../../../readme_link.html">Python module for binary_c</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../../modules.html">Binarycpython code</a></li>
@@ -94,67 +46,30 @@
<li class="toctree-l1"><a class="reference external" href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/issues/new">Submit an issue</a></li>
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<li><a href="../../index.html">Module code</a> »</li>
-
<li>binarycpython.utils.run_system_wrapper</li>
-
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<li class="wy-breadcrumbs-aside">
-
</li>
-
</ul>
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<hr/>
</div>
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
-
+
<h1>Source code for binarycpython.utils.run_system_wrapper</h1><div class="highlight"><pre>
<span></span><span class="sd">"""</span>
<span class="sd">Module containing the utility function run_system,</span>
@@ -209,7 +124,9 @@
<span class="c1"># Load available arg keywords</span>
<span class="n">available_binary_c_arg_keywords</span> <span class="o">=</span> <span class="n">get_arg_keys</span><span class="p">()</span>
- <span class="n">special_keywords</span> <span class="o">=</span> <span class="p">[</span><span class="n">el</span> <span class="k">for</span> <span class="n">el</span> <span class="ow">in</span> <span class="nb">list</span><span class="p">(</span><span class="n">available_binary_c_arg_keywords</span><span class="p">)</span> <span class="k">if</span> <span class="n">el</span><span class="o">.</span><span class="n">endswith</span><span class="p">(</span><span class="s2">"</span><span class="si">%d</span><span class="s2">"</span><span class="p">)]</span>
+ <span class="n">special_keywords</span> <span class="o">=</span> <span class="p">[</span>
+ <span class="n">el</span> <span class="k">for</span> <span class="n">el</span> <span class="ow">in</span> <span class="nb">list</span><span class="p">(</span><span class="n">available_binary_c_arg_keywords</span><span class="p">)</span> <span class="k">if</span> <span class="n">el</span><span class="o">.</span><span class="n">endswith</span><span class="p">(</span><span class="s2">"</span><span class="si">%d</span><span class="s2">"</span><span class="p">)</span>
+ <span class="p">]</span>
<span class="n">other_keywords</span> <span class="o">=</span> <span class="p">[</span><span class="s2">"custom_logging_code"</span><span class="p">,</span> <span class="s2">"log_filename"</span><span class="p">,</span> <span class="s2">"parse_function"</span><span class="p">]</span>
@@ -226,13 +143,13 @@
<span class="n">binary_c_args</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">kwargs</span><span class="p">[</span><span class="n">key</span><span class="p">]</span>
<span class="k">elif</span> <span class="nb">any</span><span class="p">(</span>
- <span class="p">[</span>
- <span class="kc">True</span>
- <span class="k">if</span> <span class="p">(</span><span class="n">key</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="n">param</span><span class="p">[:</span><span class="o">-</span><span class="mi">2</span><span class="p">])</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="n">param</span><span class="p">[:</span><span class="o">-</span><span class="mi">2</span><span class="p">])</span> <span class="o"><</span> <span class="nb">len</span><span class="p">(</span><span class="n">key</span><span class="p">))</span>
- <span class="k">else</span> <span class="kc">False</span>
- <span class="k">for</span> <span class="n">param</span> <span class="ow">in</span> <span class="n">special_keywords</span>
- <span class="p">]</span>
- <span class="p">):</span>
+ <span class="p">[</span>
+ <span class="kc">True</span>
+ <span class="k">if</span> <span class="p">(</span><span class="n">key</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="n">param</span><span class="p">[:</span><span class="o">-</span><span class="mi">2</span><span class="p">])</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="n">param</span><span class="p">[:</span><span class="o">-</span><span class="mi">2</span><span class="p">])</span> <span class="o"><</span> <span class="nb">len</span><span class="p">(</span><span class="n">key</span><span class="p">))</span>
+ <span class="k">else</span> <span class="kc">False</span>
+ <span class="k">for</span> <span class="n">param</span> <span class="ow">in</span> <span class="n">special_keywords</span>
+ <span class="p">]</span>
+ <span class="p">):</span>
<span class="n">binary_c_args</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">kwargs</span><span class="p">[</span><span class="n">key</span><span class="p">]</span>
<span class="c1"># Notify user when this key wont be used</span>
@@ -275,55 +192,36 @@
</pre></div>
</div>
-
</div>
<footer>
-
<hr/>
<div role="contentinfo">
- <p>
-
- © Copyright 2021, David Hendriks, Robert Izzard
-
- </p>
+ <p>© Copyright 2021, David Hendriks, Robert Izzard.</p>
</div>
-
-
-
- Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a
-
- <a href="https://github.com/rtfd/sphinx_rtd_theme">theme</a>
-
+
+ Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
+ <a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
provided by <a href="https://readthedocs.org">Read the Docs</a>.
+
<br><br>
-Generated on binarycpython git branch: master git revision 0886cd4f1d7f43222aac21d6ed91e917b67b20fc url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/tree/master">git url</a>.
+Generated on binarycpython git branch: auto_resolution git revision be7bd630af892a785312affc34d87c57eb337fd3 url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/tree/auto_resolution">git url</a>.
<br><br>
-Using binary_c with bit branch newmaster: git revision: "6185:20210910:1621c23a5" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/newmaster">git url</a>.
+Using binary_c with bit branch master: git revision: "6209:20211006:c4a4c332e" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/master">git url</a>.
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+ <script>
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diff --git a/docs/build/html/_modules/binarycpython/utils/spacing_functions.html b/docs/build/html/_modules/binarycpython/utils/spacing_functions.html
index ca3d72a41c8311bece9a90564db7356129545298..dd5fb06f64545c0010b265dc855b7cf820e9f1e3 100644
--- a/docs/build/html/_modules/binarycpython/utils/spacing_functions.html
+++ b/docs/build/html/_modules/binarycpython/utils/spacing_functions.html
@@ -1,69 +1,32 @@
-
-
<!DOCTYPE html>
<html class="writer-html5" lang="en" >
<head>
- <meta charset="utf-8">
-
- <meta name="viewport" content="width=device-width, initial-scale=1.0">
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+ <meta charset="utf-8" />
+ <meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>binarycpython.utils.spacing_functions — binary_c-python documentation</title>
-
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- <link rel="stylesheet" href="../../../_static/css/theme.css" type="text/css" />
- <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
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+ <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
+ <link rel="stylesheet" href="../../../_static/css/theme.css" type="text/css" />
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-
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+ <script data-url_root="../../../" id="documentation_options" src="../../../_static/documentation_options.js"></script>
<script src="../../../_static/jquery.js"></script>
<script src="../../../_static/underscore.js"></script>
<script src="../../../_static/doctools.js"></script>
- <script src="../../../_static/language_data.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
- <script async="async" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.7/latest.js?config=TeX-AMS-MML_HTMLorMML"></script>
- <script type="text/x-mathjax-config">MathJax.Hub.Config({"tex2jax": {"inlineMath": [["$", "$"], ["\\(", "\\)"]], "processEscapes": true, "ignoreClass": "document", "processClass": "math|output_area"}})</script>
-
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-
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+ <script src="../../../_static/js/theme.js"></script>
<link rel="index" title="Index" href="../../../genindex.html" />
<link rel="search" title="Search" href="../../../search.html" />
</head>
-<body class="wy-body-for-nav">
-
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+<body class="wy-body-for-nav">
<div class="wy-grid-for-nav">
-
<nav data-toggle="wy-nav-shift" class="wy-nav-side">
<div class="wy-side-scroll">
<div class="wy-side-nav-search" >
-
-
-
- <a href="../../../index.html" class="icon icon-home" alt="Documentation Home"> binary_c-python
-
-
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+ <a href="../../../index.html" class="icon icon-home"> binary_c-python
</a>
-
-
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-
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<div role="search">
<form id="rtd-search-form" class="wy-form" action="../../../search.html" method="get">
<input type="text" name="q" placeholder="Search docs" />
@@ -71,19 +34,8 @@
<input type="hidden" name="area" value="default" />
</form>
</div>
-
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- </div>
-
-
- <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
-
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-
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- <p class="caption"><span class="caption-text">Contents:</span></p>
+ </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
+ <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="../../../readme_link.html">Python module for binary_c</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../../modules.html">Binarycpython code</a></li>
@@ -94,67 +46,30 @@
<li class="toctree-l1"><a class="reference external" href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/issues/new">Submit an issue</a></li>
</ul>
-
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</nav>
- <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap">
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+ <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
<i data-toggle="wy-nav-top" class="fa fa-bars"></i>
<a href="../../../index.html">binary_c-python</a>
-
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-<div role="navigation" aria-label="breadcrumbs navigation">
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-
<li>binarycpython.utils.spacing_functions</li>
-
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<li class="wy-breadcrumbs-aside">
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<hr/>
</div>
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
-
+
<h1>Source code for binarycpython.utils.spacing_functions</h1><div class="highlight"><pre>
<span></span><span class="sd">"""</span>
<span class="sd">Module containing the spacing functions for the binarycpython package. Very under-populated at the moment, but more are likely to come soon</span>
@@ -164,10 +79,16 @@
<span class="sd">"""</span>
<span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Union</span>
+<span class="kn">import</span> <span class="nn">functools</span>
+<span class="kn">import</span> <span class="nn">math</span>
<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
+<span class="kn">import</span> <span class="nn">py_rinterpolate</span>
+<span class="kn">import</span> <span class="nn">sys</span>
+<span class="kn">from</span> <span class="nn">binarycpython.utils.grid</span> <span class="kn">import</span> <span class="n">Population</span>
-<div class="viewcode-block" id="const"><a class="viewcode-back" href="../../../spacing_functions.html#binarycpython.utils.spacing_functions.const">[docs]</a><span class="k">def</span> <span class="nf">const</span><span class="p">(</span>
+<div class="viewcode-block" id="const"><a class="viewcode-back" href="../../../spacing_functions.html#binarycpython.utils.spacing_functions.const">[docs]</a><span class="nd">@functools</span><span class="o">.</span><span class="n">lru_cache</span><span class="p">(</span><span class="n">maxsize</span><span class="o">=</span><span class="mi">16</span><span class="p">)</span>
+<span class="k">def</span> <span class="nf">const</span><span class="p">(</span>
<span class="n">min_bound</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="nb">int</span><span class="p">,</span> <span class="nb">float</span><span class="p">],</span> <span class="n">max_bound</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="nb">int</span><span class="p">,</span> <span class="nb">float</span><span class="p">],</span> <span class="n">steps</span><span class="p">:</span> <span class="nb">int</span>
<span class="p">)</span> <span class="o">-></span> <span class="nb">list</span><span class="p">:</span>
<span class="sd">"""</span>
@@ -176,65 +97,370 @@
<span class="sd"> Args:</span>
<span class="sd"> min_bound: lower bound of range</span>
<span class="sd"> max_bound: upper bound of range</span>
-<span class="sd"> steps: amount of segments between min_bound and max_bound</span>
+<span class="sd"> steps: number of segments between min_bound and max_bound</span>
<span class="sd"> Returns:</span>
<span class="sd"> np.linspace(min_bound, max_bound, steps+1)</span>
<span class="sd"> """</span>
+ <span class="k">return</span> <span class="n">np</span><span class="o">.</span><span class="n">linspace</span><span class="p">(</span><span class="n">min_bound</span><span class="p">,</span> <span class="n">max_bound</span><span class="p">,</span> <span class="n">steps</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span></div>
+
+<span class="c1">############################################################</span>
+<div class="viewcode-block" id="const_ranges"><a class="viewcode-back" href="../../../spacing_functions.html#binarycpython.utils.spacing_functions.const_ranges">[docs]</a><span class="nd">@functools</span><span class="o">.</span><span class="n">lru_cache</span><span class="p">(</span><span class="n">maxsize</span><span class="o">=</span><span class="mi">16</span><span class="p">)</span>
+<span class="k">def</span> <span class="nf">const_ranges</span><span class="p">(</span><span class="n">ranges</span><span class="p">)</span> <span class="o">-></span> <span class="nb">list</span><span class="p">:</span>
+ <span class="sd">"""</span>
+<span class="sd"> Samples a series of ranges linearly.</span>
+
+<span class="sd"> Args:</span>
+<span class="sd"> ranges: a tuple of tuples passed to the const() spacing function.</span>
- <span class="k">return</span> <span class="n">np</span><span class="o">.</span><span class="n">linspace</span><span class="p">(</span><span class="n">min_bound</span><span class="p">,</span> <span class="n">max_bound</span><span class="p">,</span> <span class="n">steps</span><span class="o">+</span><span class="mi">1</span><span class="p">)</span></div>
+<span class="sd"> Returns:</span>
+<span class="sd"> numpy array of masses</span>
+
+<span class="sd"> Example:</span>
+<span class="sd"> The following allocates 10 stars between 0.1 and 0.65, 20 stars between 0.65</span>
+<span class="sd"> and 0.85, and 10 stars between 0.85 and 10.0 Msun.</span>
+
+<span class="sd"> spacingfunc="const_ranges((({},{},{}),({},{},{}),({},{},{})))".format(</span>
+<span class="sd"> 0.1,0.65,10,</span>
+<span class="sd"> 0.65,0.85,20,</span>
+<span class="sd"> 0.85,10.0,10</span>
+<span class="sd"> ),</span>
+
+<span class="sd"> """</span>
+
+ <span class="n">masses</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">empty</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>
+ <span class="k">for</span> <span class="nb">range</span> <span class="ow">in</span> <span class="n">ranges</span><span class="p">:</span>
+ <span class="n">masses</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">masses</span><span class="p">,</span><span class="n">const</span><span class="p">(</span><span class="o">*</span><span class="nb">range</span><span class="p">))</span>
+ <span class="k">return</span> <span class="n">np</span><span class="o">.</span><span class="n">unique</span><span class="p">(</span><span class="n">masses</span><span class="p">)</span></div>
+
+<span class="c1">############################################################</span>
+<div class="viewcode-block" id="peak_normalized_gaussian_func"><a class="viewcode-back" href="../../../spacing_functions.html#binarycpython.utils.spacing_functions.peak_normalized_gaussian_func">[docs]</a><span class="k">def</span> <span class="nf">peak_normalized_gaussian_func</span><span class="p">(</span>
+ <span class="n">x</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="nb">int</span><span class="p">,</span> <span class="nb">float</span><span class="p">],</span> <span class="n">mean</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="nb">int</span><span class="p">,</span> <span class="nb">float</span><span class="p">],</span> <span class="n">sigma</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="nb">int</span><span class="p">,</span> <span class="nb">float</span><span class="p">]</span>
+<span class="p">)</span> <span class="o">-></span> <span class="n">Union</span><span class="p">[</span><span class="nb">int</span><span class="p">,</span> <span class="nb">float</span><span class="p">]:</span>
+ <span class="sd">"""</span>
+<span class="sd"> Function to evaluate a Gaussian at a given point, note</span>
+<span class="sd"> that the normalization is such that the peak is always 1.0,</span>
+<span class="sd"> not that the integral is 1.0</span>
+
+<span class="sd"> Args:</span>
+<span class="sd"> x: location at which to evaluate the distribution</span>
+<span class="sd"> mean: mean of the Gaussian</span>
+<span class="sd"> sigma: standard deviation of the Gaussian</span>
+
+<span class="sd"> Returns:</span>
+<span class="sd"> value of the Gaussian at x</span>
+<span class="sd"> """</span>
+ <span class="n">gaussian_prefactor</span> <span class="o">=</span> <span class="mf">1.0</span> <span class="c1"># / math.sqrt(2.0 * math.pi)</span>
+
+ <span class="n">r</span> <span class="o">=</span> <span class="mf">1.0</span> <span class="o">/</span> <span class="n">sigma</span>
+ <span class="n">y</span> <span class="o">=</span> <span class="p">(</span><span class="n">x</span> <span class="o">-</span> <span class="n">mean</span><span class="p">)</span> <span class="o">*</span> <span class="n">r</span>
+ <span class="k">return</span> <span class="n">math</span><span class="o">.</span><span class="n">exp</span><span class="p">(</span><span class="o">-</span><span class="mf">0.5</span> <span class="o">*</span> <span class="n">y</span> <span class="o">**</span> <span class="mi">2</span><span class="p">)</span></div>
+
+
+<span class="c1">############################################################</span>
+<div class="viewcode-block" id="gaussian_zoom"><a class="viewcode-back" href="../../../spacing_functions.html#binarycpython.utils.spacing_functions.gaussian_zoom">[docs]</a><span class="nd">@functools</span><span class="o">.</span><span class="n">lru_cache</span><span class="p">(</span><span class="n">maxsize</span><span class="o">=</span><span class="mi">16</span><span class="p">)</span>
+<span class="k">def</span> <span class="nf">gaussian_zoom</span><span class="p">(</span>
+ <span class="n">min_bound</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="nb">int</span><span class="p">,</span> <span class="nb">float</span><span class="p">],</span>
+ <span class="n">max_bound</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="nb">int</span><span class="p">,</span> <span class="nb">float</span><span class="p">],</span>
+ <span class="n">zoom_mean</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="nb">int</span><span class="p">,</span> <span class="nb">float</span><span class="p">],</span>
+ <span class="n">zoom_dispersion</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="nb">int</span><span class="p">,</span> <span class="nb">float</span><span class="p">],</span>
+ <span class="n">zoom_magnitude</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="nb">int</span><span class="p">,</span> <span class="nb">float</span><span class="p">],</span>
+ <span class="n">steps</span><span class="p">:</span> <span class="nb">int</span><span class="p">,</span>
+<span class="p">)</span> <span class="o">-></span> <span class="nb">list</span><span class="p">:</span>
+ <span class="sd">"""</span>
+<span class="sd"> Samples such that a region is zoomed in according to a 1-Gaussian function</span>
+
+<span class="sd"> Args:</span>
+<span class="sd"> min_bound: lower bound of range</span>
+<span class="sd"> max_bound: upper bound of range</span>
+<span class="sd"> zoom_mean: mean of the Gaussian zoom location</span>
+<span class="sd"> zoom_dispersion: dispersion of the Gaussian</span>
+<span class="sd"> zoom_magnitude: depth of the Gaussian (should be 0<= zoom_magntiude <1)</span>
+<span class="sd"> steps: number of segments between min_bound and max_bound assuming a linear step</span>
+<span class="sd"> this is what you'd normally call "resolution"</span>
+
+<span class="sd"> Returns:</span>
+<span class="sd"> Numpy array of sample values</span>
+<span class="sd"> """</span>
+
+ <span class="c1"># linear spacing: this is what we'd have</span>
+ <span class="c1"># in the absence of a Gaussian zoom</span>
+ <span class="n">linear_spacing</span> <span class="o">=</span> <span class="p">(</span><span class="n">max_bound</span> <span class="o">-</span> <span class="n">min_bound</span><span class="p">)</span> <span class="o">/</span> <span class="p">(</span><span class="n">steps</span> <span class="o">-</span> <span class="mi">1</span><span class="p">)</span>
+
+ <span class="c1"># make the list of values</span>
+ <span class="n">x</span> <span class="o">=</span> <span class="n">min_bound</span>
+ <span class="n">array</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([])</span>
+ <span class="k">while</span> <span class="n">x</span> <span class="o"><=</span> <span class="n">max_bound</span><span class="p">:</span>
+ <span class="n">array</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">array</span><span class="p">,</span> <span class="n">x</span><span class="p">)</span>
+ <span class="n">g</span> <span class="o">=</span> <span class="n">peak_normalized_gaussian_func</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">zoom_mean</span><span class="p">,</span> <span class="n">zoom_dispersion</span><span class="p">)</span>
+ <span class="n">f</span> <span class="o">=</span> <span class="mf">1.0</span> <span class="o">-</span> <span class="n">zoom_magnitude</span> <span class="o">*</span> <span class="n">g</span>
+ <span class="n">dx</span> <span class="o">=</span> <span class="n">linear_spacing</span> <span class="o">*</span> <span class="n">f</span>
+ <span class="n">x</span> <span class="o">=</span> <span class="n">x</span> <span class="o">+</span> <span class="n">dx</span>
+
+ <span class="c1"># force the last array member to be max_bound if it's not</span>
+ <span class="k">if</span> <span class="n">array</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span> <span class="o">!=</span> <span class="n">max_bound</span><span class="p">:</span>
+ <span class="n">array</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="n">max_bound</span>
+
+ <span class="k">return</span> <span class="n">np</span><span class="o">.</span><span class="n">unique</span><span class="p">(</span><span class="n">array</span><span class="p">)</span></div>
+
+<div class="viewcode-block" id="const_dt"><a class="viewcode-back" href="../../../spacing_functions.html#binarycpython.utils.spacing_functions.const_dt">[docs]</a><span class="nd">@functools</span><span class="o">.</span><span class="n">lru_cache</span><span class="p">(</span><span class="n">maxsize</span><span class="o">=</span><span class="mi">16</span><span class="p">)</span>
+<span class="k">def</span> <span class="nf">const_dt</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span>
+ <span class="n">dt</span><span class="o">=</span><span class="mf">1000.0</span><span class="p">,</span>
+ <span class="n">dlogt</span><span class="o">=</span><span class="mf">0.1</span><span class="p">,</span>
+ <span class="n">mmin</span><span class="o">=</span><span class="mf">0.07</span><span class="p">,</span>
+ <span class="n">mmax</span><span class="o">=</span><span class="mf">100.0</span><span class="p">,</span>
+ <span class="n">nres</span><span class="o">=</span><span class="mi">1000</span><span class="p">,</span>
+ <span class="n">logspacing</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
+ <span class="n">tmin</span><span class="o">=</span><span class="mf">3.0</span><span class="p">,</span> <span class="c1"># start at 3Myr</span>
+ <span class="n">tmax</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="c1"># use max_evolution_time by default</span>
+ <span class="n">mindm</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="c1"># tuple of tuples</span>
+ <span class="n">maxdm</span><span class="o">=</span><span class="p">((</span><span class="mf">0.07</span><span class="p">,</span><span class="mf">1.0</span><span class="p">,</span><span class="mf">0.1</span><span class="p">),(</span><span class="mf">1.0</span><span class="p">,</span><span class="mf">300.0</span><span class="p">,</span><span class="mf">1.0</span><span class="p">)),</span> <span class="c1"># tuple of tuples</span>
+ <span class="n">fsample</span><span class="o">=</span><span class="mf">1.0</span><span class="p">,</span>
+ <span class="n">factor</span><span class="o">=</span><span class="mf">1.0</span><span class="p">,</span>
+ <span class="n">showtable</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> const_dt returns a list of masses spaced at a constant age difference</span>
+
+<span class="sd"> Args:</span>
+<span class="sd"> dt: the time difference between the masses (1000.0 Myr, used when logspacing==False)</span>
+<span class="sd"> dlogt : the delta log10(time) difference between masses (0.1 dex, used when logspacing==True)</span>
+<span class="sd"> mmin: the minimum mass to be considered in the stellar lifetime interpolation table (0.07 Msun)</span>
+<span class="sd"> mmax: the maximum mass to be considered in the stellar lifetime interpolation table (100.0 Msun)</span>
+<span class="sd"> nres: the resolution of the stellar lifetime interpolation table (100)</span>
+<span class="sd"> logspacing: whether to use log-spaced time, in which case dt is actually d(log10(t))</span>
+<span class="sd"> tmin: the minimum time to consider (Myr, default 3.0 Myr)</span>
+<span class="sd"> tmax: the maximum time to consider (Myr, default None which means we use the grid option 'max_evolution_time')</span>
+<span class="sd"> mindm: a tuple of tuples containing a mass range and minimum mass spacing in that range. The default is ((0.07,1.0,0.1),(1.0,300.0,1.0)) allocated a minimum dm of 0.1Msun in the mass range 0.07 to 1.0 Msun and 1.0Msun in the range 1.0 to 300.0 Msun. Anything you set overrides this.</span>
+<span class="sd"> maxdm: a list of tuples similar to mindm but specifying a maximum mass spacing. (None)</span>
+<span class="sd"> fsample: a global sampling (Shannon-like) factor (<1) to improve resolution (default 1.0, set to smaller to improve resolution)</span>
+<span class="sd"> factor: all masses generated are multiplied by this after generation</span>
+<span class="sd"> showtable: if True, the mass list and times are shown to stdout after generation</span>
+
+<span class="sd"> Returns:</span>
+<span class="sd"> Array of masses.</span>
+
+<span class="sd"> Example:</span>
+<span class="sd"> # these are lines set as options to Population.add_grid_value(...)</span>
+
+<span class="sd"> # linear time bins of 1Gyr</span>
+<span class="sd"> spacingfunc="const_dt(self,dt=1000,nres=100,mmin=0.07,mmax=2.0,showtable=True)"</span>
+
+<span class="sd"> # logarithmic spacing in time, generally suitable for Galactic</span>
+<span class="sd"> # chemical evolution yield grids.</span>
+<span class="sd"> spacingfunc="const_dt(self,dlogt=0.1,nres=100,mmin=0.07,mmax=80.0,maxdm=((0.07,1.0,0.1),(1.0,10.0,1.0),(10.0,80.0,2.0)),showtable=True,logspacing=True,fsample=1.0/4.0)"</span>
+
+<span class="sd"> """</span>
+
+ <span class="c1"># first, make a stellar lifetime table</span>
+ <span class="c1">#</span>
+ <span class="c1"># we should use the bse_options from self</span>
+ <span class="c1"># so our lifetime_population uses the same physics</span>
+ <span class="n">lifetime_population</span> <span class="o">=</span> <span class="n">Population</span><span class="p">()</span>
+ <span class="n">lifetime_population</span><span class="o">.</span><span class="n">bse_options</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bse_options</span><span class="p">)</span>
+
+ <span class="c1"># we only want to evolve the star during nuclear burning,</span>
+ <span class="c1"># we don't want a dry run of the grid</span>
+ <span class="c1"># we want to use the right number of CPU cores</span>
+ <span class="n">lifetime_population</span><span class="o">.</span><span class="n">set</span><span class="p">(</span>
+ <span class="n">do_dry_run</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+ <span class="n">num_cores</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'num_cores'</span><span class="p">],</span>
+ <span class="n">max_stellar_type_1</span><span class="o">=</span><span class="mi">10</span>
+ <span class="p">)</span>
+
+ <span class="c1"># make a grid in M1</span>
+ <span class="n">lifetime_population</span><span class="o">.</span><span class="n">add_grid_variable</span><span class="p">(</span>
+ <span class="n">name</span><span class="o">=</span><span class="s2">"lnM_1"</span><span class="p">,</span>
+ <span class="n">longname</span><span class="o">=</span><span class="s2">"log Primary mass"</span><span class="p">,</span> <span class="c1"># == single-star mass</span>
+ <span class="n">valuerange</span><span class="o">=</span><span class="p">[</span><span class="n">math</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="n">mmin</span><span class="p">),</span><span class="n">math</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="n">mmax</span><span class="p">)],</span>
+ <span class="n">resolution</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span>
+ <span class="n">spacingfunc</span><span class="o">=</span><span class="s2">"const(math.log(</span><span class="si">{mmin}</span><span class="s2">),math.log(</span><span class="si">{mmax}</span><span class="s2">),</span><span class="si">{nres}</span><span class="s2">)"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">mmin</span><span class="o">=</span><span class="n">mmin</span><span class="p">,</span><span class="n">mmax</span><span class="o">=</span><span class="n">mmax</span><span class="p">,</span><span class="n">nres</span><span class="o">=</span><span class="n">nres</span><span class="p">),</span>
+ <span class="n">probdist</span><span class="o">=</span><span class="s2">"1"</span><span class="p">,</span> <span class="c1"># dprob/dm1 : we don't care, so just set it to 1</span>
+ <span class="n">dphasevol</span><span class="o">=</span><span class="s2">"dlnM_1"</span><span class="p">,</span>
+ <span class="n">parameter_name</span><span class="o">=</span><span class="s2">"M_1"</span><span class="p">,</span>
+ <span class="n">precode</span><span class="o">=</span><span class="s2">"M_1=math.exp(lnM_1)"</span><span class="p">,</span>
+ <span class="n">condition</span><span class="o">=</span><span class="s2">""</span><span class="p">,</span> <span class="c1"># Impose a condition on this grid variable. Mostly for a check for yourself</span>
+ <span class="n">gridtype</span><span class="o">=</span><span class="s2">"edge"</span>
+ <span class="p">)</span>
+
+ <span class="c1"># set up the parse function</span>
+ <span class="k">def</span> <span class="nf">_parse_function</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span><span class="n">output</span><span class="p">):</span>
+ <span class="k">if</span> <span class="n">output</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">output</span><span class="o">.</span><span class="n">splitlines</span><span class="p">():</span>
+ <span class="n">data</span> <span class="o">=</span> <span class="n">line</span><span class="o">.</span><span class="n">split</span><span class="p">()</span>
+ <span class="k">if</span> <span class="n">data</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="s1">'SINGLE_STAR_LIFETIME'</span><span class="p">:</span>
+ <span class="c1"># append (log10(mass), log10(lifetime)) tuples</span>
+ <span class="n">logm</span> <span class="o">=</span> <span class="n">math</span><span class="o">.</span><span class="n">log10</span><span class="p">(</span><span class="nb">float</span><span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="mi">1</span><span class="p">]))</span>
+ <span class="n">logt</span> <span class="o">=</span> <span class="n">math</span><span class="o">.</span><span class="n">log10</span><span class="p">(</span><span class="nb">float</span><span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="mi">2</span><span class="p">]))</span>
+ <span class="c1">#print(line)</span>
+ <span class="c1">#print("logM=",logm,"M=",10.0**logm," -> logt=",logt)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_results</span><span class="p">[</span><span class="s1">'interpolation table m->t'</span><span class="p">][</span><span class="n">logm</span><span class="p">]</span> <span class="o">=</span> <span class="n">logt</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_results</span><span class="p">[</span><span class="s1">'interpolation table t->m'</span><span class="p">][</span><span class="n">logt</span><span class="p">]</span> <span class="o">=</span> <span class="n">logm</span>
+
+ <span class="n">lifetime_population</span><span class="o">.</span><span class="n">set</span><span class="p">(</span>
+ <span class="n">parse_function</span><span class="o">=</span><span class="n">_parse_function</span><span class="p">,</span>
+ <span class="p">)</span>
+
+ <span class="c1"># run to build the interpolation table</span>
+ <span class="nb">print</span><span class="p">(</span><span class="s2">"Running population to make lifetime interpolation table, please wait"</span><span class="p">)</span>
+ <span class="n">lifetime_population</span><span class="o">.</span><span class="n">evolve</span><span class="p">()</span>
+ <span class="c1">#print("Data table",lifetime_population.grid_results['interpolation table t->m'])</span>
+
+ <span class="c1"># convert to nested lists for the interpolator</span>
+ <span class="c1">#</span>
+ <span class="c1"># make time -> mass table</span>
+ <span class="n">data_table_time_mass</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="n">times</span> <span class="o">=</span> <span class="nb">sorted</span><span class="p">(</span><span class="n">lifetime_population</span><span class="o">.</span><span class="n">grid_results</span><span class="p">[</span><span class="s1">'interpolation table t->m'</span><span class="p">]</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span>
+ <span class="k">for</span> <span class="n">time</span> <span class="ow">in</span> <span class="n">times</span><span class="p">:</span>
+ <span class="n">mass</span> <span class="o">=</span> <span class="n">lifetime_population</span><span class="o">.</span><span class="n">grid_results</span><span class="p">[</span><span class="s1">'interpolation table t->m'</span><span class="p">][</span><span class="n">time</span><span class="p">]</span>
+ <span class="c1"># we have to make sure the time is monotonic (not guaranteed at high mass)</span>
+ <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">data_table_time_mass</span><span class="p">)</span><span class="o">==</span><span class="mi">0</span><span class="p">:</span>
+ <span class="n">data_table_time_mass</span><span class="o">.</span><span class="n">append</span><span class="p">(</span> <span class="p">[</span> <span class="n">time</span><span class="p">,</span> <span class="n">mass</span> <span class="p">]</span> <span class="p">)</span>
+ <span class="k">elif</span> <span class="n">mass</span> <span class="o"><</span> <span class="n">data_table_time_mass</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">][</span><span class="mi">1</span><span class="p">]:</span>
+ <span class="n">data_table_time_mass</span><span class="o">.</span><span class="n">append</span><span class="p">(</span> <span class="p">[</span> <span class="n">time</span><span class="p">,</span> <span class="n">mass</span> <span class="p">]</span> <span class="p">)</span>
+
+ <span class="c1"># make mass -> time table</span>
+ <span class="n">data_table_mass_time</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="n">masses</span> <span class="o">=</span> <span class="nb">sorted</span><span class="p">(</span><span class="n">lifetime_population</span><span class="o">.</span><span class="n">grid_results</span><span class="p">[</span><span class="s1">'interpolation table m->t'</span><span class="p">]</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span>
+ <span class="k">for</span> <span class="n">mass</span> <span class="ow">in</span> <span class="n">masses</span><span class="p">:</span>
+ <span class="n">time</span> <span class="o">=</span> <span class="n">lifetime_population</span><span class="o">.</span><span class="n">grid_results</span><span class="p">[</span><span class="s1">'interpolation table m->t'</span><span class="p">][</span><span class="n">mass</span><span class="p">]</span>
+ <span class="n">data_table_mass_time</span><span class="o">.</span><span class="n">append</span><span class="p">(</span> <span class="p">[</span> <span class="n">mass</span><span class="p">,</span> <span class="n">time</span> <span class="p">]</span> <span class="p">)</span>
+
+ <span class="c1"># set up interpolators</span>
+ <span class="n">interpolator_time_mass</span> <span class="o">=</span> <span class="n">py_rinterpolate</span><span class="o">.</span><span class="n">Rinterpolate</span><span class="p">(</span>
+ <span class="n">table</span> <span class="o">=</span> <span class="n">data_table_time_mass</span><span class="p">,</span>
+ <span class="n">nparams</span> <span class="o">=</span> <span class="mi">1</span><span class="p">,</span> <span class="c1"># mass</span>
+ <span class="n">ndata</span> <span class="o">=</span> <span class="mi">1</span><span class="p">,</span> <span class="c1"># lifetime</span>
+ <span class="n">verbosity</span> <span class="o">=</span> <span class="mi">0</span><span class="p">)</span>
+ <span class="n">interpolator_mass_time</span> <span class="o">=</span> <span class="n">py_rinterpolate</span><span class="o">.</span><span class="n">Rinterpolate</span><span class="p">(</span>
+ <span class="n">table</span> <span class="o">=</span> <span class="n">data_table_mass_time</span><span class="p">,</span>
+ <span class="n">nparams</span> <span class="o">=</span> <span class="mi">1</span><span class="p">,</span> <span class="c1"># lifetime</span>
+ <span class="n">ndata</span> <span class="o">=</span> <span class="mi">1</span><span class="p">,</span> <span class="c1"># mass</span>
+ <span class="n">verbosity</span> <span class="o">=</span> <span class="mi">0</span><span class="p">)</span>
+
+ <span class="c1"># function to get a mass given a time (Myr)</span>
+ <span class="k">def</span> <span class="nf">_mass_from_time</span><span class="p">(</span><span class="n">linear_time</span><span class="p">):</span>
+ <span class="k">return</span> <span class="mf">10.0</span><span class="o">**</span><span class="n">interpolator_time_mass</span><span class="o">.</span><span class="n">interpolate</span><span class="p">([</span><span class="n">math</span><span class="o">.</span><span class="n">log10</span><span class="p">(</span><span class="n">linear_time</span><span class="p">)])[</span><span class="mi">0</span><span class="p">]</span>
+
+ <span class="c1"># function to get a time given a mass (Msun)</span>
+ <span class="k">def</span> <span class="nf">_time_from_mass</span><span class="p">(</span><span class="n">mass</span><span class="p">):</span>
+ <span class="k">return</span> <span class="mf">10.0</span><span class="o">**</span><span class="n">interpolator_mass_time</span><span class="o">.</span><span class="n">interpolate</span><span class="p">([</span><span class="n">math</span><span class="o">.</span><span class="n">log10</span><span class="p">(</span><span class="n">mass</span><span class="p">)])[</span><span class="mi">0</span><span class="p">]</span>
+
+ <span class="c1"># return a unique list</span>
+ <span class="k">def</span> <span class="nf">_uniq</span><span class="p">(</span><span class="n">_list</span><span class="p">):</span>
+ <span class="k">return</span> <span class="nb">sorted</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">_list</span><span class="p">)))</span>
+
+ <span class="c1"># format a whole list like %g</span>
+ <span class="k">def</span> <span class="nf">_format</span><span class="p">(</span><span class="n">_list</span><span class="p">):</span>
+ <span class="k">return</span> <span class="p">[</span> <span class="nb">float</span><span class="p">(</span><span class="s2">"</span><span class="si">{x:g}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">x</span><span class="o">=</span><span class="n">x</span><span class="p">))</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">_list</span><span class="p">]</span>
+
+ <span class="c1"># construct mass list, always include the min and max</span>
+ <span class="n">mass_list</span> <span class="o">=</span> <span class="p">[</span><span class="n">mmin</span><span class="p">,</span><span class="n">mmax</span><span class="p">]</span>
+
+ <span class="c1"># first, make sure the stars are separated by only</span>
+ <span class="c1"># maxdm</span>
+ <span class="k">if</span> <span class="n">maxdm</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">maxdm</span><span class="p">:</span>
+ <span class="n">range_min</span> <span class="o">=</span> <span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+ <span class="n">range_max</span> <span class="o">=</span> <span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+ <span class="n">dm</span> <span class="o">=</span> <span class="n">x</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
+ <span class="n">m</span> <span class="o">=</span> <span class="n">mmin</span>
+ <span class="k">while</span> <span class="n">m</span> <span class="o"><=</span> <span class="n">mmax</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">m</span><span class="o">>=</span><span class="n">range_min</span> <span class="ow">and</span> <span class="n">m</span><span class="o"><=</span><span class="n">range_max</span><span class="p">:</span>
+ <span class="n">mass_list</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">m</span><span class="p">)</span>
+ <span class="n">m</span> <span class="o">+=</span> <span class="n">dm</span>
+
+ <span class="c1"># start time loop at tmax or max_evolution_time</span>
+ <span class="n">t</span> <span class="o">=</span> <span class="n">tmax</span> <span class="k">if</span> <span class="n">tmax</span> <span class="k">else</span> <span class="bp">self</span><span class="o">.</span><span class="n">bse_options</span><span class="p">[</span><span class="s1">'max_evolution_time'</span><span class="p">]</span>
+
+ <span class="c1"># set default mass list</span>
+ <span class="k">if</span> <span class="n">logspacing</span><span class="p">:</span>
+ <span class="n">logt</span> <span class="o">=</span> <span class="n">math</span><span class="o">.</span><span class="n">log10</span><span class="p">(</span><span class="n">t</span><span class="p">)</span>
+ <span class="n">logtmin</span> <span class="o">=</span> <span class="n">math</span><span class="o">.</span><span class="n">log10</span><span class="p">(</span><span class="n">tmin</span><span class="p">)</span>
+ <span class="k">while</span> <span class="n">logt</span> <span class="o">></span> <span class="n">logtmin</span><span class="p">:</span>
+ <span class="n">m</span> <span class="o">=</span> <span class="n">_mass_from_time</span><span class="p">(</span><span class="mf">10.0</span><span class="o">**</span><span class="n">logt</span><span class="p">)</span>
+ <span class="n">mass_list</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">m</span><span class="p">)</span>
+ <span class="n">logt</span> <span class="o">=</span> <span class="nb">max</span><span class="p">(</span><span class="n">logtmin</span><span class="p">,</span> <span class="n">logt</span> <span class="o">-</span> <span class="n">dlogt</span> <span class="o">*</span> <span class="n">fsample</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">while</span> <span class="n">t</span> <span class="o">></span> <span class="n">tmin</span><span class="p">:</span>
+ <span class="n">m</span> <span class="o">=</span> <span class="n">_mass_from_time</span><span class="p">(</span><span class="n">t</span><span class="p">)</span>
+ <span class="n">mass_list</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">m</span><span class="p">)</span>
+ <span class="n">t</span> <span class="o">=</span> <span class="nb">max</span><span class="p">(</span><span class="n">tmin</span><span class="p">,</span><span class="n">t</span> <span class="o">-</span> <span class="n">dt</span> <span class="o">*</span> <span class="n">fsample</span><span class="p">)</span>
+
+ <span class="c1"># make mass list unique</span>
+ <span class="n">mass_list</span> <span class="o">=</span> <span class="n">_uniq</span><span class="p">(</span><span class="n">mass_list</span><span class="p">)</span>
+
+ <span class="k">if</span> <span class="n">mindm</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">mindm</span><span class="p">:</span>
+ <span class="n">range_min</span> <span class="o">=</span> <span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+ <span class="n">range_max</span> <span class="o">=</span> <span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+ <span class="n">mindm</span> <span class="o">=</span> <span class="n">x</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
+ <span class="c1"># impose a minimum dm: if two masses in the list</span>
+ <span class="c1"># are separated by < this, remove the second</span>
+ <span class="k">for</span> <span class="n">index</span><span class="p">,</span><span class="n">mass</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">mass_list</span><span class="p">):</span>
+ <span class="k">if</span> <span class="n">index</span> <span class="o">></span> <span class="mi">0</span> <span class="ow">and</span> <span class="n">mass</span><span class="o">>=</span><span class="n">range_min</span> <span class="ow">and</span> <span class="n">mass</span><span class="o"><=</span><span class="n">range_max</span><span class="p">:</span>
+ <span class="n">dm</span> <span class="o">=</span> <span class="n">mass_list</span><span class="p">[</span><span class="n">index</span><span class="p">]</span> <span class="o">-</span> <span class="n">mass_list</span><span class="p">[</span><span class="n">index</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
+ <span class="k">if</span> <span class="n">dm</span> <span class="o"><</span> <span class="n">mindm</span><span class="p">:</span>
+ <span class="n">mass_list</span><span class="p">[</span><span class="n">index</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="mf">0.0</span>
+ <span class="n">mass_list</span> <span class="o">=</span> <span class="n">_uniq</span><span class="p">(</span><span class="n">mass_list</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">mass_list</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="mf">0.0</span><span class="p">:</span>
+ <span class="n">mass_list</span><span class="o">.</span><span class="n">remove</span><span class="p">(</span><span class="mf">0.0</span><span class="p">)</span>
+
+ <span class="c1"># apply multiplication factor if given</span>
+ <span class="k">if</span> <span class="n">factor</span><span class="p">:</span>
+ <span class="n">mass_list</span> <span class="o">=</span> <span class="p">[</span><span class="n">m</span> <span class="o">*</span> <span class="n">factor</span> <span class="k">for</span> <span class="n">m</span> <span class="ow">in</span> <span class="n">mass_list</span><span class="p">]</span>
+
+ <span class="c1"># reformat numbers</span>
+ <span class="n">mass_list</span> <span class="o">=</span> <span class="n">_format</span><span class="p">(</span><span class="n">mass_list</span><span class="p">)</span>
+
+ <span class="c1"># show the mass<>time table?</span>
+ <span class="k">if</span> <span class="n">showtable</span><span class="p">:</span>
+ <span class="n">twas</span> <span class="o">=</span> <span class="mf">0.0</span>
+ <span class="n">logtwas</span> <span class="o">=</span> <span class="mf">0.0</span>
+ <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">m</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">mass_list</span><span class="p">):</span>
+ <span class="n">t</span> <span class="o">=</span> <span class="n">_time_from_mass</span><span class="p">(</span><span class="n">m</span><span class="p">)</span>
+ <span class="n">logt</span> <span class="o">=</span> <span class="n">math</span><span class="o">.</span><span class="n">log10</span><span class="p">(</span><span class="n">t</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">twas</span> <span class="o">></span> <span class="mf">0.0</span><span class="p">:</span>
+ <span class="nb">print</span><span class="p">(</span><span class="s2">"</span><span class="si">{i:4d}</span><span class="s2"> m=</span><span class="si">{m:13g}</span><span class="s2"> t=</span><span class="si">{t:13g}</span><span class="s2"> log10(t)=</span><span class="si">{logt:13g}</span><span class="s2"> dt=</span><span class="si">{dt:13g}</span><span class="s2"> dlog10(t)=</span><span class="si">{dlogt:13g}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">i</span><span class="o">=</span><span class="n">i</span><span class="p">,</span><span class="n">m</span><span class="o">=</span><span class="n">m</span><span class="p">,</span><span class="n">t</span><span class="o">=</span><span class="n">t</span><span class="p">,</span><span class="n">logt</span><span class="o">=</span><span class="n">logt</span><span class="p">,</span><span class="n">dt</span><span class="o">=</span><span class="n">twas</span><span class="o">-</span><span class="n">t</span><span class="p">,</span><span class="n">dlogt</span><span class="o">=</span><span class="n">logtwas</span><span class="o">-</span><span class="n">logt</span><span class="p">))</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="nb">print</span><span class="p">(</span><span class="s2">"</span><span class="si">{i:4d}</span><span class="s2"> m=</span><span class="si">{m:13g}</span><span class="s2"> t=</span><span class="si">{t:13g}</span><span class="s2"> log10(t)=</span><span class="si">{logt:13g}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">i</span><span class="o">=</span><span class="n">i</span><span class="p">,</span><span class="n">m</span><span class="o">=</span><span class="n">m</span><span class="p">,</span><span class="n">t</span><span class="o">=</span><span class="n">t</span><span class="p">,</span><span class="n">logt</span><span class="o">=</span><span class="n">logt</span><span class="p">))</span>
+ <span class="n">twas</span> <span class="o">=</span> <span class="n">t</span>
+ <span class="n">logtwas</span> <span class="o">=</span> <span class="n">logt</span>
+
+ <span class="c1"># return the mass list as a numpy array</span>
+ <span class="k">return</span> <span class="n">np</span><span class="o">.</span><span class="n">unique</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">mass_list</span><span class="p">))</span></div>
</pre></div>
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+ <p>© Copyright 2021, David Hendriks, Robert Izzard.</p>
</div>
-
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- Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a
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+ <a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
provided by <a href="https://readthedocs.org">Read the Docs</a>.
+
<br><br>
-Generated on binarycpython git branch: master git revision 0886cd4f1d7f43222aac21d6ed91e917b67b20fc url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/tree/master">git url</a>.
+Generated on binarycpython git branch: auto_resolution git revision be7bd630af892a785312affc34d87c57eb337fd3 url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/tree/auto_resolution">git url</a>.
<br><br>
-Using binary_c with bit branch newmaster: git revision: "6185:20210910:1621c23a5" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/newmaster">git url</a>.
+Using binary_c with bit branch master: git revision: "6209:20211006:c4a4c332e" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/master">git url</a>.
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diff --git a/docs/build/html/_modules/binarycpython/utils/useful_funcs.html b/docs/build/html/_modules/binarycpython/utils/useful_funcs.html
index 975a7c7001f642d9246248da3f2496562ab6f78f..adbf92ee66366e7cc1d93571152095a4afe44723 100644
--- a/docs/build/html/_modules/binarycpython/utils/useful_funcs.html
+++ b/docs/build/html/_modules/binarycpython/utils/useful_funcs.html
@@ -1,69 +1,32 @@
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- <script async="async" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.7/latest.js?config=TeX-AMS-MML_HTMLorMML"></script>
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@@ -71,19 +34,8 @@
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+ </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
+ <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
<ul>
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<li class="toctree-l1"><a class="reference internal" href="../../../modules.html">Binarycpython code</a></li>
@@ -94,67 +46,30 @@
<li class="toctree-l1"><a class="reference external" href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/issues/new">Submit an issue</a></li>
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<div itemprop="articleBody">
-
+
<h1>Source code for binarycpython.utils.useful_funcs</h1><div class="highlight"><pre>
<span></span><span class="sd">"""</span>
<span class="sd">Collection of useful functions.</span>
@@ -543,55 +458,36 @@
</pre></div>
</div>
-
</div>
<footer>
-
<hr/>
<div role="contentinfo">
- <p>
-
- © Copyright 2021, David Hendriks, Robert Izzard
-
- </p>
+ <p>© Copyright 2021, David Hendriks, Robert Izzard.</p>
</div>
-
-
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- Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a
-
- <a href="https://github.com/rtfd/sphinx_rtd_theme">theme</a>
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+ Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
+ <a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
provided by <a href="https://readthedocs.org">Read the Docs</a>.
+
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-Generated on binarycpython git branch: master git revision 0886cd4f1d7f43222aac21d6ed91e917b67b20fc url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/tree/master">git url</a>.
+Generated on binarycpython git branch: auto_resolution git revision be7bd630af892a785312affc34d87c57eb337fd3 url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/tree/auto_resolution">git url</a>.
<br><br>
-Using binary_c with bit branch newmaster: git revision: "6185:20210910:1621c23a5" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/newmaster">git url</a>.
+Using binary_c with bit branch master: git revision: "6209:20211006:c4a4c332e" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/master">git url</a>.
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index b050c7170f1c8ef67d525360ffd21071db5e3d5c..f6dbcf7476da90e43de6a9c5d7296430fe6df1cc 100644
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+++ b/docs/build/html/_modules/index.html
@@ -1,69 +1,32 @@
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+ <a href="../index.html" class="icon icon-home"> binary_c-python
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@@ -71,19 +34,8 @@
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+ </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
+ <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="../readme_link.html">Python module for binary_c</a></li>
<li class="toctree-l1"><a class="reference internal" href="../modules.html">Binarycpython code</a></li>
@@ -94,65 +46,29 @@
<li class="toctree-l1"><a class="reference external" href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/issues/new">Submit an issue</a></li>
</ul>
-
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-
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-
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<hr/>
</div>
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
-
+
<h1>All modules for which code is available</h1>
<ul><li><a href="binarycpython/utils/custom_logging_functions.html">binarycpython.utils.custom_logging_functions</a></li>
<li><a href="binarycpython/utils/distribution_functions.html">binarycpython.utils.distribution_functions</a></li>
@@ -166,55 +82,36 @@
</ul>
</div>
-
</div>
<footer>
-
<hr/>
<div role="contentinfo">
- <p>
-
- © Copyright 2021, David Hendriks, Robert Izzard
-
- </p>
+ <p>© Copyright 2021, David Hendriks, Robert Izzard.</p>
</div>
-
-
-
- Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a
-
- <a href="https://github.com/rtfd/sphinx_rtd_theme">theme</a>
-
+
+ Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
+ <a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
provided by <a href="https://readthedocs.org">Read the Docs</a>.
+
<br><br>
-Generated on binarycpython git branch: master git revision 0886cd4f1d7f43222aac21d6ed91e917b67b20fc url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/tree/master">git url</a>.
+Generated on binarycpython git branch: auto_resolution git revision be7bd630af892a785312affc34d87c57eb337fd3 url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/tree/auto_resolution">git url</a>.
<br><br>
-Using binary_c with bit branch newmaster: git revision: "6185:20210910:1621c23a5" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/newmaster">git url</a>.
+Using binary_c with bit branch master: git revision: "6209:20211006:c4a4c332e" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/master">git url</a>.
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diff --git a/docs/build/html/_sources/binary_c_parameters.rst.txt b/docs/build/html/_sources/binary_c_parameters.rst.txt
index cdce51580c9e3478b29c356fadc3e11bb84ac62b..a47b428512a8495e31b1c6224fec98e3c4ffd247 100644
--- a/docs/build/html/_sources/binary_c_parameters.rst.txt
+++ b/docs/build/html/_sources/binary_c_parameters.rst.txt
@@ -4,7 +4,7 @@ The following chapter contains all the parameters that the current version of bi
This information was obtained by the following binary_c build:
- **binary_c git branch**: newmaster **binary_c git revision**: 6185:20210910:1621c23a5 **Built on**: Sep 10 2021 15:05:46
+ **binary_c git branch**: master **binary_c git revision**: 6209:20211006:c4a4c332e **Built on**: Oct 6 2021 08:31:27
Section: stars
@@ -2537,6 +2537,12 @@ Section: output
| **Default value**: NULL
| **Extra**: Ignore
+| **Parameter**: tides_diagnosis_log
+| **Description**: Enable logging to test MINT tides. Requires MINT. Choices are: 0 disabled, 1 enable lambda test.
+| **Parameter input type**: Integer
+| **Default value**: 0
+| **Extra**: Ignore
+
Section: input
--------------
diff --git a/docs/build/html/_sources/grid_options_descriptions.rst.txt b/docs/build/html/_sources/grid_options_descriptions.rst.txt
index 84538e2c4a51e19e6c1e6299dcea91c1c5e2d5f2..21095484f9b57a46dc4b825c59c2ac450bacb08f 100644
--- a/docs/build/html/_sources/grid_options_descriptions.rst.txt
+++ b/docs/build/html/_sources/grid_options_descriptions.rst.txt
@@ -1,7 +1,7 @@
Population grid code options
============================
The following chapter contains all grid code options, along with their descriptions
-There are 2 options that are not described yet.
+There are 4 options that are not described yet.
Public options
@@ -13,8 +13,6 @@ The following options are meant to be changed by the user.
| **C_logging_code**: Variable to store the exact code that is used for the custom_logging. In this way the user can do more complex logging, as well as putting these logging strings in files.
-| **amt_cores**: The amount of cores that the population grid will use. The multiprocessing is useful but make sure to figure out how many logical cores the machine has. The core is multi processed, not multi threaded, and will gain no extra speed when amt_cores exceeds the amount of logical cores. Input: int
-
| **combine_ensemble_with_thread_joining**: Boolean flag on whether to combine everything and return it to the user or if false: write it to data_dir/ensemble_output_{population_id}_{thread_id}.json
| **condor**: Int flag whether to use a condor type population evolution. Not implemented yet.
@@ -27,7 +25,9 @@ The following options are meant to be changed by the user.
| **evolution_type**: Variable containing the type of evolution used of the grid. Multiprocessing or linear processing
-| **failed_systems_threshold**: Variable storing the maximum amount of systems that are allowed to fail before logging their command line arguments to failed_systems log files
+| **exit_after_dry_run**: No description available yet
+
+| **failed_systems_threshold**: Variable storing the maximum number of systems that are allowed to fail before logging their command line arguments to failed_systems log files
| **gridcode_filename**: Filename for the grid code. Set and used by the population object. TODO: allow the user to provide their own function, rather than only a generated function.
@@ -49,6 +49,10 @@ The following options are meant to be changed by the user.
| **multiplicity_fraction_function**: Which multiplicity fraction function to use. 0: None, 1: Arenou 2010, 2: Rhagavan 2010, 3: M&S 2017
+| **n_logging_stats**: No description available yet
+
+| **num_cores**: The number of cores that the population grid will use. The multiprocessing is useful but make sure to figure out how many logical cores the machine has (use e.g. psutil.cpu_count(logical=False) to find the true number of cores, psutil.cpu_count(logical=True) to find the number of logical cores). The core is multi processed, not multi threaded, and will gain no extra speed when num_cores exceeds the number of logical cores. Input: int
+
| **parse_function**: Function that the user can provide to handle the output the binary_c. This function has to take the arguments (self, output). Its best not to return anything in this function, and just store stuff in the self.grid_results dictionary, or just output results to a file
| **repeat**: Factor of how many times a system should be repeated. Consider the evolution splitting binary_c argument for supernovae kick repeating.
@@ -164,13 +168,13 @@ The following options are not meant to be changed by the user, as these options
| **_end_time_evolution**: Variable storing the end timestamp of the population evolution. Set by the object itself
-| **_errors_exceeded**: Variable storing a Boolean flag whether the amount of errors was higher than the set threshold (failed_systems_threshold). If True, then the command line arguments of the failing systems will not be stored in the failed_system_log files.
+| **_errors_exceeded**: Variable storing a Boolean flag whether the number of errors was higher than the set threshold (failed_systems_threshold). If True, then the command line arguments of the failing systems will not be stored in the failed_system_log files.
| **_errors_found**: Variable storing a Boolean flag whether errors by binary_c are encountered.
| **_evolution_type_options**: List containing the evolution type options.
-| **_failed_count**: Variable storing the amount of failed systems.
+| **_failed_count**: Variable storing the number of failed systems.
| **_failed_prob**: Variable storing the total probability of all the failed systems
@@ -198,7 +202,7 @@ The following options are not meant to be changed by the user, as these options
| **_total_probability_weighted_mass_run**: To count the total mass * probability for each system that thread/process has ran
-| **_total_starcount**: Variable storing the total amount of systems in the generator. Used and set by the population object.
+| **_total_starcount**: Variable storing the total number of systems in the generator. Used and set by the population object.
| **_zero_prob_stars_skipped**: Internal counter to track how many systems are skipped because they have 0 probability
diff --git a/docs/build/html/_sources/notebook_HRD.ipynb.txt b/docs/build/html/_sources/notebook_HRD.ipynb.txt
index 52590f8a2a6abc7245e9ea0c08d274432cd2a1ad..bf95d554d2125de449ec4b8404550132e06091f7 100644
--- a/docs/build/html/_sources/notebook_HRD.ipynb.txt
+++ b/docs/build/html/_sources/notebook_HRD.ipynb.txt
@@ -264,7 +264,7 @@
"## Evolving the grid\n",
"Now that we configured all the main parts of the population object, we can actually run the population! Doing this is straightforward: `population.evolve()`\n",
"\n",
- "This will start up the processing of all the systems. We can control how many cores are used by settings `amt_cores`. By setting the `verbosity` of the population object to a higher value we can get a lot of verbose information about the run, but for now we will set it to 0.\n",
+ "This will start up the processing of all the systems. We can control how many cores are used by settings `num_cores`. By setting the `verbosity` of the population object to a higher value we can get a lot of verbose information about the run, but for now we will set it to 0.\n",
"\n",
"There are many grid_options that can lead to different behaviour of the evolution of the grid. Please do have a look at those: [grid options docs](https://ri0005.pages.surrey.ac.uk/binary_c-python/grid_options_descriptions.html), and try "
]
@@ -300,7 +300,7 @@
" # verbose output is not required \n",
" verbosity=0,\n",
" # set number of threads (i.e. number of CPU cores we use)\n",
- " amt_cores=4,\n",
+ " num_cores=4,\n",
" )\n",
"\n",
"# Evolve the population - this is the slow, number-crunching step\n",
@@ -796,7 +796,7 @@
],
"metadata": {
"kernelspec": {
- "display_name": "Python 3",
+ "display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
@@ -810,7 +810,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
- "version": "3.6.4"
+ "version": "3.9.5"
}
},
"nbformat": 4,
diff --git a/docs/build/html/_sources/notebook_common_envelope_evolution.ipynb.txt b/docs/build/html/_sources/notebook_common_envelope_evolution.ipynb.txt
index 526320ccf954c1ed86c6d5c641204c4a9345bbe5..feb6b18e6a264b08eab1e52d639106123f494cf5 100644
--- a/docs/build/html/_sources/notebook_common_envelope_evolution.ipynb.txt
+++ b/docs/build/html/_sources/notebook_common_envelope_evolution.ipynb.txt
@@ -363,7 +363,7 @@
"metadata": {},
"source": [
"## Evolving the grid\n",
- "Now we actually run the population. This may take a little while. You can set amt_cores higher if you have a powerful machine."
+ "Now we actually run the population. This may take a little while. You can set num_cores higher if you have a powerful machine."
]
},
{
@@ -378,7 +378,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "adding: amt_cores=4 to grid_options\n",
+ "adding: num_cores=4 to grid_options\n",
"Creating and loading custom logging functionality\n",
"Generating grid code\n",
"Generating grid code\n",
@@ -540,7 +540,7 @@
"# set number of threads\n",
"population.set(\n",
" # set number of threads (i.e. number of CPU cores we use)\n",
- " amt_cores=4,\n",
+ " num_cores=4,\n",
" )\n",
"\n",
"# Evolve the population - this is the slow, number-crunching step\n",
@@ -686,7 +686,7 @@
],
"metadata": {
"kernelspec": {
- "display_name": "Python 3",
+ "display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
@@ -700,7 +700,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
- "version": "3.6.4"
+ "version": "3.9.5"
}
},
"nbformat": 4,
diff --git a/docs/build/html/_sources/notebook_individual_systems.ipynb.txt b/docs/build/html/_sources/notebook_individual_systems.ipynb.txt
index 85aef1e3962a1626f37a9ef36bf5e16f479eb68e..50c604385e0365b3404fb8d6427b9b9f0c0f7fbf 100644
--- a/docs/build/html/_sources/notebook_individual_systems.ipynb.txt
+++ b/docs/build/html/_sources/notebook_individual_systems.ipynb.txt
@@ -8,19 +8,22 @@
"# Tutorial: Running individual systems with binary_c-python\n",
"This notebook will show you how to run single systems and analyze their results.\n",
"\n",
- "It can be useful to have some functions to quickly run a single system to e.g. inspect what evolutionary steps a specific system goes through, to plot the mass loss evolution of a single star, etc. "
+ "It can be useful to have some functions to quickly run a single system to, for example, inspect what evolutionary steps a specific system goes through, to plot the mass loss evolution of a single system, etc. "
]
},
{
"cell_type": "markdown",
"id": "dd5d9ec7-5791-45f1-afbd-225947e2a583",
- "metadata": {},
+ "metadata": {
+ "tags": []
+ },
"source": [
- "## Single system with run_wrapper\n",
+ "## Single system with run_system_wrapper\n",
+ "\n",
"The simplest method to run a single system is to use the run_system wrapper. This function deals with setting up the argument string, makes sure all the required parameters are included and handles setting and cleaning up the custom logging functionality (see notebook_custom_logging).\n",
"\n",
"As arguments to this function we can add any of the parameters that binary_c itself actually knows, as well as:\n",
- "- custom_logging_code: string containing a print statement that binary_c can use to print information\n",
+ "- custom_logging_code: string containing a Printf statement that binary_c can use to print information\n",
"- log_filename: path of the logfile that binary_c generates\n",
"- parse_function: function that handles parsing the output of binary-c"
]
@@ -86,7 +89,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- " TIME M1 M2 K1 K2 SEP PER ECC R1/ROL1 R2/ROL2 TYPE RANDOM_SEED=17089 RANDOM_COUNT=0\n",
+ " TIME M1 M2 K1 K2 SEP PER ECC R1/ROL1 R2/ROL2 TYPE RANDOM_SEED=12122 RANDOM_COUNT=0\n",
" 0.0000 1.000 0.000 1 15 -1 -1 -1.00 0.000 0.000 \"INITIAL \"\n",
" 11003.1302 1.000 0.000 2 15 -1 -1 -1.00 0.000 0.000 \"OFF_MS\"\n",
" 11003.1302 1.000 0.000 2 15 -1 -1 -1.00 0.000 0.000 \"TYPE_CHNGE\"\n",
@@ -225,18 +228,18 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "0 time mass initial_mass stellar_type\n",
- "1 0 1 1 1\n",
- "2 0 1 1 1\n",
- "3 1e-06 1 1 1\n",
- "4 2e-06 1 1 1\n",
- "5 3e-06 1 1 1\n",
- "... ... ... ... ...\n",
- "1617 12461.8 0.546683 1 6\n",
- "1618 12461.9 0.517749 1 11\n",
- "1619 13461.9 0.517749 1 11\n",
- "1620 14461.9 0.517749 1 11\n",
- "1621 15000 0.517749 1 11\n",
+ "0 time mass initial_mass stellar_type\n",
+ "1 0.0 1.0 1.0 1.0\n",
+ "2 0.0 1.0 1.0 1.0\n",
+ "3 0.000001 1.0 1.0 1.0\n",
+ "4 0.000002 1.0 1.0 1.0\n",
+ "5 0.000003 1.0 1.0 1.0\n",
+ "... ... ... ... ...\n",
+ "1617 12461.819616 0.546683 1.0 6.0\n",
+ "1618 12461.945773 0.517749 1.0 11.0\n",
+ "1619 13461.945773 0.517749 1.0 11.0\n",
+ "1620 14461.945773 0.517749 1.0 11.0\n",
+ "1621 15000.0 0.517749 1.0 11.0\n",
"\n",
"[1621 rows x 4 columns]\n"
]
@@ -358,7 +361,7 @@
"Creating and loading custom logging functionality\n",
"Running binary_c M_1 10 api_log_filename_prefix /tmp/binary_c_python/notebooks/notebook_individual_systems\n",
"Cleaning up the custom logging stuff. type: single\n",
- "Removed /tmp/binary_c_python/custom_logging/libcustom_logging_8967553693ac4e11a49c42d4eef773e8.so\n",
+ "Removed /tmp/binary_c_python/custom_logging/libcustom_logging_6d4ed30fa6684630885c08523336d45f.so\n",
"EXAMPLE_MASSLOSS 0.000000000000e+00 10 0 10 1\n",
"EXAMPLE_MASSLOSS 0.000000000000e+00 10 10 10 1\n",
"EXAMPLE_MASSLOSS 1.000000000000e-06 10 10 10 1\n",
@@ -460,13 +463,13 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "adding: parse_function=<function object_parse_function at 0x7fb4d41ebbf8> to grid_options\n",
+ "adding: parse_function=<function object_parse_function at 0x14938275de50> to grid_options\n",
"<<<< Warning: Key does not match previously known parameter: adding: output_dir=/tmp/binary_c_python/notebooks/notebook_individual_systems to custom_options >>>>\n",
"adding: api_log_filename_prefix=/tmp/binary_c_python/notebooks/notebook_individual_systems to BSE_options\n",
"Creating and loading custom logging functionality\n",
"Running binary_c M_1 10 api_log_filename_prefix /tmp/binary_c_python/notebooks/notebook_individual_systems\n",
"Cleaning up the custom logging stuff. type: single\n",
- "Removed /tmp/binary_c_python/custom_logging/libcustom_logging_5d7779e8190e4b79b10c7e6a44cb0e7e.so\n",
+ "Removed /tmp/binary_c_python/custom_logging/libcustom_logging_3bc2f679982a4df6a2b83d382e83d724.so\n",
"[['time', 'mass', 'initial_mass', 'stellar_type'], [0.0, 10.0, 0.0, 10.0, 1.0], [0.0, 10.0, 10.0, 10.0, 1.0], [1e-06, 10.0, 10.0, 10.0, 1.0]]\n",
"dict_keys(['time', 'mass', 'initial_mass', 'stellar_type'])\n"
]
@@ -496,7 +499,7 @@
"## Single system via API functionality\n",
"It is possible to construct your own functionality to run a single system by directly calling the API function to run a system. Under the hood all the other functions and wrappers actually use this API.\n",
"\n",
- "There are less failsafes for this method, so this make sure the input is correct and binary_c knows all the arguments you pass in.\n",
+ "There are fewer failsafes for this method, so this make sure the input is correct and binary_c knows all the arguments you pass in.\n",
"\n",
"for more details on this API function see `notebook_api_functions`"
]
@@ -519,7 +522,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "SINGLE_STAR_LIFETIME 15 14.9947\n",
+ "SINGLE_STAR_LIFETIME 15 14.9927\n",
"\n"
]
}
diff --git a/docs/build/html/_sources/notebook_luminosity_function_binaries.ipynb.txt b/docs/build/html/_sources/notebook_luminosity_function_binaries.ipynb.txt
index c6b5f1e64cc36c684fdf5cefe0fae4b450a1c936..f054310a62ea8a37e55df724be75879dababbe38 100644
--- a/docs/build/html/_sources/notebook_luminosity_function_binaries.ipynb.txt
+++ b/docs/build/html/_sources/notebook_luminosity_function_binaries.ipynb.txt
@@ -5,7 +5,7 @@
"id": "bbbaafbb-fd7d-4b73-a970-93506ba35d71",
"metadata": {},
"source": [
- "# Zero-age stellar luminosity function in binaries\n",
+ "# Example use case: Zero-age stellar luminosity function in binaries\n",
"\n",
"In this notebook we compute the luminosity function of the zero-age main-sequence by running a population of binary stars using binary_c. \n",
"\n",
@@ -369,7 +369,7 @@
"## Evolving the grid\n",
"Now that we configured all the main parts of the population object, we can actually run the population! Doing this is straightforward: `population.evolve()`\n",
"\n",
- "This will start up the processing of all the systems. We can control how many cores are used by settings `amt_cores`. By setting the `verbosity` of the population object to a higher value we can get a lot of verbose information about the run, but for now we will set it to 0.\n",
+ "This will start up the processing of all the systems. We can control how many cores are used by settings `num_cores`. By setting the `verbosity` of the population object to a higher value we can get a lot of verbose information about the run, but for now we will set it to 0.\n",
"\n",
"There are many grid_options that can lead to different behaviour of the evolution of the grid. Please do have a look at those: [grid options docs](https://ri0005.pages.surrey.ac.uk/binary_c-python/grid_options_descriptions.html), and try "
]
@@ -386,7 +386,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "adding: amt_cores=4 to grid_options\n",
+ "adding: num_cores=4 to grid_options\n",
"Running the population now, this may take a little while...\n",
"Creating and loading custom logging functionality\n",
"Generating grid code\n",
@@ -547,7 +547,7 @@
" # verbose output is not required \n",
" verbosity=1,\n",
" # set number of threads (i.e. number of CPU cores we use)\n",
- " amt_cores=4,\n",
+ " num_cores=4,\n",
" )\n",
"\n",
"# Evolve the population - this is the slow, number-crunching step\n",
diff --git a/docs/build/html/_sources/notebook_luminosity_function_single.ipynb.txt b/docs/build/html/_sources/notebook_luminosity_function_single.ipynb.txt
index cdae316f90802fe46611ea17732506c0410aef55..09af8acc59f26e909901c0649e02a0d0864b789a 100644
--- a/docs/build/html/_sources/notebook_luminosity_function_single.ipynb.txt
+++ b/docs/build/html/_sources/notebook_luminosity_function_single.ipynb.txt
@@ -297,7 +297,7 @@
"## Evolving the grid\n",
"Now that we configured all the main parts of the population object, we can actually run the population! Doing this is straightforward: `population.evolve()`\n",
"\n",
- "This will start up the processing of all the systems. We can control how many cores are used by settings `amt_cores`. By setting the `verbosity` of the population object to a higher value we can get a lot of verbose information about the run, but for now we will set it to 0.\n",
+ "This will start up the processing of all the systems. We can control how many cores are used by settings `num_cores`. By setting the `verbosity` of the population object to a higher value we can get a lot of verbose information about the run, but for now we will set it to 0.\n",
"\n",
"There are many grid_options that can lead to different behaviour of the evolution of the grid. Please do have a look at those: [grid options docs](https://ri0005.pages.surrey.ac.uk/binary_c-python/grid_options_descriptions.html), and try "
]
@@ -332,7 +332,7 @@
" # verbose output is not required \n",
" verbosity=0,\n",
" # set number of threads (i.e. number of CPU cores we use)\n",
- " amt_cores=2,\n",
+ " num_cores=2,\n",
" )\n",
"\n",
"# Evolve the population - this is the slow, number-crunching step\n",
@@ -703,7 +703,7 @@
],
"metadata": {
"kernelspec": {
- "display_name": "Python 3",
+ "display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
@@ -717,7 +717,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
- "version": "3.6.4"
+ "version": "3.9.5"
}
},
"nbformat": 4,
diff --git a/docs/build/html/_sources/notebook_population.ipynb.txt b/docs/build/html/_sources/notebook_population.ipynb.txt
index a24638c0bd3a15a57bbf611fccb71b2100c75945..1ec2f94d3b03db0bccabe6ea2d2c100946add611 100644
--- a/docs/build/html/_sources/notebook_population.ipynb.txt
+++ b/docs/build/html/_sources/notebook_population.ipynb.txt
@@ -62,7 +62,7 @@
"adding: orbital_period=45000000080 to BSE_options\n",
"adding: max_evolution_time=15000 to BSE_options\n",
"adding: eccentricity=0.02 to BSE_options\n",
- "adding: amt_cores=2 to grid_options\n",
+ "adding: num_cores=2 to grid_options\n",
"adding: tmp_dir=/tmp/binary_c_python/notebooks/notebook_population to grid_options\n",
"<<<< Warning: Key does not match previously known parameter: adding: data_dir=/tmp/binary_c_python/notebooks/notebook_population/example_python_population_result to custom_options >>>>\n",
"<<<< Warning: Key does not match previously known parameter: adding: base_filename=example_pop.dat to custom_options >>>>\n",
@@ -92,7 +92,7 @@
"\n",
"\n",
" # grid_options\n",
- " amt_cores=2,\n",
+ " num_cores=2,\n",
" tmp_dir=TMP_DIR,\n",
" \n",
" # Custom options # TODO: need to be set in grid_options probably\n",
@@ -219,7 +219,7 @@
" Examples:\n",
" range = [math.log(m_min), math.log(m_max)]\n",
" resolution:\n",
- " Resolution of the sampled range (amount of samples).\n",
+ " Resolution of the sampled range (number of samples).\n",
" TODO: check if this is used anywhere\n",
" \n",
" Examples:\n",
@@ -496,7 +496,7 @@
" print(line)\n",
" \n",
" if not len(parameters) == len(values):\n",
- " print(\"Amount of column names isnt equal to amount of columns\")\n",
+ " print(\"Number of column names isnt equal to number of columns\")\n",
" raise ValueError\n",
"\n",
" if not os.path.exists(outfilename):\n",
@@ -520,7 +520,7 @@
"## Evolving the grid\n",
"Now that we configured all the main parts of the population object, we can actually run the population! Doing this is straightforward: `example_pop.evolve()`\n",
"\n",
- "This will start up the processing of all the systems. We can control how many cores are used by settings `amt_cores`. By setting the `verbosity` of the population object to a higher value we can get a lot of verbose information about the run, but for now we will set it to 0.\n",
+ "This will start up the processing of all the systems. We can control how many cores are used by settings `num_cores`. By setting the `verbosity` of the population object to a higher value we can get a lot of verbose information about the run, but for now we will set it to 0.\n",
"\n",
"There are many grid_options that can lead to different behaviour of the evolution of the grid. Please do have a look at those: [grid options docs](https://ri0005.pages.surrey.ac.uk/binary_c-python/grid_options_descriptions.html), and try "
]
@@ -770,7 +770,7 @@
" values = el.split()[1:]\n",
"\n",
" if not len(parameters) == len(values):\n",
- " print(\"Amount of column names isnt equal to amount of columns\")\n",
+ " print(\"Number of column names isnt equal to number of columns\")\n",
" raise ValueError\n",
"\n",
" if not os.path.exists(outfilename):\n",
@@ -797,7 +797,7 @@
" eccentricity=0.02, # bse_options\n",
" \n",
" # grid_options\n",
- " amt_cores=2,\n",
+ " num_cores=2,\n",
" tmp_dir=TMP_DIR,\n",
"\n",
" # Custom options: the data directory and the output filename\n",
@@ -963,7 +963,7 @@
" values = el.split()[1:]\n",
"\n",
" if not len(parameters) == len(values):\n",
- " print(\"Amount of column names isnt equal to amount of columns\")\n",
+ " print(\"Number of column names isnt equal to number of columns\")\n",
" raise ValueError\n",
"\n",
" if not os.path.exists(outfilename):\n",
@@ -990,7 +990,7 @@
" eccentricity=0.02, # bse_options\n",
" \n",
" # grid_options\n",
- " amt_cores=2, # grid_options\n",
+ " num_cores=2, # grid_options\n",
" tmp_dir=TMP_DIR,\n",
"\n",
" # Custom options: the data directory and the output filename\n",
diff --git a/docs/build/html/_static/basic.css b/docs/build/html/_static/basic.css
index 24a49f09b5a52dc32775ed946bcceca8156e7439..912859b55d96750bff001bb79037a83a6c02332c 100644
--- a/docs/build/html/_static/basic.css
+++ b/docs/build/html/_static/basic.css
@@ -4,7 +4,7 @@
*
* Sphinx stylesheet -- basic theme.
*
- * :copyright: Copyright 2007-2020 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2021 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
@@ -130,7 +130,7 @@ ul.search li a {
font-weight: bold;
}
-ul.search li div.context {
+ul.search li p.context {
color: #888;
margin: 2px 0 0 30px;
text-align: left;
@@ -277,25 +277,25 @@ p.rubric {
font-weight: bold;
}
-img.align-left, .figure.align-left, object.align-left {
+img.align-left, figure.align-left, .figure.align-left, object.align-left {
clear: left;
float: left;
margin-right: 1em;
}
-img.align-right, .figure.align-right, object.align-right {
+img.align-right, figure.align-right, .figure.align-right, object.align-right {
clear: right;
float: right;
margin-left: 1em;
}
-img.align-center, .figure.align-center, object.align-center {
+img.align-center, figure.align-center, .figure.align-center, object.align-center {
display: block;
margin-left: auto;
margin-right: auto;
}
-img.align-default, .figure.align-default {
+img.align-default, figure.align-default, .figure.align-default {
display: block;
margin-left: auto;
margin-right: auto;
@@ -319,7 +319,8 @@ img.align-default, .figure.align-default {
/* -- sidebars -------------------------------------------------------------- */
-div.sidebar {
+div.sidebar,
+aside.sidebar {
margin: 0 0 0.5em 1em;
border: 1px solid #ddb;
padding: 7px;
@@ -377,12 +378,14 @@ div.body p.centered {
/* -- content of sidebars/topics/admonitions -------------------------------- */
div.sidebar > :last-child,
+aside.sidebar > :last-child,
div.topic > :last-child,
div.admonition > :last-child {
margin-bottom: 0;
}
div.sidebar::after,
+aside.sidebar::after,
div.topic::after,
div.admonition::after,
blockquote::after {
@@ -455,20 +458,22 @@ td > :last-child {
/* -- figures --------------------------------------------------------------- */
-div.figure {
+div.figure, figure {
margin: 0.5em;
padding: 0.5em;
}
-div.figure p.caption {
+div.figure p.caption, figcaption {
padding: 0.3em;
}
-div.figure p.caption span.caption-number {
+div.figure p.caption span.caption-number,
+figcaption span.caption-number {
font-style: italic;
}
-div.figure p.caption span.caption-text {
+div.figure p.caption span.caption-text,
+figcaption span.caption-text {
}
/* -- field list styles ----------------------------------------------------- */
@@ -503,6 +508,63 @@ table.hlist td {
vertical-align: top;
}
+/* -- object description styles --------------------------------------------- */
+
+.sig {
+ font-family: 'Consolas', 'Menlo', 'DejaVu Sans Mono', 'Bitstream Vera Sans Mono', monospace;
+}
+
+.sig-name, code.descname {
+ background-color: transparent;
+ font-weight: bold;
+}
+
+.sig-name {
+ font-size: 1.1em;
+}
+
+code.descname {
+ font-size: 1.2em;
+}
+
+.sig-prename, code.descclassname {
+ background-color: transparent;
+}
+
+.optional {
+ font-size: 1.3em;
+}
+
+.sig-paren {
+ font-size: larger;
+}
+
+.sig-param.n {
+ font-style: italic;
+}
+
+/* C++ specific styling */
+
+.sig-inline.c-texpr,
+.sig-inline.cpp-texpr {
+ font-family: unset;
+}
+
+.sig.c .k, .sig.c .kt,
+.sig.cpp .k, .sig.cpp .kt {
+ color: #0033B3;
+}
+
+.sig.c .m,
+.sig.cpp .m {
+ color: #1750EB;
+}
+
+.sig.c .s, .sig.c .sc,
+.sig.cpp .s, .sig.cpp .sc {
+ color: #067D17;
+}
+
/* -- other body styles ----------------------------------------------------- */
@@ -629,14 +691,6 @@ dl.glossary dt {
font-size: 1.1em;
}
-.optional {
- font-size: 1.3em;
-}
-
-.sig-paren {
- font-size: larger;
-}
-
.versionmodified {
font-style: italic;
}
@@ -765,8 +819,12 @@ div.code-block-caption code {
table.highlighttable td.linenos,
span.linenos,
-div.doctest > div.highlight span.gp { /* gp: Generic.Prompt */
- user-select: none;
+div.highlight span.gp { /* gp: Generic.Prompt */
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diff --git a/docs/build/html/_static/doctools.js b/docs/build/html/_static/doctools.js
index 7d88f807dc9ad9d1b5a320f2e27daa2f5196d875..8cbf1b161a6527c8c6ad1c4f1fdc156e065ab262 100644
--- a/docs/build/html/_static/doctools.js
+++ b/docs/build/html/_static/doctools.js
@@ -4,7 +4,7 @@
*
* Sphinx JavaScript utilities for all documentation.
*
- * :copyright: Copyright 2007-2020 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2021 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
@@ -29,9 +29,14 @@ if (!window.console || !console.firebug) {
/**
* small helper function to urldecode strings
+ *
+ * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL
*/
jQuery.urldecode = function(x) {
- return decodeURIComponent(x).replace(/\+/g, ' ');
+ if (!x) {
+ return x
+ }
+ return decodeURIComponent(x.replace(/\+/g, ' '));
};
/**
@@ -296,12 +301,14 @@ var Documentation = {
window.location.href = prevHref;
return false;
}
+ break;
case 39: // right
var nextHref = $('link[rel="next"]').prop('href');
if (nextHref) {
window.location.href = nextHref;
return false;
}
+ break;
}
}
});
diff --git a/docs/build/html/_static/fonts/FontAwesome.otf b/docs/build/html/_static/fonts/FontAwesome.otf
deleted file mode 100644
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diff --git a/docs/build/html/_static/fonts/Lato/lato-bold.eot b/docs/build/html/_static/fonts/Lato/lato-bold.eot
deleted file mode 100644
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diff --git a/docs/build/html/_static/fonts/Lato/lato-bold.ttf b/docs/build/html/_static/fonts/Lato/lato-bold.ttf
deleted file mode 100644
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Binary files a/docs/build/html/_static/fonts/Lato/lato-bold.ttf and /dev/null differ
diff --git a/docs/build/html/_static/fonts/Lato/lato-bold.woff b/docs/build/html/_static/fonts/Lato/lato-bold.woff
deleted file mode 100644
index c6dff51f063cc732fdb5fe786a8966de85f4ebec..0000000000000000000000000000000000000000
Binary files a/docs/build/html/_static/fonts/Lato/lato-bold.woff and /dev/null differ
diff --git a/docs/build/html/_static/fonts/Lato/lato-bold.woff2 b/docs/build/html/_static/fonts/Lato/lato-bold.woff2
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diff --git a/docs/build/html/_static/js/theme.js b/docs/build/html/_static/js/theme.js
index 839d07e2b8e9091dea25b2b4e3081adb1906d1f7..1fddb6ee4a60f30b4a4c4b3ad1f1604043f77981 100644
--- a/docs/build/html/_static/js/theme.js
+++ b/docs/build/html/_static/js/theme.js
@@ -1 +1 @@
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\ No newline at end of file
+!function(n){var e={};function t(i){if(e[i])return e[i].exports;var o=e[i]={i:i,l:!1,exports:{}};return n[i].call(o.exports,o,o.exports,t),o.l=!0,o.exports}t.m=n,t.c=e,t.d=function(n,e,i){t.o(n,e)||Object.defineProperty(n,e,{enumerable:!0,get:i})},t.r=function(n){"undefined"!=typeof Symbol&&Symbol.toStringTag&&Object.defineProperty(n,Symbol.toStringTag,{value:"Module"}),Object.defineProperty(n,"__esModule",{value:!0})},t.t=function(n,e){if(1&e&&(n=t(n)),8&e)return n;if(4&e&&"object"==typeof n&&n&&n.__esModule)return n;var i=Object.create(null);if(t.r(i),Object.defineProperty(i,"default",{enumerable:!0,value:n}),2&e&&"string"!=typeof n)for(var o in n)t.d(i,o,function(e){return n[e]}.bind(null,o));return i},t.n=function(n){var e=n&&n.__esModule?function(){return n.default}:function(){return n};return t.d(e,"a",e),e},t.o=function(n,e){return Object.prototype.hasOwnProperty.call(n,e)},t.p="",t(t.s=0)}([function(n,e,t){t(1),n.exports=t(3)},function(n,e,t){(function(){var e="undefined"!=typeof window?window.jQuery:t(2);n.exports.ThemeNav={navBar:null,win:null,winScroll:!1,winResize:!1,linkScroll:!1,winPosition:0,winHeight:null,docHeight:null,isRunning:!1,enable:function(n){var t=this;void 0===n&&(n=!0),t.isRunning||(t.isRunning=!0,e((function(e){t.init(e),t.reset(),t.win.on("hashchange",t.reset),n&&t.win.on("scroll",(function(){t.linkScroll||t.winScroll||(t.winScroll=!0,requestAnimationFrame((function(){t.onScroll()})))})),t.win.on("resize",(function(){t.winResize||(t.winResize=!0,requestAnimationFrame((function(){t.onResize()})))})),t.onResize()})))},enableSticky:function(){this.enable(!0)},init:function(n){n(document);var e=this;this.navBar=n("div.wy-side-scroll:first"),this.win=n(window),n(document).on("click","[data-toggle='wy-nav-top']",(function(){n("[data-toggle='wy-nav-shift']").toggleClass("shift"),n("[data-toggle='rst-versions']").toggleClass("shift")})).on("click",".wy-menu-vertical .current ul li a",(function(){var 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[id="'+n.substring(1)+'"]').closest("div.section");0===(t=e.find('[href="#'+i.attr("id")+'"]')).length&&(t=e.find('[href="#"]'))}if(t.length>0){$(".wy-menu-vertical .current").removeClass("current").attr("aria-expanded","false"),t.addClass("current").attr("aria-expanded","true"),t.closest("li.toctree-l1").parent().addClass("current").attr("aria-expanded","true");for(let n=1;n<=10;n++)t.closest("li.toctree-l"+n).addClass("current").attr("aria-expanded","true");t[0].scrollIntoView()}}catch(n){console.log("Error expanding nav for anchor",n)}},onScroll:function(){this.winScroll=!1;var n=this.win.scrollTop(),e=n+this.winHeight,t=this.navBar.scrollTop()+(n-this.winPosition);n<0||e>this.docHeight||(this.navBar.scrollTop(t),this.winPosition=n)},onResize:function(){this.winResize=!1,this.winHeight=this.win.height(),this.docHeight=$(document).height()},hashChange:function(){this.linkScroll=!0,this.win.one("hashchange",(function(){this.linkScroll=!1}))},toggleCurrent:function(n){var e=n.closest("li");e.siblings("li.current").removeClass("current").attr("aria-expanded","false"),e.siblings().find("li.current").removeClass("current").attr("aria-expanded","false");var t=e.find("> ul li");t.length&&(t.removeClass("current").attr("aria-expanded","false"),e.toggleClass("current").attr("aria-expanded",(function(n,e){return"true"==e?"false":"true"})))}},"undefined"!=typeof window&&(window.SphinxRtdTheme={Navigation:n.exports.ThemeNav,StickyNav:n.exports.ThemeNav}),function(){for(var n=0,e=["ms","moz","webkit","o"],t=0;t<e.length&&!window.requestAnimationFrame;++t)window.requestAnimationFrame=window[e[t]+"RequestAnimationFrame"],window.cancelAnimationFrame=window[e[t]+"CancelAnimationFrame"]||window[e[t]+"CancelRequestAnimationFrame"];window.requestAnimationFrame||(window.requestAnimationFrame=function(e,t){var i=(new Date).getTime(),o=Math.max(0,16-(i-n)),r=window.setTimeout((function(){e(i+o)}),o);return n=i+o,r}),window.cancelAnimationFrame||(window.cancelAnimationFrame=function(n){clearTimeout(n)})}()}).call(window)},function(n,e){n.exports=jQuery},function(n,e,t){}]);
\ No newline at end of file
diff --git a/docs/build/html/_static/language_data.js b/docs/build/html/_static/language_data.js
index d2b4ee91b0da7308cf5693804779c7b18c26252a..863704b310d1539241ef20e26ccce6af27f0ffce 100644
--- a/docs/build/html/_static/language_data.js
+++ b/docs/build/html/_static/language_data.js
@@ -5,7 +5,7 @@
* This script contains the language-specific data used by searchtools.js,
* namely the list of stopwords, stemmer, scorer and splitter.
*
- * :copyright: Copyright 2007-2020 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2021 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
@@ -13,7 +13,8 @@
var stopwords = ["a","and","are","as","at","be","but","by","for","if","in","into","is","it","near","no","not","of","on","or","such","that","the","their","then","there","these","they","this","to","was","will","with"];
-/* Non-minified version JS is _stemmer.js if file is provided */
+/* Non-minified version is copied as a separate JS file, is available */
+
/**
* Porter Stemmer
*/
@@ -199,7 +200,6 @@ var Stemmer = function() {
-
var splitChars = (function() {
var result = {};
var singles = [96, 180, 187, 191, 215, 247, 749, 885, 903, 907, 909, 930, 1014, 1648,
diff --git a/docs/build/html/_static/pygments.css b/docs/build/html/_static/pygments.css
index 13b72433793c507cc1e692df52b62b1f1aebd030..582d5c3adaddbab2178a4e1ea270afe51e5437d2 100644
--- a/docs/build/html/_static/pygments.css
+++ b/docs/build/html/_static/pygments.css
@@ -1,7 +1,7 @@
pre { line-height: 125%; }
-td.linenos pre { color: #000000; background-color: #f0f0f0; padding-left: 5px; padding-right: 5px; }
-span.linenos { color: #000000; background-color: #f0f0f0; padding-left: 5px; padding-right: 5px; }
-td.linenos pre.special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; }
+td.linenos .normal { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; }
+span.linenos { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; }
+td.linenos .special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; }
span.linenos.special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; }
.highlight .hll { background-color: #ffffcc }
.highlight { background: #f8f8f8; }
diff --git a/docs/build/html/_static/searchtools.js b/docs/build/html/_static/searchtools.js
index 261ecaa92829538b506bc4794a14df56b151690e..58ff35c4345d19830352048b89abc8e7c06e4f20 100644
--- a/docs/build/html/_static/searchtools.js
+++ b/docs/build/html/_static/searchtools.js
@@ -4,7 +4,7 @@
*
* Sphinx JavaScript utilities for the full-text search.
*
- * :copyright: Copyright 2007-2020 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2021 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
@@ -248,7 +248,7 @@ var Search = {
// results left, load the summary and display it
if (results.length) {
var item = results.pop();
- var listItem = $('<li style="display:none"></li>');
+ var listItem = $('<li></li>');
var requestUrl = "";
var linkUrl = "";
if (DOCUMENTATION_OPTIONS.BUILDER === 'dirhtml') {
@@ -273,28 +273,31 @@ var Search = {
if (item[3]) {
listItem.append($('<span> (' + item[3] + ')</span>'));
Search.output.append(listItem);
- listItem.slideDown(5, function() {
+ setTimeout(function() {
displayNextItem();
- });
+ }, 5);
} else if (DOCUMENTATION_OPTIONS.HAS_SOURCE) {
$.ajax({url: requestUrl,
dataType: "text",
complete: function(jqxhr, textstatus) {
var data = jqxhr.responseText;
if (data !== '' && data !== undefined) {
- listItem.append(Search.makeSearchSummary(data, searchterms, hlterms));
+ var summary = Search.makeSearchSummary(data, searchterms, hlterms);
+ if (summary) {
+ listItem.append(summary);
+ }
}
Search.output.append(listItem);
- listItem.slideDown(5, function() {
+ setTimeout(function() {
displayNextItem();
- });
+ }, 5);
}});
} else {
// no source available, just display title
Search.output.append(listItem);
- listItem.slideDown(5, function() {
+ setTimeout(function() {
displayNextItem();
- });
+ }, 5);
}
}
// search finished, update title and status message
@@ -379,6 +382,13 @@ var Search = {
return results;
},
+ /**
+ * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions
+ */
+ escapeRegExp : function(string) {
+ return string.replace(/[.*+\-?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string
+ },
+
/**
* search for full-text terms in the index
*/
@@ -402,13 +412,14 @@ var Search = {
];
// add support for partial matches
if (word.length > 2) {
+ var word_regex = this.escapeRegExp(word);
for (var w in terms) {
- if (w.match(word) && !terms[word]) {
+ if (w.match(word_regex) && !terms[word]) {
_o.push({files: terms[w], score: Scorer.partialTerm})
}
}
for (var w in titleterms) {
- if (w.match(word) && !titleterms[word]) {
+ if (w.match(word_regex) && !titleterms[word]) {
_o.push({files: titleterms[w], score: Scorer.partialTitle})
}
}
@@ -490,6 +501,9 @@ var Search = {
*/
makeSearchSummary : function(htmlText, keywords, hlwords) {
var text = Search.htmlToText(htmlText);
+ if (text == "") {
+ return null;
+ }
var textLower = text.toLowerCase();
var start = 0;
$.each(keywords, function() {
@@ -501,7 +515,7 @@ var Search = {
var excerpt = ((start > 0) ? '...' : '') +
$.trim(text.substr(start, 240)) +
((start + 240 - text.length) ? '...' : '');
- var rv = $('<div class="context"></div>').text(excerpt);
+ var rv = $('<p class="context"></p>').text(excerpt);
$.each(hlwords, function() {
rv = rv.highlightText(this, 'highlighted');
});
diff --git a/docs/build/html/_static/underscore-1.3.1.js b/docs/build/html/_static/underscore-1.3.1.js
deleted file mode 100644
index 208d4cd890c3183d946092ebe982738ade565061..0000000000000000000000000000000000000000
--- a/docs/build/html/_static/underscore-1.3.1.js
+++ /dev/null
@@ -1,999 +0,0 @@
-// Underscore.js 1.3.1
-// (c) 2009-2012 Jeremy Ashkenas, DocumentCloud Inc.
-// Underscore is freely distributable under the MIT license.
-// Portions of Underscore are inspired or borrowed from Prototype,
-// Oliver Steele's Functional, and John Resig's Micro-Templating.
-// For all details and documentation:
-// http://documentcloud.github.com/underscore
-
-(function() {
-
- // Baseline setup
- // --------------
-
- // Establish the root object, `window` in the browser, or `global` on the server.
- var root = this;
-
- // Save the previous value of the `_` variable.
- var previousUnderscore = root._;
-
- // Establish the object that gets returned to break out of a loop iteration.
- var breaker = {};
-
- // Save bytes in the minified (but not gzipped) version:
- var ArrayProto = Array.prototype, ObjProto = Object.prototype, FuncProto = Function.prototype;
-
- // Create quick reference variables for speed access to core prototypes.
- var slice = ArrayProto.slice,
- unshift = ArrayProto.unshift,
- toString = ObjProto.toString,
- hasOwnProperty = ObjProto.hasOwnProperty;
-
- // All **ECMAScript 5** native function implementations that we hope to use
- // are declared here.
- var
- nativeForEach = ArrayProto.forEach,
- nativeMap = ArrayProto.map,
- nativeReduce = ArrayProto.reduce,
- nativeReduceRight = ArrayProto.reduceRight,
- nativeFilter = ArrayProto.filter,
- nativeEvery = ArrayProto.every,
- nativeSome = ArrayProto.some,
- nativeIndexOf = ArrayProto.indexOf,
- nativeLastIndexOf = ArrayProto.lastIndexOf,
- nativeIsArray = Array.isArray,
- nativeKeys = Object.keys,
- nativeBind = FuncProto.bind;
-
- // Create a safe reference to the Underscore object for use below.
- var _ = function(obj) { return new wrapper(obj); };
-
- // Export the Underscore object for **Node.js**, with
- // backwards-compatibility for the old `require()` API. If we're in
- // the browser, add `_` as a global object via a string identifier,
- // for Closure Compiler "advanced" mode.
- if (typeof exports !== 'undefined') {
- if (typeof module !== 'undefined' && module.exports) {
- exports = module.exports = _;
- }
- exports._ = _;
- } else {
- root['_'] = _;
- }
-
- // Current version.
- _.VERSION = '1.3.1';
-
- // Collection Functions
- // --------------------
-
- // The cornerstone, an `each` implementation, aka `forEach`.
- // Handles objects with the built-in `forEach`, arrays, and raw objects.
- // Delegates to **ECMAScript 5**'s native `forEach` if available.
- var each = _.each = _.forEach = function(obj, iterator, context) {
- if (obj == null) return;
- if (nativeForEach && obj.forEach === nativeForEach) {
- obj.forEach(iterator, context);
- } else if (obj.length === +obj.length) {
- for (var i = 0, l = obj.length; i < l; i++) {
- if (i in obj && iterator.call(context, obj[i], i, obj) === breaker) return;
- }
- } else {
- for (var key in obj) {
- if (_.has(obj, key)) {
- if (iterator.call(context, obj[key], key, obj) === breaker) return;
- }
- }
- }
- };
-
- // Return the results of applying the iterator to each element.
- // Delegates to **ECMAScript 5**'s native `map` if available.
- _.map = _.collect = function(obj, iterator, context) {
- var results = [];
- if (obj == null) return results;
- if (nativeMap && obj.map === nativeMap) return obj.map(iterator, context);
- each(obj, function(value, index, list) {
- results[results.length] = iterator.call(context, value, index, list);
- });
- if (obj.length === +obj.length) results.length = obj.length;
- return results;
- };
-
- // **Reduce** builds up a single result from a list of values, aka `inject`,
- // or `foldl`. Delegates to **ECMAScript 5**'s native `reduce` if available.
- _.reduce = _.foldl = _.inject = function(obj, iterator, memo, context) {
- var initial = arguments.length > 2;
- if (obj == null) obj = [];
- if (nativeReduce && obj.reduce === nativeReduce) {
- if (context) iterator = _.bind(iterator, context);
- return initial ? obj.reduce(iterator, memo) : obj.reduce(iterator);
- }
- each(obj, function(value, index, list) {
- if (!initial) {
- memo = value;
- initial = true;
- } else {
- memo = iterator.call(context, memo, value, index, list);
- }
- });
- if (!initial) throw new TypeError('Reduce of empty array with no initial value');
- return memo;
- };
-
- // The right-associative version of reduce, also known as `foldr`.
- // Delegates to **ECMAScript 5**'s native `reduceRight` if available.
- _.reduceRight = _.foldr = function(obj, iterator, memo, context) {
- var initial = arguments.length > 2;
- if (obj == null) obj = [];
- if (nativeReduceRight && obj.reduceRight === nativeReduceRight) {
- if (context) iterator = _.bind(iterator, context);
- return initial ? obj.reduceRight(iterator, memo) : obj.reduceRight(iterator);
- }
- var reversed = _.toArray(obj).reverse();
- if (context && !initial) iterator = _.bind(iterator, context);
- return initial ? _.reduce(reversed, iterator, memo, context) : _.reduce(reversed, iterator);
- };
-
- // Return the first value which passes a truth test. Aliased as `detect`.
- _.find = _.detect = function(obj, iterator, context) {
- var result;
- any(obj, function(value, index, list) {
- if (iterator.call(context, value, index, list)) {
- result = value;
- return true;
- }
- });
- return result;
- };
-
- // Return all the elements that pass a truth test.
- // Delegates to **ECMAScript 5**'s native `filter` if available.
- // Aliased as `select`.
- _.filter = _.select = function(obj, iterator, context) {
- var results = [];
- if (obj == null) return results;
- if (nativeFilter && obj.filter === nativeFilter) return obj.filter(iterator, context);
- each(obj, function(value, index, list) {
- if (iterator.call(context, value, index, list)) results[results.length] = value;
- });
- return results;
- };
-
- // Return all the elements for which a truth test fails.
- _.reject = function(obj, iterator, context) {
- var results = [];
- if (obj == null) return results;
- each(obj, function(value, index, list) {
- if (!iterator.call(context, value, index, list)) results[results.length] = value;
- });
- return results;
- };
-
- // Determine whether all of the elements match a truth test.
- // Delegates to **ECMAScript 5**'s native `every` if available.
- // Aliased as `all`.
- _.every = _.all = function(obj, iterator, context) {
- var result = true;
- if (obj == null) return result;
- if (nativeEvery && obj.every === nativeEvery) return obj.every(iterator, context);
- each(obj, function(value, index, list) {
- if (!(result = result && iterator.call(context, value, index, list))) return breaker;
- });
- return result;
- };
-
- // Determine if at least one element in the object matches a truth test.
- // Delegates to **ECMAScript 5**'s native `some` if available.
- // Aliased as `any`.
- var any = _.some = _.any = function(obj, iterator, context) {
- iterator || (iterator = _.identity);
- var result = false;
- if (obj == null) return result;
- if (nativeSome && obj.some === nativeSome) return obj.some(iterator, context);
- each(obj, function(value, index, list) {
- if (result || (result = iterator.call(context, value, index, list))) return breaker;
- });
- return !!result;
- };
-
- // Determine if a given value is included in the array or object using `===`.
- // Aliased as `contains`.
- _.include = _.contains = function(obj, target) {
- var found = false;
- if (obj == null) return found;
- if (nativeIndexOf && obj.indexOf === nativeIndexOf) return obj.indexOf(target) != -1;
- found = any(obj, function(value) {
- return value === target;
- });
- return found;
- };
-
- // Invoke a method (with arguments) on every item in a collection.
- _.invoke = function(obj, method) {
- var args = slice.call(arguments, 2);
- return _.map(obj, function(value) {
- return (_.isFunction(method) ? method || value : value[method]).apply(value, args);
- });
- };
-
- // Convenience version of a common use case of `map`: fetching a property.
- _.pluck = function(obj, key) {
- return _.map(obj, function(value){ return value[key]; });
- };
-
- // Return the maximum element or (element-based computation).
- _.max = function(obj, iterator, context) {
- if (!iterator && _.isArray(obj)) return Math.max.apply(Math, obj);
- if (!iterator && _.isEmpty(obj)) return -Infinity;
- var result = {computed : -Infinity};
- each(obj, function(value, index, list) {
- var computed = iterator ? iterator.call(context, value, index, list) : value;
- computed >= result.computed && (result = {value : value, computed : computed});
- });
- return result.value;
- };
-
- // Return the minimum element (or element-based computation).
- _.min = function(obj, iterator, context) {
- if (!iterator && _.isArray(obj)) return Math.min.apply(Math, obj);
- if (!iterator && _.isEmpty(obj)) return Infinity;
- var result = {computed : Infinity};
- each(obj, function(value, index, list) {
- var computed = iterator ? iterator.call(context, value, index, list) : value;
- computed < result.computed && (result = {value : value, computed : computed});
- });
- return result.value;
- };
-
- // Shuffle an array.
- _.shuffle = function(obj) {
- var shuffled = [], rand;
- each(obj, function(value, index, list) {
- if (index == 0) {
- shuffled[0] = value;
- } else {
- rand = Math.floor(Math.random() * (index + 1));
- shuffled[index] = shuffled[rand];
- shuffled[rand] = value;
- }
- });
- return shuffled;
- };
-
- // Sort the object's values by a criterion produced by an iterator.
- _.sortBy = function(obj, iterator, context) {
- return _.pluck(_.map(obj, function(value, index, list) {
- return {
- value : value,
- criteria : iterator.call(context, value, index, list)
- };
- }).sort(function(left, right) {
- var a = left.criteria, b = right.criteria;
- return a < b ? -1 : a > b ? 1 : 0;
- }), 'value');
- };
-
- // Groups the object's values by a criterion. Pass either a string attribute
- // to group by, or a function that returns the criterion.
- _.groupBy = function(obj, val) {
- var result = {};
- var iterator = _.isFunction(val) ? val : function(obj) { return obj[val]; };
- each(obj, function(value, index) {
- var key = iterator(value, index);
- (result[key] || (result[key] = [])).push(value);
- });
- return result;
- };
-
- // Use a comparator function to figure out at what index an object should
- // be inserted so as to maintain order. Uses binary search.
- _.sortedIndex = function(array, obj, iterator) {
- iterator || (iterator = _.identity);
- var low = 0, high = array.length;
- while (low < high) {
- var mid = (low + high) >> 1;
- iterator(array[mid]) < iterator(obj) ? low = mid + 1 : high = mid;
- }
- return low;
- };
-
- // Safely convert anything iterable into a real, live array.
- _.toArray = function(iterable) {
- if (!iterable) return [];
- if (iterable.toArray) return iterable.toArray();
- if (_.isArray(iterable)) return slice.call(iterable);
- if (_.isArguments(iterable)) return slice.call(iterable);
- return _.values(iterable);
- };
-
- // Return the number of elements in an object.
- _.size = function(obj) {
- return _.toArray(obj).length;
- };
-
- // Array Functions
- // ---------------
-
- // Get the first element of an array. Passing **n** will return the first N
- // values in the array. Aliased as `head`. The **guard** check allows it to work
- // with `_.map`.
- _.first = _.head = function(array, n, guard) {
- return (n != null) && !guard ? slice.call(array, 0, n) : array[0];
- };
-
- // Returns everything but the last entry of the array. Especcialy useful on
- // the arguments object. Passing **n** will return all the values in
- // the array, excluding the last N. The **guard** check allows it to work with
- // `_.map`.
- _.initial = function(array, n, guard) {
- return slice.call(array, 0, array.length - ((n == null) || guard ? 1 : n));
- };
-
- // Get the last element of an array. Passing **n** will return the last N
- // values in the array. The **guard** check allows it to work with `_.map`.
- _.last = function(array, n, guard) {
- if ((n != null) && !guard) {
- return slice.call(array, Math.max(array.length - n, 0));
- } else {
- return array[array.length - 1];
- }
- };
-
- // Returns everything but the first entry of the array. Aliased as `tail`.
- // Especially useful on the arguments object. Passing an **index** will return
- // the rest of the values in the array from that index onward. The **guard**
- // check allows it to work with `_.map`.
- _.rest = _.tail = function(array, index, guard) {
- return slice.call(array, (index == null) || guard ? 1 : index);
- };
-
- // Trim out all falsy values from an array.
- _.compact = function(array) {
- return _.filter(array, function(value){ return !!value; });
- };
-
- // Return a completely flattened version of an array.
- _.flatten = function(array, shallow) {
- return _.reduce(array, function(memo, value) {
- if (_.isArray(value)) return memo.concat(shallow ? value : _.flatten(value));
- memo[memo.length] = value;
- return memo;
- }, []);
- };
-
- // Return a version of the array that does not contain the specified value(s).
- _.without = function(array) {
- return _.difference(array, slice.call(arguments, 1));
- };
-
- // Produce a duplicate-free version of the array. If the array has already
- // been sorted, you have the option of using a faster algorithm.
- // Aliased as `unique`.
- _.uniq = _.unique = function(array, isSorted, iterator) {
- var initial = iterator ? _.map(array, iterator) : array;
- var result = [];
- _.reduce(initial, function(memo, el, i) {
- if (0 == i || (isSorted === true ? _.last(memo) != el : !_.include(memo, el))) {
- memo[memo.length] = el;
- result[result.length] = array[i];
- }
- return memo;
- }, []);
- return result;
- };
-
- // Produce an array that contains the union: each distinct element from all of
- // the passed-in arrays.
- _.union = function() {
- return _.uniq(_.flatten(arguments, true));
- };
-
- // Produce an array that contains every item shared between all the
- // passed-in arrays. (Aliased as "intersect" for back-compat.)
- _.intersection = _.intersect = function(array) {
- var rest = slice.call(arguments, 1);
- return _.filter(_.uniq(array), function(item) {
- return _.every(rest, function(other) {
- return _.indexOf(other, item) >= 0;
- });
- });
- };
-
- // Take the difference between one array and a number of other arrays.
- // Only the elements present in just the first array will remain.
- _.difference = function(array) {
- var rest = _.flatten(slice.call(arguments, 1));
- return _.filter(array, function(value){ return !_.include(rest, value); });
- };
-
- // Zip together multiple lists into a single array -- elements that share
- // an index go together.
- _.zip = function() {
- var args = slice.call(arguments);
- var length = _.max(_.pluck(args, 'length'));
- var results = new Array(length);
- for (var i = 0; i < length; i++) results[i] = _.pluck(args, "" + i);
- return results;
- };
-
- // If the browser doesn't supply us with indexOf (I'm looking at you, **MSIE**),
- // we need this function. Return the position of the first occurrence of an
- // item in an array, or -1 if the item is not included in the array.
- // Delegates to **ECMAScript 5**'s native `indexOf` if available.
- // If the array is large and already in sort order, pass `true`
- // for **isSorted** to use binary search.
- _.indexOf = function(array, item, isSorted) {
- if (array == null) return -1;
- var i, l;
- if (isSorted) {
- i = _.sortedIndex(array, item);
- return array[i] === item ? i : -1;
- }
- if (nativeIndexOf && array.indexOf === nativeIndexOf) return array.indexOf(item);
- for (i = 0, l = array.length; i < l; i++) if (i in array && array[i] === item) return i;
- return -1;
- };
-
- // Delegates to **ECMAScript 5**'s native `lastIndexOf` if available.
- _.lastIndexOf = function(array, item) {
- if (array == null) return -1;
- if (nativeLastIndexOf && array.lastIndexOf === nativeLastIndexOf) return array.lastIndexOf(item);
- var i = array.length;
- while (i--) if (i in array && array[i] === item) return i;
- return -1;
- };
-
- // Generate an integer Array containing an arithmetic progression. A port of
- // the native Python `range()` function. See
- // [the Python documentation](http://docs.python.org/library/functions.html#range).
- _.range = function(start, stop, step) {
- if (arguments.length <= 1) {
- stop = start || 0;
- start = 0;
- }
- step = arguments[2] || 1;
-
- var len = Math.max(Math.ceil((stop - start) / step), 0);
- var idx = 0;
- var range = new Array(len);
-
- while(idx < len) {
- range[idx++] = start;
- start += step;
- }
-
- return range;
- };
-
- // Function (ahem) Functions
- // ------------------
-
- // Reusable constructor function for prototype setting.
- var ctor = function(){};
-
- // Create a function bound to a given object (assigning `this`, and arguments,
- // optionally). Binding with arguments is also known as `curry`.
- // Delegates to **ECMAScript 5**'s native `Function.bind` if available.
- // We check for `func.bind` first, to fail fast when `func` is undefined.
- _.bind = function bind(func, context) {
- var bound, args;
- if (func.bind === nativeBind && nativeBind) return nativeBind.apply(func, slice.call(arguments, 1));
- if (!_.isFunction(func)) throw new TypeError;
- args = slice.call(arguments, 2);
- return bound = function() {
- if (!(this instanceof bound)) return func.apply(context, args.concat(slice.call(arguments)));
- ctor.prototype = func.prototype;
- var self = new ctor;
- var result = func.apply(self, args.concat(slice.call(arguments)));
- if (Object(result) === result) return result;
- return self;
- };
- };
-
- // Bind all of an object's methods to that object. Useful for ensuring that
- // all callbacks defined on an object belong to it.
- _.bindAll = function(obj) {
- var funcs = slice.call(arguments, 1);
- if (funcs.length == 0) funcs = _.functions(obj);
- each(funcs, function(f) { obj[f] = _.bind(obj[f], obj); });
- return obj;
- };
-
- // Memoize an expensive function by storing its results.
- _.memoize = function(func, hasher) {
- var memo = {};
- hasher || (hasher = _.identity);
- return function() {
- var key = hasher.apply(this, arguments);
- return _.has(memo, key) ? memo[key] : (memo[key] = func.apply(this, arguments));
- };
- };
-
- // Delays a function for the given number of milliseconds, and then calls
- // it with the arguments supplied.
- _.delay = function(func, wait) {
- var args = slice.call(arguments, 2);
- return setTimeout(function(){ return func.apply(func, args); }, wait);
- };
-
- // Defers a function, scheduling it to run after the current call stack has
- // cleared.
- _.defer = function(func) {
- return _.delay.apply(_, [func, 1].concat(slice.call(arguments, 1)));
- };
-
- // Returns a function, that, when invoked, will only be triggered at most once
- // during a given window of time.
- _.throttle = function(func, wait) {
- var context, args, timeout, throttling, more;
- var whenDone = _.debounce(function(){ more = throttling = false; }, wait);
- return function() {
- context = this; args = arguments;
- var later = function() {
- timeout = null;
- if (more) func.apply(context, args);
- whenDone();
- };
- if (!timeout) timeout = setTimeout(later, wait);
- if (throttling) {
- more = true;
- } else {
- func.apply(context, args);
- }
- whenDone();
- throttling = true;
- };
- };
-
- // Returns a function, that, as long as it continues to be invoked, will not
- // be triggered. The function will be called after it stops being called for
- // N milliseconds.
- _.debounce = function(func, wait) {
- var timeout;
- return function() {
- var context = this, args = arguments;
- var later = function() {
- timeout = null;
- func.apply(context, args);
- };
- clearTimeout(timeout);
- timeout = setTimeout(later, wait);
- };
- };
-
- // Returns a function that will be executed at most one time, no matter how
- // often you call it. Useful for lazy initialization.
- _.once = function(func) {
- var ran = false, memo;
- return function() {
- if (ran) return memo;
- ran = true;
- return memo = func.apply(this, arguments);
- };
- };
-
- // Returns the first function passed as an argument to the second,
- // allowing you to adjust arguments, run code before and after, and
- // conditionally execute the original function.
- _.wrap = function(func, wrapper) {
- return function() {
- var args = [func].concat(slice.call(arguments, 0));
- return wrapper.apply(this, args);
- };
- };
-
- // Returns a function that is the composition of a list of functions, each
- // consuming the return value of the function that follows.
- _.compose = function() {
- var funcs = arguments;
- return function() {
- var args = arguments;
- for (var i = funcs.length - 1; i >= 0; i--) {
- args = [funcs[i].apply(this, args)];
- }
- return args[0];
- };
- };
-
- // Returns a function that will only be executed after being called N times.
- _.after = function(times, func) {
- if (times <= 0) return func();
- return function() {
- if (--times < 1) { return func.apply(this, arguments); }
- };
- };
-
- // Object Functions
- // ----------------
-
- // Retrieve the names of an object's properties.
- // Delegates to **ECMAScript 5**'s native `Object.keys`
- _.keys = nativeKeys || function(obj) {
- if (obj !== Object(obj)) throw new TypeError('Invalid object');
- var keys = [];
- for (var key in obj) if (_.has(obj, key)) keys[keys.length] = key;
- return keys;
- };
-
- // Retrieve the values of an object's properties.
- _.values = function(obj) {
- return _.map(obj, _.identity);
- };
-
- // Return a sorted list of the function names available on the object.
- // Aliased as `methods`
- _.functions = _.methods = function(obj) {
- var names = [];
- for (var key in obj) {
- if (_.isFunction(obj[key])) names.push(key);
- }
- return names.sort();
- };
-
- // Extend a given object with all the properties in passed-in object(s).
- _.extend = function(obj) {
- each(slice.call(arguments, 1), function(source) {
- for (var prop in source) {
- obj[prop] = source[prop];
- }
- });
- return obj;
- };
-
- // Fill in a given object with default properties.
- _.defaults = function(obj) {
- each(slice.call(arguments, 1), function(source) {
- for (var prop in source) {
- if (obj[prop] == null) obj[prop] = source[prop];
- }
- });
- return obj;
- };
-
- // Create a (shallow-cloned) duplicate of an object.
- _.clone = function(obj) {
- if (!_.isObject(obj)) return obj;
- return _.isArray(obj) ? obj.slice() : _.extend({}, obj);
- };
-
- // Invokes interceptor with the obj, and then returns obj.
- // The primary purpose of this method is to "tap into" a method chain, in
- // order to perform operations on intermediate results within the chain.
- _.tap = function(obj, interceptor) {
- interceptor(obj);
- return obj;
- };
-
- // Internal recursive comparison function.
- function eq(a, b, stack) {
- // Identical objects are equal. `0 === -0`, but they aren't identical.
- // See the Harmony `egal` proposal: http://wiki.ecmascript.org/doku.php?id=harmony:egal.
- if (a === b) return a !== 0 || 1 / a == 1 / b;
- // A strict comparison is necessary because `null == undefined`.
- if (a == null || b == null) return a === b;
- // Unwrap any wrapped objects.
- if (a._chain) a = a._wrapped;
- if (b._chain) b = b._wrapped;
- // Invoke a custom `isEqual` method if one is provided.
- if (a.isEqual && _.isFunction(a.isEqual)) return a.isEqual(b);
- if (b.isEqual && _.isFunction(b.isEqual)) return b.isEqual(a);
- // Compare `[[Class]]` names.
- var className = toString.call(a);
- if (className != toString.call(b)) return false;
- switch (className) {
- // Strings, numbers, dates, and booleans are compared by value.
- case '[object String]':
- // Primitives and their corresponding object wrappers are equivalent; thus, `"5"` is
- // equivalent to `new String("5")`.
- return a == String(b);
- case '[object Number]':
- // `NaN`s are equivalent, but non-reflexive. An `egal` comparison is performed for
- // other numeric values.
- return a != +a ? b != +b : (a == 0 ? 1 / a == 1 / b : a == +b);
- case '[object Date]':
- case '[object Boolean]':
- // Coerce dates and booleans to numeric primitive values. Dates are compared by their
- // millisecond representations. Note that invalid dates with millisecond representations
- // of `NaN` are not equivalent.
- return +a == +b;
- // RegExps are compared by their source patterns and flags.
- case '[object RegExp]':
- return a.source == b.source &&
- a.global == b.global &&
- a.multiline == b.multiline &&
- a.ignoreCase == b.ignoreCase;
- }
- if (typeof a != 'object' || typeof b != 'object') return false;
- // Assume equality for cyclic structures. The algorithm for detecting cyclic
- // structures is adapted from ES 5.1 section 15.12.3, abstract operation `JO`.
- var length = stack.length;
- while (length--) {
- // Linear search. Performance is inversely proportional to the number of
- // unique nested structures.
- if (stack[length] == a) return true;
- }
- // Add the first object to the stack of traversed objects.
- stack.push(a);
- var size = 0, result = true;
- // Recursively compare objects and arrays.
- if (className == '[object Array]') {
- // Compare array lengths to determine if a deep comparison is necessary.
- size = a.length;
- result = size == b.length;
- if (result) {
- // Deep compare the contents, ignoring non-numeric properties.
- while (size--) {
- // Ensure commutative equality for sparse arrays.
- if (!(result = size in a == size in b && eq(a[size], b[size], stack))) break;
- }
- }
- } else {
- // Objects with different constructors are not equivalent.
- if ('constructor' in a != 'constructor' in b || a.constructor != b.constructor) return false;
- // Deep compare objects.
- for (var key in a) {
- if (_.has(a, key)) {
- // Count the expected number of properties.
- size++;
- // Deep compare each member.
- if (!(result = _.has(b, key) && eq(a[key], b[key], stack))) break;
- }
- }
- // Ensure that both objects contain the same number of properties.
- if (result) {
- for (key in b) {
- if (_.has(b, key) && !(size--)) break;
- }
- result = !size;
- }
- }
- // Remove the first object from the stack of traversed objects.
- stack.pop();
- return result;
- }
-
- // Perform a deep comparison to check if two objects are equal.
- _.isEqual = function(a, b) {
- return eq(a, b, []);
- };
-
- // Is a given array, string, or object empty?
- // An "empty" object has no enumerable own-properties.
- _.isEmpty = function(obj) {
- if (_.isArray(obj) || _.isString(obj)) return obj.length === 0;
- for (var key in obj) if (_.has(obj, key)) return false;
- return true;
- };
-
- // Is a given value a DOM element?
- _.isElement = function(obj) {
- return !!(obj && obj.nodeType == 1);
- };
-
- // Is a given value an array?
- // Delegates to ECMA5's native Array.isArray
- _.isArray = nativeIsArray || function(obj) {
- return toString.call(obj) == '[object Array]';
- };
-
- // Is a given variable an object?
- _.isObject = function(obj) {
- return obj === Object(obj);
- };
-
- // Is a given variable an arguments object?
- _.isArguments = function(obj) {
- return toString.call(obj) == '[object Arguments]';
- };
- if (!_.isArguments(arguments)) {
- _.isArguments = function(obj) {
- return !!(obj && _.has(obj, 'callee'));
- };
- }
-
- // Is a given value a function?
- _.isFunction = function(obj) {
- return toString.call(obj) == '[object Function]';
- };
-
- // Is a given value a string?
- _.isString = function(obj) {
- return toString.call(obj) == '[object String]';
- };
-
- // Is a given value a number?
- _.isNumber = function(obj) {
- return toString.call(obj) == '[object Number]';
- };
-
- // Is the given value `NaN`?
- _.isNaN = function(obj) {
- // `NaN` is the only value for which `===` is not reflexive.
- return obj !== obj;
- };
-
- // Is a given value a boolean?
- _.isBoolean = function(obj) {
- return obj === true || obj === false || toString.call(obj) == '[object Boolean]';
- };
-
- // Is a given value a date?
- _.isDate = function(obj) {
- return toString.call(obj) == '[object Date]';
- };
-
- // Is the given value a regular expression?
- _.isRegExp = function(obj) {
- return toString.call(obj) == '[object RegExp]';
- };
-
- // Is a given value equal to null?
- _.isNull = function(obj) {
- return obj === null;
- };
-
- // Is a given variable undefined?
- _.isUndefined = function(obj) {
- return obj === void 0;
- };
-
- // Has own property?
- _.has = function(obj, key) {
- return hasOwnProperty.call(obj, key);
- };
-
- // Utility Functions
- // -----------------
-
- // Run Underscore.js in *noConflict* mode, returning the `_` variable to its
- // previous owner. Returns a reference to the Underscore object.
- _.noConflict = function() {
- root._ = previousUnderscore;
- return this;
- };
-
- // Keep the identity function around for default iterators.
- _.identity = function(value) {
- return value;
- };
-
- // Run a function **n** times.
- _.times = function (n, iterator, context) {
- for (var i = 0; i < n; i++) iterator.call(context, i);
- };
-
- // Escape a string for HTML interpolation.
- _.escape = function(string) {
- return (''+string).replace(/&/g, '&').replace(/</g, '<').replace(/>/g, '>').replace(/"/g, '"').replace(/'/g, ''').replace(/\//g,'/');
- };
-
- // Add your own custom functions to the Underscore object, ensuring that
- // they're correctly added to the OOP wrapper as well.
- _.mixin = function(obj) {
- each(_.functions(obj), function(name){
- addToWrapper(name, _[name] = obj[name]);
- });
- };
-
- // Generate a unique integer id (unique within the entire client session).
- // Useful for temporary DOM ids.
- var idCounter = 0;
- _.uniqueId = function(prefix) {
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- // By default, Underscore uses ERB-style template delimiters, change the
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- _.templateSettings = {
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- interpolate : /<%=([\s\S]+?)%>/g,
- escape : /<%-([\s\S]+?)%>/g
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-
- // Within an interpolation, evaluation, or escaping, remove HTML escaping
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- var unescape = function(code) {
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- };
-
- // JavaScript micro-templating, similar to John Resig's implementation.
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- _.template = function(str, data) {
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- })
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- _.chain = function(obj) {
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- };
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- // can be used OO-style. This wrapper holds altered versions of all the
- // underscore functions. Wrapped objects may be chained.
- var wrapper = function(obj) { this._wrapped = obj; };
-
- // Expose `wrapper.prototype` as `_.prototype`
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- };
-
- // Add all of the Underscore functions to the wrapper object.
- _.mixin(_);
-
- // Add all mutator Array functions to the wrapper.
- each(['pop', 'push', 'reverse', 'shift', 'sort', 'splice', 'unshift'], function(name) {
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- return this;
- };
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- // Extracts the result from a wrapped and chained object.
- wrapper.prototype.value = function() {
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diff --git a/docs/build/html/_static/underscore.js b/docs/build/html/_static/underscore.js
index 5b55f32beaca186f84cca115514f02cddbd1bbd5..cf177d4285ab55fbc16406a5ec827b80e7eecd53 100644
--- a/docs/build/html/_static/underscore.js
+++ b/docs/build/html/_static/underscore.js
@@ -1,31 +1,6 @@
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diff --git a/docs/build/html/binary_c_parameters.html b/docs/build/html/binary_c_parameters.html
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@@ -106,69 +59,30 @@
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@@ -193,15 +107,15 @@
text-align: unset;
}
</style>
-<div class="section" id="binary-c-parameters">
-<h1>Binary_c parameters<a class="headerlink" href="#binary-c-parameters" title="Permalink to this headline">¶</a></h1>
+<section id="binary-c-parameters">
+<h1>Binary_c parameters<a class="headerlink" href="#binary-c-parameters" title="Permalink to this headline">ïƒ</a></h1>
<p>The following chapter contains all the parameters that the current version of binary_c can handle, along with their descriptions and other properties.</p>
<dl class="simple">
-<dt>This information was obtained by the following binary_c build:</dt><dd><p><strong>binary_c git branch</strong>: newmaster <strong>binary_c git revision</strong>: 6185:20210910:1621c23a5 <strong>Built on</strong>: Sep 10 2021 15:05:46</p>
+<dt>This information was obtained by the following binary_c build:</dt><dd><p><strong>binary_c git branch</strong>: master <strong>binary_c git revision</strong>: 6209:20211006:c4a4c332e <strong>Built on</strong>: Oct 6 2021 08:31:27</p>
</dd>
</dl>
-<div class="section" id="section-stars">
-<h2>Section: stars<a class="headerlink" href="#section-stars" title="Permalink to this headline">¶</a></h2>
+<section id="section-stars">
+<h2>Section: stars<a class="headerlink" href="#section-stars" title="Permalink to this headline">ïƒ</a></h2>
<div class="line-block">
<div class="line"><strong>Parameter</strong>: metallicity</div>
<div class="line"><strong>Description</strong>: This sets the metallicity of the stars, i.e. the amount (by mass) of matter which is not hydrogen or helium. If you are using the BSE algorithm, this must be 1e-4 <= metallicity <= 0.03. See also nucsyn_metallicity and effective_metallicity.</div>
@@ -1493,9 +1407,9 @@
<div class="line"><strong>Parameter input type</strong>: Float</div>
<div class="line"><strong>Default value</strong>: 0</div>
</div>
-</div>
-<div class="section" id="section-binary">
-<h2>Section: binary<a class="headerlink" href="#section-binary" title="Permalink to this headline">¶</a></h2>
+</section>
+<section id="section-binary">
+<h2>Section: binary<a class="headerlink" href="#section-binary" title="Permalink to this headline">ïƒ</a></h2>
<div class="line-block">
<div class="line"><strong>Parameter</strong>: separation</div>
<div class="line"><strong>Description</strong>: Set the orbital separation (actually the semi-major axis) of the binary (internal index 0, stellar indices 0 and 1) in solar radii. Note that if the orbital period is given, it is used to calculate the separation. So if you want to set the separation instead, either do not set the orbital period or set the orbital period to zero (0.0).</div>
@@ -2657,9 +2571,9 @@
<div class="line"><strong>Parameter input type</strong>: Float</div>
<div class="line"><strong>Default value</strong>: 0.05</div>
</div>
-</div>
-<div class="section" id="section-nucsyn">
-<h2>Section: nucsyn<a class="headerlink" href="#section-nucsyn" title="Permalink to this headline">¶</a></h2>
+</section>
+<section id="section-nucsyn">
+<h2>Section: nucsyn<a class="headerlink" href="#section-nucsyn" title="Permalink to this headline">ïƒ</a></h2>
<div class="line-block">
<div class="line"><strong>Parameter</strong>: third_dup</div>
<div class="line"><strong>Description</strong>: If True, enables third dredge up. Requires NUCSYN and NUCSYN_THIRD_DREDGE_UP.</div>
@@ -2923,9 +2837,9 @@
<div class="line"><strong>Parameter input type</strong>: Float</div>
<div class="line"><strong>Default value</strong>: NULL</div>
</div>
-</div>
-<div class="section" id="section-output">
-<h2>Section: output<a class="headerlink" href="#section-output" title="Permalink to this headline">¶</a></h2>
+</section>
+<section id="section-output">
+<h2>Section: output<a class="headerlink" href="#section-output" title="Permalink to this headline">ïƒ</a></h2>
<div class="line-block">
<div class="line"><strong>Parameter</strong>: cf_amanda_log</div>
<div class="line"><strong>Description</strong>: Enable logging to compare to Amanda’s models.</div>
@@ -3203,9 +3117,16 @@
<div class="line"><strong>Default value</strong>: NULL</div>
<div class="line"><strong>Extra</strong>: Ignore</div>
</div>
+<div class="line-block">
+<div class="line"><strong>Parameter</strong>: tides_diagnosis_log</div>
+<div class="line"><strong>Description</strong>: Enable logging to test MINT tides. Requires MINT. Choices are: 0 disabled, 1 enable lambda test.</div>
+<div class="line"><strong>Parameter input type</strong>: Integer</div>
+<div class="line"><strong>Default value</strong>: 0</div>
+<div class="line"><strong>Extra</strong>: Ignore</div>
</div>
-<div class="section" id="section-input">
-<h2>Section: input<a class="headerlink" href="#section-input" title="Permalink to this headline">¶</a></h2>
+</section>
+<section id="section-input">
+<h2>Section: input<a class="headerlink" href="#section-input" title="Permalink to this headline">ïƒ</a></h2>
<div class="line-block">
<div class="line"><strong>Parameter</strong>: MINT_dir</div>
<div class="line"><strong>Description</strong>: Location of MINT algorithm data.</div>
@@ -3320,9 +3241,9 @@
<div class="line"><strong>Default value</strong>: 0.1</div>
<div class="line"><strong>Extra</strong>:</div>
</div>
-</div>
-<div class="section" id="section-i-o">
-<h2>Section: i/o<a class="headerlink" href="#section-i-o" title="Permalink to this headline">¶</a></h2>
+</section>
+<section id="section-i-o">
+<h2>Section: i/o<a class="headerlink" href="#section-i-o" title="Permalink to this headline">ïƒ</a></h2>
<div class="line-block">
<div class="line"><strong>Parameter</strong>: go</div>
<div class="line"><strong>Description</strong>: batchmode control command</div>
@@ -3383,9 +3304,9 @@
<div class="line"><strong>Description</strong>: Output batchmode status information.</div>
<div class="line"><strong>Extra</strong>: Ignore</div>
</div>
-</div>
-<div class="section" id="section-algorithms">
-<h2>Section: algorithms<a class="headerlink" href="#section-algorithms" title="Permalink to this headline">¶</a></h2>
+</section>
+<section id="section-algorithms">
+<h2>Section: algorithms<a class="headerlink" href="#section-algorithms" title="Permalink to this headline">ïƒ</a></h2>
<div class="line-block">
<div class="line"><strong>Parameter</strong>: repeat</div>
<div class="line"><strong>Description</strong>: If > 1, repeats the system as many times as required. Handy if you’re using Monte-Carlo kicks and want to sample the parameter space well. Also, if you are running speed tests this is good to give a statistically more reasonable result. (See e.g. ‘tbse pgo’).</div>
@@ -3398,9 +3319,9 @@
<div class="line"><strong>Parameter input type</strong>: Integer</div>
<div class="line"><strong>Default value</strong>: 0</div>
</div>
-</div>
-<div class="section" id="section-misc">
-<h2>Section: misc<a class="headerlink" href="#section-misc" title="Permalink to this headline">¶</a></h2>
+</section>
+<section id="section-misc">
+<h2>Section: misc<a class="headerlink" href="#section-misc" title="Permalink to this headline">ïƒ</a></h2>
<div class="line-block">
<div class="line"><strong>Parameter</strong>: random_seed</div>
<div class="line"><strong>Description</strong>: Random number seed, usually a (possibly negative) integer. Useful for exactly reproducing the evolution of a system which involves a kick (which is a Monte-Carlo, i.e. pseudorandom, process).</div>
@@ -3472,69 +3393,44 @@
<div class="line"><strong>Default value</strong>: NULL</div>
<div class="line"><strong>Extra</strong>: Ignore</div>
</div>
-</div>
-</div>
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+Generated on binarycpython git branch: auto_resolution git revision be7bd630af892a785312affc34d87c57eb337fd3 url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/tree/auto_resolution">git url</a>.
<br><br>
-Using binary_c with bit branch newmaster: git revision: "6185:20210910:1621c23a5" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/newmaster">git url</a>.
+Using binary_c with bit branch master: git revision: "6209:20211006:c4a4c332e" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/master">git url</a>.
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-<div class="section" id="module-binarycpython.utils.custom_logging_functions">
-<span id="custom-logging-functions-module"></span><h1>custom_logging_functions module<a class="headerlink" href="#module-binarycpython.utils.custom_logging_functions" title="Permalink to this headline">¶</a></h1>
+<section id="module-binarycpython.utils.custom_logging_functions">
+<span id="custom-logging-functions-module"></span><h1>custom_logging_functions module<a class="headerlink" href="#module-binarycpython.utils.custom_logging_functions" title="Permalink to this headline">ïƒ</a></h1>
<p>Module containing functions for the custom logging functionality.
The functions here make it possible for the user to define binaryc output logs on runtime</p>
<dl class="py function">
-<dt id="binarycpython.utils.custom_logging_functions.autogen_C_logging_code">
-<code class="sig-prename descclassname">binarycpython.utils.custom_logging_functions.</code><code class="sig-name descname">autogen_C_logging_code</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">logging_dict</span></em>, <em class="sig-param"><span class="n">verbosity</span><span class="o">=</span><span class="default_value">0</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/custom_logging_functions.html#autogen_C_logging_code"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.custom_logging_functions.autogen_C_logging_code" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.custom_logging_functions.autogen_C_logging_code">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.custom_logging_functions.</span></span><span class="sig-name descname"><span class="pre">autogen_C_logging_code</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">logging_dict</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">verbosity</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/custom_logging_functions.html#autogen_C_logging_code"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.custom_logging_functions.autogen_C_logging_code" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function that auto-generates PRINTF statements for binaryc.
Input is a dictionary where the key is the header of that logging line
and items which are lists of parameters that will be put in that logging line</p>
@@ -238,8 +151,8 @@ and items which are lists of parameters that will be put in that logging line</p
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.custom_logging_functions.binary_c_log_code">
-<code class="sig-prename descclassname">binarycpython.utils.custom_logging_functions.</code><code class="sig-name descname">binary_c_log_code</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">code</span></em>, <em class="sig-param"><span class="n">verbosity</span><span class="o">=</span><span class="default_value">0</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/custom_logging_functions.html#binary_c_log_code"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.custom_logging_functions.binary_c_log_code" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.custom_logging_functions.binary_c_log_code">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.custom_logging_functions.</span></span><span class="sig-name descname"><span class="pre">binary_c_log_code</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">code</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">verbosity</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/custom_logging_functions.html#binary_c_log_code"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.custom_logging_functions.binary_c_log_code" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function to construct the code to construct the custom logging function</p>
<p class="rubric">Example</p>
<p>Code to log and terminate evolution when the primary star becomes a NS:</p>
@@ -283,8 +196,8 @@ and items which are lists of parameters that will be put in that logging line</p
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.custom_logging_functions.binary_c_write_log_code">
-<code class="sig-prename descclassname">binarycpython.utils.custom_logging_functions.</code><code class="sig-name descname">binary_c_write_log_code</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">code</span></em>, <em class="sig-param"><span class="n">filename</span></em>, <em class="sig-param"><span class="n">verbosity</span><span class="o">=</span><span class="default_value">0</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/custom_logging_functions.html#binary_c_write_log_code"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.custom_logging_functions.binary_c_write_log_code" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.custom_logging_functions.binary_c_write_log_code">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.custom_logging_functions.</span></span><span class="sig-name descname"><span class="pre">binary_c_write_log_code</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">code</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">filename</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">verbosity</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/custom_logging_functions.html#binary_c_write_log_code"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.custom_logging_functions.binary_c_write_log_code" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function to write the generated logging code to a file</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
@@ -301,8 +214,8 @@ and items which are lists of parameters that will be put in that logging line</p
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.custom_logging_functions.compile_shared_lib">
-<code class="sig-prename descclassname">binarycpython.utils.custom_logging_functions.</code><code class="sig-name descname">compile_shared_lib</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">code</span></em>, <em class="sig-param"><span class="n">sourcefile_name</span></em>, <em class="sig-param"><span class="n">outfile_name</span></em>, <em class="sig-param"><span class="n">verbosity</span><span class="o">=</span><span class="default_value">0</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/custom_logging_functions.html#compile_shared_lib"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.custom_logging_functions.compile_shared_lib" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.custom_logging_functions.compile_shared_lib">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.custom_logging_functions.</span></span><span class="sig-name descname"><span class="pre">compile_shared_lib</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">code</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sourcefile_name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">outfile_name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">verbosity</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/custom_logging_functions.html#compile_shared_lib"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.custom_logging_functions.compile_shared_lib" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function to write the custom logging code to a file and then compile it.</p>
<p>TODO: nicely put in the -fPIC
TODO: consider returning a status</p>
@@ -322,8 +235,8 @@ TODO: consider returning a status</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.custom_logging_functions.create_and_load_logging_function">
-<code class="sig-prename descclassname">binarycpython.utils.custom_logging_functions.</code><code class="sig-name descname">create_and_load_logging_function</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">custom_logging_code</span></em>, <em class="sig-param"><span class="n">verbosity</span><span class="o">=</span><span class="default_value">0</span></em>, <em class="sig-param"><span class="n">custom_tmp_dir</span><span class="o">=</span><span class="default_value">None</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/custom_logging_functions.html#create_and_load_logging_function"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.custom_logging_functions.create_and_load_logging_function" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.custom_logging_functions.create_and_load_logging_function">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.custom_logging_functions.</span></span><span class="sig-name descname"><span class="pre">create_and_load_logging_function</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">custom_logging_code</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">verbosity</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">custom_tmp_dir</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/custom_logging_functions.html#create_and_load_logging_function"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.custom_logging_functions.create_and_load_logging_function" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function to automatically compile the shared library with the given
custom logging code and load it with ctypes.</p>
<p>This function is more or less the main function of this module and unless you know what you’re doing with the other functions
@@ -345,8 +258,8 @@ I recommend using this in function in combination with a function that generates
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.custom_logging_functions.from_binary_c_config">
-<code class="sig-prename descclassname">binarycpython.utils.custom_logging_functions.</code><code class="sig-name descname">from_binary_c_config</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">config_file</span></em>, <em class="sig-param"><span class="n">flag</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/custom_logging_functions.html#from_binary_c_config"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.custom_logging_functions.from_binary_c_config" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.custom_logging_functions.from_binary_c_config">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.custom_logging_functions.</span></span><span class="sig-name descname"><span class="pre">from_binary_c_config</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">config_file</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">flag</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/custom_logging_functions.html#from_binary_c_config"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.custom_logging_functions.from_binary_c_config" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function to run the binaryc_config command with flags</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
@@ -365,8 +278,8 @@ I recommend using this in function in combination with a function that generates
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.custom_logging_functions.return_compilation_dict">
-<code class="sig-prename descclassname">binarycpython.utils.custom_logging_functions.</code><code class="sig-name descname">return_compilation_dict</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">verbosity</span><span class="o">=</span><span class="default_value">0</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/custom_logging_functions.html#return_compilation_dict"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.custom_logging_functions.return_compilation_dict" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.custom_logging_functions.return_compilation_dict">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.custom_logging_functions.</span></span><span class="sig-name descname"><span class="pre">return_compilation_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">verbosity</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/custom_logging_functions.html#return_compilation_dict"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.custom_logging_functions.return_compilation_dict" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function to build the compile command for the shared library</p>
<p>Inspired by binary_c_inline_config command in Perl</p>
<p>TODO: this function still has some cleaning up to do w.r.t. default values for the compile command
@@ -384,68 +297,43 @@ I recommend using this in function in combination with a function that generates
</dl>
</dd></dl>
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+Generated on binarycpython git branch: auto_resolution git revision be7bd630af892a785312affc34d87c57eb337fd3 url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/tree/auto_resolution">git url</a>.
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-Using binary_c with bit branch newmaster: git revision: "6185:20210910:1621c23a5" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/newmaster">git url</a>.
+Using binary_c with bit branch master: git revision: "6209:20211006:c4a4c332e" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/master">git url</a>.
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-<div class="section" id="module-binarycpython.utils.distribution_functions">
-<span id="distribution-functions-module"></span><h1>distribution_functions module<a class="headerlink" href="#module-binarycpython.utils.distribution_functions" title="Permalink to this headline">¶</a></h1>
+<section id="module-binarycpython.utils.distribution_functions">
+<span id="distribution-functions-module"></span><h1>distribution_functions module<a class="headerlink" href="#module-binarycpython.utils.distribution_functions" title="Permalink to this headline">ïƒ</a></h1>
<p>Module containing the predefined distribution functions</p>
<p>The user can use any of these distribution functions to
generate probability distributions for sampling populations</p>
@@ -226,8 +139,8 @@ generate probability distributions for sampling populations</p>
</dd>
</dl>
<dl class="py function">
-<dt id="binarycpython.utils.distribution_functions.Arenou2010_binary_fraction">
-<code class="sig-prename descclassname">binarycpython.utils.distribution_functions.</code><code class="sig-name descname">Arenou2010_binary_fraction</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">m</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#Arenou2010_binary_fraction"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.Arenou2010_binary_fraction" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.distribution_functions.Arenou2010_binary_fraction">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.distribution_functions.</span></span><span class="sig-name descname"><span class="pre">Arenou2010_binary_fraction</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">m</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#Arenou2010_binary_fraction"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.Arenou2010_binary_fraction" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Arenou 2010 function for the binary fraction as f(M1)</p>
<p>GAIA-C2-SP-OPM-FA-054
www.rssd.esa.int/doc_fetch.php?id=2969346</p>
@@ -245,8 +158,8 @@ www.rssd.esa.int/doc_fetch.php?id=2969346</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.distribution_functions.Izzard2012_period_distribution">
-<code class="sig-prename descclassname">binarycpython.utils.distribution_functions.</code><code class="sig-name descname">Izzard2012_period_distribution</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">P</span></em>, <em class="sig-param"><span class="n">M1</span></em>, <em class="sig-param"><span class="n">log10Pmin</span><span class="o">=</span><span class="default_value">1</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#Izzard2012_period_distribution"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.Izzard2012_period_distribution" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.distribution_functions.Izzard2012_period_distribution">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.distribution_functions.</span></span><span class="sig-name descname"><span class="pre">Izzard2012_period_distribution</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">P</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">M1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">log10Pmin</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#Izzard2012_period_distribution"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.Izzard2012_period_distribution" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>period distribution which interpolates between
Duquennoy and Mayor 1991 at low mass (G/K spectral type <~1.15Msun)
and Sana et al 2012 at high mass (O spectral type >~16.3Msun)</p>
@@ -271,8 +184,8 @@ and Sana’s power law (as a function of logP) at high mass</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.distribution_functions.Kroupa2001">
-<code class="sig-prename descclassname">binarycpython.utils.distribution_functions.</code><code class="sig-name descname">Kroupa2001</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">m</span></em>, <em class="sig-param"><span class="n">newopts</span><span class="o">=</span><span class="default_value">None</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#Kroupa2001"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.Kroupa2001" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.distribution_functions.Kroupa2001">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.distribution_functions.</span></span><span class="sig-name descname"><span class="pre">Kroupa2001</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">m</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">newopts</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#Kroupa2001"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.Kroupa2001" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Probability distribution function for Kroupa 2001 IMF, where the default values to the
three_part_powerlaw are: default = {“m0â€: 0.1, “m1â€: 0.5, “m2â€: 1, “mmaxâ€: 100, “p1â€: -1.3, “p2â€: -2.3,â€p3â€: -2.3}</p>
<dl class="field-list simple">
@@ -292,8 +205,8 @@ three_part_powerlaw are: default = {“m0â€: 0.1, “m1â€: 0.5, “m2â€: 1,
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.distribution_functions.Moe_di_Stefano_2017_multiplicity_fractions">
-<code class="sig-prename descclassname">binarycpython.utils.distribution_functions.</code><code class="sig-name descname">Moe_di_Stefano_2017_multiplicity_fractions</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">options</span></em>, <em class="sig-param"><span class="n">verbosity</span><span class="o">=</span><span class="default_value">0</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#Moe_di_Stefano_2017_multiplicity_fractions"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.Moe_di_Stefano_2017_multiplicity_fractions" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.distribution_functions.Moe_di_Stefano_2017_multiplicity_fractions">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.distribution_functions.</span></span><span class="sig-name descname"><span class="pre">Moe_di_Stefano_2017_multiplicity_fractions</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">options</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">verbosity</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#Moe_di_Stefano_2017_multiplicity_fractions"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.Moe_di_Stefano_2017_multiplicity_fractions" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function that creates a list of probability fractions and
normalises and merges them according to the users choice.</p>
<p>TODO: make an extrapolation functionality in this. log10(1.6e1)
@@ -304,8 +217,8 @@ of the mass range is now the last known value</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.distribution_functions.Moe_di_Stefano_2017_pdf">
-<code class="sig-prename descclassname">binarycpython.utils.distribution_functions.</code><code class="sig-name descname">Moe_di_Stefano_2017_pdf</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">options</span></em>, <em class="sig-param"><span class="n">verbosity</span><span class="o">=</span><span class="default_value">0</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#Moe_di_Stefano_2017_pdf"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.Moe_di_Stefano_2017_pdf" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.distribution_functions.Moe_di_Stefano_2017_pdf">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.distribution_functions.</span></span><span class="sig-name descname"><span class="pre">Moe_di_Stefano_2017_pdf</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">options</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">verbosity</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#Moe_di_Stefano_2017_pdf"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.Moe_di_Stefano_2017_pdf" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Moe & diStefano function to calculate the probability density.</p>
<p>takes a dictionary as input (in options) with options:</p>
<p>M1, M2, M3, M4 => masses (Msun) [M1 required, rest optional]
@@ -316,33 +229,33 @@ mmax => maximum allowed stellar mass (default 80.0)</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.distribution_functions.build_q_table">
-<code class="sig-prename descclassname">binarycpython.utils.distribution_functions.</code><code class="sig-name descname">build_q_table</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">options</span></em>, <em class="sig-param"><span class="n">m</span></em>, <em class="sig-param"><span class="n">p</span></em>, <em class="sig-param"><span class="n">verbosity</span><span class="o">=</span><span class="default_value">0</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#build_q_table"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.build_q_table" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.distribution_functions.build_q_table">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.distribution_functions.</span></span><span class="sig-name descname"><span class="pre">build_q_table</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">options</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">m</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">p</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">verbosity</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#build_q_table"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.build_q_table" title="Permalink to this definition">ïƒ</a></dt>
<dd></dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.distribution_functions.calc_P_integral">
-<code class="sig-prename descclassname">binarycpython.utils.distribution_functions.</code><code class="sig-name descname">calc_P_integral</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">options</span></em>, <em class="sig-param"><span class="n">min_P</span></em>, <em class="sig-param"><span class="n">integrals_string</span></em>, <em class="sig-param"><span class="n">interpolator_name</span></em>, <em class="sig-param"><span class="n">mass_string</span></em>, <em class="sig-param"><span class="n">verbosity</span><span class="o">=</span><span class="default_value">0</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#calc_P_integral"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.calc_P_integral" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.distribution_functions.calc_P_integral">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.distribution_functions.</span></span><span class="sig-name descname"><span class="pre">calc_P_integral</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">options</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">min_P</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">integrals_string</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interpolator_name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mass_string</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">verbosity</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#calc_P_integral"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.calc_P_integral" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function to calculate the P integral</p>
<p>We need to renormalise this because min_per > 0, and not all periods should be included</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.distribution_functions.calc_e_integral">
-<code class="sig-prename descclassname">binarycpython.utils.distribution_functions.</code><code class="sig-name descname">calc_e_integral</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">options</span></em>, <em class="sig-param"><span class="n">integrals_string</span></em>, <em class="sig-param"><span class="n">interpolator_name</span></em>, <em class="sig-param"><span class="n">mass_string</span></em>, <em class="sig-param"><span class="n">period_string</span></em>, <em class="sig-param"><span class="n">verbosity</span><span class="o">=</span><span class="default_value">0</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#calc_e_integral"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.calc_e_integral" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.distribution_functions.calc_e_integral">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.distribution_functions.</span></span><span class="sig-name descname"><span class="pre">calc_e_integral</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">options</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">integrals_string</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interpolator_name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mass_string</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">period_string</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">verbosity</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#calc_e_integral"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.calc_e_integral" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function to calculate the P integral</p>
<p>We need to renormalise this because min_per > 0, and not all periods should be included</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.distribution_functions.calc_total_probdens">
-<code class="sig-prename descclassname">binarycpython.utils.distribution_functions.</code><code class="sig-name descname">calc_total_probdens</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">prob_dict</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#calc_total_probdens"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.calc_total_probdens" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.distribution_functions.calc_total_probdens">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.distribution_functions.</span></span><span class="sig-name descname"><span class="pre">calc_total_probdens</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">prob_dict</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#calc_total_probdens"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.calc_total_probdens" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function to calculate the total probability density</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.distribution_functions.calculate_constants_three_part_powerlaw">
-<code class="sig-prename descclassname">binarycpython.utils.distribution_functions.</code><code class="sig-name descname">calculate_constants_three_part_powerlaw</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">m0</span></em>, <em class="sig-param"><span class="n">m1</span></em>, <em class="sig-param"><span class="n">m2</span></em>, <em class="sig-param"><span class="n">m_max</span></em>, <em class="sig-param"><span class="n">p1</span></em>, <em class="sig-param"><span class="n">p2</span></em>, <em class="sig-param"><span class="n">p3</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#calculate_constants_three_part_powerlaw"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.calculate_constants_three_part_powerlaw" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.distribution_functions.calculate_constants_three_part_powerlaw">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.distribution_functions.</span></span><span class="sig-name descname"><span class="pre">calculate_constants_three_part_powerlaw</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">m0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">m1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">m2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">m_max</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">p1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">p2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">p3</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#calculate_constants_three_part_powerlaw"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.calculate_constants_three_part_powerlaw" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function to calculate the constants for a three-part power law</p>
<p>TODO: use the power law_constant function to calculate all these values</p>
<dl class="field-list simple">
@@ -367,8 +280,8 @@ mmax => maximum allowed stellar mass (default 80.0)</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.distribution_functions.const">
-<code class="sig-prename descclassname">binarycpython.utils.distribution_functions.</code><code class="sig-name descname">const</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">min_bound</span></em>, <em class="sig-param"><span class="n">max_bound</span></em>, <em class="sig-param"><span class="n">val</span><span class="o">=</span><span class="default_value">None</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#const"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.const" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.distribution_functions.const">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.distribution_functions.</span></span><span class="sig-name descname"><span class="pre">const</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">min_bound</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_bound</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">val</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#const"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.const" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>a constant distribution function between min=min_bound and max=max_bound.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
@@ -387,8 +300,8 @@ mmax => maximum allowed stellar mass (default 80.0)</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.distribution_functions.cosmic_SFH_madau_dickinson2014">
-<code class="sig-prename descclassname">binarycpython.utils.distribution_functions.</code><code class="sig-name descname">cosmic_SFH_madau_dickinson2014</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">z</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#cosmic_SFH_madau_dickinson2014"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.cosmic_SFH_madau_dickinson2014" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.distribution_functions.cosmic_SFH_madau_dickinson2014">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.distribution_functions.</span></span><span class="sig-name descname"><span class="pre">cosmic_SFH_madau_dickinson2014</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">z</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#cosmic_SFH_madau_dickinson2014"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.cosmic_SFH_madau_dickinson2014" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Cosmic star formation history distribution from Madau & Dickonson 2014 (<a class="reference external" href="https://arxiv.org/pdf/1403.0007.pdf">https://arxiv.org/pdf/1403.0007.pdf</a>)</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
@@ -401,8 +314,8 @@ mmax => maximum allowed stellar mass (default 80.0)</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.distribution_functions.duquennoy1991">
-<code class="sig-prename descclassname">binarycpython.utils.distribution_functions.</code><code class="sig-name descname">duquennoy1991</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">logper</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#duquennoy1991"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.duquennoy1991" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.distribution_functions.duquennoy1991">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.distribution_functions.</span></span><span class="sig-name descname"><span class="pre">duquennoy1991</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">logper</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#duquennoy1991"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.duquennoy1991" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Period distribution from Duquennoy + Mayor 1991. Evaluated the function gaussian(logper, 4.8, 2.3, -2, 12)</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
@@ -418,16 +331,16 @@ mmax => maximum allowed stellar mass (default 80.0)</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.distribution_functions.fill_data">
-<code class="sig-prename descclassname">binarycpython.utils.distribution_functions.</code><code class="sig-name descname">fill_data</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">sample_values</span></em>, <em class="sig-param"><span class="n">data_dict</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#fill_data"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.fill_data" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.distribution_functions.fill_data">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.distribution_functions.</span></span><span class="sig-name descname"><span class="pre">fill_data</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">sample_values</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_dict</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#fill_data"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.fill_data" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function that returns the normalised array of values for given logmass and logperiod
used for the e and q values</p>
<p>TODO: make sure we do the correct thing with the dstep</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.distribution_functions.flat">
-<code class="sig-prename descclassname">binarycpython.utils.distribution_functions.</code><code class="sig-name descname">flat</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#flat"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.flat" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.distribution_functions.flat">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.distribution_functions.</span></span><span class="sig-name descname"><span class="pre">flat</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#flat"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.flat" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Dummy distribution function that returns 1</p>
<dl class="field-list simple">
<dt class="field-odd">Returns</dt>
@@ -440,8 +353,8 @@ used for the e and q values</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.distribution_functions.flatsections">
-<code class="sig-prename descclassname">binarycpython.utils.distribution_functions.</code><code class="sig-name descname">flatsections</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">x</span></em>, <em class="sig-param"><span class="n">opts</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#flatsections"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.flatsections" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.distribution_functions.flatsections">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.distribution_functions.</span></span><span class="sig-name descname"><span class="pre">flatsections</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">x</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">opts</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#flatsections"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.flatsections" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function to generate flat distributions, possibly in multiple sections</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
@@ -460,8 +373,8 @@ used for the e and q values</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.distribution_functions.gaussian">
-<code class="sig-prename descclassname">binarycpython.utils.distribution_functions.</code><code class="sig-name descname">gaussian</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">x</span></em>, <em class="sig-param"><span class="n">mean</span></em>, <em class="sig-param"><span class="n">sigma</span></em>, <em class="sig-param"><span class="n">gmin</span></em>, <em class="sig-param"><span class="n">gmax</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#gaussian"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.gaussian" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.distribution_functions.gaussian">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.distribution_functions.</span></span><span class="sig-name descname"><span class="pre">gaussian</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">x</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mean</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sigma</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">gmin</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">gmax</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#gaussian"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.gaussian" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Gaussian distribution function. used for e..g Duquennoy + Mayor 1991</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
@@ -483,8 +396,8 @@ used for the e and q values</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.distribution_functions.gaussian_func">
-<code class="sig-prename descclassname">binarycpython.utils.distribution_functions.</code><code class="sig-name descname">gaussian_func</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">x</span></em>, <em class="sig-param"><span class="n">mean</span></em>, <em class="sig-param"><span class="n">sigma</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#gaussian_func"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.gaussian_func" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.distribution_functions.gaussian_func">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.distribution_functions.</span></span><span class="sig-name descname"><span class="pre">gaussian_func</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">x</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mean</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sigma</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#gaussian_func"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.gaussian_func" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function to evaluate a Gaussian at a given point, but this time without any boundaries.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
@@ -504,8 +417,8 @@ used for the e and q values</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.distribution_functions.gaussian_normalizing_const">
-<code class="sig-prename descclassname">binarycpython.utils.distribution_functions.</code><code class="sig-name descname">gaussian_normalizing_const</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">mean</span></em>, <em class="sig-param"><span class="n">sigma</span></em>, <em class="sig-param"><span class="n">gmin</span></em>, <em class="sig-param"><span class="n">gmax</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#gaussian_normalizing_const"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.gaussian_normalizing_const" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.distribution_functions.gaussian_normalizing_const">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.distribution_functions.</span></span><span class="sig-name descname"><span class="pre">gaussian_normalizing_const</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">mean</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sigma</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">gmin</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">gmax</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#gaussian_normalizing_const"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.gaussian_normalizing_const" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function to calculate the normalisation constant for the Gaussian</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
@@ -526,20 +439,20 @@ used for the e and q values</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.distribution_functions.get_integration_constant_q">
-<code class="sig-prename descclassname">binarycpython.utils.distribution_functions.</code><code class="sig-name descname">get_integration_constant_q</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">q_interpolator</span></em>, <em class="sig-param"><span class="n">tmp_table</span></em>, <em class="sig-param"><span class="n">qdata</span></em>, <em class="sig-param"><span class="n">verbosity</span><span class="o">=</span><span class="default_value">0</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#get_integration_constant_q"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.get_integration_constant_q" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.distribution_functions.get_integration_constant_q">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.distribution_functions.</span></span><span class="sig-name descname"><span class="pre">get_integration_constant_q</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">q_interpolator</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tmp_table</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">qdata</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">verbosity</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#get_integration_constant_q"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.get_integration_constant_q" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function to integrate the q interpolator and return the integration constant</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.distribution_functions.get_max_multiplicity">
-<code class="sig-prename descclassname">binarycpython.utils.distribution_functions.</code><code class="sig-name descname">get_max_multiplicity</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">multiplicity_array</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#get_max_multiplicity"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.get_max_multiplicity" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.distribution_functions.get_max_multiplicity">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.distribution_functions.</span></span><span class="sig-name descname"><span class="pre">get_max_multiplicity</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">multiplicity_array</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#get_max_multiplicity"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.get_max_multiplicity" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function to get the maximum multiplicity</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.distribution_functions.imf_chabrier2003">
-<code class="sig-prename descclassname">binarycpython.utils.distribution_functions.</code><code class="sig-name descname">imf_chabrier2003</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">m</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#imf_chabrier2003"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.imf_chabrier2003" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.distribution_functions.imf_chabrier2003">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.distribution_functions.</span></span><span class="sig-name descname"><span class="pre">imf_chabrier2003</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">m</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#imf_chabrier2003"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.imf_chabrier2003" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Probability distribution function for IMF of Chabrier 2003 PASP 115:763-795</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
@@ -555,8 +468,8 @@ used for the e and q values</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.distribution_functions.imf_scalo1986">
-<code class="sig-prename descclassname">binarycpython.utils.distribution_functions.</code><code class="sig-name descname">imf_scalo1986</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">m</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#imf_scalo1986"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.imf_scalo1986" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.distribution_functions.imf_scalo1986">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.distribution_functions.</span></span><span class="sig-name descname"><span class="pre">imf_scalo1986</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">m</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#imf_scalo1986"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.imf_scalo1986" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Probability distribution function for Scalo 1986 IMF (defined up until 80Msol): three_part_powerlaw(m, 0.1, 1.0, 2.0, 80.0, -2.35, -2.35, -2.70)</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
@@ -572,8 +485,8 @@ used for the e and q values</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.distribution_functions.imf_scalo1998">
-<code class="sig-prename descclassname">binarycpython.utils.distribution_functions.</code><code class="sig-name descname">imf_scalo1998</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">m</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#imf_scalo1998"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.imf_scalo1998" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.distribution_functions.imf_scalo1998">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.distribution_functions.</span></span><span class="sig-name descname"><span class="pre">imf_scalo1998</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">m</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#imf_scalo1998"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.imf_scalo1998" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>From Scalo 1998</p>
<p>Probability distribution function for Scalo 1998 IMF (defined up until 80Msol): three_part_powerlaw(m, 0.1, 1.0, 10.0, 80.0, -1.2, -2.7, -2.3)</p>
<dl class="field-list simple">
@@ -590,8 +503,8 @@ used for the e and q values</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.distribution_functions.imf_tinsley1980">
-<code class="sig-prename descclassname">binarycpython.utils.distribution_functions.</code><code class="sig-name descname">imf_tinsley1980</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">m</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#imf_tinsley1980"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.imf_tinsley1980" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.distribution_functions.imf_tinsley1980">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.distribution_functions.</span></span><span class="sig-name descname"><span class="pre">imf_tinsley1980</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">m</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#imf_tinsley1980"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.imf_tinsley1980" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Probability distribution function for Tinsley 1980 IMF (defined up until 80Msol): three_part_powerlaw(m, 0.1, 2.0, 10.0, 80.0, -2.0, -2.3, -3.3)</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
@@ -607,8 +520,8 @@ used for the e and q values</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.distribution_functions.interpolate_in_mass_izzard2012">
-<code class="sig-prename descclassname">binarycpython.utils.distribution_functions.</code><code class="sig-name descname">interpolate_in_mass_izzard2012</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">M</span></em>, <em class="sig-param"><span class="n">high</span></em>, <em class="sig-param"><span class="n">low</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#interpolate_in_mass_izzard2012"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.interpolate_in_mass_izzard2012" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.distribution_functions.interpolate_in_mass_izzard2012">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.distribution_functions.</span></span><span class="sig-name descname"><span class="pre">interpolate_in_mass_izzard2012</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">M</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">high</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">low</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#interpolate_in_mass_izzard2012"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.interpolate_in_mass_izzard2012" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function to interpolate in mass</p>
<p>TODO: fix this function.
TODO: describe the args
@@ -632,8 +545,8 @@ low: at 1.15</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.distribution_functions.ktg93">
-<code class="sig-prename descclassname">binarycpython.utils.distribution_functions.</code><code class="sig-name descname">ktg93</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">m</span></em>, <em class="sig-param"><span class="n">newopts</span><span class="o">=</span><span class="default_value">None</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#ktg93"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.ktg93" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.distribution_functions.ktg93">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.distribution_functions.</span></span><span class="sig-name descname"><span class="pre">ktg93</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">m</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">newopts</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#ktg93"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.ktg93" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Probability distribution function for KTG93 IMF, where the default values to the three_part_powerlaw are: default = {“m0â€: 0.1, “m1â€: 0.5, “m2â€: 1, “mmaxâ€: 80, “p1â€: -1.3, “p2â€: -2.2,â€p3â€: -2.7}</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
@@ -652,14 +565,14 @@ low: at 1.15</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.distribution_functions.linear_extrapolation_q">
-<code class="sig-prename descclassname">binarycpython.utils.distribution_functions.</code><code class="sig-name descname">linear_extrapolation_q</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">qs</span></em>, <em class="sig-param"><span class="n">indices</span></em>, <em class="sig-param"><span class="n">qlimit</span></em>, <em class="sig-param"><span class="n">qdata</span></em>, <em class="sig-param"><span class="n">end_index</span></em>, <em class="sig-param"><span class="n">verbosity</span><span class="o">=</span><span class="default_value">0</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#linear_extrapolation_q"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.linear_extrapolation_q" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.distribution_functions.linear_extrapolation_q">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.distribution_functions.</span></span><span class="sig-name descname"><span class="pre">linear_extrapolation_q</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">qs</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">indices</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">qlimit</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">qdata</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">end_index</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">verbosity</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#linear_extrapolation_q"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.linear_extrapolation_q" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function to do the linear extrapolation for q.</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.distribution_functions.merge_multiplicities">
-<code class="sig-prename descclassname">binarycpython.utils.distribution_functions.</code><code class="sig-name descname">merge_multiplicities</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">result_array</span></em>, <em class="sig-param"><span class="n">max_multiplicity</span></em>, <em class="sig-param"><span class="n">verbosity</span><span class="o">=</span><span class="default_value">0</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#merge_multiplicities"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.merge_multiplicities" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.distribution_functions.merge_multiplicities">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.distribution_functions.</span></span><span class="sig-name descname"><span class="pre">merge_multiplicities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">result_array</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_multiplicity</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">verbosity</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#merge_multiplicities"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.merge_multiplicities" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function to fold the multiplicities higher than the max_multiplicity onto the max_multiplicity</p>
<dl class="simple">
<dt>if max_multiplicity == 1:</dt><dd><p>All the multiplicities are folded onto multiplicity == 1. This will always total to 1</p>
@@ -672,14 +585,14 @@ low: at 1.15</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.distribution_functions.normalize_dict">
-<code class="sig-prename descclassname">binarycpython.utils.distribution_functions.</code><code class="sig-name descname">normalize_dict</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">result_dict</span></em>, <em class="sig-param"><span class="n">verbosity</span><span class="o">=</span><span class="default_value">0</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#normalize_dict"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.normalize_dict" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.distribution_functions.normalize_dict">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.distribution_functions.</span></span><span class="sig-name descname"><span class="pre">normalize_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">result_dict</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">verbosity</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#normalize_dict"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.normalize_dict" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function to normalise a dictionary</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.distribution_functions.number">
-<code class="sig-prename descclassname">binarycpython.utils.distribution_functions.</code><code class="sig-name descname">number</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">value</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#number"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.number" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.distribution_functions.number">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.distribution_functions.</span></span><span class="sig-name descname"><span class="pre">number</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">value</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#number"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.number" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Dummy distribution function that returns the input</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
@@ -695,15 +608,15 @@ low: at 1.15</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.distribution_functions.poisson">
-<code class="sig-prename descclassname">binarycpython.utils.distribution_functions.</code><code class="sig-name descname">poisson</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">lambda_val</span></em>, <em class="sig-param"><span class="n">n</span></em>, <em class="sig-param"><span class="n">nmax</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">verbosity</span><span class="o">=</span><span class="default_value">0</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#poisson"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.poisson" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.distribution_functions.poisson">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.distribution_functions.</span></span><span class="sig-name descname"><span class="pre">poisson</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">lambda_val</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">n</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nmax</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">verbosity</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#poisson"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.poisson" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function that calculates the Poisson value and normalises
TODO: improve the description</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.distribution_functions.powerlaw">
-<code class="sig-prename descclassname">binarycpython.utils.distribution_functions.</code><code class="sig-name descname">powerlaw</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">min_val</span></em>, <em class="sig-param"><span class="n">max_val</span></em>, <em class="sig-param"><span class="n">k</span></em>, <em class="sig-param"><span class="n">x</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#powerlaw"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.powerlaw" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.distribution_functions.powerlaw">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.distribution_functions.</span></span><span class="sig-name descname"><span class="pre">powerlaw</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">min_val</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_val</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">k</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">x</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#powerlaw"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.powerlaw" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Single power law with index k at x from min to max</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
@@ -724,8 +637,8 @@ TODO: improve the description</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.distribution_functions.powerlaw_constant">
-<code class="sig-prename descclassname">binarycpython.utils.distribution_functions.</code><code class="sig-name descname">powerlaw_constant</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">min_val</span></em>, <em class="sig-param"><span class="n">max_val</span></em>, <em class="sig-param"><span class="n">k</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#powerlaw_constant"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.powerlaw_constant" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.distribution_functions.powerlaw_constant">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.distribution_functions.</span></span><span class="sig-name descname"><span class="pre">powerlaw_constant</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">min_val</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_val</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">k</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#powerlaw_constant"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.powerlaw_constant" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function that returns the constant to normalise a power law</p>
<p>TODO: what if k is -1?</p>
<dl class="field-list simple">
@@ -746,14 +659,14 @@ TODO: improve the description</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.distribution_functions.powerlaw_extrapolation_q">
-<code class="sig-prename descclassname">binarycpython.utils.distribution_functions.</code><code class="sig-name descname">powerlaw_extrapolation_q</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">qdata</span></em>, <em class="sig-param"><span class="n">qs</span></em>, <em class="sig-param"><span class="n">indices</span></em>, <em class="sig-param"><span class="n">verbosity</span><span class="o">=</span><span class="default_value">0</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#powerlaw_extrapolation_q"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.powerlaw_extrapolation_q" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.distribution_functions.powerlaw_extrapolation_q">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.distribution_functions.</span></span><span class="sig-name descname"><span class="pre">powerlaw_extrapolation_q</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">qdata</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">qs</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">indices</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">verbosity</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#powerlaw_extrapolation_q"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.powerlaw_extrapolation_q" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function to do the power law extrapolation at the lower end of the q range</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.distribution_functions.prepare_dict">
-<code class="sig-prename descclassname">binarycpython.utils.distribution_functions.</code><code class="sig-name descname">prepare_dict</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">global_dict</span></em>, <em class="sig-param"><span class="n">list_of_sub_keys</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#prepare_dict"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.prepare_dict" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.distribution_functions.prepare_dict">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.distribution_functions.</span></span><span class="sig-name descname"><span class="pre">prepare_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">global_dict</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">list_of_sub_keys</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#prepare_dict"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.prepare_dict" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function that makes sure that the global dict is prepared to have a value set there.
This dictionary will store values and factors for the distribution functions,
so that they don’t have to be calculated each time.</p>
@@ -771,8 +684,8 @@ so that they don’t have to be calculated each time.</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.distribution_functions.raghavan2010_binary_fraction">
-<code class="sig-prename descclassname">binarycpython.utils.distribution_functions.</code><code class="sig-name descname">raghavan2010_binary_fraction</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">m</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#raghavan2010_binary_fraction"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.raghavan2010_binary_fraction" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.distribution_functions.raghavan2010_binary_fraction">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.distribution_functions.</span></span><span class="sig-name descname"><span class="pre">raghavan2010_binary_fraction</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">m</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#raghavan2010_binary_fraction"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.raghavan2010_binary_fraction" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Fit to the Raghavan 2010 binary fraction as a function of
spectral type (Fig 12). Valid for local stars (Z=Zsolar).</p>
<p>The spectral type is converted mass by use of the ZAMS
@@ -794,8 +707,8 @@ and the new “long_spectral_type†function of binary_c
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.distribution_functions.sana12">
-<code class="sig-prename descclassname">binarycpython.utils.distribution_functions.</code><code class="sig-name descname">sana12</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">M1</span></em>, <em class="sig-param"><span class="n">M2</span></em>, <em class="sig-param"><span class="n">a</span></em>, <em class="sig-param"><span class="n">P</span></em>, <em class="sig-param"><span class="n">amin</span></em>, <em class="sig-param"><span class="n">amax</span></em>, <em class="sig-param"><span class="n">x0</span></em>, <em class="sig-param"><span class="n">x1</span></em>, <em class="sig-param"><span class="n">p</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#sana12"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.sana12" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.distribution_functions.sana12">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.distribution_functions.</span></span><span class="sig-name descname"><span class="pre">sana12</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">M1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">M2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">a</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">P</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">amin</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">amax</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">x0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">x1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">p</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#sana12"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.sana12" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>distribution of initial orbital periods as found by Sana et al. (2012)
which is a flat distribution in ln(a) and ln(P) respectively for stars
* less massive than 15Msun (no O-stars)
@@ -829,8 +742,8 @@ and is be given by dp/dlogP ~ (logP)^p for all other binary configurations (defa
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.distribution_functions.set_opts">
-<code class="sig-prename descclassname">binarycpython.utils.distribution_functions.</code><code class="sig-name descname">set_opts</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">opts</span></em>, <em class="sig-param"><span class="n">newopts</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#set_opts"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.set_opts" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.distribution_functions.set_opts">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.distribution_functions.</span></span><span class="sig-name descname"><span class="pre">set_opts</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">opts</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">newopts</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#set_opts"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.set_opts" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function to take a default dict and override it with newer values.</p>
<p># TODO: consider changing this to just a dict.update</p>
<dl class="field-list simple">
@@ -850,8 +763,8 @@ and is be given by dp/dlogP ~ (logP)^p for all other binary configurations (defa
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.distribution_functions.three_part_powerlaw">
-<code class="sig-prename descclassname">binarycpython.utils.distribution_functions.</code><code class="sig-name descname">three_part_powerlaw</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">m</span></em>, <em class="sig-param"><span class="n">m0</span></em>, <em class="sig-param"><span class="n">m1</span></em>, <em class="sig-param"><span class="n">m2</span></em>, <em class="sig-param"><span class="n">m_max</span></em>, <em class="sig-param"><span class="n">p1</span></em>, <em class="sig-param"><span class="n">p2</span></em>, <em class="sig-param"><span class="n">p3</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#three_part_powerlaw"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.three_part_powerlaw" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.distribution_functions.three_part_powerlaw">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.distribution_functions.</span></span><span class="sig-name descname"><span class="pre">three_part_powerlaw</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">m</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">m0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">m1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">m2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">m_max</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">p1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">p2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">p3</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/distribution_functions.html#three_part_powerlaw"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.distribution_functions.three_part_powerlaw" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Generalised three-part power law, usually used for mass distributions</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
@@ -875,68 +788,43 @@ and is be given by dp/dlogP ~ (logP)^p for all other binary configurations (defa
</dl>
</dd></dl>
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+Generated on binarycpython git branch: auto_resolution git revision be7bd630af892a785312affc34d87c57eb337fd3 url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/tree/auto_resolution">git url</a>.
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-Using binary_c with bit branch newmaster: git revision: "6185:20210910:1621c23a5" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/newmaster">git url</a>.
+Using binary_c with bit branch master: git revision: "6209:20211006:c4a4c332e" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/master">git url</a>.
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index f4596c160a423df339f7f5d286605a2a0c5aa47e..abce16b5b7298e561d7691e83c61c2261672cc1a 100644
--- a/docs/build/html/example_notebooks.html
+++ b/docs/build/html/example_notebooks.html
@@ -1,71 +1,35 @@
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<head>
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+ <title>Example notebooks — binary_c-python documentation</title>
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+ </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
+ <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
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<li class="toctree-l1"><a class="reference internal" href="readme_link.html">Python module for binary_c</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules.html">Binarycpython code</a></li>
@@ -96,7 +49,7 @@
<li class="toctree-l2"><a class="reference internal" href="notebook_extra_features.html">Tutorial: Extra features and functionality of binary_c-python</a></li>
<li class="toctree-l2"><a class="reference internal" href="notebook_api_functionality.html">Tutorial: Using the API functionality of binary_c-python</a></li>
<li class="toctree-l2"><a class="reference internal" href="notebook_luminosity_function_single.html">Example use case: Zero-age stellar luminosity function</a></li>
-<li class="toctree-l2"><a class="reference internal" href="notebook_luminosity_function_binaries.html">Zero-age stellar luminosity function in binaries</a></li>
+<li class="toctree-l2"><a class="reference internal" href="notebook_luminosity_function_binaries.html">Example use case: Zero-age stellar luminosity function in binaries</a></li>
<li class="toctree-l2"><a class="reference internal" href="notebook_HRD.html">Example use case: Hertzsprung-Russell diagrams</a></li>
<li class="toctree-l2"><a class="reference internal" href="notebook_common_envelope_evolution.html">Example use case: Common-envelope evolution</a></li>
</ul>
@@ -107,69 +60,30 @@
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</style>
-<div class="section" id="example-notebooks">
-<h1>Example notebooks<a class="headerlink" href="#example-notebooks" title="Permalink to this headline">¶</a></h1>
+<section id="example-notebooks">
+<h1>Example notebooks<a class="headerlink" href="#example-notebooks" title="Permalink to this headline">ïƒ</a></h1>
<p>We have a set of notebooks that explain and show the usage of the binarycpython features. The notebooks are also stored in the examples/ directory in the <a class="reference external" href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/tree/master/examples">repository</a></p>
<p>The order of the notebooks below is more or less the recommended order to read. The last couple of notebooks are example usecases</p>
<div class="toctree-wrapper compound">
-<p class="caption"><span class="caption-text">Contents:</span></p>
+<p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="notebook_individual_systems.html">Tutorial: Running individual systems with binary_c-python</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="notebook_individual_systems.html#Single-system-with-run_wrapper">Single system with run_wrapper</a></li>
+<li class="toctree-l2"><a class="reference internal" href="notebook_individual_systems.html#Single-system-with-run_system_wrapper">Single system with run_system_wrapper</a></li>
<li class="toctree-l2"><a class="reference internal" href="notebook_individual_systems.html#Single-system-via-population-object">Single system via population object</a></li>
<li class="toctree-l2"><a class="reference internal" href="notebook_individual_systems.html#Single-system-via-API-functionality">Single system via API functionality</a></li>
</ul>
@@ -242,7 +156,7 @@
<li class="toctree-l2"><a class="reference internal" href="notebook_luminosity_function_single.html#A-better-sampled-grid">A better-sampled grid</a></li>
</ul>
</li>
-<li class="toctree-l1"><a class="reference internal" href="notebook_luminosity_function_binaries.html">Zero-age stellar luminosity function in binaries</a><ul>
+<li class="toctree-l1"><a class="reference internal" href="notebook_luminosity_function_binaries.html">Example use case: Zero-age stellar luminosity function in binaries</a><ul>
<li class="toctree-l2"><a class="reference internal" href="notebook_luminosity_function_binaries.html#Setting-up-the-Population-object">Setting up the Population object</a></li>
<li class="toctree-l2"><a class="reference internal" href="notebook_luminosity_function_binaries.html#Adding-grid-variables">Adding grid variables</a></li>
<li class="toctree-l2"><a class="reference internal" href="notebook_luminosity_function_binaries.html#Setting-logging-and-handling-the-output">Setting logging and handling the output</a></li>
@@ -266,68 +180,43 @@
</li>
</ul>
</div>
-</div>
+</section>
</div>
-
</div>
- <footer>
-
- <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
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+ <a href="notebook_individual_systems.html" class="btn btn-neutral float-right" title="Tutorial: Running individual systems with binary_c-python" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
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-
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<div role="contentinfo">
- <p>
-
- © Copyright 2021, David Hendriks, Robert Izzard
-
- </p>
+ <p>© Copyright 2021, David Hendriks, Robert Izzard.</p>
</div>
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- Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a
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+ <a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
provided by <a href="https://readthedocs.org">Read the Docs</a>.
+
<br><br>
-Generated on binarycpython git branch: master git revision 0886cd4f1d7f43222aac21d6ed91e917b67b20fc url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/tree/master">git url</a>.
+Generated on binarycpython git branch: auto_resolution git revision be7bd630af892a785312affc34d87c57eb337fd3 url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/tree/auto_resolution">git url</a>.
<br><br>
-Using binary_c with bit branch newmaster: git revision: "6185:20210910:1621c23a5" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/newmaster">git url</a>.
+Using binary_c with bit branch master: git revision: "6209:20211006:c4a4c332e" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/master">git url</a>.
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diff --git a/docs/build/html/functions.html b/docs/build/html/functions.html
index e27f55452a0768903bdc8dabdce9282aa10c51d0..b0c580094f11251bb194f703a94159bd6dbc6567 100644
--- a/docs/build/html/functions.html
+++ b/docs/build/html/functions.html
@@ -1,71 +1,35 @@
-
-
<!DOCTYPE html>
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- <meta charset="utf-8">
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- <meta name="viewport" content="width=device-width, initial-scale=1.0">
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- <script async="async" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.7/latest.js?config=TeX-AMS-MML_HTMLorMML"></script>
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+ <script src="_static/js/theme.js"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="next" title="grid_class module" href="grid.html" />
<link rel="prev" title="distribution_functions module" href="distribution_functions.html" />
</head>
-<body class="wy-body-for-nav">
-
-
+<body class="wy-body-for-nav">
<div class="wy-grid-for-nav">
-
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<div class="wy-side-scroll">
<div class="wy-side-nav-search" >
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- <a href="index.html" class="icon icon-home" alt="Documentation Home"> binary_c-python
-
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+ <a href="index.html" class="icon icon-home"> binary_c-python
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@@ -73,19 +37,8 @@
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-
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+ </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
+ <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="readme_link.html">Python module for binary_c</a></li>
<li class="toctree-l1 current"><a class="reference internal" href="modules.html">Binarycpython code</a><ul class="current">
@@ -109,71 +62,31 @@
<li class="toctree-l1"><a class="reference external" href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/issues/new">Submit an issue</a></li>
</ul>
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<ul class="wy-breadcrumbs">
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-
<li><a href="modules.html">Binarycpython code</a> »</li>
-
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-
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<div itemprop="articleBody">
-
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<style>
/* CSS overrides for sphinx_rtd_theme */
@@ -198,8 +111,8 @@
text-align: unset;
}
</style>
-<div class="section" id="module-binarycpython.utils.functions">
-<span id="functions-module"></span><h1>functions module<a class="headerlink" href="#module-binarycpython.utils.functions" title="Permalink to this headline">¶</a></h1>
+<section id="module-binarycpython.utils.functions">
+<span id="functions-module"></span><h1>functions module<a class="headerlink" href="#module-binarycpython.utils.functions" title="Permalink to this headline">ïƒ</a></h1>
<p>Module containing most of the utility functions for the binarycpython package</p>
<p>Functions here are mostly functions used in other classes/functions, or
useful functions for the user</p>
@@ -209,9 +122,14 @@ useful functions for the user</p>
</ul>
</dd>
</dl>
+<dl class="py function">
+<dt class="sig sig-object py" id="binarycpython.utils.functions.ANSI_colours">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.functions.</span></span><span class="sig-name descname"><span class="pre">ANSI_colours</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#ANSI_colours"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.functions.ANSI_colours" title="Permalink to this definition">ïƒ</a></dt>
+<dd></dd></dl>
+
<dl class="py class">
-<dt id="binarycpython.utils.functions.AutoVivificationDict">
-<em class="property">class </em><code class="sig-prename descclassname">binarycpython.utils.functions.</code><code class="sig-name descname">AutoVivificationDict</code><a class="reference internal" href="_modules/binarycpython/utils/functions.html#AutoVivificationDict"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.functions.AutoVivificationDict" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.functions.AutoVivificationDict">
+<em class="property"><span class="pre">class</span> </em><span class="sig-prename descclassname"><span class="pre">binarycpython.utils.functions.</span></span><span class="sig-name descname"><span class="pre">AutoVivificationDict</span></span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#AutoVivificationDict"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.functions.AutoVivificationDict" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">dict</span></code></p>
<p>Implementation of perl’s autovivification feature, by overriding the
get item and the __iadd__ operator (<a class="reference external" href="https://docs.python.org/3/reference/datamodel.html?highlight=iadd#object.__iadd__">https://docs.python.org/3/reference/datamodel.html?highlight=iadd#object.__iadd__</a>)</p>
@@ -224,60 +142,60 @@ print(newdict)
</dd></dl>
<dl class="py class">
-<dt id="binarycpython.utils.functions.BinaryCEncoder">
-<em class="property">class </em><code class="sig-prename descclassname">binarycpython.utils.functions.</code><code class="sig-name descname">BinaryCEncoder</code><span class="sig-paren">(</span><em class="sig-param"><span class="o">*</span></em>, <em class="sig-param"><span class="n">skipkeys</span><span class="o">=</span><span class="default_value">False</span></em>, <em class="sig-param"><span class="n">ensure_ascii</span><span class="o">=</span><span class="default_value">True</span></em>, <em class="sig-param"><span class="n">check_circular</span><span class="o">=</span><span class="default_value">True</span></em>, <em class="sig-param"><span class="n">allow_nan</span><span class="o">=</span><span class="default_value">True</span></em>, <em class="sig-param"><span class="n">sort_keys</span><span class="o">=</span><span class="default_value">False</span></em>, <em class="sig-param"><span class="n">indent</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">separators</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">default</span><span class="o">=</span><span class="default_value">None</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#BinaryCEncoder"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.functions.BinaryCEncoder" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.functions.BinaryCEncoder">
+<em class="property"><span class="pre">class</span> </em><span class="sig-prename descclassname"><span class="pre">binarycpython.utils.functions.</span></span><span class="sig-name descname"><span class="pre">BinaryCEncoder</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">skipkeys</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ensure_ascii</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">check_circular</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">allow_nan</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sort_keys</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">indent</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">separators</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">default</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#BinaryCEncoder"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.functions.BinaryCEncoder" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">json.encoder.JSONEncoder</span></code></p>
<p>Encoding class function to attempt to convert things to strings.</p>
<dl class="py method">
-<dt id="binarycpython.utils.functions.BinaryCEncoder.default">
-<code class="sig-name descname">default</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">o</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#BinaryCEncoder.default"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.functions.BinaryCEncoder.default" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.functions.BinaryCEncoder.default">
+<span class="sig-name descname"><span class="pre">default</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">o</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#BinaryCEncoder.default"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.functions.BinaryCEncoder.default" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Converting function. Well, could be more precise. look at the JSON module</p>
</dd></dl>
</dd></dl>
<dl class="py class">
-<dt id="binarycpython.utils.functions.Capturing">
-<em class="property">class </em><code class="sig-prename descclassname">binarycpython.utils.functions.</code><code class="sig-name descname">Capturing</code><a class="reference internal" href="_modules/binarycpython/utils/functions.html#Capturing"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.functions.Capturing" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.functions.Capturing">
+<em class="property"><span class="pre">class</span> </em><span class="sig-prename descclassname"><span class="pre">binarycpython.utils.functions.</span></span><span class="sig-name descname"><span class="pre">Capturing</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">iterable</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">/</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#Capturing"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.functions.Capturing" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></p>
<p>Context manager to capture output and store it</p>
<dl class="py method">
-<dt id="binarycpython.utils.functions.Capturing.__enter__">
-<code class="sig-name descname">__enter__</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#Capturing.__enter__"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.functions.Capturing.__enter__" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.functions.Capturing.__enter__">
+<span class="sig-name descname"><span class="pre">__enter__</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#Capturing.__enter__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.functions.Capturing.__enter__" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>On entry we capture the stdout output</p>
</dd></dl>
<dl class="py method">
-<dt id="binarycpython.utils.functions.Capturing.__exit__">
-<code class="sig-name descname">__exit__</code><span class="sig-paren">(</span><em class="sig-param"><span class="o">*</span><span class="n">args</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#Capturing.__exit__"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.functions.Capturing.__exit__" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.functions.Capturing.__exit__">
+<span class="sig-name descname"><span class="pre">__exit__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#Capturing.__exit__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.functions.Capturing.__exit__" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>On exit we release the capture again</p>
</dd></dl>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.functions.bin_data">
-<code class="sig-prename descclassname">binarycpython.utils.functions.</code><code class="sig-name descname">bin_data</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">value</span></em>, <em class="sig-param"><span class="n">binwidth</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#bin_data"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.functions.bin_data" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.functions.bin_data">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.functions.</span></span><span class="sig-name descname"><span class="pre">bin_data</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">value</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">binwidth</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#bin_data"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.functions.bin_data" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function that bins the data</p>
<p>Uses the absolute value of binwidth</p>
</dd></dl>
<dl class="py class">
-<dt id="binarycpython.utils.functions.binarycDecoder">
-<em class="property">class </em><code class="sig-prename descclassname">binarycpython.utils.functions.</code><code class="sig-name descname">binarycDecoder</code><span class="sig-paren">(</span><em class="sig-param"><span class="o">*</span></em>, <em class="sig-param"><span class="n">object_hook</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">parse_float</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">parse_int</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">parse_constant</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">strict</span><span class="o">=</span><span class="default_value">True</span></em>, <em class="sig-param"><span class="n">object_pairs_hook</span><span class="o">=</span><span class="default_value">None</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#binarycDecoder"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.functions.binarycDecoder" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.functions.binarycDecoder">
+<em class="property"><span class="pre">class</span> </em><span class="sig-prename descclassname"><span class="pre">binarycpython.utils.functions.</span></span><span class="sig-name descname"><span class="pre">binarycDecoder</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">object_hook</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parse_float</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parse_int</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parse_constant</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">strict</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">object_pairs_hook</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#binarycDecoder"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.functions.binarycDecoder" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">json.decoder.JSONDecoder</span></code></p>
<p>Custom decoder to transform the numbers that are strings to actual floats</p>
<dl class="py method">
-<dt id="binarycpython.utils.functions.binarycDecoder.decode">
-<code class="sig-name descname">decode</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">s</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#binarycDecoder.decode"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.functions.binarycDecoder.decode" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.functions.binarycDecoder.decode">
+<span class="sig-name descname"><span class="pre">decode</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">s</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#binarycDecoder.decode"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.functions.binarycDecoder.decode" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Entry point function for decoding</p>
</dd></dl>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.functions.binaryc_json_serializer">
-<code class="sig-prename descclassname">binarycpython.utils.functions.</code><code class="sig-name descname">binaryc_json_serializer</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">obj</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#binaryc_json_serializer"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.functions.binaryc_json_serializer" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.functions.binaryc_json_serializer">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.functions.</span></span><span class="sig-name descname"><span class="pre">binaryc_json_serializer</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">obj</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#binaryc_json_serializer"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.functions.binaryc_json_serializer" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Custom serialiser for binary_c to use when functions are present in the dictionary
that we want to export.</p>
<p>Function objects will be turned into str representations of themselves</p>
@@ -295,8 +213,8 @@ that we want to export.</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.functions.call_binary_c_config">
-<code class="sig-prename descclassname">binarycpython.utils.functions.</code><code class="sig-name descname">call_binary_c_config</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">argument</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#call_binary_c_config"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.functions.call_binary_c_config" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.functions.call_binary_c_config">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.functions.</span></span><span class="sig-name descname"><span class="pre">call_binary_c_config</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">argument</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#call_binary_c_config"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.functions.call_binary_c_config" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function to interface with the binary_c config file</p>
<dl class="simple">
<dt>input:</dt><dd><ul class="simple">
@@ -315,45 +233,57 @@ that we want to export.</p>
</dd></dl>
<dl class="py class">
-<dt id="binarycpython.utils.functions.catchtime">
-<em class="property">class </em><code class="sig-prename descclassname">binarycpython.utils.functions.</code><code class="sig-name descname">catchtime</code><a class="reference internal" href="_modules/binarycpython/utils/functions.html#catchtime"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.functions.catchtime" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.functions.catchtime">
+<em class="property"><span class="pre">class</span> </em><span class="sig-prename descclassname"><span class="pre">binarycpython.utils.functions.</span></span><span class="sig-name descname"><span class="pre">catchtime</span></span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#catchtime"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.functions.catchtime" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
<p>Context manager to calculate time spent</p>
<dl class="py method">
-<dt id="binarycpython.utils.functions.catchtime.__enter__">
-<code class="sig-name descname">__enter__</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#catchtime.__enter__"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.functions.catchtime.__enter__" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.functions.catchtime.__enter__">
+<span class="sig-name descname"><span class="pre">__enter__</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#catchtime.__enter__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.functions.catchtime.__enter__" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>On entry we start the clock</p>
</dd></dl>
<dl class="py method">
-<dt id="binarycpython.utils.functions.catchtime.__exit__">
-<code class="sig-name descname">__exit__</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">type</span></em>, <em class="sig-param"><span class="n">value</span></em>, <em class="sig-param"><span class="n">traceback</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#catchtime.__exit__"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.functions.catchtime.__exit__" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.functions.catchtime.__exit__">
+<span class="sig-name descname"><span class="pre">__exit__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">type</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">value</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">traceback</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#catchtime.__exit__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.functions.catchtime.__exit__" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>On exit we stop the clock and measure the time spent</p>
</dd></dl>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.functions.convert_bytes">
-<code class="sig-prename descclassname">binarycpython.utils.functions.</code><code class="sig-name descname">convert_bytes</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">size</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#convert_bytes"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.functions.convert_bytes" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.functions.check_if_in_shell">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.functions.</span></span><span class="sig-name descname"><span class="pre">check_if_in_shell</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#check_if_in_shell"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.functions.check_if_in_shell" title="Permalink to this definition">ïƒ</a></dt>
+<dd><p>Function to check whether the script is running from a shell</p>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="binarycpython.utils.functions.conv_time_units">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.functions.</span></span><span class="sig-name descname"><span class="pre">conv_time_units</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">t</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#conv_time_units"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.functions.conv_time_units" title="Permalink to this definition">ïƒ</a></dt>
+<dd><p>Converts time (t, in seconds, passing in as the only argument) to seconds, minutes or hours depending on its magnitude. Returns a tuple (t,units).</p>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="binarycpython.utils.functions.convert_bytes">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.functions.</span></span><span class="sig-name descname"><span class="pre">convert_bytes</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">size</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#convert_bytes"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.functions.convert_bytes" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function to return the size + a magnitude string</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.functions.convfloat">
-<code class="sig-prename descclassname">binarycpython.utils.functions.</code><code class="sig-name descname">convfloat</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">x</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#convfloat"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.functions.convfloat" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.functions.convfloat">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.functions.</span></span><span class="sig-name descname"><span class="pre">convfloat</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">x</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#convfloat"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.functions.convfloat" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Convert scalar x to a float if we can, in which case return the float, otherwise just return x without changing it. Usually, x is a string, but could be anything that float() can handle without failure.</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.functions.count_keys_recursive">
-<code class="sig-prename descclassname">binarycpython.utils.functions.</code><code class="sig-name descname">count_keys_recursive</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">input_dict</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#count_keys_recursive"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.functions.count_keys_recursive" title="Permalink to this definition">¶</a></dt>
-<dd><p>Function to count the total amount of keys in a dictionary</p>
+<dt class="sig sig-object py" id="binarycpython.utils.functions.count_keys_recursive">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.functions.</span></span><span class="sig-name descname"><span class="pre">count_keys_recursive</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">input_dict</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#count_keys_recursive"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.functions.count_keys_recursive" title="Permalink to this definition">ïƒ</a></dt>
+<dd><p>Function to count the total number of keys in a dictionary</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.functions.create_arg_string">
-<code class="sig-prename descclassname">binarycpython.utils.functions.</code><code class="sig-name descname">create_arg_string</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">arg_dict</span></em>, <em class="sig-param"><span class="n">sort</span><span class="o">=</span><span class="default_value">False</span></em>, <em class="sig-param"><span class="n">filter_values</span><span class="o">=</span><span class="default_value">False</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#create_arg_string"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.functions.create_arg_string" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.functions.create_arg_string">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.functions.</span></span><span class="sig-name descname"><span class="pre">create_arg_string</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">arg_dict</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sort</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">filter_values</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#create_arg_string"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.functions.create_arg_string" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function that creates the arg string for binary_c. Takes a dictionary containing the arguments
and writes them to a string
This string is missing the ‘binary_c ‘ at the start.</p>
@@ -375,8 +305,8 @@ This string is missing the ‘binary_c ‘ at the start.</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.functions.create_hdf5">
-<code class="sig-prename descclassname">binarycpython.utils.functions.</code><code class="sig-name descname">create_hdf5</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">data_dir</span></em>, <em class="sig-param"><span class="n">name</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#create_hdf5"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.functions.create_hdf5" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.functions.create_hdf5">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.functions.</span></span><span class="sig-name descname"><span class="pre">create_hdf5</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">data_dir</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">name</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#create_hdf5"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.functions.create_hdf5" title="Permalink to this definition">ïƒ</a></dt>
<dd><dl class="simple">
<dt>Function to create an hdf5 file from the contents of a directory:</dt><dd><ul class="simple">
<li><p>settings file is selected by checking on files ending on settings</p></li>
@@ -399,8 +329,8 @@ This string is missing the ‘binary_c ‘ at the start.</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.functions.custom_sort_dict">
-<code class="sig-prename descclassname">binarycpython.utils.functions.</code><code class="sig-name descname">custom_sort_dict</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">input_dict</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#custom_sort_dict"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.functions.custom_sort_dict" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.functions.custom_sort_dict">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.functions.</span></span><span class="sig-name descname"><span class="pre">custom_sort_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">input_dict</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#custom_sort_dict"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.functions.custom_sort_dict" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Returns a dictionary that is ordered, but can handle numbers better than normal OrderedDict</p>
<p>When the keys of the current dictionary are of mixed type, we first find all the unique types.
Sort that list of type names. Then find the values that fit that type.
@@ -410,8 +340,8 @@ This is done until all the keys are sorted.</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.functions.datalinedict">
-<code class="sig-prename descclassname">binarycpython.utils.functions.</code><code class="sig-name descname">datalinedict</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">line</span></em>, <em class="sig-param"><span class="n">parameters</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#datalinedict"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.functions.datalinedict" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.functions.datalinedict">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.functions.</span></span><span class="sig-name descname"><span class="pre">datalinedict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">line</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parameters</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#datalinedict"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.functions.datalinedict" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Convert a line of data to a more convenient dictionary.
:param line = a line of data as a string:
:param parameters = a list of the parameter names:</p>
@@ -419,8 +349,8 @@ This is done until all the keys are sorted.</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.functions.example_parse_output">
-<code class="sig-prename descclassname">binarycpython.utils.functions.</code><code class="sig-name descname">example_parse_output</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">output</span></em>, <em class="sig-param"><span class="n">selected_header</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#example_parse_output"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.functions.example_parse_output" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.functions.example_parse_output">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.functions.</span></span><span class="sig-name descname"><span class="pre">example_parse_output</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">output</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">selected_header</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#example_parse_output"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.functions.example_parse_output" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function that parses output of binary_c. This version serves as an example and is quite
detailed. Custom functions can be easier:</p>
<p>This function works in two cases:
@@ -455,8 +385,8 @@ process)</p></li>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.functions.extract_ensemble_json_from_string">
-<code class="sig-prename descclassname">binarycpython.utils.functions.</code><code class="sig-name descname">extract_ensemble_json_from_string</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">binary_c_output</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#extract_ensemble_json_from_string"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.functions.extract_ensemble_json_from_string" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.functions.extract_ensemble_json_from_string">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.functions.</span></span><span class="sig-name descname"><span class="pre">extract_ensemble_json_from_string</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">binary_c_output</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#extract_ensemble_json_from_string"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.functions.extract_ensemble_json_from_string" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function to extract the ensemble_json information from a raw binary_c output string</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
@@ -472,8 +402,8 @@ process)</p></li>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.functions.filter_arg_dict">
-<code class="sig-prename descclassname">binarycpython.utils.functions.</code><code class="sig-name descname">filter_arg_dict</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">arg_dict</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#filter_arg_dict"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.functions.filter_arg_dict" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.functions.filter_arg_dict">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.functions.</span></span><span class="sig-name descname"><span class="pre">filter_arg_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">arg_dict</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#filter_arg_dict"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.functions.filter_arg_dict" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function to filter out keys that contain values included in [‘NULL’, ‘Function’, ‘’]</p>
<p>This function is called by get_defaults()</p>
<dl class="field-list simple">
@@ -490,8 +420,8 @@ process)</p></li>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.functions.format_ensemble_results">
-<code class="sig-prename descclassname">binarycpython.utils.functions.</code><code class="sig-name descname">format_ensemble_results</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">ensemble_dictionary</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#format_ensemble_results"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.functions.format_ensemble_results" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.functions.format_ensemble_results">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.functions.</span></span><span class="sig-name descname"><span class="pre">format_ensemble_results</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ensemble_dictionary</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#format_ensemble_results"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.functions.format_ensemble_results" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function to handle all the steps of formatting the ensemble output again.</p>
<dl class="simple">
<dt>Input:</dt><dd><p>ensemble_dictionary: dictionary containing all the ensemble results</p>
@@ -500,8 +430,13 @@ process)</p></li>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.functions.get_arg_keys">
-<code class="sig-prename descclassname">binarycpython.utils.functions.</code><code class="sig-name descname">get_arg_keys</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#get_arg_keys"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.functions.get_arg_keys" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.functions.format_number">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.functions.</span></span><span class="sig-name descname"><span class="pre">format_number</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">number</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#format_number"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.functions.format_number" title="Permalink to this definition">ïƒ</a></dt>
+<dd></dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="binarycpython.utils.functions.get_arg_keys">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.functions.</span></span><span class="sig-name descname"><span class="pre">get_arg_keys</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#get_arg_keys"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.functions.get_arg_keys" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function that return the list of possible keys to give in the arg string.
This function calls get_defaults()</p>
<dl class="field-list simple">
@@ -516,8 +451,8 @@ we call get_defaults())</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.functions.get_defaults">
-<code class="sig-prename descclassname">binarycpython.utils.functions.</code><code class="sig-name descname">get_defaults</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">filter_values</span><span class="o">=</span><span class="default_value">False</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#get_defaults"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.functions.get_defaults" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.functions.get_defaults">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.functions.</span></span><span class="sig-name descname"><span class="pre">get_defaults</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">filter_values</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#get_defaults"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.functions.get_defaults" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function that calls the binaryc get args function and cast it into a dictionary.</p>
<p>All the values are strings</p>
<dl class="field-list simple">
@@ -534,8 +469,8 @@ we call get_defaults())</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.functions.get_help">
-<code class="sig-prename descclassname">binarycpython.utils.functions.</code><code class="sig-name descname">get_help</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">param_name</span><span class="o">=</span><span class="default_value">''</span></em>, <em class="sig-param"><span class="n">print_help</span><span class="o">=</span><span class="default_value">True</span></em>, <em class="sig-param"><span class="n">fail_silently</span><span class="o">=</span><span class="default_value">False</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#get_help"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.functions.get_help" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.functions.get_help">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.functions.</span></span><span class="sig-name descname"><span class="pre">get_help</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">param_name</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">''</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">print_help</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fail_silently</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#get_help"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.functions.get_help" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function that returns the help info for a given parameter, by interfacing with binary_c</p>
<p>Will check whether it is a valid parameter.</p>
<p>Binary_c will output things in the following order;
@@ -557,7 +492,7 @@ we call get_defaults())</p>
valid parameter name</p></li>
<li><p><strong>print_help</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code>) – (optional, default = True) whether to print out the help information</p></li>
<li><p><strong>fail_silently</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code>) – (optional, default = False) Whether to print the errors raised if the</p></li>
-<li><p><strong>isn't valid</strong> (<em>parameter</em>) – </p></li>
+<li><p><strong>valid</strong> (<em>parameter isn't</em>) – </p></li>
</ul>
</dd>
<dt class="field-even">Return type</dt>
@@ -571,8 +506,8 @@ valid parameter name</p></li>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.functions.get_help_all">
-<code class="sig-prename descclassname">binarycpython.utils.functions.</code><code class="sig-name descname">get_help_all</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">print_help</span><span class="o">=</span><span class="default_value">True</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#get_help_all"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.functions.get_help_all" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.functions.get_help_all">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.functions.</span></span><span class="sig-name descname"><span class="pre">get_help_all</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">print_help</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#get_help_all"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.functions.get_help_all" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function that reads out the output of the return_help_all API call to binary_c. This return_help_all binary_c returns all the information for the parameters, their descriptions and other properties. The output is categorised in sections.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
@@ -588,8 +523,8 @@ valid parameter name</p></li>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.functions.get_help_super">
-<code class="sig-prename descclassname">binarycpython.utils.functions.</code><code class="sig-name descname">get_help_super</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">print_help</span><span class="o">=</span><span class="default_value">False</span></em>, <em class="sig-param"><span class="n">fail_silently</span><span class="o">=</span><span class="default_value">True</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#get_help_super"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.functions.get_help_super" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.functions.get_help_super">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.functions.</span></span><span class="sig-name descname"><span class="pre">get_help_super</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">print_help</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fail_silently</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#get_help_super"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.functions.get_help_super" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function that first runs get_help_all, and then per argument also run
the help function to get as much information as possible.</p>
<dl class="field-list simple">
@@ -609,21 +544,26 @@ the help function to get as much information as possible.</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.functions.get_moe_di_stefano_dataset">
-<code class="sig-prename descclassname">binarycpython.utils.functions.</code><code class="sig-name descname">get_moe_di_stefano_dataset</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">options</span></em>, <em class="sig-param"><span class="n">verbosity</span><span class="o">=</span><span class="default_value">0</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#get_moe_di_stefano_dataset"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.functions.get_moe_di_stefano_dataset" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.functions.get_moe_di_stefano_dataset">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.functions.</span></span><span class="sig-name descname"><span class="pre">get_moe_di_stefano_dataset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">options</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">verbosity</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#get_moe_di_stefano_dataset"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.functions.get_moe_di_stefano_dataset" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function to get the default moe and di Stefano dataset or accept a user input.</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.functions.get_size">
-<code class="sig-prename descclassname">binarycpython.utils.functions.</code><code class="sig-name descname">get_size</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">obj</span></em>, <em class="sig-param"><span class="n">seen</span><span class="o">=</span><span class="default_value">None</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#get_size"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.functions.get_size" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.functions.get_size">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.functions.</span></span><span class="sig-name descname"><span class="pre">get_size</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">obj</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">seen</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#get_size"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.functions.get_size" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Recursively finds size of objects</p>
<p>From <a class="reference external" href="https://github.com/bosswissam/pysize">https://github.com/bosswissam/pysize</a></p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.functions.handle_ensemble_string_to_json">
-<code class="sig-prename descclassname">binarycpython.utils.functions.</code><code class="sig-name descname">handle_ensemble_string_to_json</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">raw_output</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#handle_ensemble_string_to_json"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.functions.handle_ensemble_string_to_json" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.functions.get_username">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.functions.</span></span><span class="sig-name descname"><span class="pre">get_username</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#get_username"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.functions.get_username" title="Permalink to this definition">ïƒ</a></dt>
+<dd></dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="binarycpython.utils.functions.handle_ensemble_string_to_json">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.functions.</span></span><span class="sig-name descname"><span class="pre">handle_ensemble_string_to_json</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">raw_output</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#handle_ensemble_string_to_json"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.functions.handle_ensemble_string_to_json" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function that deals with the raw output of the ensemble and
creates a working JSON dictionary out of it.</p>
<p>Having this wrapper makes it easy to</p>
@@ -638,13 +578,13 @@ creates a working JSON dictionary out of it.</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.functions.imports">
-<code class="sig-prename descclassname">binarycpython.utils.functions.</code><code class="sig-name descname">imports</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#imports"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.functions.imports" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.functions.imports">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.functions.</span></span><span class="sig-name descname"><span class="pre">imports</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#imports"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.functions.imports" title="Permalink to this definition">ïƒ</a></dt>
<dd></dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.functions.inspect_dict">
-<code class="sig-prename descclassname">binarycpython.utils.functions.</code><code class="sig-name descname">inspect_dict</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">input_dict</span></em>, <em class="sig-param"><span class="n">indent</span><span class="o">=</span><span class="default_value">0</span></em>, <em class="sig-param"><span class="n">print_structure</span><span class="o">=</span><span class="default_value">True</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#inspect_dict"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.functions.inspect_dict" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.functions.inspect_dict">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.functions.</span></span><span class="sig-name descname"><span class="pre">inspect_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">input_dict</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">indent</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">print_structure</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#inspect_dict"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.functions.inspect_dict" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function to (recursively) inspect a (nested) dictionary.
The object that is returned is a dictionary containing the key of the input_dict, but as value
it will return the type of what the value would be in the input_dict</p>
@@ -671,14 +611,14 @@ it will return the type of what the value would be in the input_dict</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.functions.is_capsule">
-<code class="sig-prename descclassname">binarycpython.utils.functions.</code><code class="sig-name descname">is_capsule</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">o</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#is_capsule"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.functions.is_capsule" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.functions.is_capsule">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.functions.</span></span><span class="sig-name descname"><span class="pre">is_capsule</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">o</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#is_capsule"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.functions.is_capsule" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function to tell whether object is a capsule</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.functions.load_logfile">
-<code class="sig-prename descclassname">binarycpython.utils.functions.</code><code class="sig-name descname">load_logfile</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">logfile</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#load_logfile"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.functions.load_logfile" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.functions.load_logfile">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.functions.</span></span><span class="sig-name descname"><span class="pre">load_logfile</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">logfile</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#load_logfile"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.functions.load_logfile" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Experimental function that parses the generated log file of binary_c.</p>
<p>This function is not finished and shouldn’t be used yet.</p>
<dl class="simple">
@@ -701,8 +641,8 @@ it will return the type of what the value would be in the input_dict</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.functions.make_build_text">
-<code class="sig-prename descclassname">binarycpython.utils.functions.</code><code class="sig-name descname">make_build_text</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#make_build_text"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.functions.make_build_text" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.functions.make_build_text">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.functions.</span></span><span class="sig-name descname"><span class="pre">make_build_text</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#make_build_text"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.functions.make_build_text" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function to make build text</p>
<dl class="field-list simple">
<dt class="field-odd">Return type</dt>
@@ -715,8 +655,14 @@ it will return the type of what the value would be in the input_dict</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.functions.merge_dicts">
-<code class="sig-prename descclassname">binarycpython.utils.functions.</code><code class="sig-name descname">merge_dicts</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">dict_1</span></em>, <em class="sig-param"><span class="n">dict_2</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#merge_dicts"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.functions.merge_dicts" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.functions.mem_use">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.functions.</span></span><span class="sig-name descname"><span class="pre">mem_use</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#mem_use"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.functions.mem_use" title="Permalink to this definition">ïƒ</a></dt>
+<dd><p>Return current process memory use in MB. (Takes no arguments) Note: this is per-thread only.</p>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="binarycpython.utils.functions.merge_dicts">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.functions.</span></span><span class="sig-name descname"><span class="pre">merge_dicts</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dict_1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dict_2</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#merge_dicts"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.functions.merge_dicts" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function to merge two dictionaries in a custom way.</p>
<p>Behaviour:</p>
<dl class="simple">
@@ -749,15 +695,15 @@ it will return the type of what the value would be in the input_dict</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.functions.multiply_values_dict">
-<code class="sig-prename descclassname">binarycpython.utils.functions.</code><code class="sig-name descname">multiply_values_dict</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">input_dict</span></em>, <em class="sig-param"><span class="n">factor</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#multiply_values_dict"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.functions.multiply_values_dict" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.functions.multiply_values_dict">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.functions.</span></span><span class="sig-name descname"><span class="pre">multiply_values_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">input_dict</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">factor</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#multiply_values_dict"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.functions.multiply_values_dict" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function that goes over dictionary recursively and multiplies the value if possible by a factor</p>
<p>If the key equals “general_infoâ€, the multiplication gets skipped</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.functions.output_lines">
-<code class="sig-prename descclassname">binarycpython.utils.functions.</code><code class="sig-name descname">output_lines</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">output</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#output_lines"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.functions.output_lines" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.functions.output_lines">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.functions.</span></span><span class="sig-name descname"><span class="pre">output_lines</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">output</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#output_lines"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.functions.output_lines" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function that outputs the lines that were received from the binary_c run, but now as an iterator.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
@@ -773,14 +719,14 @@ it will return the type of what the value would be in the input_dict</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.functions.pad_output_distribution">
-<code class="sig-prename descclassname">binarycpython.utils.functions.</code><code class="sig-name descname">pad_output_distribution</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">dist</span></em>, <em class="sig-param"><span class="n">binwidth</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#pad_output_distribution"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.functions.pad_output_distribution" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.functions.pad_output_distribution">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.functions.</span></span><span class="sig-name descname"><span class="pre">pad_output_distribution</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dist</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">binwidth</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#pad_output_distribution"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.functions.pad_output_distribution" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Given a distribution, dist (a dictionary), which should be binned every binwidth (float), fill the distribution with zeros when there is no data. Note: this changes the data in place.</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.functions.parse_binary_c_version_info">
-<code class="sig-prename descclassname">binarycpython.utils.functions.</code><code class="sig-name descname">parse_binary_c_version_info</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">version_info_string</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#parse_binary_c_version_info"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.functions.parse_binary_c_version_info" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.functions.parse_binary_c_version_info">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.functions.</span></span><span class="sig-name descname"><span class="pre">parse_binary_c_version_info</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">version_info_string</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#parse_binary_c_version_info"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.functions.parse_binary_c_version_info" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function that parses the binary_c version info. Long function with a lot of branches</p>
<p>TODO: fix this function. stuff is missing: isotopes, macros, nucleosynthesis_sources</p>
<dl class="field-list simple">
@@ -797,22 +743,22 @@ it will return the type of what the value would be in the input_dict</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.functions.recursive_change_key_to_float">
-<code class="sig-prename descclassname">binarycpython.utils.functions.</code><code class="sig-name descname">recursive_change_key_to_float</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">input_dict</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#recursive_change_key_to_float"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.functions.recursive_change_key_to_float" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.functions.recursive_change_key_to_float">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.functions.</span></span><span class="sig-name descname"><span class="pre">recursive_change_key_to_float</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">input_dict</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#recursive_change_key_to_float"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.functions.recursive_change_key_to_float" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function to recursively change the key to float</p>
<p>This only works if the dict contains just sub-dicts or numbers/strings.
Does not work with lists as values</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.functions.recursive_change_key_to_string">
-<code class="sig-prename descclassname">binarycpython.utils.functions.</code><code class="sig-name descname">recursive_change_key_to_string</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">input_dict</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#recursive_change_key_to_string"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.functions.recursive_change_key_to_string" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.functions.recursive_change_key_to_string">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.functions.</span></span><span class="sig-name descname"><span class="pre">recursive_change_key_to_string</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">input_dict</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#recursive_change_key_to_string"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.functions.recursive_change_key_to_string" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function to recursively change the key back to a string but this time in a format that we decide</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.functions.remove_file">
-<code class="sig-prename descclassname">binarycpython.utils.functions.</code><code class="sig-name descname">remove_file</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">file</span></em>, <em class="sig-param"><span class="n">verbosity</span><span class="o">=</span><span class="default_value">0</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#remove_file"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.functions.remove_file" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.functions.remove_file">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.functions.</span></span><span class="sig-name descname"><span class="pre">remove_file</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">file</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">verbosity</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#remove_file"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.functions.remove_file" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function to remove files but with verbosity</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
@@ -831,8 +777,8 @@ Does not work with lists as values</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.functions.return_binary_c_version_info">
-<code class="sig-prename descclassname">binarycpython.utils.functions.</code><code class="sig-name descname">return_binary_c_version_info</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">parsed</span><span class="o">=</span><span class="default_value">True</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#return_binary_c_version_info"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.functions.return_binary_c_version_info" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.functions.return_binary_c_version_info">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.functions.</span></span><span class="sig-name descname"><span class="pre">return_binary_c_version_info</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">parsed</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#return_binary_c_version_info"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.functions.return_binary_c_version_info" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function that returns the version information of binary_c. This function calls the function
_binary_c_bindings.return_version_info()</p>
<dl class="field-list simple">
@@ -850,8 +796,8 @@ dictionary</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.functions.subtract_dicts">
-<code class="sig-prename descclassname">binarycpython.utils.functions.</code><code class="sig-name descname">subtract_dicts</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">dict_1</span></em>, <em class="sig-param"><span class="n">dict_2</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#subtract_dicts"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.functions.subtract_dicts" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.functions.subtract_dicts">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.functions.</span></span><span class="sig-name descname"><span class="pre">subtract_dicts</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dict_1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dict_2</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#subtract_dicts"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.functions.subtract_dicts" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function to subtract two dictionaries.</p>
<p>Only allows values to be either a dict or a numerical type</p>
<dl class="simple">
@@ -896,8 +842,8 @@ If that results in an empty dict, the dict will be removed too.</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.functions.temp_dir">
-<code class="sig-prename descclassname">binarycpython.utils.functions.</code><code class="sig-name descname">temp_dir</code><span class="sig-paren">(</span><em class="sig-param"><span class="o">*</span><span class="n">args</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#temp_dir"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.functions.temp_dir" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.functions.temp_dir">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.functions.</span></span><span class="sig-name descname"><span class="pre">temp_dir</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#temp_dir"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.functions.temp_dir" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function to create directory within the TMP directory of the file system</p>
<p>Makes use of os.makedirs exist_ok which requires python 3.2+</p>
<dl class="field-list simple">
@@ -914,8 +860,14 @@ If that results in an empty dict, the dict will be removed too.</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.functions.update_dicts">
-<code class="sig-prename descclassname">binarycpython.utils.functions.</code><code class="sig-name descname">update_dicts</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">dict_1</span></em>, <em class="sig-param"><span class="n">dict_2</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#update_dicts"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.functions.update_dicts" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.functions.trem">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.functions.</span></span><span class="sig-name descname"><span class="pre">trem</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dt</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">count</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dn</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">n</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#trem"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.functions.trem" title="Permalink to this definition">ïƒ</a></dt>
+<dd><p>Estimate time remaining (seconds) given a differential time and count (i.e. progress = $count/$n). $dt is the time since the last call, $count is the current progress count, $dn is the number run since the last call, and $n is the total number required.</p>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="binarycpython.utils.functions.update_dicts">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.functions.</span></span><span class="sig-name descname"><span class="pre">update_dicts</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dict_1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dict_2</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#update_dicts"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.functions.update_dicts" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function to update dict_1 with values of dict_2 in a recursive way.</p>
<p>Behaviour:</p>
<dl class="simple">
@@ -945,8 +897,8 @@ If that results in an empty dict, the dict will be removed too.</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.functions.verbose_print">
-<code class="sig-prename descclassname">binarycpython.utils.functions.</code><code class="sig-name descname">verbose_print</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">message</span></em>, <em class="sig-param"><span class="n">verbosity</span></em>, <em class="sig-param"><span class="n">minimal_verbosity</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#verbose_print"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.functions.verbose_print" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.functions.verbose_print">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.functions.</span></span><span class="sig-name descname"><span class="pre">verbose_print</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">message</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">verbosity</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">minimal_verbosity</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#verbose_print"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.functions.verbose_print" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function that decides whether to print a message based on the current verbosity
and its minimum verbosity</p>
<p>if verbosity is equal or higher than the minimum, then we print</p>
@@ -965,8 +917,8 @@ and its minimum verbosity</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.functions.write_binary_c_parameter_descriptions_to_rst_file">
-<code class="sig-prename descclassname">binarycpython.utils.functions.</code><code class="sig-name descname">write_binary_c_parameter_descriptions_to_rst_file</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">output_file</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#write_binary_c_parameter_descriptions_to_rst_file"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.functions.write_binary_c_parameter_descriptions_to_rst_file" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.functions.write_binary_c_parameter_descriptions_to_rst_file">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.functions.</span></span><span class="sig-name descname"><span class="pre">write_binary_c_parameter_descriptions_to_rst_file</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">output_file</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/functions.html#write_binary_c_parameter_descriptions_to_rst_file"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.functions.write_binary_c_parameter_descriptions_to_rst_file" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function that calls the get_help_super() to get the help text/descriptions for all the
parameters available in that build.
Writes the results to a .rst file that can be included in the docs.</p>
@@ -991,68 +943,43 @@ of all the binary_c parameters.</p>
</dl>
</dd></dl>
-</div>
+</section>
</div>
-
</div>
- <footer>
-
- <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
-
- <a href="grid.html" class="btn btn-neutral float-right" title="grid_class module" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
-
-
- <a href="distribution_functions.html" class="btn btn-neutral float-left" title="distribution_functions module" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
-
+ <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
+ <a href="distribution_functions.html" class="btn btn-neutral float-left" title="distribution_functions module" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
+ <a href="grid.html" class="btn btn-neutral float-right" title="grid_class module" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
</div>
-
<hr/>
<div role="contentinfo">
- <p>
-
- © Copyright 2021, David Hendriks, Robert Izzard
-
- </p>
+ <p>© Copyright 2021, David Hendriks, Robert Izzard.</p>
</div>
-
-
-
- Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a
-
- <a href="https://github.com/rtfd/sphinx_rtd_theme">theme</a>
-
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+ Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
+ <a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
provided by <a href="https://readthedocs.org">Read the Docs</a>.
+
<br><br>
-Generated on binarycpython git branch: master git revision 0886cd4f1d7f43222aac21d6ed91e917b67b20fc url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/tree/master">git url</a>.
+Generated on binarycpython git branch: auto_resolution git revision be7bd630af892a785312affc34d87c57eb337fd3 url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/tree/auto_resolution">git url</a>.
<br><br>
-Using binary_c with bit branch newmaster: git revision: "6185:20210910:1621c23a5" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/newmaster">git url</a>.
+Using binary_c with bit branch master: git revision: "6209:20211006:c4a4c332e" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/master">git url</a>.
</footer>
-
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- <script type="text/javascript">
+ <script>
jQuery(function () {
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- </script>
-
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+ </script>
</body>
</html>
\ No newline at end of file
diff --git a/docs/build/html/genindex.html b/docs/build/html/genindex.html
index 0c51efc2fc6eb6e5c1a18aac6ad144c79dbfe851..e3c0fd0f6f1870e695b7d0983d60a4c8f390a8b9 100644
--- a/docs/build/html/genindex.html
+++ b/docs/build/html/genindex.html
@@ -1,69 +1,32 @@
-
-
<!DOCTYPE html>
<html class="writer-html5" lang="en" >
<head>
- <meta charset="utf-8">
-
- <meta name="viewport" content="width=device-width, initial-scale=1.0">
-
+ <meta charset="utf-8" />
+ <meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Index — binary_c-python documentation</title>
-
-
-
- <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
- <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-
-
-
-
-
-
-
+ <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+ <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
<!--[if lt IE 9]>
<script src="_static/js/html5shiv.min.js"></script>
<![endif]-->
-
- <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
+ <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
<script src="_static/jquery.js"></script>
<script src="_static/underscore.js"></script>
<script src="_static/doctools.js"></script>
- <script src="_static/language_data.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
- <script async="async" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.7/latest.js?config=TeX-AMS-MML_HTMLorMML"></script>
- <script type="text/x-mathjax-config">MathJax.Hub.Config({"tex2jax": {"inlineMath": [["$", "$"], ["\\(", "\\)"]], "processEscapes": true, "ignoreClass": "document", "processClass": "math|output_area"}})</script>
-
- <script type="text/javascript" src="_static/js/theme.js"></script>
-
-
+ <script src="_static/js/theme.js"></script>
<link rel="index" title="Index" href="#" />
<link rel="search" title="Search" href="search.html" />
</head>
-<body class="wy-body-for-nav">
-
-
+<body class="wy-body-for-nav">
<div class="wy-grid-for-nav">
-
<nav data-toggle="wy-nav-shift" class="wy-nav-side">
<div class="wy-side-scroll">
<div class="wy-side-nav-search" >
-
-
-
- <a href="index.html" class="icon icon-home" alt="Documentation Home"> binary_c-python
-
-
-
+ <a href="index.html" class="icon icon-home"> binary_c-python
</a>
-
-
-
-
-
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<div role="search">
<form id="rtd-search-form" class="wy-form" action="search.html" method="get">
<input type="text" name="q" placeholder="Search docs" />
@@ -71,19 +34,8 @@
<input type="hidden" name="area" value="default" />
</form>
</div>
-
-
- </div>
-
-
- <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
-
-
-
-
-
-
- <p class="caption"><span class="caption-text">Contents:</span></p>
+ </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
+ <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="readme_link.html">Python module for binary_c</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules.html">Binarycpython code</a></li>
@@ -94,67 +46,29 @@
<li class="toctree-l1"><a class="reference external" href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/issues/new">Submit an issue</a></li>
</ul>
-
-
</div>
-
</div>
</nav>
- <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap">
-
-
- <nav class="wy-nav-top" aria-label="top navigation">
-
+ <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
<i data-toggle="wy-nav-top" class="fa fa-bars"></i>
<a href="index.html">binary_c-python</a>
-
</nav>
-
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-
<div class="rst-content">
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-
-<div role="navigation" aria-label="breadcrumbs navigation">
-
+ <div role="navigation" aria-label="Page navigation">
<ul class="wy-breadcrumbs">
-
<li><a href="index.html" class="icon icon-home"></a> »</li>
-
<li>Index</li>
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</ul>
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<hr/>
</div>
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
-
+
<h1 id="index">Index</h1>
@@ -209,10 +123,12 @@
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="grid.html#binarycpython.utils.grid.Population.add_grid_variable">add_grid_variable() (binarycpython.utils.grid.Population method)</a>
</li>
- <li><a href="distribution_functions.html#binarycpython.utils.distribution_functions.Arenou2010_binary_fraction">Arenou2010_binary_fraction() (in module binarycpython.utils.distribution_functions)</a>
+ <li><a href="functions.html#binarycpython.utils.functions.ANSI_colours">ANSI_colours() (in module binarycpython.utils.functions)</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="distribution_functions.html#binarycpython.utils.distribution_functions.Arenou2010_binary_fraction">Arenou2010_binary_fraction() (in module binarycpython.utils.distribution_functions)</a>
+</li>
<li><a href="custom_logging_functions.html#binarycpython.utils.custom_logging_functions.autogen_C_logging_code">autogen_C_logging_code() (in module binarycpython.utils.custom_logging_functions)</a>
</li>
<li><a href="functions.html#binarycpython.utils.functions.AutoVivificationDict">AutoVivificationDict (class in binarycpython.utils.functions)</a>
@@ -339,21 +255,29 @@
<li><a href="functions.html#binarycpython.utils.functions.Capturing">Capturing (class in binarycpython.utils.functions)</a>
</li>
<li><a href="functions.html#binarycpython.utils.functions.catchtime">catchtime (class in binarycpython.utils.functions)</a>
+</li>
+ <li><a href="functions.html#binarycpython.utils.functions.check_if_in_shell">check_if_in_shell() (in module binarycpython.utils.functions)</a>
</li>
<li><a href="grid.html#binarycpython.utils.grid.Population.clean">clean() (binarycpython.utils.grid.Population method)</a>
</li>
<li><a href="plot_functions.html#binarycpython.utils.plot_functions.color_by_index">color_by_index() (in module binarycpython.utils.plot_functions)</a>
</li>
- </ul></td>
- <td style="width: 33%; vertical-align: top;"><ul>
<li><a href="custom_logging_functions.html#binarycpython.utils.custom_logging_functions.compile_shared_lib">compile_shared_lib() (in module binarycpython.utils.custom_logging_functions)</a>
</li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
<li><a href="distribution_functions.html#binarycpython.utils.distribution_functions.const">const() (in module binarycpython.utils.distribution_functions)</a>
<ul>
<li><a href="spacing_functions.html#binarycpython.utils.spacing_functions.const">(in module binarycpython.utils.spacing_functions)</a>
</li>
</ul></li>
+ <li><a href="spacing_functions.html#binarycpython.utils.spacing_functions.const_dt">const_dt() (in module binarycpython.utils.spacing_functions)</a>
+</li>
+ <li><a href="spacing_functions.html#binarycpython.utils.spacing_functions.const_ranges">const_ranges() (in module binarycpython.utils.spacing_functions)</a>
+</li>
+ <li><a href="functions.html#binarycpython.utils.functions.conv_time_units">conv_time_units() (in module binarycpython.utils.functions)</a>
+</li>
<li><a href="functions.html#binarycpython.utils.functions.convert_bytes">convert_bytes() (in module binarycpython.utils.functions)</a>
</li>
<li><a href="functions.html#binarycpython.utils.functions.convfloat">convfloat() (in module binarycpython.utils.functions)</a>
@@ -379,10 +303,12 @@
<li><a href="functions.html#binarycpython.utils.functions.datalinedict">datalinedict() (in module binarycpython.utils.functions)</a>
</li>
<li><a href="functions.html#binarycpython.utils.functions.binarycDecoder.decode">decode() (binarycpython.utils.functions.binarycDecoder method)</a>
+</li>
+ <li><a href="functions.html#binarycpython.utils.functions.BinaryCEncoder.default">default() (binarycpython.utils.functions.BinaryCEncoder method)</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
- <li><a href="functions.html#binarycpython.utils.functions.BinaryCEncoder.default">default() (binarycpython.utils.functions.BinaryCEncoder method)</a>
+ <li><a href="grid.html#binarycpython.utils.grid.Population.delete_grid_variable">delete_grid_variable() (binarycpython.utils.grid.Population method)</a>
</li>
<li><a href="plot_functions.html#binarycpython.utils.plot_functions.dummy">dummy() (in module binarycpython.utils.plot_functions)</a>
</li>
@@ -423,6 +349,8 @@
<li><a href="distribution_functions.html#binarycpython.utils.distribution_functions.flatsections">flatsections() (in module binarycpython.utils.distribution_functions)</a>
</li>
<li><a href="functions.html#binarycpython.utils.functions.format_ensemble_results">format_ensemble_results() (in module binarycpython.utils.functions)</a>
+</li>
+ <li><a href="functions.html#binarycpython.utils.functions.format_number">format_number() (in module binarycpython.utils.functions)</a>
</li>
<li><a href="custom_logging_functions.html#binarycpython.utils.custom_logging_functions.from_binary_c_config">from_binary_c_config() (in module binarycpython.utils.custom_logging_functions)</a>
</li>
@@ -437,6 +365,8 @@
<li><a href="distribution_functions.html#binarycpython.utils.distribution_functions.gaussian_func">gaussian_func() (in module binarycpython.utils.distribution_functions)</a>
</li>
<li><a href="distribution_functions.html#binarycpython.utils.distribution_functions.gaussian_normalizing_const">gaussian_normalizing_const() (in module binarycpython.utils.distribution_functions)</a>
+</li>
+ <li><a href="spacing_functions.html#binarycpython.utils.spacing_functions.gaussian_zoom">gaussian_zoom() (in module binarycpython.utils.spacing_functions)</a>
</li>
<li><a href="functions.html#binarycpython.utils.functions.get_arg_keys">get_arg_keys() (in module binarycpython.utils.functions)</a>
</li>
@@ -457,6 +387,8 @@
<li><a href="functions.html#binarycpython.utils.functions.get_moe_di_stefano_dataset">get_moe_di_stefano_dataset() (in module binarycpython.utils.functions)</a>
</li>
<li><a href="functions.html#binarycpython.utils.functions.get_size">get_size() (in module binarycpython.utils.functions)</a>
+</li>
+ <li><a href="functions.html#binarycpython.utils.functions.get_username">get_username() (in module binarycpython.utils.functions)</a>
</li>
<li><a href="grid_options_defaults.html#binarycpython.utils.grid_options_defaults.grid_options_description_checker">grid_options_description_checker() (in module binarycpython.utils.grid_options_defaults)</a>
</li>
@@ -529,6 +461,8 @@
<li><a href="functions.html#binarycpython.utils.functions.make_build_text">make_build_text() (in module binarycpython.utils.functions)</a>
</li>
<li><a href="useful_funcs.html#binarycpython.utils.useful_funcs.maximum_mass_ratio_for_RLOF">maximum_mass_ratio_for_RLOF() (in module binarycpython.utils.useful_funcs)</a>
+</li>
+ <li><a href="functions.html#binarycpython.utils.functions.mem_use">mem_use() (in module binarycpython.utils.functions)</a>
</li>
<li><a href="functions.html#binarycpython.utils.functions.merge_dicts">merge_dicts() (in module binarycpython.utils.functions)</a>
</li>
@@ -612,6 +546,8 @@
<li><a href="plot_functions.html#binarycpython.utils.plot_functions.parse_function_masses">parse_function_masses() (in module binarycpython.utils.plot_functions)</a>
</li>
<li><a href="plot_functions.html#binarycpython.utils.plot_functions.parse_function_orbit">parse_function_orbit() (in module binarycpython.utils.plot_functions)</a>
+</li>
+ <li><a href="spacing_functions.html#binarycpython.utils.spacing_functions.peak_normalized_gaussian_func">peak_normalized_gaussian_func() (in module binarycpython.utils.spacing_functions)</a>
</li>
<li><a href="plot_functions.html#binarycpython.utils.plot_functions.plot_HR_diagram">plot_HR_diagram() (in module binarycpython.utils.plot_functions)</a>
</li>
@@ -706,6 +642,8 @@
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="distribution_functions.html#binarycpython.utils.distribution_functions.three_part_powerlaw">three_part_powerlaw() (in module binarycpython.utils.distribution_functions)</a>
+</li>
+ <li><a href="functions.html#binarycpython.utils.functions.trem">trem() (in module binarycpython.utils.functions)</a>
</li>
</ul></td>
</tr></table>
@@ -729,6 +667,8 @@
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="grid.html#binarycpython.utils.grid.Population.vb2print">vb2print() (binarycpython.utils.grid.Population method)</a>
+</li>
<li><a href="functions.html#binarycpython.utils.functions.verbose_print">verbose_print() (in module binarycpython.utils.functions)</a>
</li>
</ul></td>
@@ -759,55 +699,36 @@
</div>
-
</div>
<footer>
-
<hr/>
<div role="contentinfo">
- <p>
-
- © Copyright 2021, David Hendriks, Robert Izzard
-
- </p>
+ <p>© Copyright 2021, David Hendriks, Robert Izzard.</p>
</div>
-
-
-
- Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a
-
- <a href="https://github.com/rtfd/sphinx_rtd_theme">theme</a>
-
+
+ Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
+ <a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
provided by <a href="https://readthedocs.org">Read the Docs</a>.
+
<br><br>
-Generated on binarycpython git branch: master git revision 0886cd4f1d7f43222aac21d6ed91e917b67b20fc url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/tree/master">git url</a>.
+Generated on binarycpython git branch: auto_resolution git revision be7bd630af892a785312affc34d87c57eb337fd3 url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/tree/auto_resolution">git url</a>.
<br><br>
-Using binary_c with bit branch newmaster: git revision: "6185:20210910:1621c23a5" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/newmaster">git url</a>.
+Using binary_c with bit branch master: git revision: "6209:20211006:c4a4c332e" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/master">git url</a>.
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+ <script>
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\ No newline at end of file
diff --git a/docs/build/html/grid.html b/docs/build/html/grid.html
index f94395fa76ca654e0dd5fb5b3d7a929f672d58b4..93bf82824f3764b20a086f3549cb36c35470251f 100644
--- a/docs/build/html/grid.html
+++ b/docs/build/html/grid.html
@@ -1,71 +1,35 @@
-
-
<!DOCTYPE html>
<html class="writer-html5" lang="en" >
<head>
- <meta charset="utf-8">
-
- <meta name="viewport" content="width=device-width, initial-scale=1.0">
-
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- <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-
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-
+ <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+ <title>grid_class module — binary_c-python documentation</title>
+ <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+ <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
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+ <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
<script src="_static/jquery.js"></script>
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- <script src="_static/language_data.js"></script>
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- <script async="async" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.7/latest.js?config=TeX-AMS-MML_HTMLorMML"></script>
- <script type="text/x-mathjax-config">MathJax.Hub.Config({"tex2jax": {"inlineMath": [["$", "$"], ["\\(", "\\)"]], "processEscapes": true, "ignoreClass": "document", "processClass": "math|output_area"}})</script>
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+ <script src="_static/js/theme.js"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="next" title="Grid options and descriptions" href="grid_options_defaults.html" />
<link rel="prev" title="functions module" href="functions.html" />
</head>
-<body class="wy-body-for-nav">
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+<body class="wy-body-for-nav">
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-
<nav data-toggle="wy-nav-shift" class="wy-nav-side">
<div class="wy-side-scroll">
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@@ -73,19 +37,8 @@
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-
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+ </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
+ <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
<ul class="current">
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<li class="toctree-l1 current"><a class="reference internal" href="modules.html">Binarycpython code</a><ul class="current">
@@ -109,71 +62,31 @@
<li class="toctree-l1"><a class="reference external" href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/issues/new">Submit an issue</a></li>
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-<div role="navigation" aria-label="breadcrumbs navigation">
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<ul class="wy-breadcrumbs">
-
<li><a href="index.html" class="icon icon-home"></a> »</li>
-
<li><a href="modules.html">Binarycpython code</a> »</li>
-
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-
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<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
-
+
<style>
/* CSS overrides for sphinx_rtd_theme */
@@ -198,8 +111,8 @@
text-align: unset;
}
</style>
-<div class="section" id="module-binarycpython.utils.grid">
-<span id="grid-class-module"></span><h1>grid_class module<a class="headerlink" href="#module-binarycpython.utils.grid" title="Permalink to this headline">¶</a></h1>
+<section id="module-binarycpython.utils.grid">
+<span id="grid-class-module"></span><h1>grid_class module<a class="headerlink" href="#module-binarycpython.utils.grid" title="Permalink to this headline">ïƒ</a></h1>
<p>Module containing the Population grid class object.</p>
<p>Here all the functionality of a Population object is defined.</p>
<dl class="simple">
@@ -222,14 +135,14 @@
</dd>
</dl>
<dl class="py class">
-<dt id="binarycpython.utils.grid.Population">
-<em class="property">class </em><code class="sig-prename descclassname">binarycpython.utils.grid.</code><code class="sig-name descname">Population</code><a class="reference internal" href="_modules/binarycpython/utils/grid.html#Population"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.grid.Population" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.grid.Population">
+<em class="property"><span class="pre">class</span> </em><span class="sig-prename descclassname"><span class="pre">binarycpython.utils.grid.</span></span><span class="sig-name descname"><span class="pre">Population</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/grid.html#Population"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.grid.Population" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
<p>Population Object. Contains all the necessary functions to set up, run and process a
population of systems</p>
<dl class="py method">
-<dt id="binarycpython.utils.grid.Population.Moe_di_Stefano_2017">
-<code class="sig-name descname">Moe_di_Stefano_2017</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">options</span><span class="o">=</span><span class="default_value">None</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/grid.html#Population.Moe_di_Stefano_2017"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.grid.Population.Moe_di_Stefano_2017" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.grid.Population.Moe_di_Stefano_2017">
+<span class="sig-name descname"><span class="pre">Moe_di_Stefano_2017</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">options</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/grid.html#Population.Moe_di_Stefano_2017"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.grid.Population.Moe_di_Stefano_2017" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function to handle setting the user input settings,
set up the data and load that into interpolators and
then set the distribution functions</p>
@@ -237,8 +150,8 @@ then set the distribution functions</p>
</dd></dl>
<dl class="py method">
-<dt id="binarycpython.utils.grid.Population.add_grid_variable">
-<code class="sig-name descname">add_grid_variable</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">name</span></em>, <em class="sig-param"><span class="n">longname</span></em>, <em class="sig-param"><span class="n">valuerange</span></em>, <em class="sig-param"><span class="n">resolution</span></em>, <em class="sig-param"><span class="n">spacingfunc</span></em>, <em class="sig-param"><span class="n">probdist</span></em>, <em class="sig-param"><span class="n">dphasevol</span></em>, <em class="sig-param"><span class="n">parameter_name</span></em>, <em class="sig-param"><span class="n">gridtype</span><span class="o">=</span><span class="default_value">'centred'</span></em>, <em class="sig-param"><span class="n">branchpoint</span><span class="o">=</span><span class="default_value">0</span></em>, <em class="sig-param"><span class="n">precode</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">condition</span><span class="o">=</span><span class="default_value">None</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/grid.html#Population.add_grid_variable"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.grid.Population.add_grid_variable" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.grid.Population.add_grid_variable">
+<span class="sig-name descname"><span class="pre">add_grid_variable</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">longname</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">valuerange</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resolution</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">spacingfunc</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">probdist</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dphasevol</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parameter_name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">gridtype</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'centred'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">branchpoint</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">precode</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">condition</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/grid.html#Population.add_grid_variable"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.grid.Population.add_grid_variable" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function to add grid variables to the grid_options.</p>
<p>The execution of the grid generation will be through a nested for loop.
Each of the grid variables will get create a deeper for loop.</p>
@@ -264,21 +177,21 @@ the rest of the function</p>
<p class="rubric">Examples</p>
<p>longname = ‘Primary mass’</p>
</p></li>
-<li><p><strong>range</strong> – <p>Range of values to take. Does not get used really, the spacingfunction is used to
+<li><p><strong>range</strong> – <p>Range of values to take. Does not get used really, the spacingfunc is used to
get the values from</p>
<p class="rubric">Examples</p>
<p>range = [math.log(m_min), math.log(m_max)]</p>
</p></li>
-<li><p><strong>resolution</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code>) – <p>Resolution of the sampled range (amount of samples).
+<li><p><strong>resolution</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code>) – <p>Resolution of the sampled range (number of samples).
TODO: check if this is used anywhere</p>
<p class="rubric">Examples</p>
<p>resolution = resolution[“M_1â€]</p>
</p></li>
-<li><p><strong>spacingfunction</strong> – <p>Function determining how the range is sampled. You can either use a real function,
+<li><p><strong>spacingfunc</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code>) – <p>Function determining how the range is sampled. You can either use a real function,
or a string representation of a function call. Will get written to a file and
then evaluated.</p>
<p class="rubric">Examples</p>
-<p>spacingfunction = “const(math.log(m_min), math.log(m_max), {})â€.format(resolution[‘M_1’])</p>
+<p>spacingfunc = “const(math.log(m_min), math.log(m_max), {})â€.format(resolution[‘M_1’])</p>
</p></li>
<li><p><strong>precode</strong> (<code class="xref py py-data docutils literal notranslate"><span class="pre">Optional</span></code>[<code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code>]) – <p>Extra room for some code. This code will be evaluated within the loop of the
sampling function (i.e. a value for lnm1 is chosen already)</p>
@@ -310,8 +223,8 @@ the lower edge of the value range) or ‘centred’
</dd></dl>
<dl class="py method">
-<dt id="binarycpython.utils.grid.Population.clean">
-<code class="sig-name descname">clean</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/grid.html#Population.clean"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.grid.Population.clean" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.grid.Population.clean">
+<span class="sig-name descname"><span class="pre">clean</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/grid.html#Population.clean"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.grid.Population.clean" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Clean the contents of the population object so it can be reused.</p>
<p>Calling _pre_run_cleanup()</p>
<p>TODO: decide to deprecate this function</p>
@@ -323,8 +236,18 @@ the lower edge of the value range) or ‘centred’
</dd></dl>
<dl class="py method">
-<dt id="binarycpython.utils.grid.Population.evolve">
-<code class="sig-name descname">evolve</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/grid.html#Population.evolve"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.grid.Population.evolve" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.grid.Population.delete_grid_variable">
+<span class="sig-name descname"><span class="pre">delete_grid_variable</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/grid.html#Population.delete_grid_variable"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.grid.Population.delete_grid_variable" title="Permalink to this definition">ïƒ</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">None</span></code></p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="binarycpython.utils.grid.Population.evolve">
+<span class="sig-name descname"><span class="pre">evolve</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/grid.html#Population.evolve"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.grid.Population.evolve" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Entry point function of the whole object. From here, based on the settings,
we set up a SLURM or CONDOR grid, or if no setting is given we go straight
to evolving the population.</p>
@@ -336,7 +259,7 @@ grid_options[‘condor’]: integer Boolean whether to use a condor_grid evoluti
<p>If neither of the above is set, we continue without using HPC routines
(that doesn’t mean this cannot be run on a server with many cores)</p>
<p>Returns an dictionary containing the analytics of the run</p>
-<p>TODO: change the way this is done. Slurm & CONDOR should probably do this different
+<p>TODO: change the way this is done. Slurm & CONDOR should probably do this differently
NOTE: SLURM and CONDOR options are not working properly yet</p>
<dl class="field-list simple">
<dt class="field-odd">Return type</dt>
@@ -346,8 +269,8 @@ NOTE: SLURM and CONDOR options are not working properly yet</p>
</dd></dl>
<dl class="py method">
-<dt id="binarycpython.utils.grid.Population.evolve_single">
-<code class="sig-name descname">evolve_single</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">clean_up_custom_logging_files</span><span class="o">=</span><span class="default_value">True</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/grid.html#Population.evolve_single"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.grid.Population.evolve_single" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.grid.Population.evolve_single">
+<span class="sig-name descname"><span class="pre">evolve_single</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">clean_up_custom_logging_files</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/grid.html#Population.evolve_single"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.grid.Population.evolve_single" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function to run a single system, based on the settings in the grid_options</p>
<p>The output of the run gets returned, unless a parse function is given to this function.</p>
<dl class="field-list simple">
@@ -364,8 +287,8 @@ NOTE: SLURM and CONDOR options are not working properly yet</p>
</dd></dl>
<dl class="py method">
-<dt id="binarycpython.utils.grid.Population.export_all_info">
-<code class="sig-name descname">export_all_info</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">use_datadir</span><span class="o">=</span><span class="default_value">True</span></em>, <em class="sig-param"><span class="n">outfile</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">include_population_settings</span><span class="o">=</span><span class="default_value">True</span></em>, <em class="sig-param"><span class="n">include_binary_c_defaults</span><span class="o">=</span><span class="default_value">True</span></em>, <em class="sig-param"><span class="n">include_binary_c_version_info</span><span class="o">=</span><span class="default_value">True</span></em>, <em class="sig-param"><span class="n">include_binary_c_help_all</span><span class="o">=</span><span class="default_value">True</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/grid.html#Population.export_all_info"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.grid.Population.export_all_info" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.grid.Population.export_all_info">
+<span class="sig-name descname"><span class="pre">export_all_info</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">use_datadir</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">outfile</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">include_population_settings</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">include_binary_c_defaults</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">include_binary_c_version_info</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">include_binary_c_help_all</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/grid.html#Population.export_all_info"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.grid.Population.export_all_info" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function that exports the all_info to a JSON file</p>
<dl class="simple">
<dt>Tasks:</dt><dd><ul class="simple">
@@ -410,22 +333,16 @@ simulation_<date+time>_settings.json will be created</p></li>
</dd></dl>
<dl class="py method">
-<dt id="binarycpython.utils.grid.Population.parse_cmdline">
-<code class="sig-name descname">parse_cmdline</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/grid.html#Population.parse_cmdline"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.grid.Population.parse_cmdline" title="Permalink to this definition">¶</a></dt>
-<dd><p>Function to handle settings values via the command line.
-Best to be called after all the .set(..) lines, and just before the .evolve() is called</p>
+<dt class="sig sig-object py" id="binarycpython.utils.grid.Population.parse_cmdline">
+<span class="sig-name descname"><span class="pre">parse_cmdline</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/grid.html#Population.parse_cmdline"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.grid.Population.parse_cmdline" title="Permalink to this definition">ïƒ</a></dt>
+<dd><p>Function to handle settings values via the command line in the form x=y, w=z, etc.</p>
+<p>Best to be called after all the .set(..) lines, and just before the .evolve() is called</p>
<p>If you input any known parameter (i.e. contained in grid_options, defaults/bse_options
or custom_options), this function will attempt to convert the input from string
(because everything is string) to the type of the value that option had before.</p>
<p>The values of the bse_options are initially all strings, but after user input they
can change to ints.</p>
<p>The value of any new parameter (which will go to custom_options) will be a string.</p>
-<dl class="simple">
-<dt>Tasks:</dt><dd><ul class="simple">
-<li><p>TODO: remove the need for –cmdline</p></li>
-</ul>
-</dd>
-</dl>
<dl class="field-list simple">
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">None</span></code></p>
@@ -434,8 +351,8 @@ can change to ints.</p>
</dd></dl>
<dl class="py method">
-<dt id="binarycpython.utils.grid.Population.rename_grid_variable">
-<code class="sig-name descname">rename_grid_variable</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">oldname</span></em>, <em class="sig-param"><span class="n">newname</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/grid.html#Population.rename_grid_variable"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.grid.Population.rename_grid_variable" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.grid.Population.rename_grid_variable">
+<span class="sig-name descname"><span class="pre">rename_grid_variable</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">oldname</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">newname</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/grid.html#Population.rename_grid_variable"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.grid.Population.rename_grid_variable" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function to rename a grid variable.</p>
<p>note: this does NOT alter the order
of the self.grid_options[“_grid_variablesâ€] dictionary.</p>
@@ -455,8 +372,8 @@ of the self.grid_options[“_grid_variablesâ€] dictionary.</p>
</dd></dl>
<dl class="py method">
-<dt id="binarycpython.utils.grid.Population.return_all_info">
-<code class="sig-name descname">return_all_info</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">include_population_settings</span><span class="o">=</span><span class="default_value">True</span></em>, <em class="sig-param"><span class="n">include_binary_c_defaults</span><span class="o">=</span><span class="default_value">True</span></em>, <em class="sig-param"><span class="n">include_binary_c_version_info</span><span class="o">=</span><span class="default_value">True</span></em>, <em class="sig-param"><span class="n">include_binary_c_help_all</span><span class="o">=</span><span class="default_value">True</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/grid.html#Population.return_all_info"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.grid.Population.return_all_info" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.grid.Population.return_all_info">
+<span class="sig-name descname"><span class="pre">return_all_info</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">include_population_settings</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">include_binary_c_defaults</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">include_binary_c_version_info</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">include_binary_c_help_all</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/grid.html#Population.return_all_info"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.grid.Population.return_all_info" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function that returns all the information about the population and binary_c</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
@@ -480,20 +397,20 @@ the binary_c parameters (see get_help_all)</p></li>
</dd></dl>
<dl class="py method">
-<dt id="binarycpython.utils.grid.Population.return_binary_c_defaults">
-<code class="sig-name descname">return_binary_c_defaults</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/grid.html#Population.return_binary_c_defaults"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.grid.Population.return_binary_c_defaults" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.grid.Population.return_binary_c_defaults">
+<span class="sig-name descname"><span class="pre">return_binary_c_defaults</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/grid.html#Population.return_binary_c_defaults"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.grid.Population.return_binary_c_defaults" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function that returns the defaults of the binary_c version that is used.</p>
</dd></dl>
<dl class="py method">
-<dt id="binarycpython.utils.grid.Population.return_binary_c_version_info">
-<code class="sig-name descname">return_binary_c_version_info</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">parsed</span><span class="o">=</span><span class="default_value">False</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/grid.html#Population.return_binary_c_version_info"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.grid.Population.return_binary_c_version_info" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.grid.Population.return_binary_c_version_info">
+<span class="sig-name descname"><span class="pre">return_binary_c_version_info</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">parsed</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/grid.html#Population.return_binary_c_version_info"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.grid.Population.return_binary_c_version_info" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function that returns the version information of binary_c</p>
</dd></dl>
<dl class="py method">
-<dt id="binarycpython.utils.grid.Population.return_population_settings">
-<code class="sig-name descname">return_population_settings</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/grid.html#Population.return_population_settings"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.grid.Population.return_population_settings" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.grid.Population.return_population_settings">
+<span class="sig-name descname"><span class="pre">return_population_settings</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/grid.html#Population.return_population_settings"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.grid.Population.return_population_settings" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function that returns all the options that have been set.</p>
<p>Can be combined with JSON to make a nice file.</p>
<dl class="field-list simple">
@@ -507,8 +424,8 @@ the binary_c parameters (see get_help_all)</p></li>
</dd></dl>
<dl class="py method">
-<dt id="binarycpython.utils.grid.Population.set">
-<code class="sig-name descname">set</code><span class="sig-paren">(</span><em class="sig-param"><span class="o">**</span><span class="n">kwargs</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/grid.html#Population.set"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.grid.Population.set" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.grid.Population.set">
+<span class="sig-name descname"><span class="pre">set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/grid.html#Population.set"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.grid.Population.set" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function to set the values of the population. This is the preferred method to set values
of functions, as it provides checks on the input.</p>
<p>the bse_options will get populated with all the those that have a key that is present
@@ -519,8 +436,8 @@ in the self.grid_options</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>kwargs all the arguments are either set to binary_c parameters</strong> (<em>via</em>) – </p></li>
-<li><p><strong>or custom_options</strong> (<em>grid_options</em>) – </p></li>
+<li><p><strong>parameters</strong> (<em>via kwargs all the arguments are either set to binary_c</em>) – </p></li>
+<li><p><strong>custom_options</strong> (<em>grid_options or</em>) – </p></li>
</ul>
</dd>
<dt class="field-even">Return type</dt>
@@ -530,15 +447,15 @@ in the self.grid_options</p>
</dd></dl>
<dl class="py method">
-<dt id="binarycpython.utils.grid.Population.set_moe_di_stefano_settings">
-<code class="sig-name descname">set_moe_di_stefano_settings</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">options</span><span class="o">=</span><span class="default_value">None</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/grid.html#Population.set_moe_di_stefano_settings"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.grid.Population.set_moe_di_stefano_settings" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.grid.Population.set_moe_di_stefano_settings">
+<span class="sig-name descname"><span class="pre">set_moe_di_stefano_settings</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">options</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/grid.html#Population.set_moe_di_stefano_settings"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.grid.Population.set_moe_di_stefano_settings" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function to set user input configurations for the moe & di Stefano methods</p>
<p>If nothing is passed then we just use the default options</p>
</dd></dl>
<dl class="py method">
-<dt id="binarycpython.utils.grid.Population.update_grid_variable">
-<code class="sig-name descname">update_grid_variable</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">name</span></em>, <em class="sig-param"><span class="o">**</span><span class="n">kwargs</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/grid.html#Population.update_grid_variable"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.grid.Population.update_grid_variable" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.grid.Population.update_grid_variable">
+<span class="sig-name descname"><span class="pre">update_grid_variable</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/grid.html#Population.update_grid_variable"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.grid.Population.update_grid_variable" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function to update the values of a grid variable.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
@@ -554,17 +471,23 @@ in the self.grid_options</p>
</dd></dl>
<dl class="py method">
-<dt id="binarycpython.utils.grid.Population.vb1print">
-<code class="sig-name descname">vb1print</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">ID</span></em>, <em class="sig-param"><span class="n">now</span></em>, <em class="sig-param"><span class="n">system_number</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/grid.html#Population.vb1print"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.grid.Population.vb1print" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.grid.Population.vb1print">
+<span class="sig-name descname"><span class="pre">vb1print</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ID</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">now</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">system_number</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">system_dict</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/grid.html#Population.vb1print"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.grid.Population.vb1print" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Verbosity-level 1 printing, to keep an eye on a grid.
:param ID: thread ID for debugging (int)
:param now: the time now as a UNIX-style epoch in seconds (float)
:param system_number: the system number</p>
+<p>TODO: add information about the number of cores. the TPR shows the dt/dn but i want to see the number per core too</p>
</dd></dl>
<dl class="py method">
-<dt id="binarycpython.utils.grid.Population.write_binary_c_calls_to_file">
-<code class="sig-name descname">write_binary_c_calls_to_file</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">output_dir</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">output_filename</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">include_defaults</span><span class="o">=</span><span class="default_value">False</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/grid.html#Population.write_binary_c_calls_to_file"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.grid.Population.write_binary_c_calls_to_file" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.grid.Population.vb2print">
+<span class="sig-name descname"><span class="pre">vb2print</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">system_dict</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cmdline_string</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/grid.html#Population.vb2print"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.grid.Population.vb2print" title="Permalink to this definition">ïƒ</a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="binarycpython.utils.grid.Population.write_binary_c_calls_to_file">
+<span class="sig-name descname"><span class="pre">write_binary_c_calls_to_file</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">output_dir</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_filename</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">include_defaults</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/grid.html#Population.write_binary_c_calls_to_file"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.grid.Population.write_binary_c_calls_to_file" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function that loops over the grid code and writes the generated parameters to a file.
In the form of a command line call</p>
<p>Only useful when you have a variable grid as system_generator. MC wouldn’t be that useful</p>
@@ -597,68 +520,43 @@ like m1,m2,sep, orb-per, ecc, probability etc.</p>
</dd></dl>
-</div>
+</section>
</div>
-
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+ <p>© Copyright 2021, David Hendriks, Robert Izzard.</p>
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+
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+Generated on binarycpython git branch: auto_resolution git revision be7bd630af892a785312affc34d87c57eb337fd3 url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/tree/auto_resolution">git url</a>.
<br><br>
-Using binary_c with bit branch newmaster: git revision: "6185:20210910:1621c23a5" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/newmaster">git url</a>.
+Using binary_c with bit branch master: git revision: "6209:20211006:c4a4c332e" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/master">git url</a>.
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diff --git a/docs/build/html/grid_options_defaults.html b/docs/build/html/grid_options_defaults.html
index 8bb1e5cb9fdc61bc1ec582d5d5b3778d5656962e..61d15382140406cad60bb06139fc2641382de4cb 100644
--- a/docs/build/html/grid_options_defaults.html
+++ b/docs/build/html/grid_options_defaults.html
@@ -1,71 +1,35 @@
-
-
<!DOCTYPE html>
<html class="writer-html5" lang="en" >
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- <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+ <meta charset="utf-8" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
-
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+ <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+ <title>Grid options and descriptions — binary_c-python documentation</title>
+ <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
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+ </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
+ <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
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<li class="toctree-l1 current"><a class="reference internal" href="modules.html">Binarycpython code</a><ul class="current">
@@ -109,71 +62,31 @@
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/* CSS overrides for sphinx_rtd_theme */
@@ -198,8 +111,8 @@
text-align: unset;
}
</style>
-<div class="section" id="module-binarycpython.utils.grid_options_defaults">
-<span id="grid-options-and-descriptions"></span><h1>Grid options and descriptions<a class="headerlink" href="#module-binarycpython.utils.grid_options_defaults" title="Permalink to this headline">¶</a></h1>
+<section id="module-binarycpython.utils.grid_options_defaults">
+<span id="grid-options-and-descriptions"></span><h1>Grid options and descriptions<a class="headerlink" href="#module-binarycpython.utils.grid_options_defaults" title="Permalink to this headline">ïƒ</a></h1>
<dl class="simple">
<dt>Module that contains the default options for the population grid code along with the description for these options, in the form of dictionaries:</dt><dd><ul class="simple">
<li><p>grid_options_defaults_dict: dictionary containing the default values for all the options</p></li>
@@ -216,8 +129,8 @@
<p>With this its also possible to automatically generate a document containing all the setting names + descriptions.</p>
<p>All the options starting with _ should not be changed by the user except when you really know what you’re doing (which is probably hacking the code :P)</p>
<dl class="py function">
-<dt id="binarycpython.utils.grid_options_defaults.grid_options_description_checker">
-<code class="sig-prename descclassname">binarycpython.utils.grid_options_defaults.</code><code class="sig-name descname">grid_options_description_checker</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">print_info</span><span class="o">=</span><span class="default_value">True</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/grid_options_defaults.html#grid_options_description_checker"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.grid_options_defaults.grid_options_description_checker" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.grid_options_defaults.grid_options_description_checker">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.grid_options_defaults.</span></span><span class="sig-name descname"><span class="pre">grid_options_description_checker</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">print_info</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/grid_options_defaults.html#grid_options_description_checker"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.grid_options_defaults.grid_options_description_checker" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function that checks which descriptions are missing</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
@@ -227,14 +140,14 @@
<dd class="field-even"><p><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></p>
</dd>
<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>the amount of undescribed keys</p>
+<dd class="field-odd"><p>the number of undescribed keys</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.grid_options_defaults.grid_options_help">
-<code class="sig-prename descclassname">binarycpython.utils.grid_options_defaults.</code><code class="sig-name descname">grid_options_help</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">option</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/grid_options_defaults.html#grid_options_help"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.grid_options_defaults.grid_options_help" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.grid_options_defaults.grid_options_help">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.grid_options_defaults.</span></span><span class="sig-name descname"><span class="pre">grid_options_help</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">option</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/grid_options_defaults.html#grid_options_help"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.grid_options_defaults.grid_options_help" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function that prints out the description of a grid option. Useful function for the user.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
@@ -250,13 +163,13 @@
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.grid_options_defaults.print_option_descriptions">
-<code class="sig-prename descclassname">binarycpython.utils.grid_options_defaults.</code><code class="sig-name descname">print_option_descriptions</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">filehandle</span></em>, <em class="sig-param"><span class="n">options</span></em>, <em class="sig-param"><span class="n">descriptions</span></em>, <em class="sig-param"><span class="n">title</span></em>, <em class="sig-param"><span class="n">extra_text</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/grid_options_defaults.html#print_option_descriptions"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.grid_options_defaults.print_option_descriptions" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.grid_options_defaults.print_option_descriptions">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.grid_options_defaults.</span></span><span class="sig-name descname"><span class="pre">print_option_descriptions</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">filehandle</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">options</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">descriptions</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">title</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">extra_text</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/grid_options_defaults.html#print_option_descriptions"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.grid_options_defaults.print_option_descriptions" title="Permalink to this definition">ïƒ</a></dt>
<dd></dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.grid_options_defaults.write_grid_options_to_rst_file">
-<code class="sig-prename descclassname">binarycpython.utils.grid_options_defaults.</code><code class="sig-name descname">write_grid_options_to_rst_file</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">output_file</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/grid_options_defaults.html#write_grid_options_to_rst_file"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.grid_options_defaults.write_grid_options_to_rst_file" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.grid_options_defaults.write_grid_options_to_rst_file">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.grid_options_defaults.</span></span><span class="sig-name descname"><span class="pre">write_grid_options_to_rst_file</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">output_file</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/grid_options_defaults.html#write_grid_options_to_rst_file"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.grid_options_defaults.write_grid_options_to_rst_file" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function that writes the descriptions of the grid options to a rst file</p>
<dl class="simple">
<dt>Tasks:</dt><dd><p>TODO: separate things into private and public options</p>
@@ -272,68 +185,43 @@
</dl>
</dd></dl>
-</div>
+</section>
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-
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- <footer>
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- <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
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+ <p>© Copyright 2021, David Hendriks, Robert Izzard.</p>
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provided by <a href="https://readthedocs.org">Read the Docs</a>.
+
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-Generated on binarycpython git branch: master git revision 0886cd4f1d7f43222aac21d6ed91e917b67b20fc url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/tree/master">git url</a>.
+Generated on binarycpython git branch: auto_resolution git revision be7bd630af892a785312affc34d87c57eb337fd3 url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/tree/auto_resolution">git url</a>.
<br><br>
-Using binary_c with bit branch newmaster: git revision: "6185:20210910:1621c23a5" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/newmaster">git url</a>.
+Using binary_c with bit branch master: git revision: "6209:20211006:c4a4c332e" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/master">git url</a>.
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diff --git a/docs/build/html/grid_options_descriptions.html b/docs/build/html/grid_options_descriptions.html
index 17724a27ef3dadaaaebdbf0bcda15487fc27fb48..730d09b6de5d76772b87db673b4e5e829bec1c6c 100644
--- a/docs/build/html/grid_options_descriptions.html
+++ b/docs/build/html/grid_options_descriptions.html
@@ -1,70 +1,34 @@
-
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<!DOCTYPE html>
<html class="writer-html5" lang="en" >
<head>
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- <meta name="viewport" content="width=device-width, initial-scale=1.0">
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+ <meta charset="utf-8" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
-
+ <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+ <title>Population grid code options — binary_c-python documentation</title>
+ <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+ <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
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+ <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
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- <script async="async" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.7/latest.js?config=TeX-AMS-MML_HTMLorMML"></script>
- <script type="text/x-mathjax-config">MathJax.Hub.Config({"tex2jax": {"inlineMath": [["$", "$"], ["\\(", "\\)"]], "processEscapes": true, "ignoreClass": "document", "processClass": "math|output_area"}})</script>
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+ <script src="_static/js/theme.js"></script>
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@@ -72,19 +36,8 @@
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+ </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
+ <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
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<li class="toctree-l1"><a class="reference internal" href="readme_link.html">Python module for binary_c</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules.html">Binarycpython code</a></li>
@@ -100,69 +53,30 @@
<li class="toctree-l1"><a class="reference external" href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/issues/new">Submit an issue</a></li>
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@@ -187,12 +101,12 @@
text-align: unset;
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</style>
-<div class="section" id="population-grid-code-options">
-<h1>Population grid code options<a class="headerlink" href="#population-grid-code-options" title="Permalink to this headline">¶</a></h1>
+<section id="population-grid-code-options">
+<h1>Population grid code options<a class="headerlink" href="#population-grid-code-options" title="Permalink to this headline">ïƒ</a></h1>
<p>The following chapter contains all grid code options, along with their descriptions
-There are 2 options that are not described yet.</p>
-<div class="section" id="public-options">
-<h2>Public options<a class="headerlink" href="#public-options" title="Permalink to this headline">¶</a></h2>
+There are 4 options that are not described yet.</p>
+<section id="public-options">
+<h2>Public options<a class="headerlink" href="#public-options" title="Permalink to this headline">ïƒ</a></h2>
<p>The following options are meant to be changed by the user.</p>
<div class="line-block">
<div class="line"><strong>C_auto_logging</strong>: Dictionary containing parameters to be logged by binary_c. The structure of this dictionary is as follows: the key is used as the headline which the user can then catch. The value at that key is a list of binary_c system parameters (like star[0].mass)</div>
@@ -201,9 +115,6 @@ There are 2 options that are not described yet.</p>
<div class="line"><strong>C_logging_code</strong>: Variable to store the exact code that is used for the custom_logging. In this way the user can do more complex logging, as well as putting these logging strings in files.</div>
</div>
<div class="line-block">
-<div class="line"><strong>amt_cores</strong>: The amount of cores that the population grid will use. The multiprocessing is useful but make sure to figure out how many logical cores the machine has. The core is multi processed, not multi threaded, and will gain no extra speed when amt_cores exceeds the amount of logical cores. Input: int</div>
-</div>
-<div class="line-block">
<div class="line"><strong>combine_ensemble_with_thread_joining</strong>: Boolean flag on whether to combine everything and return it to the user or if false: write it to data_dir/ensemble_output_{population_id}_{thread_id}.json</div>
</div>
<div class="line-block">
@@ -222,7 +133,10 @@ There are 2 options that are not described yet.</p>
<div class="line"><strong>evolution_type</strong>: Variable containing the type of evolution used of the grid. Multiprocessing or linear processing</div>
</div>
<div class="line-block">
-<div class="line"><strong>failed_systems_threshold</strong>: Variable storing the maximum amount of systems that are allowed to fail before logging their command line arguments to failed_systems log files</div>
+<div class="line"><strong>exit_after_dry_run</strong>: No description available yet</div>
+</div>
+<div class="line-block">
+<div class="line"><strong>failed_systems_threshold</strong>: Variable storing the maximum number of systems that are allowed to fail before logging their command line arguments to failed_systems log files</div>
</div>
<div class="line-block">
<div class="line"><strong>gridcode_filename</strong>: Filename for the grid code. Set and used by the population object. TODO: allow the user to provide their own function, rather than only a generated function.</div>
@@ -255,6 +169,12 @@ There are 2 options that are not described yet.</p>
<div class="line"><strong>multiplicity_fraction_function</strong>: Which multiplicity fraction function to use. 0: None, 1: Arenou 2010, 2: Rhagavan 2010, 3: M&S 2017</div>
</div>
<div class="line-block">
+<div class="line"><strong>n_logging_stats</strong>: No description available yet</div>
+</div>
+<div class="line-block">
+<div class="line"><strong>num_cores</strong>: The number of cores that the population grid will use. The multiprocessing is useful but make sure to figure out how many logical cores the machine has (use e.g. psutil.cpu_count(logical=False) to find the true number of cores, psutil.cpu_count(logical=True) to find the number of logical cores). The core is multi processed, not multi threaded, and will gain no extra speed when num_cores exceeds the number of logical cores. Input: int</div>
+</div>
+<div class="line-block">
<div class="line"><strong>parse_function</strong>: Function that the user can provide to handle the output the binary_c. This function has to take the arguments (self, output). Its best not to return anything in this function, and just store stuff in the self.grid_results dictionary, or just output results to a file</div>
</div>
<div class="line-block">
@@ -278,9 +198,9 @@ There are 2 options that are not described yet.</p>
<div class="line-block">
<div class="line"><strong>weight</strong>: Weight factor for each system. The calculated probability is multiplied by this. If the user wants each system to be repeated several times, then this variable should not be changed, rather change the _repeat variable instead, as that handles the reduction in probability per system. This is useful for systems that have a process with some random element in it.</div>
</div>
-</div>
-<div class="section" id="moe-di-stefano-sampler-options">
-<h2>Moe & di Stefano sampler options<a class="headerlink" href="#moe-di-stefano-sampler-options" title="Permalink to this headline">¶</a></h2>
+</section>
+<section id="moe-di-stefano-sampler-options">
+<h2>Moe & di Stefano sampler options<a class="headerlink" href="#moe-di-stefano-sampler-options" title="Permalink to this headline">ïƒ</a></h2>
<p>The following options are meant to be changed by the user.</p>
<div class="line-block">
<div class="line"><strong>Mmin</strong>: Minimum stellar mass</div>
@@ -359,9 +279,9 @@ q extrapolation (below 0.15) method
<div class="line-block">
<div class="line"><strong>resolutions</strong>:</div>
</div>
-</div>
-<div class="section" id="private-options">
-<h2>Private options<a class="headerlink" href="#private-options" title="Permalink to this headline">¶</a></h2>
+</section>
+<section id="private-options">
+<h2>Private options<a class="headerlink" href="#private-options" title="Permalink to this headline">ïƒ</a></h2>
<p>The following options are not meant to be changed by the user, as these options are used and set internally by the object itself. The description still is provided, but just for documentation purposes.</p>
<div class="line-block">
<div class="line"><strong>_actually_evolve_system</strong>: Whether to actually evolve the systems of just act as if. for testing. used in _process_run_population_grid</div>
@@ -391,7 +311,7 @@ q extrapolation (below 0.15) method
<div class="line"><strong>_end_time_evolution</strong>: Variable storing the end timestamp of the population evolution. Set by the object itself</div>
</div>
<div class="line-block">
-<div class="line"><strong>_errors_exceeded</strong>: Variable storing a Boolean flag whether the amount of errors was higher than the set threshold (failed_systems_threshold). If True, then the command line arguments of the failing systems will not be stored in the failed_system_log files.</div>
+<div class="line"><strong>_errors_exceeded</strong>: Variable storing a Boolean flag whether the number of errors was higher than the set threshold (failed_systems_threshold). If True, then the command line arguments of the failing systems will not be stored in the failed_system_log files.</div>
</div>
<div class="line-block">
<div class="line"><strong>_errors_found</strong>: Variable storing a Boolean flag whether errors by binary_c are encountered.</div>
@@ -400,7 +320,7 @@ q extrapolation (below 0.15) method
<div class="line"><strong>_evolution_type_options</strong>: List containing the evolution type options.</div>
</div>
<div class="line-block">
-<div class="line"><strong>_failed_count</strong>: Variable storing the amount of failed systems.</div>
+<div class="line"><strong>_failed_count</strong>: Variable storing the number of failed systems.</div>
</div>
<div class="line-block">
<div class="line"><strong>_failed_prob</strong>: Variable storing the total probability of all the failed systems</div>
@@ -442,72 +362,48 @@ q extrapolation (below 0.15) method
<div class="line"><strong>_total_probability_weighted_mass_run</strong>: To count the total mass * probability for each system that thread/process has ran</div>
</div>
<div class="line-block">
-<div class="line"><strong>_total_starcount</strong>: Variable storing the total amount of systems in the generator. Used and set by the population object.</div>
+<div class="line"><strong>_total_starcount</strong>: Variable storing the total number of systems in the generator. Used and set by the population object.</div>
</div>
<div class="line-block">
<div class="line"><strong>_zero_prob_stars_skipped</strong>: Internal counter to track how many systems are skipped because they have 0 probability</div>
</div>
-</div>
-</div>
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+Generated on binarycpython git branch: auto_resolution git revision be7bd630af892a785312affc34d87c57eb337fd3 url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/tree/auto_resolution">git url</a>.
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-Using binary_c with bit branch newmaster: git revision: "6185:20210910:1621c23a5" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/newmaster">git url</a>.
+Using binary_c with bit branch master: git revision: "6209:20211006:c4a4c332e" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/master">git url</a>.
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--- a/docs/build/html/hpc_functions.html
+++ b/docs/build/html/hpc_functions.html
@@ -1,71 +1,35 @@
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+ </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
+ <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
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<li class="toctree-l1 current"><a class="reference internal" href="modules.html">Binarycpython code</a><ul class="current">
@@ -109,71 +62,31 @@
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@@ -198,73 +111,48 @@
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-<div class="section" id="module-binarycpython.utils.hpc_functions">
-<span id="hpc-functions-module"></span><h1>hpc_functions module<a class="headerlink" href="#module-binarycpython.utils.hpc_functions" title="Permalink to this headline">¶</a></h1>
+<section id="module-binarycpython.utils.hpc_functions">
+<span id="hpc-functions-module"></span><h1>hpc_functions module<a class="headerlink" href="#module-binarycpython.utils.hpc_functions" title="Permalink to this headline">ïƒ</a></h1>
<p>File containing functions for HPC computing, distributed tasks on clusters etc.</p>
<p>Functions that the Slurm and Condor subroutines of the population object use.</p>
<p>Mainly divided in 2 sections: Slurm and Condor</p>
-</div>
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+
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+Generated on binarycpython git branch: auto_resolution git revision be7bd630af892a785312affc34d87c57eb337fd3 url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/tree/auto_resolution">git url</a>.
<br><br>
-Using binary_c with bit branch newmaster: git revision: "6185:20210910:1621c23a5" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/newmaster">git url</a>.
+Using binary_c with bit branch master: git revision: "6209:20211006:c4a4c332e" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/master">git url</a>.
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<li class="toctree-l1"><a class="reference internal" href="readme_link.html">Python module for binary_c</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules.html">Binarycpython code</a></li>
@@ -95,69 +48,30 @@
<li class="toctree-l1"><a class="reference external" href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/issues/new">Submit an issue</a></li>
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@@ -182,19 +96,19 @@
text-align: unset;
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</style>
-<div class="section" id="welcome-to-binary-c-python-s-documentation">
-<h1>Welcome to binary_c-python’s documentation!<a class="headerlink" href="#welcome-to-binary-c-python-s-documentation" title="Permalink to this headline">¶</a></h1>
-</div>
-<div class="section" id="python-module-for-binary-c">
-<h1>Python module for binary_c<a class="headerlink" href="#python-module-for-binary-c" title="Permalink to this headline">¶</a></h1>
+<section id="welcome-to-binary-c-python-s-documentation">
+<h1>Welcome to binary_c-python’s documentation!<a class="headerlink" href="#welcome-to-binary-c-python-s-documentation" title="Permalink to this headline">ïƒ</a></h1>
+</section>
+<section id="python-module-for-binary-c">
+<h1>Python module for binary_c<a class="headerlink" href="#python-module-for-binary-c" title="Permalink to this headline">ïƒ</a></h1>
<p>Docstring coverage:</p>
<a class="reference external image-reference" href="./badges/docstring_coverage.svg"><img alt="docstring coverage" src="_images/docstring_coverage.svg" /></a>
<p>Test coverage:</p>
<a class="reference external image-reference" href="./badges/test_coverage.svg"><img alt="test coverage" src="_images/test_coverage.svg" /></a>
<p>Binary population synthesis code that interfaces with binary_c. Based on a original work by Jeff Andrews (can be found in old_solution/ directory). Updated and extended for Python3 by David Hendriks, Robert Izzard.</p>
<p>The current release is version 0.9.1, make sure to use that version number when installing!</p>
-<div class="section" id="requirements">
-<h2>Requirements<a class="headerlink" href="#requirements" title="Permalink to this headline">¶</a></h2>
+<section id="requirements">
+<h2>Requirements<a class="headerlink" href="#requirements" title="Permalink to this headline">ïƒ</a></h2>
<p>To run this code you need to at least have installations of:</p>
<ul class="simple">
<li><p>Python 3.6 or higher</p></li>
@@ -211,9 +125,9 @@
<li><p>matplotlib</p></li>
<li><p>py_rinterpolate</p></li>
</ul>
-</div>
-<div class="section" id="environment-variables">
-<h2>Environment variables<a class="headerlink" href="#environment-variables" title="Permalink to this headline">¶</a></h2>
+</section>
+<section id="environment-variables">
+<h2>Environment variables<a class="headerlink" href="#environment-variables" title="Permalink to this headline">ïƒ</a></h2>
<p>Before compilation you need to have certain environment variables:</p>
<p>Required:</p>
<ul class="simple">
@@ -222,51 +136,50 @@
<li><p><code class="docutils literal notranslate"><span class="pre">LIBRARY_PATH</span></code> should include whatever directories are required to build binary_c (e.g. locations of libgsl, libmemoize, librinterpolate, etc.)</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">GSL_DIR</span></code> should point to the root location where you installed GSL to. This root dir should contain <code class="docutils literal notranslate"><span class="pre">bin/</span></code>, <code class="docutils literal notranslate"><span class="pre">lib/</span></code> etc</p></li>
</ul>
-</div>
-<div class="section" id="build-instructions">
-<h2>Build instructions<a class="headerlink" href="#build-instructions" title="Permalink to this headline">¶</a></h2>
+</section>
+<section id="build-instructions">
+<h2>Build instructions<a class="headerlink" href="#build-instructions" title="Permalink to this headline">ïƒ</a></h2>
<p>First, make sure you have built binary_c (See <code class="docutils literal notranslate"><span class="pre">$BINARY_C/doc/binary_c2.pdf</span></code> section: installation for all the installation instructions for <code class="docutils literal notranslate"><span class="pre">binary_c</span></code>)) and that it functions correctly.</p>
-<div class="section" id="installation-via-pip">
-<h3>Installation via PIP:<a class="headerlink" href="#installation-via-pip" title="Permalink to this headline">¶</a></h3>
+<section id="installation-via-pip">
+<h3>Installation via PIP:<a class="headerlink" href="#installation-via-pip" title="Permalink to this headline">ïƒ</a></h3>
<p>To install this package via pip:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">pip</span> <span class="n">install</span> <span class="n">binarycpython</span>
</pre></div>
</div>
-</div>
-<div class="section" id="installation-from-source">
-<h3>Installation from source:<a class="headerlink" href="#installation-from-source" title="Permalink to this headline">¶</a></h3>
+</section>
+<section id="installation-from-source">
+<h3>Installation from source:<a class="headerlink" href="#installation-from-source" title="Permalink to this headline">ïƒ</a></h3>
<p>For this it is best to set up a virtual environment. Activate the virtualenvironment and enter the cloned version of the repo.</p>
<p>Then run:</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">python</span> <span class="n">setup</span><span class="o">.</span><span class="n">py</span> <span class="n">clean</span> <span class="o">&&</span> <span class="n">python</span> <span class="n">setup</span><span class="o">.</span><span class="n">py</span> <span class="n">build</span> <span class="o">--</span><span class="n">force</span> <span class="o">&&</span> <span class="n">python</span> <span class="n">setup</span><span class="o">.</span><span class="n">py</span> <span class="n">sdist</span> <span class="o">&&</span> <span class="n">pip</span> <span class="n">install</span> <span class="o">-</span><span class="n">v</span> <span class="n">dist</span><span class="o">/</span><span class="n">binarycpython</span><span class="o">-<</span><span class="n">version</span> <span class="n">of</span> <span class="n">this</span> <span class="n">package</span><span class="o">>.</span><span class="n">tar</span><span class="o">.</span><span class="n">gz</span>
-<span class="n">python</span> <span class="n">setup</span><span class="o">.</span><span class="n">py</span> <span class="n">clean</span> <span class="o">&&</span> <span class="n">pip</span> <span class="n">uninstall</span> <span class="n">binarycpython</span> <span class="o">&&</span> <span class="n">rm</span> <span class="n">dist</span><span class="o">/*</span> <span class="o">&&</span> <span class="n">python</span> <span class="n">setup</span><span class="o">.</span><span class="n">py</span> <span class="n">build</span> <span class="o">--</span><span class="n">force</span> <span class="o">&&</span> <span class="n">python</span> <span class="n">setup</span><span class="o">.</span><span class="n">py</span> <span class="n">sdist</span> <span class="o">&&</span> <span class="n">pip</span> <span class="n">install</span> <span class="o">-</span><span class="n">v</span> <span class="n">dist</span><span class="o">/</span><span class="n">binarycpython</span><span class="o">-<</span><span class="n">version</span> <span class="n">of</span> <span class="n">this</span> <span class="n">package</span><span class="o">>.</span><span class="n">tar</span><span class="o">.</span><span class="n">gz</span>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">python</span> <span class="n">setup</span><span class="o">.</span><span class="n">py</span> <span class="n">clean</span> <span class="o">&&</span> <span class="n">pip</span> <span class="n">uninstall</span> <span class="n">binarycpython</span> <span class="o">&&</span> <span class="n">python</span> <span class="n">setup</span><span class="o">.</span><span class="n">py</span> <span class="n">build</span> <span class="o">--</span><span class="n">force</span> <span class="o">&&</span> <span class="n">python</span> <span class="n">setup</span><span class="o">.</span><span class="n">py</span> <span class="n">sdist</span> <span class="o">&&</span> <span class="n">pip</span> <span class="n">install</span> <span class="o">-</span><span class="n">v</span> <span class="n">dist</span><span class="o">/</span><span class="n">binarycpython</span><span class="o">-<</span><span class="n">version</span> <span class="n">of</span> <span class="n">this</span> <span class="n">package</span><span class="o">>.</span><span class="n">tar</span><span class="o">.</span><span class="n">gz</span>
</pre></div>
</div>
<p>This will clean the build directory, remove binarycpython from the venv, remove the dist packages, and then rebuilding and reinstalling the package. You can find the version of this package in setup.py.</p>
<p>This will install this package into the virtual environment. Making changes to the sourcecode can be “installed†into the virtual env with the same command.</p>
<p>If this is not the first time you install the package, but rather rebuild it because you make changes in either binary_c or binarycpython, you should ignore the currently installed version, and also skip installing the dependencies again, by executing the following command:</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">python</span> <span class="n">setup</span><span class="o">.</span><span class="n">py</span> <span class="n">clean</span> <span class="o">&&</span> <span class="n">pip</span> <span class="n">uninstall</span> <span class="n">binarycpython</span> <span class="o">&&</span> <span class="n">rm</span> <span class="n">dist</span><span class="o">/*</span> <span class="o">&&</span> <span class="n">python</span> <span class="n">setup</span><span class="o">.</span><span class="n">py</span> <span class="n">build</span> <span class="o">--</span><span class="n">force</span> <span class="o">&&</span> <span class="n">python</span> <span class="n">setup</span><span class="o">.</span><span class="n">py</span> <span class="n">sdist</span> <span class="o">&&</span> <span class="n">pip</span> <span class="n">install</span> <span class="o">--</span><span class="n">ignore</span><span class="o">-</span><span class="n">installed</span> <span class="o">--</span><span class="n">no</span><span class="o">-</span><span class="n">dependencies</span> <span class="o">-</span><span class="n">v</span> <span class="n">dist</span><span class="o">/</span><span class="n">binarycpython</span><span class="o">-<</span><span class="n">version</span> <span class="n">of</span> <span class="n">this</span> <span class="n">package</span><span class="o">>.</span><span class="n">tar</span><span class="o">.</span><span class="n">gz</span>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">python</span> <span class="n">setup</span><span class="o">.</span><span class="n">py</span> <span class="n">clean</span> <span class="o">&&</span> <span class="n">pip</span> <span class="n">uninstall</span> <span class="n">binarycpython</span> <span class="o">&&</span> <span class="n">python</span> <span class="n">setup</span><span class="o">.</span><span class="n">py</span> <span class="n">build</span> <span class="o">--</span><span class="n">force</span> <span class="o">&&</span> <span class="n">python</span> <span class="n">setup</span><span class="o">.</span><span class="n">py</span> <span class="n">sdist</span> <span class="o">&&</span> <span class="n">pip</span> <span class="n">install</span> <span class="o">--</span><span class="n">ignore</span><span class="o">-</span><span class="n">installed</span> <span class="o">--</span><span class="n">no</span><span class="o">-</span><span class="n">dependencies</span> <span class="o">-</span><span class="n">v</span> <span class="n">dist</span><span class="o">/</span><span class="n">binarycpython</span><span class="o">-<</span><span class="n">version</span> <span class="n">of</span> <span class="n">this</span> <span class="n">package</span><span class="o">>.</span><span class="n">tar</span><span class="o">.</span><span class="n">gz</span>
</pre></div>
</div>
-<div class="section" id="after-installation">
-<h4>After installation<a class="headerlink" href="#after-installation" title="Permalink to this headline">¶</a></h4>
+<section id="after-installation">
+<h4>After installation<a class="headerlink" href="#after-installation" title="Permalink to this headline">ïƒ</a></h4>
<p>After installing the code via source it is useful to run the test suite before doing any programming with it. The test suite is stored in <code class="docutils literal notranslate"><span class="pre">binarycpython/tests</span></code> and running <code class="docutils literal notranslate"><span class="pre">python</span> <span class="pre">main.py</span></code> in there will run all the tests.</p>
-</div>
-</div>
-</div>
-<div class="section" id="examples">
-<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
+</section>
+</section>
+</section>
+<section id="examples">
+<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">ïƒ</a></h2>
<p>See the examples/ directory for example scripts and notebooks. The documentation contains example pages as well.</p>
-</div>
-<div class="section" id="usage-notes">
-<h2>Usage notes<a class="headerlink" href="#usage-notes" title="Permalink to this headline">¶</a></h2>
+</section>
+<section id="usage-notes">
+<h2>Usage notes<a class="headerlink" href="#usage-notes" title="Permalink to this headline">ïƒ</a></h2>
<p>Make sure that with every change/recompilation you make in <code class="docutils literal notranslate"><span class="pre">binary_c</span></code>, you also rebuild this package. Whenever you change the sourcecode of this package, you need to reinstall it into your virtualenvironment as well</p>
-</div>
-<div class="section" id="documentation">
-<h2>Documentation<a class="headerlink" href="#documentation" title="Permalink to this headline">¶</a></h2>
+</section>
+<section id="documentation">
+<h2>Documentation<a class="headerlink" href="#documentation" title="Permalink to this headline">ïƒ</a></h2>
<p>Look in the docs/ directory. Within the build/html/ there is the html version of the documentation. The</p>
-</div>
-<div class="section" id="faq-issues">
-<h2>FAQ/Issues:<a class="headerlink" href="#faq-issues" title="Permalink to this headline">¶</a></h2>
+</section>
+<section id="faq-issues">
+<h2>FAQ/Issues:<a class="headerlink" href="#faq-issues" title="Permalink to this headline">ïƒ</a></h2>
<p>Building issues with binary_c itself:</p>
<ul class="simple">
<li><p>see the documentation of binary_c (in doc/).</p></li>
@@ -285,7 +198,7 @@
<li><p>When the output of binary_c seems to be different than expected, you might need to rebuild this python package. Everytime binary_c is compiled, this package needs to be rebuilt too.</p></li>
</ul>
<div class="toctree-wrapper compound">
-<p class="caption"><span class="caption-text">Contents:</span></p>
+<p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="readme_link.html">Python module for binary_c</a><ul>
<li class="toctree-l2"><a class="reference internal" href="readme_link.html#requirements">Requirements</a></li>
@@ -318,7 +231,7 @@
<li class="toctree-l2"><a class="reference internal" href="notebook_extra_features.html">Tutorial: Extra features and functionality of binary_c-python</a></li>
<li class="toctree-l2"><a class="reference internal" href="notebook_api_functionality.html">Tutorial: Using the API functionality of binary_c-python</a></li>
<li class="toctree-l2"><a class="reference internal" href="notebook_luminosity_function_single.html">Example use case: Zero-age stellar luminosity function</a></li>
-<li class="toctree-l2"><a class="reference internal" href="notebook_luminosity_function_binaries.html">Zero-age stellar luminosity function in binaries</a></li>
+<li class="toctree-l2"><a class="reference internal" href="notebook_luminosity_function_binaries.html">Example use case: Zero-age stellar luminosity function in binaries</a></li>
<li class="toctree-l2"><a class="reference internal" href="notebook_HRD.html">Example use case: Hertzsprung-Russell diagrams</a></li>
<li class="toctree-l2"><a class="reference internal" href="notebook_common_envelope_evolution.html">Example use case: Common-envelope evolution</a></li>
</ul>
@@ -344,75 +257,51 @@
<li class="toctree-l1"><a class="reference external" href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/issues/new">Submit an issue</a></li>
</ul>
</div>
-</div>
-</div>
-<div class="section" id="indices-and-tables">
-<h1>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Permalink to this headline">¶</a></h1>
+</section>
+</section>
+<section id="indices-and-tables">
+<h1>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Permalink to this headline">ïƒ</a></h1>
<ul class="simple">
<li><p><a class="reference internal" href="genindex.html"><span class="std std-ref">Index</span></a></p></li>
<li><p><a class="reference internal" href="py-modindex.html"><span class="std std-ref">Module Index</span></a></p></li>
<li><p><a class="reference internal" href="search.html"><span class="std std-ref">Search Page</span></a></p></li>
</ul>
-</div>
+</section>
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-
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- <footer>
-
- <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
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+ <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
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- <p>
-
- © Copyright 2021, David Hendriks, Robert Izzard
-
- </p>
+ <p>© Copyright 2021, David Hendriks, Robert Izzard.</p>
</div>
-
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-
- Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a
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+
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-Generated on binarycpython git branch: master git revision 0886cd4f1d7f43222aac21d6ed91e917b67b20fc url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/tree/master">git url</a>.
+Generated on binarycpython git branch: auto_resolution git revision be7bd630af892a785312affc34d87c57eb337fd3 url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/tree/auto_resolution">git url</a>.
<br><br>
-Using binary_c with bit branch newmaster: git revision: "6185:20210910:1621c23a5" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/newmaster">git url</a>.
+Using binary_c with bit branch master: git revision: "6209:20211006:c4a4c332e" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/master">git url</a>.
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diff --git a/docs/build/html/modules.html b/docs/build/html/modules.html
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<li class="toctree-l1 current"><a class="current reference internal" href="#">Binarycpython code</a><ul>
@@ -109,69 +62,30 @@
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</style>
-<div class="section" id="binarycpython-code">
-<h1>Binarycpython code<a class="headerlink" href="#binarycpython-code" title="Permalink to this headline">¶</a></h1>
+<section id="binarycpython-code">
+<h1>Binarycpython code<a class="headerlink" href="#binarycpython-code" title="Permalink to this headline">ïƒ</a></h1>
<p>This chapter contains the (auto)documentation for all the functions and modules in the source code of binarycpython</p>
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<ul>
@@ -214,68 +128,43 @@
<li class="toctree-l1"><a class="reference internal" href="useful_funcs.html">useful_funcs module</a></li>
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+ <p>© Copyright 2021, David Hendriks, Robert Izzard.</p>
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+
<br><br>
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+Generated on binarycpython git branch: auto_resolution git revision be7bd630af892a785312affc34d87c57eb337fd3 url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/tree/auto_resolution">git url</a>.
<br><br>
-Using binary_c with bit branch newmaster: git revision: "6185:20210910:1621c23a5" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/newmaster">git url</a>.
+Using binary_c with bit branch master: git revision: "6209:20211006:c4a4c332e" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/master">git url</a>.
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diff --git a/docs/build/html/notebook_HRD.html b/docs/build/html/notebook_HRD.html
index e0d4a842f252ca092e7f18ac0928089bacc6a709..9ad5d96012c9ed01abb335b09353ae8576c49cbb 100644
--- a/docs/build/html/notebook_HRD.html
+++ b/docs/build/html/notebook_HRD.html
@@ -1,71 +1,37 @@
-
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<!DOCTYPE html>
<html class="writer-html5" lang="en" >
<head>
- <meta charset="utf-8">
-
- <meta name="viewport" content="width=device-width, initial-scale=1.0">
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+ <title>Example use case: Hertzsprung-Russell diagrams — binary_c-python documentation</title>
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+ <script src="_static/js/theme.js"></script>
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- <link rel="prev" title="Zero-age stellar luminosity function in binaries" href="notebook_luminosity_function_binaries.html" />
+ <link rel="prev" title="Example use case: Zero-age stellar luminosity function in binaries" href="notebook_luminosity_function_binaries.html" />
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+ </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
+ <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="readme_link.html">Python module for binary_c</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules.html">Binarycpython code</a></li>
@@ -96,7 +51,7 @@
<li class="toctree-l2"><a class="reference internal" href="notebook_extra_features.html">Tutorial: Extra features and functionality of binary_c-python</a></li>
<li class="toctree-l2"><a class="reference internal" href="notebook_api_functionality.html">Tutorial: Using the API functionality of binary_c-python</a></li>
<li class="toctree-l2"><a class="reference internal" href="notebook_luminosity_function_single.html">Example use case: Zero-age stellar luminosity function</a></li>
-<li class="toctree-l2"><a class="reference internal" href="notebook_luminosity_function_binaries.html">Zero-age stellar luminosity function in binaries</a></li>
+<li class="toctree-l2"><a class="reference internal" href="notebook_luminosity_function_binaries.html">Example use case: Zero-age stellar luminosity function in binaries</a></li>
<li class="toctree-l2 current"><a class="current reference internal" href="#">Example use case: Hertzsprung-Russell diagrams</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#Setting-up-the-Population-object">Setting up the Population object</a></li>
<li class="toctree-l3"><a class="reference internal" href="#Stellar-Grid">Stellar Grid</a></li>
@@ -114,71 +69,31 @@
<li class="toctree-l1"><a class="reference external" href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/issues/new">Submit an issue</a></li>
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<ul class="wy-breadcrumbs">
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-
<li>Example use case: Hertzsprung-Russell diagrams</li>
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@@ -449,8 +364,8 @@ div.rendered_html tbody tr:hover {
text-align: unset;
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-<div class="section" id="Example-use-case:-Hertzsprung-Russell-diagrams">
-<h1>Example use case: Hertzsprung-Russell diagrams<a class="headerlink" href="#Example-use-case:-Hertzsprung-Russell-diagrams" title="Permalink to this headline">¶</a></h1>
+<section id="Example-use-case:-Hertzsprung-Russell-diagrams">
+<h1>Example use case: Hertzsprung-Russell diagrams<a class="headerlink" href="#Example-use-case:-Hertzsprung-Russell-diagrams" title="Permalink to this headline">ïƒ</a></h1>
<p>In this notebook we compute Hertzsprung-Russell diagrams (HRDs) of single and binary stars.</p>
<div class="nbinput nblast docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[1]:
@@ -469,8 +384,8 @@ div.rendered_html tbody tr:hover {
</pre></div>
</div>
</div>
-<div class="section" id="Setting-up-the-Population-object">
-<h2>Setting up the Population object<a class="headerlink" href="#Setting-up-the-Population-object" title="Permalink to this headline">¶</a></h2>
+<section id="Setting-up-the-Population-object">
+<h2>Setting up the Population object<a class="headerlink" href="#Setting-up-the-Population-object" title="Permalink to this headline">ïƒ</a></h2>
<p>First we set up a new population object. Our stars evolve to <span class="math notranslate nohighlight">\(13.7\mathrm{Gyr}\)</span>, the age of the Universe, and we assume the metallicity <span class="math notranslate nohighlight">\(Z=0.02\)</span>. These are rough approximations: a real population was born some finite time ago, so cannot possibly evolve to <span class="math notranslate nohighlight">\(13.7\mathrm{Gyr}\)</span>, and stars are not really born with a metallicity of <span class="math notranslate nohighlight">\(0.02\)</span>. These approximations only affect very low mass stars, so we assume all our stars have mass <span class="math notranslate nohighlight">\(M\geq 1 \mathrm{M}_\odot\)</span>, and metallicity
does not change evolution too much except in massive stars through the dependence of their winds on metallicity, so we limit our study to <span class="math notranslate nohighlight">\(M\leq 10 \mathrm{M}_\odot\)</span>.</p>
<div class="nbinput nblast docutils container">
@@ -496,9 +411,9 @@ does not change evolution too much except in massive stars through the dependenc
</pre></div>
</div>
</div>
-</div>
-<div class="section" id="Stellar-Grid">
-<h2>Stellar Grid<a class="headerlink" href="#Stellar-Grid" title="Permalink to this headline">¶</a></h2>
+</section>
+<section id="Stellar-Grid">
+<h2>Stellar Grid<a class="headerlink" href="#Stellar-Grid" title="Permalink to this headline">ïƒ</a></h2>
<p>We now construct a grid of stars, varying the mass from <span class="math notranslate nohighlight">\(1\)</span> to <span class="math notranslate nohighlight">\(10\mathrm{M}_\odot\)</span> in nine steps (so the masses are integers).</p>
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@@ -550,9 +465,9 @@ Added grid variable: {
}
</pre></div></div>
</div>
-</div>
-<div class="section" id="Setting-logging-and-handling-the-output">
-<h2>Setting logging and handling the output<a class="headerlink" href="#Setting-logging-and-handling-the-output" title="Permalink to this headline">¶</a></h2>
+</section>
+<section id="Setting-logging-and-handling-the-output">
+<h2>Setting logging and handling the output<a class="headerlink" href="#Setting-logging-and-handling-the-output" title="Permalink to this headline">ïƒ</a></h2>
<p>We now construct the HRD output.</p>
<p>We choose stars prior to and including the thermally-pulsing asymptotic giant branch (TPAGB) phase that have <span class="math notranslate nohighlight">\(>0.1\mathrm{M}_\odot\)</span> of material in their outer hydrogen envelope (remember the core of an evolved star is made of helium or carbon/oxygen/neon). This prevents us showing the post-AGB phase which is a bit messy and we avoid the white-dwarf cooling track.</p>
<div class="nbinput docutils container">
@@ -617,7 +532,7 @@ Foreach_star(star)
to grid_options
</pre></div></div>
</div>
-<p>The parse function must now catch lines that start with “HRD*n*â€, where <em>n</em> is 0 (primary star) or 1 (secondary star, which doesn’t exist in single-star systems), and process the associated data.</p>
+<p>The parse function must now catch lines that start with “HRD<em>n</em>â€, where <em>n</em> is 0 (primary star) or 1 (secondary star, which doesn’t exist in single-star systems), and process the associated data.</p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[5]:
</pre></div>
@@ -670,11 +585,11 @@ Foreach_star(star)
adding: parse_function=<function parse_function at 0x14565763dca0> to grid_options
</pre></div></div>
</div>
-</div>
-<div class="section" id="Evolving-the-grid">
-<h2>Evolving the grid<a class="headerlink" href="#Evolving-the-grid" title="Permalink to this headline">¶</a></h2>
+</section>
+<section id="Evolving-the-grid">
+<h2>Evolving the grid<a class="headerlink" href="#Evolving-the-grid" title="Permalink to this headline">ïƒ</a></h2>
<p>Now that we configured all the main parts of the population object, we can actually run the population! Doing this is straightforward: <code class="docutils literal notranslate"><span class="pre">population.evolve()</span></code></p>
-<p>This will start up the processing of all the systems. We can control how many cores are used by settings <code class="docutils literal notranslate"><span class="pre">amt_cores</span></code>. By setting the <code class="docutils literal notranslate"><span class="pre">verbosity</span></code> of the population object to a higher value we can get a lot of verbose information about the run, but for now we will set it to 0.</p>
+<p>This will start up the processing of all the systems. We can control how many cores are used by settings <code class="docutils literal notranslate"><span class="pre">num_cores</span></code>. By setting the <code class="docutils literal notranslate"><span class="pre">verbosity</span></code> of the population object to a higher value we can get a lot of verbose information about the run, but for now we will set it to 0.</p>
<p>There are many grid_options that can lead to different behaviour of the evolution of the grid. Please do have a look at those: <a class="reference external" href="https://ri0005.pages.surrey.ac.uk/binary_c-python/grid_options_descriptions.html">grid options docs</a>, and try</p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[6]:
@@ -686,7 +601,7 @@ adding: parse_function=<function parse_function at 0x14565763dca0> to grid
<span class="c1"># verbose output is not required</span>
<span class="n">verbosity</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span>
<span class="c1"># set number of threads (i.e. number of CPU cores we use)</span>
- <span class="n">amt_cores</span><span class="o">=</span><span class="mi">4</span><span class="p">,</span>
+ <span class="n">num_cores</span><span class="o">=</span><span class="mi">4</span><span class="p">,</span>
<span class="p">)</span>
<span class="c1"># Evolve the population - this is the slow, number-crunching step</span>
@@ -714,7 +629,7 @@ Population-20bee5b0c58d49c5bc47eced240685bb finished! The total probability was:
There were no errors found in this run.
</pre></div></div>
</div>
-<p>After the run is complete, some technical report on the run is returned. I stored that in <code class="docutils literal notranslate"><span class="pre">analytics</span></code>. As we can see below, this dictionary is like a status report of the evolution. Useful for e.g. debugging.</p>
+<p>After the run is complete, some technical report on the run is returned. I stored that in <code class="docutils literal notranslate"><span class="pre">analytics</span></code>. As we can see below, this dictionary is like a status report of the evolution. Useful for e.g. debugging.</p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[7]:
</pre></div>
@@ -816,9 +731,9 @@ Text(0, 0.5, '$\\log_{10} (L/$L$_{☉})$')
</div>
</div>
<p>We now have an HRD. It took longer to make the plot than to run the stars with <em>binary_c</em>!</p>
-</div>
-<div class="section" id="Binary-stars">
-<h2>Binary stars<a class="headerlink" href="#Binary-stars" title="Permalink to this headline">¶</a></h2>
+</section>
+<section id="Binary-stars">
+<h2>Binary stars<a class="headerlink" href="#Binary-stars" title="Permalink to this headline">ïƒ</a></h2>
<p>Now we put a secondary star of mass <span class="math notranslate nohighlight">\(0.5\mathrm{M}_\odot\)</span> at a distance of <span class="math notranslate nohighlight">\(10\mathrm{R}_\odot\)</span> to see how this changes things. Then we rerun the population. At such short separations, we expect mass transfer to begin on or shortly after the main sequence.</p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[9]:
@@ -1108,69 +1023,44 @@ Text(0, 0.5, '$\\log_{10} (L/$L$_{☉})$')
<p>Remember, all these stars start with a <span class="math notranslate nohighlight">\(1\mathrm{M}_\odot\)</span> binary, which begins at <span class="math notranslate nohighlight">\(\log_{10}(T_\mathrm{eff}/\mathrm{K})\sim 3.750\)</span>, <span class="math notranslate nohighlight">\(\log_{10}L/\mathrm{L}_\odot \sim 0\)</span>. The <span class="math notranslate nohighlight">\(1\mathrm{M}_\odot\)</span>-<span class="math notranslate nohighlight">\(1\mathrm{M}_\odot\)</span> binary evolves like two single stars until they interact up the giant branch at about <span class="math notranslate nohighlight">\(\log_{10} (L/\mathrm{L}_\odot) \sim 2.5\)</span>, the others interact long before they evolve very far on the main sequence: you can just about see their tracks at the
very start.</p>
<p>This is, of course, a very simple introduction to what happens in binaries. We haven’t talked about the remnants that are produced by interactions. When the stars do evolve on the giant branch, white dwarfs are made which can go on to suffer novae and (perhaps) thermonuclear explosions. The merging process itself leads to luminosus red novae and, in the case of neutron stars and black holes, kilonovae and gravitational wave events.</p>
-</div>
-</div>
+</section>
+</section>
</div>
-
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- <footer>
-
- <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
-
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+ <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
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+ <a href="notebook_common_envelope_evolution.html" class="btn btn-neutral float-right" title="Example use case: Common-envelope evolution" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
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-
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- <p>
-
- © Copyright 2021, David Hendriks, Robert Izzard
-
- </p>
+ <p>© Copyright 2021, David Hendriks, Robert Izzard.</p>
</div>
-
-
-
- Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a
-
- <a href="https://github.com/rtfd/sphinx_rtd_theme">theme</a>
-
+
+ Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
+ <a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
provided by <a href="https://readthedocs.org">Read the Docs</a>.
+
<br><br>
-Generated on binarycpython git branch: master git revision 0886cd4f1d7f43222aac21d6ed91e917b67b20fc url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/tree/master">git url</a>.
+Generated on binarycpython git branch: auto_resolution git revision be7bd630af892a785312affc34d87c57eb337fd3 url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/tree/auto_resolution">git url</a>.
<br><br>
-Using binary_c with bit branch newmaster: git revision: "6185:20210910:1621c23a5" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/newmaster">git url</a>.
+Using binary_c with bit branch master: git revision: "6209:20211006:c4a4c332e" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/master">git url</a>.
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diff --git a/docs/build/html/notebook_HRD.ipynb b/docs/build/html/notebook_HRD.ipynb
index 52590f8a2a6abc7245e9ea0c08d274432cd2a1ad..bf95d554d2125de449ec4b8404550132e06091f7 100644
--- a/docs/build/html/notebook_HRD.ipynb
+++ b/docs/build/html/notebook_HRD.ipynb
@@ -264,7 +264,7 @@
"## Evolving the grid\n",
"Now that we configured all the main parts of the population object, we can actually run the population! Doing this is straightforward: `population.evolve()`\n",
"\n",
- "This will start up the processing of all the systems. We can control how many cores are used by settings `amt_cores`. By setting the `verbosity` of the population object to a higher value we can get a lot of verbose information about the run, but for now we will set it to 0.\n",
+ "This will start up the processing of all the systems. We can control how many cores are used by settings `num_cores`. By setting the `verbosity` of the population object to a higher value we can get a lot of verbose information about the run, but for now we will set it to 0.\n",
"\n",
"There are many grid_options that can lead to different behaviour of the evolution of the grid. Please do have a look at those: [grid options docs](https://ri0005.pages.surrey.ac.uk/binary_c-python/grid_options_descriptions.html), and try "
]
@@ -300,7 +300,7 @@
" # verbose output is not required \n",
" verbosity=0,\n",
" # set number of threads (i.e. number of CPU cores we use)\n",
- " amt_cores=4,\n",
+ " num_cores=4,\n",
" )\n",
"\n",
"# Evolve the population - this is the slow, number-crunching step\n",
@@ -796,7 +796,7 @@
],
"metadata": {
"kernelspec": {
- "display_name": "Python 3",
+ "display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
@@ -810,7 +810,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
- "version": "3.6.4"
+ "version": "3.9.5"
}
},
"nbformat": 4,
diff --git a/docs/build/html/notebook_api_functionality.html b/docs/build/html/notebook_api_functionality.html
index cdd5ae1fc1192b9ad98e7531f77ac917ff204c55..de13fbd804c6cfa7e062f36bff422e670e99e4a9 100644
--- a/docs/build/html/notebook_api_functionality.html
+++ b/docs/build/html/notebook_api_functionality.html
@@ -1,71 +1,37 @@
-
-
<!DOCTYPE html>
<html class="writer-html5" lang="en" >
<head>
- <meta charset="utf-8">
-
- <meta name="viewport" content="width=device-width, initial-scale=1.0">
-
- <title>Tutorial: Using the API functionality of binary_c-python — binary_c-python documentation</title>
-
-
-
- <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
- <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+ <meta charset="utf-8" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
-
-
-
-
-
-
+ <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+ <title>Tutorial: Using the API functionality of binary_c-python — binary_c-python documentation</title>
+ <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+ <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
<!--[if lt IE 9]>
<script src="_static/js/html5shiv.min.js"></script>
<![endif]-->
-
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+ <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
<script src="_static/jquery.js"></script>
<script src="_static/underscore.js"></script>
<script src="_static/doctools.js"></script>
- <script src="_static/language_data.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
- <script async="async" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.7/latest.js?config=TeX-AMS-MML_HTMLorMML"></script>
- <script type="text/x-mathjax-config">MathJax.Hub.Config({"tex2jax": {"inlineMath": [["$", "$"], ["\\(", "\\)"]], "processEscapes": true, "ignoreClass": "document", "processClass": "math|output_area"}})</script>
-
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-
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+ <script async="async" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
+ <script>window.MathJax = {"tex": {"inlineMath": [["$", "$"], ["\\(", "\\)"]], "processEscapes": true}, "options": {"ignoreHtmlClass": "tex2jax_ignore|mathjax_ignore|document", "processHtmlClass": "tex2jax_process|mathjax_process|math|output_area"}}</script>
+ <script src="_static/js/theme.js"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="next" title="Example use case: Zero-age stellar luminosity function" href="notebook_luminosity_function_single.html" />
<link rel="prev" title="Tutorial: Extra features and functionality of binary_c-python" href="notebook_extra_features.html" />
</head>
-<body class="wy-body-for-nav">
-
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+<body class="wy-body-for-nav">
<div class="wy-grid-for-nav">
-
<nav data-toggle="wy-nav-shift" class="wy-nav-side">
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<div class="wy-side-nav-search" >
-
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- <a href="index.html" class="icon icon-home" alt="Documentation Home"> binary_c-python
-
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+ <a href="index.html" class="icon icon-home"> binary_c-python
</a>
-
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<div role="search">
<form id="rtd-search-form" class="wy-form" action="search.html" method="get">
<input type="text" name="q" placeholder="Search docs" />
@@ -73,19 +39,8 @@
<input type="hidden" name="area" value="default" />
</form>
</div>
-
-
- </div>
-
-
- <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
-
-
-
-
-
-
- <p class="caption"><span class="caption-text">Contents:</span></p>
+ </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
+ <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="readme_link.html">Python module for binary_c</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules.html">Binarycpython code</a></li>
@@ -103,7 +58,7 @@
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="notebook_luminosity_function_single.html">Example use case: Zero-age stellar luminosity function</a></li>
-<li class="toctree-l2"><a class="reference internal" href="notebook_luminosity_function_binaries.html">Zero-age stellar luminosity function in binaries</a></li>
+<li class="toctree-l2"><a class="reference internal" href="notebook_luminosity_function_binaries.html">Example use case: Zero-age stellar luminosity function in binaries</a></li>
<li class="toctree-l2"><a class="reference internal" href="notebook_HRD.html">Example use case: Hertzsprung-Russell diagrams</a></li>
<li class="toctree-l2"><a class="reference internal" href="notebook_common_envelope_evolution.html">Example use case: Common-envelope evolution</a></li>
</ul>
@@ -114,71 +69,31 @@
<li class="toctree-l1"><a class="reference external" href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/issues/new">Submit an issue</a></li>
</ul>
-
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- <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap">
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<ul class="wy-breadcrumbs">
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-
<li><a href="example_notebooks.html">Example notebooks</a> »</li>
-
<li>Tutorial: Using the API functionality of binary_c-python</li>
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<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
-
+
<style>
/* CSS for nbsphinx extension */
@@ -449,9 +364,9 @@ div.rendered_html tbody tr:hover {
text-align: unset;
}
</style>
-<div class="section" id="Tutorial:-Using-the-API-functionality-of-binary_c-python">
-<h1>Tutorial: Using the API functionality of binary_c-python<a class="headerlink" href="#Tutorial:-Using-the-API-functionality-of-binary_c-python" title="Permalink to this headline">¶</a></h1>
-<p>This notebook shows how to use the API functions that interface with binary_c. It usually is better to use wrapper functions that internally use these API functions, because most of the output here is very raw</p>
+<section id="Tutorial:-Using-the-API-functionality-of-binary_c-python">
+<h1>Tutorial: Using the API functionality of binary_c-python<a class="headerlink" href="#Tutorial:-Using-the-API-functionality-of-binary_c-python" title="Permalink to this headline">ïƒ</a></h1>
+<p>This notebook shows how to use the API functions that interface with binary_c. It usually is better to use wrapper functions that internally use these API functions, because most of the output here is very raw</p>
<p>Binarycpython uses the Python-C extension framework to interface Python with C. The sourcecode for this is contained in <code class="docutils literal notranslate"><span class="pre">src/binary_c_python.c</span></code>, and the functions are available via <code class="docutils literal notranslate"><span class="pre">from</span> <span class="pre">binarycpython</span> <span class="pre">import</span> <span class="pre">_binary_c_bindings</span></code>.</p>
<p>The following functions are available through the API: (run cell below)</p>
<div class="nbinput docutils container">
@@ -581,10 +496,10 @@ FILE
</ul>
</li>
</ul>
-<div class="section" id="Example-usage:">
-<h2>Example usage:<a class="headerlink" href="#Example-usage:" title="Permalink to this headline">¶</a></h2>
-<div class="section" id="Setting-up,-using-and-freeing-store">
-<h3>Setting up, using and freeing store<a class="headerlink" href="#Setting-up,-using-and-freeing-store" title="Permalink to this headline">¶</a></h3>
+<section id="Example-usage:">
+<h2>Example usage:<a class="headerlink" href="#Example-usage:" title="Permalink to this headline">ïƒ</a></h2>
+<section id="Setting-up,-using-and-freeing-store">
+<h3>Setting up, using and freeing store<a class="headerlink" href="#Setting-up,-using-and-freeing-store" title="Permalink to this headline">ïƒ</a></h3>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[2]:
</pre></div>
@@ -624,9 +539,9 @@ SINGLE_STAR_LIFETIME 10 28.4838
</pre></div></div>
</div>
-</div>
-<div class="section" id="Getting-information-from-binary_c">
-<h3>Getting information from binary_c<a class="headerlink" href="#Getting-information-from-binary_c" title="Permalink to this headline">¶</a></h3>
+</section>
+<section id="Getting-information-from-binary_c">
+<h3>Getting information from binary_c<a class="headerlink" href="#Getting-information-from-binary_c" title="Permalink to this headline">ïƒ</a></h3>
<p>We can get information for a parameter via return_help(parameter_name): This will return an unparsed output</p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[3]:
@@ -1349,70 +1264,45 @@ MAXIMUM MASS RATIO 0.0141
</pre></div>
</div>
</div>
-</div>
-</div>
-</div>
+</section>
+</section>
+</section>
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-
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-
- <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
-
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-
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-
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<div role="contentinfo">
- <p>
-
- © Copyright 2021, David Hendriks, Robert Izzard
-
- </p>
+ <p>© Copyright 2021, David Hendriks, Robert Izzard.</p>
</div>
-
-
-
- Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a
-
- <a href="https://github.com/rtfd/sphinx_rtd_theme">theme</a>
-
+
+ Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
+ <a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
provided by <a href="https://readthedocs.org">Read the Docs</a>.
+
<br><br>
-Generated on binarycpython git branch: master git revision 0886cd4f1d7f43222aac21d6ed91e917b67b20fc url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/tree/master">git url</a>.
+Generated on binarycpython git branch: auto_resolution git revision be7bd630af892a785312affc34d87c57eb337fd3 url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/tree/auto_resolution">git url</a>.
<br><br>
-Using binary_c with bit branch newmaster: git revision: "6185:20210910:1621c23a5" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/newmaster">git url</a>.
+Using binary_c with bit branch master: git revision: "6209:20211006:c4a4c332e" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/master">git url</a>.
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diff --git a/docs/build/html/notebook_common_envelope_evolution.html b/docs/build/html/notebook_common_envelope_evolution.html
index 6d041737c22b9e442003f5b8174b938868564e35..23bd765a400d7e068e3f01a35ef1fd418f4249b3 100644
--- a/docs/build/html/notebook_common_envelope_evolution.html
+++ b/docs/build/html/notebook_common_envelope_evolution.html
@@ -1,71 +1,37 @@
-
-
<!DOCTYPE html>
<html class="writer-html5" lang="en" >
<head>
- <meta charset="utf-8">
-
- <meta name="viewport" content="width=device-width, initial-scale=1.0">
-
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-
-
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<li class="toctree-l1"><a class="reference internal" href="readme_link.html">Python module for binary_c</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules.html">Binarycpython code</a></li>
@@ -96,7 +51,7 @@
<li class="toctree-l2"><a class="reference internal" href="notebook_extra_features.html">Tutorial: Extra features and functionality of binary_c-python</a></li>
<li class="toctree-l2"><a class="reference internal" href="notebook_api_functionality.html">Tutorial: Using the API functionality of binary_c-python</a></li>
<li class="toctree-l2"><a class="reference internal" href="notebook_luminosity_function_single.html">Example use case: Zero-age stellar luminosity function</a></li>
-<li class="toctree-l2"><a class="reference internal" href="notebook_luminosity_function_binaries.html">Zero-age stellar luminosity function in binaries</a></li>
+<li class="toctree-l2"><a class="reference internal" href="notebook_luminosity_function_binaries.html">Example use case: Zero-age stellar luminosity function in binaries</a></li>
<li class="toctree-l2"><a class="reference internal" href="notebook_HRD.html">Example use case: Hertzsprung-Russell diagrams</a></li>
<li class="toctree-l2 current"><a class="current reference internal" href="#">Example use case: Common-envelope evolution</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#Setting-up-the-Population-object">Setting up the Population object</a></li>
@@ -113,71 +68,31 @@
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<li>Example use case: Common-envelope evolution</li>
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/* CSS for nbsphinx extension */
@@ -448,8 +363,8 @@ div.rendered_html tbody tr:hover {
text-align: unset;
}
</style>
-<div class="section" id="Example-use-case:-Common-envelope-evolution">
-<h1>Example use case: Common-envelope evolution<a class="headerlink" href="#Example-use-case:-Common-envelope-evolution" title="Permalink to this headline">¶</a></h1>
+<section id="Example-use-case:-Common-envelope-evolution">
+<h1>Example use case: Common-envelope evolution<a class="headerlink" href="#Example-use-case:-Common-envelope-evolution" title="Permalink to this headline">ïƒ</a></h1>
<p>In this notebook we look at how common-envelope evolution (CEE) alters binary-star orbits. We construct a population of low- and intermediate-mass binaries and compare their orbital periods before and after CEE. Not all stars evolve into this phase, so we have to run a whole population to find those that do. We then have to construct the pre- and post-CEE distributions and plot them.</p>
<p>First, we import a few required Python modules.</p>
<div class="nbinput nblast docutils container">
@@ -466,8 +381,8 @@ div.rendered_html tbody tr:hover {
</pre></div>
</div>
</div>
-<div class="section" id="Setting-up-the-Population-object">
-<h2>Setting up the Population object<a class="headerlink" href="#Setting-up-the-Population-object" title="Permalink to this headline">¶</a></h2>
+<section id="Setting-up-the-Population-object">
+<h2>Setting up the Population object<a class="headerlink" href="#Setting-up-the-Population-object" title="Permalink to this headline">ïƒ</a></h2>
<p>We set up a new population object. Our stars evolve to <span class="math notranslate nohighlight">\(13.7\text{ }\mathrm{Gyr}\)</span>, the age of the Universe, and we assume the metallicity <span class="math notranslate nohighlight">\(Z=0.02\)</span>. We also set the common-envelope ejection efficiency <span class="math notranslate nohighlight">\(\alpha_\mathrm{CE}=1\)</span> and the envelope structure parameter <span class="math notranslate nohighlight">\(\lambda=0.5\)</span>. More complex options are available in <em>binary_c</em>, such as <span class="math notranslate nohighlight">\(\lambda\)</span> based on stellar mass, but this is just a demonstration example so let’s keep things simple.</p>
<div class="nbinput docutils container">
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@@ -503,9 +418,9 @@ adding: alpha_ce=1.0 to BSE_options
adding: lambda_ce=0.5 to BSE_options
</pre></div></div>
</div>
-</div>
-<div class="section" id="Stellar-Grid">
-<h2>Stellar Grid<a class="headerlink" href="#Stellar-Grid" title="Permalink to this headline">¶</a></h2>
+</section>
+<section id="Stellar-Grid">
+<h2>Stellar Grid<a class="headerlink" href="#Stellar-Grid" title="Permalink to this headline">ïƒ</a></h2>
<p>We now construct a grid of stars, varying the mass from <span class="math notranslate nohighlight">\(1\)</span> to <span class="math notranslate nohighlight">\(6\text{ }\mathrm{M}_\odot\)</span>. We avoid massive stars for now, and focus on the (more common) low- and intermediate-mass stars. We also limit the period range to <span class="math notranslate nohighlight">\(10^4\text{ }\mathrm{d}\)</span> because systems with longer orbital periods will probably not undergo Roche-lobe overflow and hence common-envelope evolution is impossible.</p>
<div class="nbinput docutils container">
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@@ -624,9 +539,9 @@ Added grid variable: {
}
</pre></div></div>
</div>
-</div>
-<div class="section" id="Logging-and-handling-the-output">
-<h2>Logging and handling the output<a class="headerlink" href="#Logging-and-handling-the-output" title="Permalink to this headline">¶</a></h2>
+</section>
+<section id="Logging-and-handling-the-output">
+<h2>Logging and handling the output<a class="headerlink" href="#Logging-and-handling-the-output" title="Permalink to this headline">ïƒ</a></h2>
<p>We now construct the pre- and post-common envelope evolution data for the first common envelope that forms in each binary. We look at the comenv_count variable, we can see that when it increases from 0 to 1 we have found our object. If this happens, we stop evolution of the system to save CPU time.</p>
<div class="nbinput docutils container">
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@@ -765,10 +680,10 @@ if(stardata->model.comenv_count == 1 &&
adding: parse_function=<function parse_function at 0x14736bebc040> to grid_options
</pre></div></div>
</div>
-</div>
-<div class="section" id="Evolving-the-grid">
-<h2>Evolving the grid<a class="headerlink" href="#Evolving-the-grid" title="Permalink to this headline">¶</a></h2>
-<p>Now we actually run the population. This may take a little while. You can set amt_cores higher if you have a powerful machine.</p>
+</section>
+<section id="Evolving-the-grid">
+<h2>Evolving the grid<a class="headerlink" href="#Evolving-the-grid" title="Permalink to this headline">ïƒ</a></h2>
+<p>Now we actually run the population. This may take a little while. You can set num_cores higher if you have a powerful machine.</p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[6]:
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@@ -777,7 +692,7 @@ adding: parse_function=<function parse_function at 0x14736bebc040> to grid
<span></span><span class="c1"># set number of threads</span>
<span class="n">population</span><span class="o">.</span><span class="n">set</span><span class="p">(</span>
<span class="c1"># set number of threads (i.e. number of CPU cores we use)</span>
- <span class="n">amt_cores</span><span class="o">=</span><span class="mi">4</span><span class="p">,</span>
+ <span class="n">num_cores</span><span class="o">=</span><span class="mi">4</span><span class="p">,</span>
<span class="p">)</span>
<span class="c1"># Evolve the population - this is the slow, number-crunching step</span>
@@ -793,7 +708,7 @@ adding: parse_function=<function parse_function at 0x14736bebc040> to grid
</div>
<div class="output_area docutils container">
<div class="highlight"><pre>
-adding: amt_cores=4 to grid_options
+adding: num_cores=4 to grid_options
Creating and loading custom logging functionality
Generating grid code
Generating grid code
@@ -964,7 +879,7 @@ Population-ad303100d719457c83256568f9a9887c finished! The total probability was:
There were no errors found in this run.
</pre></div></div>
</div>
-<p>After the run is complete, some technical report on the run is returned. I stored that in <code class="docutils literal notranslate"><span class="pre">analytics</span></code>. As we can see below, this dictionary is like a status report of the evolution. Useful for e.g. debugging. We check this, and then set about making the plot of the orbital period distributions using Seaborn.</p>
+<p>After the run is complete, some technical report on the run is returned. I stored that in <code class="docutils literal notranslate"><span class="pre">analytics</span></code>. As we can see below, this dictionary is like a status report of the evolution. Useful for e.g. debugging. We check this, and then set about making the plot of the orbital period distributions using Seaborn.</p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[7]:
</pre></div>
@@ -1064,69 +979,44 @@ Text(0, 0.5, 'Number of stars')
<p>You can see that common-envelope evolution shrinks stellar orbits, just as we expect. Pre-CEE, most orbits are in the range <span class="math notranslate nohighlight">\(10\)</span> to <span class="math notranslate nohighlight">\(1000\text{ }\mathrm{d}\)</span>, while after CEE the distribution peaks at about <span class="math notranslate nohighlight">\(1\text{ }\mathrm{d}\)</span>. Some of these orbits are very short: <span class="math notranslate nohighlight">\(\log_{10}(-2) = 0.01\text{ }\mathrm{d}\sim10\text{ }\mathrm{minutes}\)</span>. Such systems are prime candidates for exciting astrophysics: novae, type Ia supernovae and gravitational wave sources.</p>
<p>Things to try: * Extend the logging to output more data than just the orbital period. * What are the stellar types of the post-common envelope systems? Are they likely to undergo novae or a type-Ia supernova? * What are the lifetimes of the systems in close (<span class="math notranslate nohighlight">\(<1\text{ }\mathrm{d}\)</span>) binaries? Are they likely to merge in the life of the Universe? * How much mass is lost in common-envelope interactions? * Extend the grid to massive stars. Do you see many NS and BH compact binaries? *
Try different <span class="math notranslate nohighlight">\(\alpha_\mathrm{CE}\)</span> and <span class="math notranslate nohighlight">\(\lambda_\mathrm{CE}\)</span> options… * … and perhaps increased resolution to obtain smoother curves. * Why do long-period systems not reach common envelope evolution?</p>
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+Generated on binarycpython git branch: auto_resolution git revision be7bd630af892a785312affc34d87c57eb337fd3 url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/tree/auto_resolution">git url</a>.
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+Using binary_c with bit branch master: git revision: "6209:20211006:c4a4c332e" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/master">git url</a>.
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diff --git a/docs/build/html/notebook_common_envelope_evolution.ipynb b/docs/build/html/notebook_common_envelope_evolution.ipynb
index 526320ccf954c1ed86c6d5c641204c4a9345bbe5..feb6b18e6a264b08eab1e52d639106123f494cf5 100644
--- a/docs/build/html/notebook_common_envelope_evolution.ipynb
+++ b/docs/build/html/notebook_common_envelope_evolution.ipynb
@@ -363,7 +363,7 @@
"metadata": {},
"source": [
"## Evolving the grid\n",
- "Now we actually run the population. This may take a little while. You can set amt_cores higher if you have a powerful machine."
+ "Now we actually run the population. This may take a little while. You can set num_cores higher if you have a powerful machine."
]
},
{
@@ -378,7 +378,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "adding: amt_cores=4 to grid_options\n",
+ "adding: num_cores=4 to grid_options\n",
"Creating and loading custom logging functionality\n",
"Generating grid code\n",
"Generating grid code\n",
@@ -540,7 +540,7 @@
"# set number of threads\n",
"population.set(\n",
" # set number of threads (i.e. number of CPU cores we use)\n",
- " amt_cores=4,\n",
+ " num_cores=4,\n",
" )\n",
"\n",
"# Evolve the population - this is the slow, number-crunching step\n",
@@ -686,7 +686,7 @@
],
"metadata": {
"kernelspec": {
- "display_name": "Python 3",
+ "display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
@@ -700,7 +700,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
- "version": "3.6.4"
+ "version": "3.9.5"
}
},
"nbformat": 4,
diff --git a/docs/build/html/notebook_custom_logging.html b/docs/build/html/notebook_custom_logging.html
index aa4d05806f38293ff535db6f8bd31a1278e5428f..49a23a76f52000e45361b983a27f62b12663ba33 100644
--- a/docs/build/html/notebook_custom_logging.html
+++ b/docs/build/html/notebook_custom_logging.html
@@ -1,71 +1,37 @@
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+ <title>Tutorial: Using custom logging routines with binary_c-python — binary_c-python documentation</title>
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@@ -108,7 +63,7 @@
<li class="toctree-l2"><a class="reference internal" href="notebook_extra_features.html">Tutorial: Extra features and functionality of binary_c-python</a></li>
<li class="toctree-l2"><a class="reference internal" href="notebook_api_functionality.html">Tutorial: Using the API functionality of binary_c-python</a></li>
<li class="toctree-l2"><a class="reference internal" href="notebook_luminosity_function_single.html">Example use case: Zero-age stellar luminosity function</a></li>
-<li class="toctree-l2"><a class="reference internal" href="notebook_luminosity_function_binaries.html">Zero-age stellar luminosity function in binaries</a></li>
+<li class="toctree-l2"><a class="reference internal" href="notebook_luminosity_function_binaries.html">Example use case: Zero-age stellar luminosity function in binaries</a></li>
<li class="toctree-l2"><a class="reference internal" href="notebook_HRD.html">Example use case: Hertzsprung-Russell diagrams</a></li>
<li class="toctree-l2"><a class="reference internal" href="notebook_common_envelope_evolution.html">Example use case: Common-envelope evolution</a></li>
</ul>
@@ -119,71 +74,31 @@
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-<div class="section" id="Tutorial:-Using-custom-logging-routines-with-binary_c-python">
-<h1>Tutorial: Using custom logging routines with binary_c-python<a class="headerlink" href="#Tutorial:-Using-custom-logging-routines-with-binary_c-python" title="Permalink to this headline">¶</a></h1>
+<section id="Tutorial:-Using-custom-logging-routines-with-binary_c-python">
+<h1>Tutorial: Using custom logging routines with binary_c-python<a class="headerlink" href="#Tutorial:-Using-custom-logging-routines-with-binary_c-python" title="Permalink to this headline">ïƒ</a></h1>
<p>In this notebook you’ll learn how to use the custom logging functionality</p>
<div class="nbinput nblast docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[1]:
@@ -473,12 +388,12 @@ div.rendered_html tbody tr:hover {
</pre></div>
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-<p>The custom logging functionality allows us to decide the output of binary_c <em>without</em> modifying the actual sourcecode of binary_c (i.e. editing <code class="docutils literal notranslate"><span class="pre">src/logging/log_every_timestep</span></code> in binary_c). Rather, we can create a logging routine from within python.</p>
+<p>The custom logging functionality allows us to decide the output of binary_c <em>without</em> modifying the actual sourcecode of binary_c (i.e. editing <code class="docutils literal notranslate"><span class="pre">src/logging/log_every_timestep</span></code> in binary_c). Rather, we can create a logging routine from within python.</p>
<p>Technically, the following steps are taken: - User creates a logging print statement from within python - The logging print statement string gets wrapped into a proper c-function by <code class="docutils literal notranslate"><span class="pre">binary_c_log_code</span></code> - The c-function string gets compiled and loaded into memory by <code class="docutils literal notranslate"><span class="pre">create_and_load_logging_function</span></code> - The memory adress of the compiled and loaded print function can now be passed to C - binary_c uses the custom print function</p>
<p>The custom logging functionality can be used when running systems via <code class="docutils literal notranslate"><span class="pre">run_system()</span></code>, via <code class="docutils literal notranslate"><span class="pre">Population.evolve()</span></code> and <code class="docutils literal notranslate"><span class="pre">Population.evolve_single()</span></code>, and directly via the API</p>
<p>Within the logging statement we can access information from the stardata object, as well as use logical statements to determine when to log information. What we cannot do, however, is access functions that are not <em>publicly available</em>. For very elaborate printing routines it is still advised to actually hardcode the print statement into binary_c itself.</p>
-<div class="section" id="Usage">
-<h2>Usage<a class="headerlink" href="#Usage" title="Permalink to this headline">¶</a></h2>
+<section id="Usage">
+<h2>Usage<a class="headerlink" href="#Usage" title="Permalink to this headline">ïƒ</a></h2>
<p>There are two methods to create the C-code that will be compiled: - Automatically generate the print statement and use the wrapper to generate the full function string, by using <code class="docutils literal notranslate"><span class="pre">autogen_C_logging_code</span></code> - Create your custom print statement and use the wrapper to generate the full function string, by writing out the print statement. Here the logging statement obviously has to be valid C code</p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[2]:
@@ -559,7 +474,7 @@ void binary_c_API_function custom_output_function(struct stardata_t * stardata)
#pragma pop_macro("Max")
</pre></div></div>
</div>
-<p>Combining the above with e.g. run_system() (see notebook_individual_systems for more examples):</p>
+<p>Combining the above with e.g. run_system() (see notebook_individual_systems for more examples):</p>
<div class="nbinput docutils container">
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@@ -590,8 +505,8 @@ MY_STELLAR_DATA time=1e-06 mass=2
MY_STELLAR_DATA time=2e-06 mass=2
</pre></div></div>
</div>
-<div class="section" id="Using-custom-logging-with-the-population-object">
-<h3>Using custom logging with the population object<a class="headerlink" href="#Using-custom-logging-with-the-population-object" title="Permalink to this headline">¶</a></h3>
+<section id="Using-custom-logging-with-the-population-object">
+<h3>Using custom logging with the population object<a class="headerlink" href="#Using-custom-logging-with-the-population-object" title="Permalink to this headline">ïƒ</a></h3>
<p>Custom logging can be used for a whole population by setting the print statement (so not the entire logging script) in <code class="docutils literal notranslate"><span class="pre">C_logging_code</span></code></p>
<div class="nbinput docutils container">
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@@ -648,9 +563,9 @@ EXAMPLE_ABOVE_MS 1.044654032097e+02 4.99192 4.99192 7.81395 7.51803
EXAMPLE_ABOVE_MS 1.045084306856e+02 4.99191 4.99192 9.57443 7.81395 2 2
</pre></div></div>
</div>
-</div>
-<div class="section" id="Using-custom-logging-when-running-directly-from-the-API">
-<h3>Using custom logging when running directly from the API<a class="headerlink" href="#Using-custom-logging-when-running-directly-from-the-API" title="Permalink to this headline">¶</a></h3>
+</section>
+<section id="Using-custom-logging-when-running-directly-from-the-API">
+<h3>Using custom logging when running directly from the API<a class="headerlink" href="#Using-custom-logging-when-running-directly-from-the-API" title="Permalink to this headline">ïƒ</a></h3>
<p>When running a system directly with the API we need to manually load the custom logging into memory (via <code class="docutils literal notranslate"><span class="pre">create_and_load_logging_function</span></code>) and pass the memory address to the binary_c binding via <code class="docutils literal notranslate"><span class="pre">_binary_c_bindings.run_system(argstring,</span> <span class="pre">custom_logging_func_memaddr=custom_logging_memaddr)</span></code></p>
<div class="nbinput docutils container">
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@@ -709,13 +624,13 @@ MY_STELLAR_DATA 1e-06 15
MY_STELLAR_DATA 2e-06 15
</pre></div></div>
</div>
-</div>
-</div>
-<div class="section" id="Examples-of-logging-strings">
-<h2>Examples of logging strings<a class="headerlink" href="#Examples-of-logging-strings" title="Permalink to this headline">¶</a></h2>
+</section>
+</section>
+<section id="Examples-of-logging-strings">
+<h2>Examples of logging strings<a class="headerlink" href="#Examples-of-logging-strings" title="Permalink to this headline">ïƒ</a></h2>
<p>Below are some examples of logging strings</p>
-<div class="section" id="Compact-object">
-<h3>Compact object<a class="headerlink" href="#Compact-object" title="Permalink to this headline">¶</a></h3>
+<section id="Compact-object">
+<h3>Compact object<a class="headerlink" href="#Compact-object" title="Permalink to this headline">ïƒ</a></h3>
<p>This logging will print the timestep when the star becomes a compact object. After it does, we change the maximum time to be the current time, effectively terminating the evolution</p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[8]:
@@ -766,9 +681,9 @@ SINGLE_STAR_LIFETIME 10 28.4838
EXAMPLE_LOG_CO 2.848380621869e+01 1.33469 9.1865 1.72498e-05 724.338 13 5
</pre></div></div>
</div>
-</div>
-<div class="section" id="Logging-mass-evolution-and-the-supernova">
-<h3>Logging mass evolution and the supernova<a class="headerlink" href="#Logging-mass-evolution-and-the-supernova" title="Permalink to this headline">¶</a></h3>
+</section>
+<section id="Logging-mass-evolution-and-the-supernova">
+<h3>Logging mass evolution and the supernova<a class="headerlink" href="#Logging-mass-evolution-and-the-supernova" title="Permalink to this headline">ïƒ</a></h3>
<p>This logging code prints the mass evolution and the moment the star goes supernova</p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[10]:
@@ -846,70 +761,45 @@ EXAMPLE_SN 1.050651207308e+01 1.59452 9.34213 20 12 13 5 1 6.55458 4
</pre></div>
</div>
</div>
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+Generated on binarycpython git branch: auto_resolution git revision be7bd630af892a785312affc34d87c57eb337fd3 url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/tree/auto_resolution">git url</a>.
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-Using binary_c with bit branch newmaster: git revision: "6185:20210910:1621c23a5" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/newmaster">git url</a>.
+Using binary_c with bit branch master: git revision: "6209:20211006:c4a4c332e" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/master">git url</a>.
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+ </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
+ <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
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<li class="toctree-l1"><a class="reference internal" href="readme_link.html">Python module for binary_c</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules.html">Binarycpython code</a></li>
@@ -103,7 +58,7 @@
</li>
<li class="toctree-l2"><a class="reference internal" href="notebook_api_functionality.html">Tutorial: Using the API functionality of binary_c-python</a></li>
<li class="toctree-l2"><a class="reference internal" href="notebook_luminosity_function_single.html">Example use case: Zero-age stellar luminosity function</a></li>
-<li class="toctree-l2"><a class="reference internal" href="notebook_luminosity_function_binaries.html">Zero-age stellar luminosity function in binaries</a></li>
+<li class="toctree-l2"><a class="reference internal" href="notebook_luminosity_function_binaries.html">Example use case: Zero-age stellar luminosity function in binaries</a></li>
<li class="toctree-l2"><a class="reference internal" href="notebook_HRD.html">Example use case: Hertzsprung-Russell diagrams</a></li>
<li class="toctree-l2"><a class="reference internal" href="notebook_common_envelope_evolution.html">Example use case: Common-envelope evolution</a></li>
</ul>
@@ -114,71 +69,31 @@
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-<div class="section" id="Tutorial:-Extra-features-and-functionality-of-binary_c-python">
-<h1>Tutorial: Extra features and functionality of binary_c-python<a class="headerlink" href="#Tutorial:-Extra-features-and-functionality-of-binary_c-python" title="Permalink to this headline">¶</a></h1>
+<section id="Tutorial:-Extra-features-and-functionality-of-binary_c-python">
+<h1>Tutorial: Extra features and functionality of binary_c-python<a class="headerlink" href="#Tutorial:-Extra-features-and-functionality-of-binary_c-python" title="Permalink to this headline">ïƒ</a></h1>
<p>In this notebook we’ll go over some of the extra features and functionality that was not covered in the other notebooks.</p>
<p>Within the module <code class="docutils literal notranslate"><span class="pre">binarycpython.utils.functions</span></code> there are many functions that can be useful when using binarycpython. We can see which functions are in there, again by using the <code class="docutils literal notranslate"><span class="pre">help()</span></code></p>
<div class="nbinput nblast docutils container">
@@ -469,8 +384,8 @@ div.rendered_html tbody tr:hover {
</pre></div>
</div>
</div>
-<div class="section" id="getting-extra-information-about-binary_c-parameters">
-<h2>getting extra information about binary_c parameters<a class="headerlink" href="#getting-extra-information-about-binary_c-parameters" title="Permalink to this headline">¶</a></h2>
+<section id="getting-extra-information-about-binary_c-parameters">
+<h2>getting extra information about binary_c parameters<a class="headerlink" href="#getting-extra-information-about-binary_c-parameters" title="Permalink to this headline">ïƒ</a></h2>
<p>There are several functions that can be used to get information about the parameters in binary_c: - <code class="docutils literal notranslate"><span class="pre">get_help(parameter)</span></code>: Function to get information about the specific input parameter. Prints the output on default but returns a dictionary containing the information. - <code class="docutils literal notranslate"><span class="pre">get_help_all(print_help=True)</span></code>: Function to get information about all the parameters. Prints the output on default but returns a dictionary containing the information. - <code class="docutils literal notranslate"><span class="pre">get_help_super()</span></code>: Function to get even more
information about all the parameters. Does not print the output on default but returns a dictionary containing the information. - <code class="docutils literal notranslate"><span class="pre">get_defaults()</span></code>: Function that will get all the default values for the parameters. Returns a dictionary</p>
<div class="nbinput docutils container">
@@ -536,9 +451,9 @@ default:
</pre></div>
</div>
</div>
-</div>
-<div class="section" id="Build-information-of-binary_c">
-<h2>Build information of binary_c<a class="headerlink" href="#Build-information-of-binary_c" title="Permalink to this headline">¶</a></h2>
+</section>
+<section id="Build-information-of-binary_c">
+<h2>Build information of binary_c<a class="headerlink" href="#Build-information-of-binary_c" title="Permalink to this headline">ïƒ</a></h2>
<p>Sometimes we want to know with which settings binary_c has been built. We can use the function <code class="docutils literal notranslate"><span class="pre">return_binary_c_version_info</span></code> for this. This function will parse the version info of binary_c and return a dictionary with all the settings.</p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[32]:
@@ -558,9 +473,9 @@ default:
dict_keys(['networks', 'isotopes', 'argpairs', 'ensembles', 'macros', 'elements', 'dt_limits', 'nucleosynthesis_sources', 'miscellaneous'])
</pre></div></div>
</div>
-</div>
-<div class="section" id="Example-parse-function">
-<h2>Example parse function<a class="headerlink" href="#Example-parse-function" title="Permalink to this headline">¶</a></h2>
+</section>
+<section id="Example-parse-function">
+<h2>Example parse function<a class="headerlink" href="#Example-parse-function" title="Permalink to this headline">ïƒ</a></h2>
<p>TODO: In the functions module there is an example parse function that can be used in conjunction with run_system.</p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[34]:
@@ -591,18 +506,18 @@ get_defaults(filter_values:bool=False) -> dict
</pre></div></div>
</div>
-</div>
-<div class="section" id="Dictionary-modification">
-<h2>Dictionary modification<a class="headerlink" href="#Dictionary-modification" title="Permalink to this headline">¶</a></h2>
+</section>
+<section id="Dictionary-modification">
+<h2>Dictionary modification<a class="headerlink" href="#Dictionary-modification" title="Permalink to this headline">ïƒ</a></h2>
<ul class="simple">
<li><p>merge_dicts</p></li>
<li><p>update_dicts</p></li>
<li><p>multiply_values_dict</p></li>
</ul>
<p>TODO:</p>
-</div>
-<div class="section" id="Getting-help">
-<h2>Getting help<a class="headerlink" href="#Getting-help" title="Permalink to this headline">¶</a></h2>
+</section>
+<section id="Getting-help">
+<h2>Getting help<a class="headerlink" href="#Getting-help" title="Permalink to this headline">ïƒ</a></h2>
<p>There are sever</p>
<div class="nbinput nblast docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[ ]:
@@ -613,69 +528,44 @@ get_defaults(filter_values:bool=False) -> dict
</pre></div>
</div>
</div>
-</div>
-</div>
+</section>
+</section>
</div>
-
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- <footer>
-
- <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
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+ <p>© Copyright 2021, David Hendriks, Robert Izzard.</p>
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-
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- Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a
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+
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-Generated on binarycpython git branch: master git revision 0886cd4f1d7f43222aac21d6ed91e917b67b20fc url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/tree/master">git url</a>.
+Generated on binarycpython git branch: auto_resolution git revision be7bd630af892a785312affc34d87c57eb337fd3 url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/tree/auto_resolution">git url</a>.
<br><br>
-Using binary_c with bit branch newmaster: git revision: "6185:20210910:1621c23a5" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/newmaster">git url</a>.
+Using binary_c with bit branch master: git revision: "6209:20211006:c4a4c332e" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/master">git url</a>.
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diff --git a/docs/build/html/notebook_individual_systems.html b/docs/build/html/notebook_individual_systems.html
index 3c61e7be689f33a7b5060a2c449b21330b924200..bb649d43acc78c45503046c2994fe44382334853 100644
--- a/docs/build/html/notebook_individual_systems.html
+++ b/docs/build/html/notebook_individual_systems.html
@@ -1,71 +1,37 @@
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+ <title>Tutorial: Running individual systems with binary_c-python — binary_c-python documentation</title>
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</head>
-<body class="wy-body-for-nav">
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+<body class="wy-body-for-nav">
<div class="wy-grid-for-nav">
-
<nav data-toggle="wy-nav-shift" class="wy-nav-side">
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+ <a href="index.html" class="icon icon-home"> binary_c-python
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<input type="text" name="q" placeholder="Search docs" />
@@ -73,25 +39,14 @@
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-
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-
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+ </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
+ <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="readme_link.html">Python module for binary_c</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules.html">Binarycpython code</a></li>
<li class="toctree-l1 current"><a class="reference internal" href="example_notebooks.html">Example notebooks</a><ul class="current">
<li class="toctree-l2 current"><a class="current reference internal" href="#">Tutorial: Running individual systems with binary_c-python</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="#Single-system-with-run_wrapper">Single system with run_wrapper</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#Single-system-with-run_system_wrapper">Single system with run_system_wrapper</a></li>
<li class="toctree-l3"><a class="reference internal" href="#Single-system-via-population-object">Single system via population object</a></li>
<li class="toctree-l3"><a class="reference internal" href="#Single-system-via-API-functionality">Single system via API functionality</a></li>
</ul>
@@ -101,7 +56,7 @@
<li class="toctree-l2"><a class="reference internal" href="notebook_extra_features.html">Tutorial: Extra features and functionality of binary_c-python</a></li>
<li class="toctree-l2"><a class="reference internal" href="notebook_api_functionality.html">Tutorial: Using the API functionality of binary_c-python</a></li>
<li class="toctree-l2"><a class="reference internal" href="notebook_luminosity_function_single.html">Example use case: Zero-age stellar luminosity function</a></li>
-<li class="toctree-l2"><a class="reference internal" href="notebook_luminosity_function_binaries.html">Zero-age stellar luminosity function in binaries</a></li>
+<li class="toctree-l2"><a class="reference internal" href="notebook_luminosity_function_binaries.html">Example use case: Zero-age stellar luminosity function in binaries</a></li>
<li class="toctree-l2"><a class="reference internal" href="notebook_HRD.html">Example use case: Hertzsprung-Russell diagrams</a></li>
<li class="toctree-l2"><a class="reference internal" href="notebook_common_envelope_evolution.html">Example use case: Common-envelope evolution</a></li>
</ul>
@@ -112,71 +67,31 @@
<li class="toctree-l1"><a class="reference external" href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/issues/new">Submit an issue</a></li>
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-
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<div itemprop="articleBody">
-
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/* CSS for nbsphinx extension */
@@ -447,14 +362,14 @@ div.rendered_html tbody tr:hover {
text-align: unset;
}
</style>
-<div class="section" id="Tutorial:-Running-individual-systems-with-binary_c-python">
-<h1>Tutorial: Running individual systems with binary_c-python<a class="headerlink" href="#Tutorial:-Running-individual-systems-with-binary_c-python" title="Permalink to this headline">¶</a></h1>
+<section id="Tutorial:-Running-individual-systems-with-binary_c-python">
+<h1>Tutorial: Running individual systems with binary_c-python<a class="headerlink" href="#Tutorial:-Running-individual-systems-with-binary_c-python" title="Permalink to this headline">ïƒ</a></h1>
<p>This notebook will show you how to run single systems and analyze their results.</p>
-<p>It can be useful to have some functions to quickly run a single system to e.g. inspect what evolutionary steps a specific system goes through, to plot the mass loss evolution of a single star, etc.</p>
-<div class="section" id="Single-system-with-run_wrapper">
-<h2>Single system with run_wrapper<a class="headerlink" href="#Single-system-with-run_wrapper" title="Permalink to this headline">¶</a></h2>
+<p>It can be useful to have some functions to quickly run a single system to, for example, inspect what evolutionary steps a specific system goes through, to plot the mass loss evolution of a single system, etc.</p>
+<section id="Single-system-with-run_system_wrapper">
+<h2>Single system with run_system_wrapper<a class="headerlink" href="#Single-system-with-run_system_wrapper" title="Permalink to this headline">ïƒ</a></h2>
<p>The simplest method to run a single system is to use the run_system wrapper. This function deals with setting up the argument string, makes sure all the required parameters are included and handles setting and cleaning up the custom logging functionality (see notebook_custom_logging).</p>
-<p>As arguments to this function we can add any of the parameters that binary_c itself actually knows, as well as: - custom_logging_code: string containing a print statement that binary_c can use to print information - log_filename: path of the logfile that binary_c generates - parse_function: function that handles parsing the output of binary-c</p>
+<p>As arguments to this function we can add any of the parameters that binary_c itself actually knows, as well as: - custom_logging_code: string containing a Printf statement that binary_c can use to print information - log_filename: path of the logfile that binary_c generates - parse_function: function that handles parsing the output of binary-c</p>
<div class="nbinput nblast docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[1]:
</pre></div>
@@ -513,7 +428,7 @@ SINGLE_STAR_LIFETIME 1 12461.9
</div>
<div class="output_area docutils container">
<div class="highlight"><pre>
- TIME M1 M2 K1 K2 SEP PER ECC R1/ROL1 R2/ROL2 TYPE RANDOM_SEED=17089 RANDOM_COUNT=0
+ TIME M1 M2 K1 K2 SEP PER ECC R1/ROL1 R2/ROL2 TYPE RANDOM_SEED=12122 RANDOM_COUNT=0
0.0000 1.000 0.000 1 15 -1 -1 -1.00 0.000 0.000 "INITIAL "
11003.1302 1.000 0.000 2 15 -1 -1 -1.00 0.000 0.000 "OFF_MS"
11003.1302 1.000 0.000 2 15 -1 -1 -1.00 0.000 0.000 "TYPE_CHNGE"
@@ -608,7 +523,7 @@ EXAMPLE_MASSLOSS 2.000000000000e-06 1 1 1
[['time', 'mass', 'initial_mass', 'stellar_type'], [0.0, 1.0, 1.0, 1.0], [0.0, 1.0, 1.0, 1.0]]
</pre></div></div>
</div>
-<p>This output can now be turned into e.g. an Numpy array or Pandas dataframe (my favorite: makes querying the data very easy)</p>
+<p>This output can now be turned into e.g. an Numpy array or Pandas dataframe (my favorite: makes querying the data very easy)</p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[7]:
</pre></div>
@@ -632,25 +547,25 @@ EXAMPLE_MASSLOSS 2.000000000000e-06 1 1 1
</div>
<div class="output_area docutils container">
<div class="highlight"><pre>
-0 time mass initial_mass stellar_type
-1 0 1 1 1
-2 0 1 1 1
-3 1e-06 1 1 1
-4 2e-06 1 1 1
-5 3e-06 1 1 1
-... ... ... ... ...
-1617 12461.8 0.546683 1 6
-1618 12461.9 0.517749 1 11
-1619 13461.9 0.517749 1 11
-1620 14461.9 0.517749 1 11
-1621 15000 0.517749 1 11
+0 time mass initial_mass stellar_type
+1 0.0 1.0 1.0 1.0
+2 0.0 1.0 1.0 1.0
+3 0.000001 1.0 1.0 1.0
+4 0.000002 1.0 1.0 1.0
+5 0.000003 1.0 1.0 1.0
+... ... ... ... ...
+1617 12461.819616 0.546683 1.0 6.0
+1618 12461.945773 0.517749 1.0 11.0
+1619 13461.945773 0.517749 1.0 11.0
+1620 14461.945773 0.517749 1.0 11.0
+1621 15000.0 0.517749 1.0 11.0
[1621 rows x 4 columns]
</pre></div></div>
</div>
-</div>
-<div class="section" id="Single-system-via-population-object">
-<h2>Single system via population object<a class="headerlink" href="#Single-system-via-population-object" title="Permalink to this headline">¶</a></h2>
+</section>
+<section id="Single-system-via-population-object">
+<h2>Single system via population object<a class="headerlink" href="#Single-system-via-population-object" title="Permalink to this headline">ïƒ</a></h2>
<p>When setting up your population object (see notebook_population), and configuring all the parameters, it is possible to run a single system using that same configuration. It will use the parse_function if set, and running a single system is a good method to test if everything works accordingly.</p>
<div class="nbinput nblast docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[8]:
@@ -745,7 +660,7 @@ Printf("EXAMPLE_MASSLOSS %30.12e %g %g %g %d\n",
Creating and loading custom logging functionality
Running binary_c M_1 10 api_log_filename_prefix /tmp/binary_c_python/notebooks/notebook_individual_systems
Cleaning up the custom logging stuff. type: single
-Removed /tmp/binary_c_python/custom_logging/libcustom_logging_8967553693ac4e11a49c42d4eef773e8.so
+Removed /tmp/binary_c_python/custom_logging/libcustom_logging_6d4ed30fa6684630885c08523336d45f.so
EXAMPLE_MASSLOSS 0.000000000000e+00 10 0 10 1
EXAMPLE_MASSLOSS 0.000000000000e+00 10 10 10 1
EXAMPLE_MASSLOSS 1.000000000000e-06 10 10 10 1
@@ -830,22 +745,22 @@ EXAMPLE_MASSLOSS 2.000000000000e-06 10 10 10 1
</div>
<div class="output_area docutils container">
<div class="highlight"><pre>
-adding: parse_function=<function object_parse_function at 0x7fb4d41ebbf8> to grid_options
+adding: parse_function=<function object_parse_function at 0x14938275de50> to grid_options
<<<< Warning: Key does not match previously known parameter: adding: output_dir=/tmp/binary_c_python/notebooks/notebook_individual_systems to custom_options >>>>
adding: api_log_filename_prefix=/tmp/binary_c_python/notebooks/notebook_individual_systems to BSE_options
Creating and loading custom logging functionality
Running binary_c M_1 10 api_log_filename_prefix /tmp/binary_c_python/notebooks/notebook_individual_systems
Cleaning up the custom logging stuff. type: single
-Removed /tmp/binary_c_python/custom_logging/libcustom_logging_5d7779e8190e4b79b10c7e6a44cb0e7e.so
+Removed /tmp/binary_c_python/custom_logging/libcustom_logging_3bc2f679982a4df6a2b83d382e83d724.so
[['time', 'mass', 'initial_mass', 'stellar_type'], [0.0, 10.0, 0.0, 10.0, 1.0], [0.0, 10.0, 10.0, 10.0, 1.0], [1e-06, 10.0, 10.0, 10.0, 1.0]]
dict_keys(['time', 'mass', 'initial_mass', 'stellar_type'])
</pre></div></div>
</div>
-</div>
-<div class="section" id="Single-system-via-API-functionality">
-<h2>Single system via API functionality<a class="headerlink" href="#Single-system-via-API-functionality" title="Permalink to this headline">¶</a></h2>
+</section>
+<section id="Single-system-via-API-functionality">
+<h2>Single system via API functionality<a class="headerlink" href="#Single-system-via-API-functionality" title="Permalink to this headline">ïƒ</a></h2>
<p>It is possible to construct your own functionality to run a single system by directly calling the API function to run a system. Under the hood all the other functions and wrappers actually use this API.</p>
-<p>There are less failsafes for this method, so this make sure the input is correct and binary_c knows all the arguments you pass in.</p>
+<p>There are fewer failsafes for this method, so this make sure the input is correct and binary_c knows all the arguments you pass in.</p>
<p>for more details on this API function see <code class="docutils literal notranslate"><span class="pre">notebook_api_functions</span></code></p>
<p>First we must construct the argument string that we pass to binary_c</p>
<div class="nbinput docutils container">
@@ -889,74 +804,49 @@ dict_keys(['time', 'mass', 'initial_mass', 'stellar_
</div>
<div class="output_area docutils container">
<div class="highlight"><pre>
-SINGLE_STAR_LIFETIME 15 14.9947
+SINGLE_STAR_LIFETIME 15 14.9927
</pre></div></div>
</div>
<p>As we can see above, the output is rather empty. But if SINGLE_STAR_LIFETIME is printed we know we caught the output correctly. To get actual output we should have timesteps printed in the <code class="docutils literal notranslate"><span class="pre">log_every_timestep.c</span></code> in binary_c, or add some custom_logging (see notebook_custom_logging).</p>
-</div>
-</div>
+</section>
+</section>
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- <p>
-
- © Copyright 2021, David Hendriks, Robert Izzard
-
- </p>
+ <p>© Copyright 2021, David Hendriks, Robert Izzard.</p>
</div>
-
-
-
- Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a
-
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-
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+ <a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
provided by <a href="https://readthedocs.org">Read the Docs</a>.
+
<br><br>
-Generated on binarycpython git branch: master git revision 0886cd4f1d7f43222aac21d6ed91e917b67b20fc url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/tree/master">git url</a>.
+Generated on binarycpython git branch: auto_resolution git revision be7bd630af892a785312affc34d87c57eb337fd3 url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/tree/auto_resolution">git url</a>.
<br><br>
-Using binary_c with bit branch newmaster: git revision: "6185:20210910:1621c23a5" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/newmaster">git url</a>.
+Using binary_c with bit branch master: git revision: "6209:20211006:c4a4c332e" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/master">git url</a>.
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diff --git a/docs/build/html/notebook_individual_systems.ipynb b/docs/build/html/notebook_individual_systems.ipynb
index 85aef1e3962a1626f37a9ef36bf5e16f479eb68e..50c604385e0365b3404fb8d6427b9b9f0c0f7fbf 100644
--- a/docs/build/html/notebook_individual_systems.ipynb
+++ b/docs/build/html/notebook_individual_systems.ipynb
@@ -8,19 +8,22 @@
"# Tutorial: Running individual systems with binary_c-python\n",
"This notebook will show you how to run single systems and analyze their results.\n",
"\n",
- "It can be useful to have some functions to quickly run a single system to e.g. inspect what evolutionary steps a specific system goes through, to plot the mass loss evolution of a single star, etc. "
+ "It can be useful to have some functions to quickly run a single system to, for example, inspect what evolutionary steps a specific system goes through, to plot the mass loss evolution of a single system, etc. "
]
},
{
"cell_type": "markdown",
"id": "dd5d9ec7-5791-45f1-afbd-225947e2a583",
- "metadata": {},
+ "metadata": {
+ "tags": []
+ },
"source": [
- "## Single system with run_wrapper\n",
+ "## Single system with run_system_wrapper\n",
+ "\n",
"The simplest method to run a single system is to use the run_system wrapper. This function deals with setting up the argument string, makes sure all the required parameters are included and handles setting and cleaning up the custom logging functionality (see notebook_custom_logging).\n",
"\n",
"As arguments to this function we can add any of the parameters that binary_c itself actually knows, as well as:\n",
- "- custom_logging_code: string containing a print statement that binary_c can use to print information\n",
+ "- custom_logging_code: string containing a Printf statement that binary_c can use to print information\n",
"- log_filename: path of the logfile that binary_c generates\n",
"- parse_function: function that handles parsing the output of binary-c"
]
@@ -86,7 +89,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- " TIME M1 M2 K1 K2 SEP PER ECC R1/ROL1 R2/ROL2 TYPE RANDOM_SEED=17089 RANDOM_COUNT=0\n",
+ " TIME M1 M2 K1 K2 SEP PER ECC R1/ROL1 R2/ROL2 TYPE RANDOM_SEED=12122 RANDOM_COUNT=0\n",
" 0.0000 1.000 0.000 1 15 -1 -1 -1.00 0.000 0.000 \"INITIAL \"\n",
" 11003.1302 1.000 0.000 2 15 -1 -1 -1.00 0.000 0.000 \"OFF_MS\"\n",
" 11003.1302 1.000 0.000 2 15 -1 -1 -1.00 0.000 0.000 \"TYPE_CHNGE\"\n",
@@ -225,18 +228,18 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "0 time mass initial_mass stellar_type\n",
- "1 0 1 1 1\n",
- "2 0 1 1 1\n",
- "3 1e-06 1 1 1\n",
- "4 2e-06 1 1 1\n",
- "5 3e-06 1 1 1\n",
- "... ... ... ... ...\n",
- "1617 12461.8 0.546683 1 6\n",
- "1618 12461.9 0.517749 1 11\n",
- "1619 13461.9 0.517749 1 11\n",
- "1620 14461.9 0.517749 1 11\n",
- "1621 15000 0.517749 1 11\n",
+ "0 time mass initial_mass stellar_type\n",
+ "1 0.0 1.0 1.0 1.0\n",
+ "2 0.0 1.0 1.0 1.0\n",
+ "3 0.000001 1.0 1.0 1.0\n",
+ "4 0.000002 1.0 1.0 1.0\n",
+ "5 0.000003 1.0 1.0 1.0\n",
+ "... ... ... ... ...\n",
+ "1617 12461.819616 0.546683 1.0 6.0\n",
+ "1618 12461.945773 0.517749 1.0 11.0\n",
+ "1619 13461.945773 0.517749 1.0 11.0\n",
+ "1620 14461.945773 0.517749 1.0 11.0\n",
+ "1621 15000.0 0.517749 1.0 11.0\n",
"\n",
"[1621 rows x 4 columns]\n"
]
@@ -358,7 +361,7 @@
"Creating and loading custom logging functionality\n",
"Running binary_c M_1 10 api_log_filename_prefix /tmp/binary_c_python/notebooks/notebook_individual_systems\n",
"Cleaning up the custom logging stuff. type: single\n",
- "Removed /tmp/binary_c_python/custom_logging/libcustom_logging_8967553693ac4e11a49c42d4eef773e8.so\n",
+ "Removed /tmp/binary_c_python/custom_logging/libcustom_logging_6d4ed30fa6684630885c08523336d45f.so\n",
"EXAMPLE_MASSLOSS 0.000000000000e+00 10 0 10 1\n",
"EXAMPLE_MASSLOSS 0.000000000000e+00 10 10 10 1\n",
"EXAMPLE_MASSLOSS 1.000000000000e-06 10 10 10 1\n",
@@ -460,13 +463,13 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "adding: parse_function=<function object_parse_function at 0x7fb4d41ebbf8> to grid_options\n",
+ "adding: parse_function=<function object_parse_function at 0x14938275de50> to grid_options\n",
"<<<< Warning: Key does not match previously known parameter: adding: output_dir=/tmp/binary_c_python/notebooks/notebook_individual_systems to custom_options >>>>\n",
"adding: api_log_filename_prefix=/tmp/binary_c_python/notebooks/notebook_individual_systems to BSE_options\n",
"Creating and loading custom logging functionality\n",
"Running binary_c M_1 10 api_log_filename_prefix /tmp/binary_c_python/notebooks/notebook_individual_systems\n",
"Cleaning up the custom logging stuff. type: single\n",
- "Removed /tmp/binary_c_python/custom_logging/libcustom_logging_5d7779e8190e4b79b10c7e6a44cb0e7e.so\n",
+ "Removed /tmp/binary_c_python/custom_logging/libcustom_logging_3bc2f679982a4df6a2b83d382e83d724.so\n",
"[['time', 'mass', 'initial_mass', 'stellar_type'], [0.0, 10.0, 0.0, 10.0, 1.0], [0.0, 10.0, 10.0, 10.0, 1.0], [1e-06, 10.0, 10.0, 10.0, 1.0]]\n",
"dict_keys(['time', 'mass', 'initial_mass', 'stellar_type'])\n"
]
@@ -496,7 +499,7 @@
"## Single system via API functionality\n",
"It is possible to construct your own functionality to run a single system by directly calling the API function to run a system. Under the hood all the other functions and wrappers actually use this API.\n",
"\n",
- "There are less failsafes for this method, so this make sure the input is correct and binary_c knows all the arguments you pass in.\n",
+ "There are fewer failsafes for this method, so this make sure the input is correct and binary_c knows all the arguments you pass in.\n",
"\n",
"for more details on this API function see `notebook_api_functions`"
]
@@ -519,7 +522,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "SINGLE_STAR_LIFETIME 15 14.9947\n",
+ "SINGLE_STAR_LIFETIME 15 14.9927\n",
"\n"
]
}
diff --git a/docs/build/html/notebook_luminosity_function_binaries.html b/docs/build/html/notebook_luminosity_function_binaries.html
index 026d2e78efe298107eede50987367f4e4d47edbe..b72691b1765e2a02f0f2bc2268941a2895bd1039 100644
--- a/docs/build/html/notebook_luminosity_function_binaries.html
+++ b/docs/build/html/notebook_luminosity_function_binaries.html
@@ -1,71 +1,37 @@
-
-
<!DOCTYPE html>
<html class="writer-html5" lang="en" >
<head>
- <meta charset="utf-8">
-
- <meta name="viewport" content="width=device-width, initial-scale=1.0">
-
- <title>Zero-age stellar luminosity function in binaries — binary_c-python documentation</title>
-
-
-
- <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
- <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+ <meta charset="utf-8" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
-
-
-
-
-
-
+ <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+ <title>Example use case: Zero-age stellar luminosity function in binaries — binary_c-python documentation</title>
+ <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+ <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
<!--[if lt IE 9]>
<script src="_static/js/html5shiv.min.js"></script>
<![endif]-->
-
- <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
+ <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
<script src="_static/jquery.js"></script>
<script src="_static/underscore.js"></script>
<script src="_static/doctools.js"></script>
- <script src="_static/language_data.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
- <script async="async" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.7/latest.js?config=TeX-AMS-MML_HTMLorMML"></script>
- <script type="text/x-mathjax-config">MathJax.Hub.Config({"tex2jax": {"inlineMath": [["$", "$"], ["\\(", "\\)"]], "processEscapes": true, "ignoreClass": "document", "processClass": "math|output_area"}})</script>
-
- <script type="text/javascript" src="_static/js/theme.js"></script>
-
-
+ <script async="async" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
+ <script>window.MathJax = {"tex": {"inlineMath": [["$", "$"], ["\\(", "\\)"]], "processEscapes": true}, "options": {"ignoreHtmlClass": "tex2jax_ignore|mathjax_ignore|document", "processHtmlClass": "tex2jax_process|mathjax_process|math|output_area"}}</script>
+ <script src="_static/js/theme.js"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="next" title="Example use case: Hertzsprung-Russell diagrams" href="notebook_HRD.html" />
<link rel="prev" title="Example use case: Zero-age stellar luminosity function" href="notebook_luminosity_function_single.html" />
</head>
-<body class="wy-body-for-nav">
-
-
+<body class="wy-body-for-nav">
<div class="wy-grid-for-nav">
-
<nav data-toggle="wy-nav-shift" class="wy-nav-side">
<div class="wy-side-scroll">
<div class="wy-side-nav-search" >
-
-
-
- <a href="index.html" class="icon icon-home" alt="Documentation Home"> binary_c-python
-
-
-
+ <a href="index.html" class="icon icon-home"> binary_c-python
</a>
-
-
-
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-
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<div role="search">
<form id="rtd-search-form" class="wy-form" action="search.html" method="get">
<input type="text" name="q" placeholder="Search docs" />
@@ -73,19 +39,8 @@
<input type="hidden" name="area" value="default" />
</form>
</div>
-
-
- </div>
-
-
- <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
-
-
-
-
-
-
- <p class="caption"><span class="caption-text">Contents:</span></p>
+ </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
+ <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="readme_link.html">Python module for binary_c</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules.html">Binarycpython code</a></li>
@@ -96,7 +51,7 @@
<li class="toctree-l2"><a class="reference internal" href="notebook_extra_features.html">Tutorial: Extra features and functionality of binary_c-python</a></li>
<li class="toctree-l2"><a class="reference internal" href="notebook_api_functionality.html">Tutorial: Using the API functionality of binary_c-python</a></li>
<li class="toctree-l2"><a class="reference internal" href="notebook_luminosity_function_single.html">Example use case: Zero-age stellar luminosity function</a></li>
-<li class="toctree-l2 current"><a class="current reference internal" href="#">Zero-age stellar luminosity function in binaries</a><ul>
+<li class="toctree-l2 current"><a class="current reference internal" href="#">Example use case: Zero-age stellar luminosity function in binaries</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#Setting-up-the-Population-object">Setting up the Population object</a></li>
<li class="toctree-l3"><a class="reference internal" href="#Adding-grid-variables">Adding grid variables</a></li>
<li class="toctree-l3"><a class="reference internal" href="#Setting-logging-and-handling-the-output">Setting logging and handling the output</a></li>
@@ -113,71 +68,31 @@
<li class="toctree-l1"><a class="reference external" href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/issues/new">Submit an issue</a></li>
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-<div role="navigation" aria-label="breadcrumbs navigation">
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+ <div role="navigation" aria-label="Page navigation">
<ul class="wy-breadcrumbs">
-
<li><a href="index.html" class="icon icon-home"></a> »</li>
-
<li><a href="example_notebooks.html">Example notebooks</a> »</li>
-
- <li>Zero-age stellar luminosity function in binaries</li>
-
-
+ <li>Example use case: Zero-age stellar luminosity function in binaries</li>
<li class="wy-breadcrumbs-aside">
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<a href="_sources/notebook_luminosity_function_binaries.ipynb.txt" rel="nofollow"> View page source</a>
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<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
-
+
<style>
/* CSS for nbsphinx extension */
@@ -448,8 +363,8 @@ div.rendered_html tbody tr:hover {
text-align: unset;
}
</style>
-<div class="section" id="Zero-age-stellar-luminosity-function-in-binaries">
-<h1>Zero-age stellar luminosity function in binaries<a class="headerlink" href="#Zero-age-stellar-luminosity-function-in-binaries" title="Permalink to this headline">¶</a></h1>
+<section id="Example-use-case:-Zero-age-stellar-luminosity-function-in-binaries">
+<h1>Example use case: Zero-age stellar luminosity function in binaries<a class="headerlink" href="#Example-use-case:-Zero-age-stellar-luminosity-function-in-binaries" title="Permalink to this headline">ïƒ</a></h1>
<p>In this notebook we compute the luminosity function of the zero-age main-sequence by running a population of binary stars using binary_c.</p>
<p>Before you go through this notebook, you should look at notebook_luminosity_function.ipynb which is for the - conceptually more simple - single stars.</p>
<p>We start by loading in some standard Python modules and the binary_c module.</p>
@@ -466,8 +381,8 @@ div.rendered_html tbody tr:hover {
</pre></div>
</div>
</div>
-<div class="section" id="Setting-up-the-Population-object">
-<h2>Setting up the Population object<a class="headerlink" href="#Setting-up-the-Population-object" title="Permalink to this headline">¶</a></h2>
+<section id="Setting-up-the-Population-object">
+<h2>Setting up the Population object<a class="headerlink" href="#Setting-up-the-Population-object" title="Permalink to this headline">ïƒ</a></h2>
<p>To set up and configure the population object we need to make a new instance of the <code class="docutils literal notranslate"><span class="pre">Population</span></code> object and configure it with the <code class="docutils literal notranslate"><span class="pre">.set()</span></code> function.</p>
<p>In our case, we only need to set the maximum evolution time to something short, because we care only about zero-age main sequence stars which have, by definition, age zero.</p>
<div class="nbinput docutils container">
@@ -504,11 +419,11 @@ adding: max_evolution_time=0.1 to BSE_options
verbosity is 1
</pre></div></div>
</div>
-</div>
-<div class="section" id="Adding-grid-variables">
-<h2>Adding grid variables<a class="headerlink" href="#Adding-grid-variables" title="Permalink to this headline">¶</a></h2>
+</section>
+<section id="Adding-grid-variables">
+<h2>Adding grid variables<a class="headerlink" href="#Adding-grid-variables" title="Permalink to this headline">ïƒ</a></h2>
<p>The main purpose of the Population object is to handle the population synthesis side of running a set of stars. The main method to do this with binarycpython, as is the case with Perl binarygrid, is to use grid variables. These are loops over a predefined range of values, where a probability will be assigned to the systems based on the chosen probability distributions.</p>
-<p>Usually we use either 1 mass grid variable, or a trio of mass, mass ratio and period (other notebooks cover these examples). We can, however, also add grid sampling for e.g. eccentricity, metallicity or other parameters.</p>
+<p>Usually we use either 1 mass grid variable, or a trio of mass, mass ratio and period (other notebooks cover these examples). We can, however, also add grid sampling for e.g. eccentricity, metallicity or other parameters.</p>
<p>To add a grid variable to the population object we use <code class="docutils literal notranslate"><span class="pre">population.add_grid_variable</span></code></p>
<div class="nbinput nblast docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[3]:
@@ -530,7 +445,7 @@ verbosity is 1
</pre></div>
</div>
</div>
-<p>First let us set up some global variables that will be useful throughout. * The resolution is the number of stars we simulate in our model population. * The massrange is a list of the min and max masses * The total_probability is the theoretical integral of a probability density function, i.e. 1.0. * The binwidth sets the resolution of the final distribution. If set to 0.5, the bins in log<em>L</em> are 0.5dex wide.</p>
+<p>First let us set up some global variables that will be useful throughout. * The resolution is the number of stars we simulate in our model population. * The massrange is a list of the min and max masses * The total_probability is the theoretical integral of a probability density function, i.e. 1.0. * The binwidth sets the resolution of the final distribution. If set to 0.5, the bins in log<em>L</em> are 0.5dex wide.</p>
<div class="nbinput nblast docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[5]:
</pre></div>
@@ -610,11 +525,11 @@ verbosity is 1
</pre></div>
</div>
</div>
-</div>
-<div class="section" id="Setting-logging-and-handling-the-output">
-<h2>Setting logging and handling the output<a class="headerlink" href="#Setting-logging-and-handling-the-output" title="Permalink to this headline">¶</a></h2>
-<p>By default, binary_c will not output anything (except for ‘SINGLE STAR LIFETIME’). It is up to us to determine what will be printed. We can either do that by hardcoding the print statements into <code class="docutils literal notranslate"><span class="pre">binary_c</span></code> (see documentation binary_c) or we can use the custom logging functionality of binarycpython (see notebook <code class="docutils literal notranslate"><span class="pre">notebook_custom_logging.ipynb</span></code>), which is faster to set up and requires no recompilation of binary_c, but is somewhat more limited in its functionality. For our current purposes,
-it works perfectly well.</p>
+</section>
+<section id="Setting-logging-and-handling-the-output">
+<h2>Setting logging and handling the output<a class="headerlink" href="#Setting-logging-and-handling-the-output" title="Permalink to this headline">ïƒ</a></h2>
+<p>By default, binary_c will not output anything (except for ‘SINGLE STAR LIFETIME’). It is up to us to determine what will be printed. We can either do that by hardcoding the print statements into <code class="docutils literal notranslate"><span class="pre">binary_c</span></code> (see documentation binary_c) or we can use the custom logging functionality of binarycpython (see notebook <code class="docutils literal notranslate"><span class="pre">notebook_custom_logging.ipynb</span></code>), which is faster to set up and requires no recompilation of binary_c, but is somewhat more limited in its functionality. For our current purposes, it
+works perfectly well.</p>
<p>After configuring what will be printed, we need to make a function to parse the output. This can be done by setting the parse_function parameter in the population object (see also notebook <code class="docutils literal notranslate"><span class="pre">notebook_individual_systems.ipynb</span></code>).</p>
<p>In the code below we will set up both the custom logging and a parse function to handle that output.</p>
<div class="nbinput nblast docutils container">
@@ -738,11 +653,11 @@ it works perfectly well.</p>
</pre></div>
</div>
</div>
-</div>
-<div class="section" id="Evolving-the-grid">
-<h2>Evolving the grid<a class="headerlink" href="#Evolving-the-grid" title="Permalink to this headline">¶</a></h2>
+</section>
+<section id="Evolving-the-grid">
+<h2>Evolving the grid<a class="headerlink" href="#Evolving-the-grid" title="Permalink to this headline">ïƒ</a></h2>
<p>Now that we configured all the main parts of the population object, we can actually run the population! Doing this is straightforward: <code class="docutils literal notranslate"><span class="pre">population.evolve()</span></code></p>
-<p>This will start up the processing of all the systems. We can control how many cores are used by settings <code class="docutils literal notranslate"><span class="pre">amt_cores</span></code>. By setting the <code class="docutils literal notranslate"><span class="pre">verbosity</span></code> of the population object to a higher value we can get a lot of verbose information about the run, but for now we will set it to 0.</p>
+<p>This will start up the processing of all the systems. We can control how many cores are used by settings <code class="docutils literal notranslate"><span class="pre">num_cores</span></code>. By setting the <code class="docutils literal notranslate"><span class="pre">verbosity</span></code> of the population object to a higher value we can get a lot of verbose information about the run, but for now we will set it to 0.</p>
<p>There are many grid_options that can lead to different behaviour of the evolution of the grid. Please do have a look at those: <a class="reference external" href="https://ri0005.pages.surrey.ac.uk/binary_c-python/grid_options_descriptions.html">grid options docs</a>, and try</p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[9]:
@@ -754,7 +669,7 @@ it works perfectly well.</p>
<span class="c1"># verbose output is not required</span>
<span class="n">verbosity</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span>
<span class="c1"># set number of threads (i.e. number of CPU cores we use)</span>
- <span class="n">amt_cores</span><span class="o">=</span><span class="mi">4</span><span class="p">,</span>
+ <span class="n">num_cores</span><span class="o">=</span><span class="mi">4</span><span class="p">,</span>
<span class="p">)</span>
<span class="c1"># Evolve the population - this is the slow, number-crunching step</span>
@@ -772,7 +687,7 @@ it works perfectly well.</p>
</div>
<div class="output_area docutils container">
<div class="highlight"><pre>
-adding: amt_cores=4 to grid_options
+adding: num_cores=4 to grid_options
Running the population now, this may take a little while...
Creating and loading custom logging functionality
Generating grid code
@@ -940,7 +855,7 @@ There were no errors found in this run.
Done population run!
</pre></div></div>
</div>
-<p>After the run is complete, some technical report on the run is returned. I stored that in <code class="docutils literal notranslate"><span class="pre">analytics</span></code>. As we can see below, this dictionary is like a status report of the evolution. Useful for e.g. debugging.</p>
+<p>After the run is complete, some technical report on the run is returned. I stored that in <code class="docutils literal notranslate"><span class="pre">analytics</span></code>. As we can see below, this dictionary is like a status report of the evolution. Useful for e.g. debugging.</p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[10]:
</pre></div>
@@ -1034,69 +949,44 @@ Done population run!
</pre></div>
</div>
</div>
-</div>
-</div>
+</section>
+</section>
</div>
-
</div>
- <footer>
-
- <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
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- <a href="notebook_luminosity_function_single.html" class="btn btn-neutral float-left" title="Example use case: Zero-age stellar luminosity function" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
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+ <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
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+ <a href="notebook_HRD.html" class="btn btn-neutral float-right" title="Example use case: Hertzsprung-Russell diagrams" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
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-
<hr/>
<div role="contentinfo">
- <p>
-
- © Copyright 2021, David Hendriks, Robert Izzard
-
- </p>
+ <p>© Copyright 2021, David Hendriks, Robert Izzard.</p>
</div>
-
-
-
- Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a
-
- <a href="https://github.com/rtfd/sphinx_rtd_theme">theme</a>
-
+
+ Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
+ <a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
provided by <a href="https://readthedocs.org">Read the Docs</a>.
+
<br><br>
-Generated on binarycpython git branch: master git revision 0886cd4f1d7f43222aac21d6ed91e917b67b20fc url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/tree/master">git url</a>.
+Generated on binarycpython git branch: auto_resolution git revision be7bd630af892a785312affc34d87c57eb337fd3 url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/tree/auto_resolution">git url</a>.
<br><br>
-Using binary_c with bit branch newmaster: git revision: "6185:20210910:1621c23a5" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/newmaster">git url</a>.
+Using binary_c with bit branch master: git revision: "6209:20211006:c4a4c332e" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/master">git url</a>.
</footer>
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+ <script>
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diff --git a/docs/build/html/notebook_luminosity_function_binaries.ipynb b/docs/build/html/notebook_luminosity_function_binaries.ipynb
index c6b5f1e64cc36c684fdf5cefe0fae4b450a1c936..f054310a62ea8a37e55df724be75879dababbe38 100644
--- a/docs/build/html/notebook_luminosity_function_binaries.ipynb
+++ b/docs/build/html/notebook_luminosity_function_binaries.ipynb
@@ -5,7 +5,7 @@
"id": "bbbaafbb-fd7d-4b73-a970-93506ba35d71",
"metadata": {},
"source": [
- "# Zero-age stellar luminosity function in binaries\n",
+ "# Example use case: Zero-age stellar luminosity function in binaries\n",
"\n",
"In this notebook we compute the luminosity function of the zero-age main-sequence by running a population of binary stars using binary_c. \n",
"\n",
@@ -369,7 +369,7 @@
"## Evolving the grid\n",
"Now that we configured all the main parts of the population object, we can actually run the population! Doing this is straightforward: `population.evolve()`\n",
"\n",
- "This will start up the processing of all the systems. We can control how many cores are used by settings `amt_cores`. By setting the `verbosity` of the population object to a higher value we can get a lot of verbose information about the run, but for now we will set it to 0.\n",
+ "This will start up the processing of all the systems. We can control how many cores are used by settings `num_cores`. By setting the `verbosity` of the population object to a higher value we can get a lot of verbose information about the run, but for now we will set it to 0.\n",
"\n",
"There are many grid_options that can lead to different behaviour of the evolution of the grid. Please do have a look at those: [grid options docs](https://ri0005.pages.surrey.ac.uk/binary_c-python/grid_options_descriptions.html), and try "
]
@@ -386,7 +386,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "adding: amt_cores=4 to grid_options\n",
+ "adding: num_cores=4 to grid_options\n",
"Running the population now, this may take a little while...\n",
"Creating and loading custom logging functionality\n",
"Generating grid code\n",
@@ -547,7 +547,7 @@
" # verbose output is not required \n",
" verbosity=1,\n",
" # set number of threads (i.e. number of CPU cores we use)\n",
- " amt_cores=4,\n",
+ " num_cores=4,\n",
" )\n",
"\n",
"# Evolve the population - this is the slow, number-crunching step\n",
diff --git a/docs/build/html/notebook_luminosity_function_single.html b/docs/build/html/notebook_luminosity_function_single.html
index 8f7cb72abb8027dae19b267fa30372a65d718ffb..02a5bece0a68dc8f982f8f882a9ca3783d5844d3 100644
--- a/docs/build/html/notebook_luminosity_function_single.html
+++ b/docs/build/html/notebook_luminosity_function_single.html
@@ -1,71 +1,37 @@
-
-
<!DOCTYPE html>
<html class="writer-html5" lang="en" >
<head>
- <meta charset="utf-8">
-
- <meta name="viewport" content="width=device-width, initial-scale=1.0">
-
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-
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- <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+ <meta charset="utf-8" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
-
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+ <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+ <title>Example use case: Zero-age stellar luminosity function — binary_c-python documentation</title>
+ <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+ <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
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- <script async="async" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.7/latest.js?config=TeX-AMS-MML_HTMLorMML"></script>
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+ <script async="async" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
+ <script>window.MathJax = {"tex": {"inlineMath": [["$", "$"], ["\\(", "\\)"]], "processEscapes": true}, "options": {"ignoreHtmlClass": "tex2jax_ignore|mathjax_ignore|document", "processHtmlClass": "tex2jax_process|mathjax_process|math|output_area"}}</script>
+ <script src="_static/js/theme.js"></script>
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- <link rel="next" title="Zero-age stellar luminosity function in binaries" href="notebook_luminosity_function_binaries.html" />
+ <link rel="next" title="Example use case: Zero-age stellar luminosity function in binaries" href="notebook_luminosity_function_binaries.html" />
<link rel="prev" title="Tutorial: Using the API functionality of binary_c-python" href="notebook_api_functionality.html" />
</head>
-<body class="wy-body-for-nav">
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+<body class="wy-body-for-nav">
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+ <a href="index.html" class="icon icon-home"> binary_c-python
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<form id="rtd-search-form" class="wy-form" action="search.html" method="get">
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@@ -73,19 +39,8 @@
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-
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- <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
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- <p class="caption"><span class="caption-text">Contents:</span></p>
+ </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
+ <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="readme_link.html">Python module for binary_c</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules.html">Binarycpython code</a></li>
@@ -104,7 +59,7 @@
<li class="toctree-l3"><a class="reference internal" href="#A-better-sampled-grid">A better-sampled grid</a></li>
</ul>
</li>
-<li class="toctree-l2"><a class="reference internal" href="notebook_luminosity_function_binaries.html">Zero-age stellar luminosity function in binaries</a></li>
+<li class="toctree-l2"><a class="reference internal" href="notebook_luminosity_function_binaries.html">Example use case: Zero-age stellar luminosity function in binaries</a></li>
<li class="toctree-l2"><a class="reference internal" href="notebook_HRD.html">Example use case: Hertzsprung-Russell diagrams</a></li>
<li class="toctree-l2"><a class="reference internal" href="notebook_common_envelope_evolution.html">Example use case: Common-envelope evolution</a></li>
</ul>
@@ -115,71 +70,31 @@
<li class="toctree-l1"><a class="reference external" href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/issues/new">Submit an issue</a></li>
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-
+
<style>
/* CSS for nbsphinx extension */
@@ -450,8 +365,8 @@ div.rendered_html tbody tr:hover {
text-align: unset;
}
</style>
-<div class="section" id="Example-use-case:-Zero-age-stellar-luminosity-function">
-<h1>Example use case: Zero-age stellar luminosity function<a class="headerlink" href="#Example-use-case:-Zero-age-stellar-luminosity-function" title="Permalink to this headline">¶</a></h1>
+<section id="Example-use-case:-Zero-age-stellar-luminosity-function">
+<h1>Example use case: Zero-age stellar luminosity function<a class="headerlink" href="#Example-use-case:-Zero-age-stellar-luminosity-function" title="Permalink to this headline">ïƒ</a></h1>
<p>In this notebook we compute the luminosity function of the zero-age main-sequence by running a population of single stars using binary_c.</p>
<p>We start by loading in some standard Python modules and the binary_c module.</p>
<div class="nbinput nblast docutils container">
@@ -472,8 +387,8 @@ div.rendered_html tbody tr:hover {
</pre></div>
</div>
</div>
-<div class="section" id="Setting-up-the-Population-object">
-<h2>Setting up the Population object<a class="headerlink" href="#Setting-up-the-Population-object" title="Permalink to this headline">¶</a></h2>
+<section id="Setting-up-the-Population-object">
+<h2>Setting up the Population object<a class="headerlink" href="#Setting-up-the-Population-object" title="Permalink to this headline">ïƒ</a></h2>
<p>To set up and configure the population object we need to make a new instance of the <code class="docutils literal notranslate"><span class="pre">Population</span></code> object and configure it with the <code class="docutils literal notranslate"><span class="pre">.set()</span></code> function.</p>
<p>In our case, we only need to set the maximum evolution time to something short, because we care only about zero-age main sequence stars which have, by definition, age zero.</p>
<div class="nbinput docutils container">
@@ -512,11 +427,11 @@ adding: tmp_dir=/tmp/binary_c_python/notebooks/notebook_luminosity to grid_optio
verbosity is 1
</pre></div></div>
</div>
-</div>
-<div class="section" id="Adding-grid-variables">
-<h2>Adding grid variables<a class="headerlink" href="#Adding-grid-variables" title="Permalink to this headline">¶</a></h2>
+</section>
+<section id="Adding-grid-variables">
+<h2>Adding grid variables<a class="headerlink" href="#Adding-grid-variables" title="Permalink to this headline">ïƒ</a></h2>
<p>The main purpose of the Population object is to handle the population synthesis side of running a set of stars. The main method to do this with binarycpython, as is the case with Perl binarygrid, is to use grid variables. These are loops over a predefined range of values, where a probability will be assigned to the systems based on the chosen probability distributions.</p>
-<p>Usually we use either 1 mass grid variable, or a trio of mass, mass ratio and period (other notebooks cover these examples). We can, however, also add grid sampling for e.g. eccentricity, metallicity or other parameters.</p>
+<p>Usually we use either 1 mass grid variable, or a trio of mass, mass ratio and period (other notebooks cover these examples). We can, however, also add grid sampling for e.g. eccentricity, metallicity or other parameters.</p>
<p>To add a grid variable to the population object we use <code class="docutils literal notranslate"><span class="pre">population.add_grid_variable</span></code></p>
<div class="nbinput nblast docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[3]:
@@ -538,7 +453,7 @@ verbosity is 1
</pre></div>
</div>
</div>
-<p>First let us set up some global variables that will be useful throughout. * The resolution is the number of stars we simulate in our model population. * The massrange is a list of the min and max masses * The total_probability is the theoretical integral of a probability density function, i.e. 1.0. * The binwidth sets the resolution of the final distribution. If set to 0.5, the bins in log<em>L</em> are 0.5dex wide.</p>
+<p>First let us set up some global variables that will be useful throughout. * The resolution is the number of stars we simulate in our model population. * The massrange is a list of the min and max masses * The total_probability is the theoretical integral of a probability density function, i.e. 1.0. * The binwidth sets the resolution of the final distribution. If set to 0.5, the bins in log<em>L</em> are 0.5dex wide.</p>
<div class="nbinput nblast docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[5]:
</pre></div>
@@ -579,11 +494,11 @@ verbosity is 1
</pre></div>
</div>
</div>
-</div>
-<div class="section" id="Setting-logging-and-handling-the-output">
-<h2>Setting logging and handling the output<a class="headerlink" href="#Setting-logging-and-handling-the-output" title="Permalink to this headline">¶</a></h2>
-<p>By default, binary_c will not output anything (except for ‘SINGLE STAR LIFETIME’). It is up to us to determine what will be printed. We can either do that by hardcoding the print statements into <code class="docutils literal notranslate"><span class="pre">binary_c</span></code> (see documentation binary_c) or we can use the custom logging functionality of binarycpython (see notebook <code class="docutils literal notranslate"><span class="pre">notebook_custom_logging.ipynb</span></code>), which is faster to set up and requires no recompilation of binary_c, but is somewhat more limited in its functionality. For our current purposes,
-it works perfectly well.</p>
+</section>
+<section id="Setting-logging-and-handling-the-output">
+<h2>Setting logging and handling the output<a class="headerlink" href="#Setting-logging-and-handling-the-output" title="Permalink to this headline">ïƒ</a></h2>
+<p>By default, binary_c will not output anything (except for ‘SINGLE STAR LIFETIME’). It is up to us to determine what will be printed. We can either do that by hardcoding the print statements into <code class="docutils literal notranslate"><span class="pre">binary_c</span></code> (see documentation binary_c) or we can use the custom logging functionality of binarycpython (see notebook <code class="docutils literal notranslate"><span class="pre">notebook_custom_logging.ipynb</span></code>), which is faster to set up and requires no recompilation of binary_c, but is somewhat more limited in its functionality. For our current purposes, it
+works perfectly well.</p>
<p>After configuring what will be printed, we need to make a function to parse the output. This can be done by setting the parse_function parameter in the population object (see also notebook <code class="docutils literal notranslate"><span class="pre">notebook_individual_systems.ipynb</span></code>).</p>
<p>In the code below we will set up both the custom logging and a parse function to handle that output.</p>
<div class="nbinput nblast docutils container">
@@ -667,11 +582,11 @@ it works perfectly well.</p>
</pre></div>
</div>
</div>
-</div>
-<div class="section" id="Evolving-the-grid">
-<h2>Evolving the grid<a class="headerlink" href="#Evolving-the-grid" title="Permalink to this headline">¶</a></h2>
+</section>
+<section id="Evolving-the-grid">
+<h2>Evolving the grid<a class="headerlink" href="#Evolving-the-grid" title="Permalink to this headline">ïƒ</a></h2>
<p>Now that we configured all the main parts of the population object, we can actually run the population! Doing this is straightforward: <code class="docutils literal notranslate"><span class="pre">population.evolve()</span></code></p>
-<p>This will start up the processing of all the systems. We can control how many cores are used by settings <code class="docutils literal notranslate"><span class="pre">amt_cores</span></code>. By setting the <code class="docutils literal notranslate"><span class="pre">verbosity</span></code> of the population object to a higher value we can get a lot of verbose information about the run, but for now we will set it to 0.</p>
+<p>This will start up the processing of all the systems. We can control how many cores are used by settings <code class="docutils literal notranslate"><span class="pre">num_cores</span></code>. By setting the <code class="docutils literal notranslate"><span class="pre">verbosity</span></code> of the population object to a higher value we can get a lot of verbose information about the run, but for now we will set it to 0.</p>
<p>There are many grid_options that can lead to different behaviour of the evolution of the grid. Please do have a look at those: <a class="reference external" href="https://ri0005.pages.surrey.ac.uk/binary_c-python/grid_options_descriptions.html">grid options docs</a>, and try</p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[9]:
@@ -683,7 +598,7 @@ it works perfectly well.</p>
<span class="c1"># verbose output is not required</span>
<span class="n">verbosity</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span>
<span class="c1"># set number of threads (i.e. number of CPU cores we use)</span>
- <span class="n">amt_cores</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span>
+ <span class="n">num_cores</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span>
<span class="p">)</span>
<span class="c1"># Evolve the population - this is the slow, number-crunching step</span>
@@ -710,7 +625,7 @@ Population-e6c082aabe0849a0811761a06e50476b finished! The total probability was:
There were no errors found in this run.
</pre></div></div>
</div>
-<p>After the run is complete, some technical report on the run is returned. I stored that in <code class="docutils literal notranslate"><span class="pre">analytics</span></code>. As we can see below, this dictionary is like a status report of the evolution. Useful for e.g. debugging.</p>
+<p>After the run is complete, some technical report on the run is returned. I stored that in <code class="docutils literal notranslate"><span class="pre">analytics</span></code>. As we can see below, this dictionary is like a status report of the evolution. Useful for e.g. debugging.</p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[10]:
</pre></div>
@@ -780,9 +695,9 @@ There were no errors found in this run.
</div>
</div>
<p>Does this look like a reasonable stellar luminosity function to you? The implication is that the most likely stellar luminosity is 105.8 L☉! Clearly, this is not very realistic… let’s see what went wrong.</p>
-</div>
-<div class="section" id="ZAMS-Luminosity-distribution-with-the-initial-mass-function">
-<h2>ZAMS Luminosity distribution with the initial mass function<a class="headerlink" href="#ZAMS-Luminosity-distribution-with-the-initial-mass-function" title="Permalink to this headline">¶</a></h2>
+</section>
+<section id="ZAMS-Luminosity-distribution-with-the-initial-mass-function">
+<h2>ZAMS Luminosity distribution with the initial mass function<a class="headerlink" href="#ZAMS-Luminosity-distribution-with-the-initial-mass-function" title="Permalink to this headline">ïƒ</a></h2>
<p>In the previous example, all the stars in our grid had an equal weighting. This is very unlikely to be true in reality: indeed, we know that low mass stars are far more likely than high mass stars. So we now include an initial mass function as a three-part power law based on Kroupa (2001). Kroupa’s distribution is a three-part power law: we have a function that does this for us (it’s very common to use power laws in astrophysics).</p>
<div class="nbinput nblast docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[12]:
@@ -869,9 +784,9 @@ There were no errors found in this run.
<p>This distribution is peaked at low luminosity, as one expects from observations, but the resolution is clearly not great because it’s not smooth - it’s spiky!</p>
<p>If you noticed above, the total probability of the grid was about 0.2. Given that the total probability of a probability distribution function should be 1.0, this shows that our sampling is (very) poor.</p>
<p>We could simply increase the resolution to compensate, but this is very CPU intensive and a complete waste of time and resources. Instead, let’s try sampling the masses of the stars in a smarter way.</p>
-</div>
-<div class="section" id="A-better-sampled-grid">
-<h2>A better-sampled grid<a class="headerlink" href="#A-better-sampled-grid" title="Permalink to this headline">¶</a></h2>
+</section>
+<section id="A-better-sampled-grid">
+<h2>A better-sampled grid<a class="headerlink" href="#A-better-sampled-grid" title="Permalink to this headline">ïƒ</a></h2>
<p>The IMF has many more low-mass stars than high-mass stars. So, instead of sampling M1 linearly, we can sample it in log space.</p>
<p>To do this we first rename the mass grid variable so that it is clear we are working in (natural) logarithmic phase space.</p>
<div class="nbinput nblast docutils container">
@@ -972,69 +887,44 @@ There were no errors found in this run.
<p>Remember you can play with the binwidth too. If you want a very accurate distribution you need a narrow binwidth, but then you’ll also need high resolution (lots of stars) so lots of CPU time, hence cost, CO2, etc.</p>
<p>Things to try: * Change the resolution to make the distributions smoother: what about error bars, how would you do that? * Different initial distributions: the Kroupa distribution isn’t the only one out there * Change the metallicity and mass ranges * What about a non-constant star formation rate? This is more of a challenge! * What about evolved stars? Here we consider only the <em>zero-age</em> main sequnece. What about other main-sequence stars? What about stars in later phases of stellar
evolution? * Binary stars! (see notebook_luminosity_function_binaries.ipynb)</p>
-</div>
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+</section>
+</section>
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<div role="contentinfo">
- <p>
-
- © Copyright 2021, David Hendriks, Robert Izzard
-
- </p>
+ <p>© Copyright 2021, David Hendriks, Robert Izzard.</p>
</div>
-
-
-
- Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a
-
- <a href="https://github.com/rtfd/sphinx_rtd_theme">theme</a>
-
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+ Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
+ <a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
provided by <a href="https://readthedocs.org">Read the Docs</a>.
+
<br><br>
-Generated on binarycpython git branch: master git revision 0886cd4f1d7f43222aac21d6ed91e917b67b20fc url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/tree/master">git url</a>.
+Generated on binarycpython git branch: auto_resolution git revision be7bd630af892a785312affc34d87c57eb337fd3 url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/tree/auto_resolution">git url</a>.
<br><br>
-Using binary_c with bit branch newmaster: git revision: "6185:20210910:1621c23a5" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/newmaster">git url</a>.
+Using binary_c with bit branch master: git revision: "6209:20211006:c4a4c332e" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/master">git url</a>.
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diff --git a/docs/build/html/notebook_luminosity_function_single.ipynb b/docs/build/html/notebook_luminosity_function_single.ipynb
index cdae316f90802fe46611ea17732506c0410aef55..09af8acc59f26e909901c0649e02a0d0864b789a 100644
--- a/docs/build/html/notebook_luminosity_function_single.ipynb
+++ b/docs/build/html/notebook_luminosity_function_single.ipynb
@@ -297,7 +297,7 @@
"## Evolving the grid\n",
"Now that we configured all the main parts of the population object, we can actually run the population! Doing this is straightforward: `population.evolve()`\n",
"\n",
- "This will start up the processing of all the systems. We can control how many cores are used by settings `amt_cores`. By setting the `verbosity` of the population object to a higher value we can get a lot of verbose information about the run, but for now we will set it to 0.\n",
+ "This will start up the processing of all the systems. We can control how many cores are used by settings `num_cores`. By setting the `verbosity` of the population object to a higher value we can get a lot of verbose information about the run, but for now we will set it to 0.\n",
"\n",
"There are many grid_options that can lead to different behaviour of the evolution of the grid. Please do have a look at those: [grid options docs](https://ri0005.pages.surrey.ac.uk/binary_c-python/grid_options_descriptions.html), and try "
]
@@ -332,7 +332,7 @@
" # verbose output is not required \n",
" verbosity=0,\n",
" # set number of threads (i.e. number of CPU cores we use)\n",
- " amt_cores=2,\n",
+ " num_cores=2,\n",
" )\n",
"\n",
"# Evolve the population - this is the slow, number-crunching step\n",
@@ -703,7 +703,7 @@
],
"metadata": {
"kernelspec": {
- "display_name": "Python 3",
+ "display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
@@ -717,7 +717,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
- "version": "3.6.4"
+ "version": "3.9.5"
}
},
"nbformat": 4,
diff --git a/docs/build/html/notebook_population.html b/docs/build/html/notebook_population.html
index 055662c6446d2b0498a9accd3e75ca6953b46f23..ffe8b06c8ec59f5356bb996dad0d2ac13e96c092 100644
--- a/docs/build/html/notebook_population.html
+++ b/docs/build/html/notebook_population.html
@@ -1,71 +1,37 @@
-
-
<!DOCTYPE html>
<html class="writer-html5" lang="en" >
<head>
- <meta charset="utf-8">
-
- <meta name="viewport" content="width=device-width, initial-scale=1.0">
-
- <title>Tutorial: Running populations with binary_c-python — binary_c-python documentation</title>
-
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-
- <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
- <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+ <meta charset="utf-8" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
-
-
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-
-
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+ <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+ <title>Tutorial: Running populations with binary_c-python — binary_c-python documentation</title>
+ <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+ <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
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+ <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
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- <script src="_static/language_data.js"></script>
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- <script async="async" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.7/latest.js?config=TeX-AMS-MML_HTMLorMML"></script>
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+ <script async="async" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
+ <script>window.MathJax = {"tex": {"inlineMath": [["$", "$"], ["\\(", "\\)"]], "processEscapes": true}, "options": {"ignoreHtmlClass": "tex2jax_ignore|mathjax_ignore|document", "processHtmlClass": "tex2jax_process|mathjax_process|math|output_area"}}</script>
+ <script src="_static/js/theme.js"></script>
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+<body class="wy-body-for-nav">
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-
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+ <a href="index.html" class="icon icon-home"> binary_c-python
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<form id="rtd-search-form" class="wy-form" action="search.html" method="get">
<input type="text" name="q" placeholder="Search docs" />
@@ -73,19 +39,8 @@
<input type="hidden" name="area" value="default" />
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-
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- <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
-
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- <p class="caption"><span class="caption-text">Contents:</span></p>
+ </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
+ <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="readme_link.html">Python module for binary_c</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules.html">Binarycpython code</a></li>
@@ -104,7 +59,7 @@
<li class="toctree-l2"><a class="reference internal" href="notebook_extra_features.html">Tutorial: Extra features and functionality of binary_c-python</a></li>
<li class="toctree-l2"><a class="reference internal" href="notebook_api_functionality.html">Tutorial: Using the API functionality of binary_c-python</a></li>
<li class="toctree-l2"><a class="reference internal" href="notebook_luminosity_function_single.html">Example use case: Zero-age stellar luminosity function</a></li>
-<li class="toctree-l2"><a class="reference internal" href="notebook_luminosity_function_binaries.html">Zero-age stellar luminosity function in binaries</a></li>
+<li class="toctree-l2"><a class="reference internal" href="notebook_luminosity_function_binaries.html">Example use case: Zero-age stellar luminosity function in binaries</a></li>
<li class="toctree-l2"><a class="reference internal" href="notebook_HRD.html">Example use case: Hertzsprung-Russell diagrams</a></li>
<li class="toctree-l2"><a class="reference internal" href="notebook_common_envelope_evolution.html">Example use case: Common-envelope evolution</a></li>
</ul>
@@ -115,71 +70,31 @@
<li class="toctree-l1"><a class="reference external" href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/issues/new">Submit an issue</a></li>
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-
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<style>
/* CSS for nbsphinx extension */
@@ -450,8 +365,8 @@ div.rendered_html tbody tr:hover {
text-align: unset;
}
</style>
-<div class="section" id="Tutorial:-Running-populations-with-binary_c-python">
-<h1>Tutorial: Running populations with binary_c-python<a class="headerlink" href="#Tutorial:-Running-populations-with-binary_c-python" title="Permalink to this headline">¶</a></h1>
+<section id="Tutorial:-Running-populations-with-binary_c-python">
+<h1>Tutorial: Running populations with binary_c-python<a class="headerlink" href="#Tutorial:-Running-populations-with-binary_c-python" title="Permalink to this headline">ïƒ</a></h1>
<p>This notebook will show you how to evolve a population of stars</p>
<p>Much of the code in the binarycpython package is written to evolve a population of stars through the Population object, rather than running a single system. Let’s go through the functionality of this object step by step and set up some example populations.</p>
<p>At the bottom of this notebook there are some complete example scripts</p>
@@ -471,11 +386,11 @@ div.rendered_html tbody tr:hover {
</pre></div>
</div>
</div>
-<div class="section" id="Setting-up-the-Population-object">
-<h2>Setting up the Population object<a class="headerlink" href="#Setting-up-the-Population-object" title="Permalink to this headline">¶</a></h2>
+<section id="Setting-up-the-Population-object">
+<h2>Setting up the Population object<a class="headerlink" href="#Setting-up-the-Population-object" title="Permalink to this headline">ïƒ</a></h2>
<p>To set up and configure the population object we need to make an object instance of the <code class="docutils literal notranslate"><span class="pre">Population</span></code> object, and add configuration via the <code class="docutils literal notranslate"><span class="pre">.set()</span></code> function.</p>
-<p>There are three categories of options that the Population object can set: - BSE options: these options will be used for the binary_c calls, and are recognized by comparing the arguments to a known list of available arguments of binary_c. To see which options are available, see section <code class="docutils literal notranslate"><span class="pre">`binary_c</span> <span class="pre">parameters</span></code> in the documentation <<a class="reference external" href="https://ri0005.pages.surrey.ac.uk/binary_c-python/binary_c_parameters.html">https://ri0005.pages.surrey.ac.uk/binary_c-python/binary_c_parameters.html</a>>`__. You can access these through <code class="docutils literal notranslate"><span class="pre">population.bse_options['<bse</span> <span class="pre">option</span> <span class="pre">name>']</span></code> after
-you have set them.</p>
+<p>There are three categories of options that the Population object can set: - BSE options: these options will be used for the binary_c calls, and are recognized by comparing the arguments to a known list of available arguments of binary_c. To see which options are available, see section <code class="docutils literal notranslate"><span class="pre">`binary_c</span> <span class="pre">parameters</span></code> in the documentation <<a class="reference external" href="https://ri0005.pages.surrey.ac.uk/binary_c-python/binary_c_parameters.html">https://ri0005.pages.surrey.ac.uk/binary_c-python/binary_c_parameters.html</a>>`__. You can access these through <code class="docutils literal notranslate"><span class="pre">population.bse_options['<bse</span> <span class="pre">option</span> <span class="pre">name>']</span></code> after you
+have set them.</p>
<ul class="simple">
<li><p>Grid options: these options will be used to configure the behaviour of the Population object. To see which options are available, see section <code class="docutils literal notranslate"><span class="pre">`Population</span> <span class="pre">grid</span> <span class="pre">code</span> <span class="pre">options</span></code> in the documentation <<a class="reference external" href="https://ri0005.pages.surrey.ac.uk/binary_c-python/grid_options_descriptions.html">https://ri0005.pages.surrey.ac.uk/binary_c-python/grid_options_descriptions.html</a>>`__. They can be accessed via <code class="docutils literal notranslate"><span class="pre">population.grid_options['<grid</span> <span class="pre">option</span> <span class="pre">name>']</span></code> after you have set them.</p></li>
<li><p>Custom options: these options are not recognized as either of the above, so they will be stored in the custom_options, and can be accessed via <code class="docutils literal notranslate"><span class="pre">population.custom_options['<custom</span> <span class="pre">option</span> <span class="pre">name>']</span></code></p></li>
@@ -504,7 +419,7 @@ you have set them.</p>
<span class="c1"># grid_options</span>
- <span class="n">amt_cores</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span>
+ <span class="n">num_cores</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span>
<span class="n">tmp_dir</span><span class="o">=</span><span class="n">TMP_DIR</span><span class="p">,</span>
<span class="c1"># Custom options # TODO: need to be set in grid_options probably</span>
@@ -530,7 +445,7 @@ adding: M_1=10 to BSE_options
adding: orbital_period=45000000080 to BSE_options
adding: max_evolution_time=15000 to BSE_options
adding: eccentricity=0.02 to BSE_options
-adding: amt_cores=2 to grid_options
+adding: num_cores=2 to grid_options
adding: tmp_dir=/tmp/binary_c_python/notebooks/notebook_population to grid_options
<<<< Warning: Key does not match previously known parameter: adding: data_dir=/tmp/binary_c_python/notebooks/notebook_population/example_python_population_result to custom_options >>>>
<<<< Warning: Key does not match previously known parameter: adding: base_filename=example_pop.dat to custom_options >>>>
@@ -540,8 +455,8 @@ example_pop.dat
</pre></div></div>
</div>
<p>After configuring the population, but before running the actual population, its usually a good idea to export the full configuration (including version info of binary_c and all the parameters) to a file. To do this we use <code class="docutils literal notranslate"><span class="pre">example_pop.export_all_info()</span></code>.</p>
-<p>On default this exports everything, each of the sections can be disabled: - population settings (bse_options, grid_options, custom_options), turn off with include_population settings=False - binary_c_defaults (all the commandline arguments that binary c accepts, and their defaults). turn off with include_binary_c_defaults=False - include_binary_c_version_info (all the compilation info, and information about the compiled parameters), turn off with
-include_binary_c_version_info=False - include_binary_c_help_all (all the help information for all the binary_c parameters), turn off with include_binary_c_help_all=Fase</p>
+<p>On default this exports everything, each of the sections can be disabled: - population settings (bse_options, grid_options, custom_options), turn off with include_population settings=False - binary_c_defaults (all the commandline arguments that binary c accepts, and their defaults). turn off with include_binary_c_defaults=False - include_binary_c_version_info (all the compilation info, and information about the compiled parameters), turn off with include_binary_c_version_info=False -
+include_binary_c_help_all (all the help information for all the binary_c parameters), turn off with include_binary_c_help_all=Fase</p>
<p>On default it will write this to the custom_options[‘data_dir’], but that can be overriden by setting use_datadir=False and providing an outfile=<></p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[3]:
@@ -569,12 +484,12 @@ Writing settings to /tmp/binary_c_python/notebooks/notebook_population/example_p
'/tmp/binary_c_python/notebooks/notebook_population/example_python_population_result/example_pop_settings.json'
</pre></div></div>
</div>
-</div>
-<div class="section" id="Adding-grid-variables">
-<h2>Adding grid variables<a class="headerlink" href="#Adding-grid-variables" title="Permalink to this headline">¶</a></h2>
+</section>
+<section id="Adding-grid-variables">
+<h2>Adding grid variables<a class="headerlink" href="#Adding-grid-variables" title="Permalink to this headline">ïƒ</a></h2>
<p>The main purpose of the Population object is to handle the population synthesis side of running a set of stars. The main method to do this with binarycpython, as is the case with Perl binarygrid, is to use grid variables. These are loops over a predefined range of values, where a probability will be assigned to the systems based on the chosen probability distributions.</p>
-<p>Usually we use either 1 mass grid variable, or a trio of mass, mass ratio and period (See below for full examples of all of these). We can, however, also add grid sampling for e.g. eccentricity, metallicity or other parameters.</p>
-<p>In some cases it could be easier to set up a for loop that sets that parameter and calls the evolve function several times, e.g. when you want to vary a prescription (usually a discrete, unweighted parameter)</p>
+<p>Usually we use either 1 mass grid variable, or a trio of mass, mass ratio and period (See below for full examples of all of these). We can, however, also add grid sampling for e.g. eccentricity, metallicity or other parameters.</p>
+<p>In some cases it could be easier to set up a for loop that sets that parameter and calls the evolve function several times, e.g. when you want to vary a prescription (usually a discrete, unweighted parameter)</p>
<p>A notable special type of grid variable is that of the Moe & di Stefano 2017 dataset (see further down in the notebook).</p>
<p>To add a grid variable to the population object we use <code class="docutils literal notranslate"><span class="pre">example_pop.add_grid_variable</span></code> (see next cell)</p>
<div class="nbinput docutils container">
@@ -626,7 +541,7 @@ add_grid_variable(name:str, longname:str, valuerange:Union[list, str], resolutio
Examples:
range = [math.log(m_min), math.log(m_max)]
resolution:
- Resolution of the sampled range (amount of samples).
+ Resolution of the sampled range (number of samples).
TODO: check if this is used anywhere
Examples:
@@ -758,9 +673,9 @@ Added grid variable: {
}
</pre></div></div>
</div>
-</div>
-<div class="section" id="Setting-logging-and-handling-the-output">
-<h2>Setting logging and handling the output<a class="headerlink" href="#Setting-logging-and-handling-the-output" title="Permalink to this headline">¶</a></h2>
+</section>
+<section id="Setting-logging-and-handling-the-output">
+<h2>Setting logging and handling the output<a class="headerlink" href="#Setting-logging-and-handling-the-output" title="Permalink to this headline">ïƒ</a></h2>
<p>On default, binary_c will not output anything (except for ‘SINGLE STAR LIFETIME’). It is up to us to determine what will be printed. We can either do that by hardcoding the print statements into <code class="docutils literal notranslate"><span class="pre">binary_c</span></code> (see documentation binary_c). Or, we can use the custom logging functionality of binarycpython (see notebook <code class="docutils literal notranslate"><span class="pre">notebook_custom_logging.ipynb</span></code>), which is faster to set up and requires no recompilation of binary_c, but is somewhat more limited in its functionality.</p>
<p>After configuring what will be printed, we need to make a function to parse the output. This can be done by setting the parse_function parameter in the population object (see also notebook <code class="docutils literal notranslate"><span class="pre">notebook_individual_systems.ipynb</span></code>).</p>
<p>In the code below we will set up both the custom logging, and a parse function to handle that output</p>
@@ -855,7 +770,7 @@ if(stardata->star[0].stellar_type >= 13)
<span class="nb">print</span><span class="p">(</span><span class="n">line</span><span class="p">)</span>
<span class="k">if</span> <span class="ow">not</span> <span class="nb">len</span><span class="p">(</span><span class="n">parameters</span><span class="p">)</span> <span class="o">==</span> <span class="nb">len</span><span class="p">(</span><span class="n">values</span><span class="p">):</span>
- <span class="nb">print</span><span class="p">(</span><span class="s2">"Amount of column names isnt equal to amount of columns"</span><span class="p">)</span>
+ <span class="nb">print</span><span class="p">(</span><span class="s2">"Number of column names isnt equal to number of columns"</span><span class="p">)</span>
<span class="k">raise</span> <span class="ne">ValueError</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">outfilename</span><span class="p">):</span>
@@ -880,11 +795,11 @@ if(stardata->star[0].stellar_type >= 13)
adding: parse_function=<function parse_function at 0x7f531bc3b6a8> to grid_options
</pre></div></div>
</div>
-</div>
-<div class="section" id="Evolving-the-grid">
-<h2>Evolving the grid<a class="headerlink" href="#Evolving-the-grid" title="Permalink to this headline">¶</a></h2>
+</section>
+<section id="Evolving-the-grid">
+<h2>Evolving the grid<a class="headerlink" href="#Evolving-the-grid" title="Permalink to this headline">ïƒ</a></h2>
<p>Now that we configured all the main parts of the population object, we can actually run the population! Doing this is straightforward: <code class="docutils literal notranslate"><span class="pre">example_pop.evolve()</span></code></p>
-<p>This will start up the processing of all the systems. We can control how many cores are used by settings <code class="docutils literal notranslate"><span class="pre">amt_cores</span></code>. By setting the <code class="docutils literal notranslate"><span class="pre">verbosity</span></code> of the population object to a higher value we can get a lot of verbose information about the run, but for now we will set it to 0.</p>
+<p>This will start up the processing of all the systems. We can control how many cores are used by settings <code class="docutils literal notranslate"><span class="pre">num_cores</span></code>. By setting the <code class="docutils literal notranslate"><span class="pre">verbosity</span></code> of the population object to a higher value we can get a lot of verbose information about the run, but for now we will set it to 0.</p>
<p>There are many grid_options that can lead to different behaviour of the evolution of the grid. Please do have a look at those: <a class="reference external" href="https://ri0005.pages.surrey.ac.uk/binary_c-python/grid_options_descriptions.html">grid options docs</a>, and try</p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[9]:
@@ -931,7 +846,7 @@ Population-f28b5f98d7ef40dcb17fc2481a6d3ced finished! The total probability was:
There were no errors found in this run.
</pre></div></div>
</div>
-<p>After the run is complete, some technical report on the run is returned. I stored that in <code class="docutils literal notranslate"><span class="pre">analytics</span></code>. As we can see below, this dictionary is like a status report of the evolution. Useful for e.g. debugging.</p>
+<p>After the run is complete, some technical report on the run is returned. I stored that in <code class="docutils literal notranslate"><span class="pre">analytics</span></code>. As we can see below, this dictionary is like a status report of the evolution. Useful for e.g. debugging.</p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[10]:
</pre></div>
@@ -949,9 +864,9 @@ There were no errors found in this run.
{'population_name': 'f28b5f98d7ef40dcb17fc2481a6d3ced', 'evolution_type': 'grid', 'failed_count': 0, 'failed_prob': 0, 'failed_systems_error_codes': [], 'errors_exceeded': False, 'errors_found': False, 'total_probability': 0.04440288843805411, 'total_count': 20, 'start_timestamp': 1629459533.935186, 'end_timestamp': 1629459536.7203987, 'total_mass_run': 684.2544031669779, 'total_probability_weighted_mass_run': 0.28134439269236855, 'zero_prob_stars_skipped': 0}
</pre></div></div>
</div>
-</div>
-<div class="section" id="Noteworthy-functionality">
-<h2>Noteworthy functionality<a class="headerlink" href="#Noteworthy-functionality" title="Permalink to this headline">¶</a></h2>
+</section>
+<section id="Noteworthy-functionality">
+<h2>Noteworthy functionality<a class="headerlink" href="#Noteworthy-functionality" title="Permalink to this headline">ïƒ</a></h2>
<p>Some extra features that are available from via the population object are: - write_binary_c_calls_to_file: Function to write the calls that would be passed to binary_c to a file</p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[11]:
@@ -1030,9 +945,9 @@ binary_c M_1 3.4309362899259503 eccentricity 0.02 max_evolution_time 15000 orbit
binary_c M_1 4.257608426597089 eccentricity 0.02 max_evolution_time 15000 orbital_period 45000000080 phasevol 0.21587440567681548 probability 0.004698855121516278
</pre></div></div>
</div>
-</div>
-<div class="section" id="Full-examples-of-population-scripts">
-<h2>Full examples of population scripts<a class="headerlink" href="#Full-examples-of-population-scripts" title="Permalink to this headline">¶</a></h2>
+</section>
+<section id="Full-examples-of-population-scripts">
+<h2>Full examples of population scripts<a class="headerlink" href="#Full-examples-of-population-scripts" title="Permalink to this headline">ïƒ</a></h2>
<p>Below is a full setup for a population of single stars</p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[13]:
@@ -1071,7 +986,7 @@ binary_c M_1 4.257608426597089 eccentricity 0.02 max_evolution_time 15000 orbita
<span class="n">values</span> <span class="o">=</span> <span class="n">el</span><span class="o">.</span><span class="n">split</span><span class="p">()[</span><span class="mi">1</span><span class="p">:]</span>
<span class="k">if</span> <span class="ow">not</span> <span class="nb">len</span><span class="p">(</span><span class="n">parameters</span><span class="p">)</span> <span class="o">==</span> <span class="nb">len</span><span class="p">(</span><span class="n">values</span><span class="p">):</span>
- <span class="nb">print</span><span class="p">(</span><span class="s2">"Amount of column names isnt equal to amount of columns"</span><span class="p">)</span>
+ <span class="nb">print</span><span class="p">(</span><span class="s2">"Number of column names isnt equal to number of columns"</span><span class="p">)</span>
<span class="k">raise</span> <span class="ne">ValueError</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">outfilename</span><span class="p">):</span>
@@ -1098,7 +1013,7 @@ binary_c M_1 4.257608426597089 eccentricity 0.02 max_evolution_time 15000 orbita
<span class="n">eccentricity</span><span class="o">=</span><span class="mf">0.02</span><span class="p">,</span> <span class="c1"># bse_options</span>
<span class="c1"># grid_options</span>
- <span class="n">amt_cores</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span>
+ <span class="n">num_cores</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span>
<span class="n">tmp_dir</span><span class="o">=</span><span class="n">TMP_DIR</span><span class="p">,</span>
<span class="c1"># Custom options: the data directory and the output filename</span>
@@ -1250,7 +1165,7 @@ time mass zams_mass probability radius stellar_type
<span class="n">values</span> <span class="o">=</span> <span class="n">el</span><span class="o">.</span><span class="n">split</span><span class="p">()[</span><span class="mi">1</span><span class="p">:]</span>
<span class="k">if</span> <span class="ow">not</span> <span class="nb">len</span><span class="p">(</span><span class="n">parameters</span><span class="p">)</span> <span class="o">==</span> <span class="nb">len</span><span class="p">(</span><span class="n">values</span><span class="p">):</span>
- <span class="nb">print</span><span class="p">(</span><span class="s2">"Amount of column names isnt equal to amount of columns"</span><span class="p">)</span>
+ <span class="nb">print</span><span class="p">(</span><span class="s2">"Number of column names isnt equal to number of columns"</span><span class="p">)</span>
<span class="k">raise</span> <span class="ne">ValueError</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">outfilename</span><span class="p">):</span>
@@ -1277,7 +1192,7 @@ time mass zams_mass probability radius stellar_type
<span class="n">eccentricity</span><span class="o">=</span><span class="mf">0.02</span><span class="p">,</span> <span class="c1"># bse_options</span>
<span class="c1"># grid_options</span>
- <span class="n">amt_cores</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span> <span class="c1"># grid_options</span>
+ <span class="n">num_cores</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span> <span class="c1"># grid_options</span>
<span class="n">tmp_dir</span><span class="o">=</span><span class="n">TMP_DIR</span><span class="p">,</span>
<span class="c1"># Custom options: the data directory and the output filename</span>
@@ -1434,69 +1349,44 @@ time mass_1 zams_mass_1 mass_2 zams_mass_2 stellar_type_1 prev_stellar_type_1 st
</pre></div></div>
</div>
-</div>
-</div>
+</section>
+</section>
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- © Copyright 2021, David Hendriks, Robert Izzard
-
- </p>
+ <p>© Copyright 2021, David Hendriks, Robert Izzard.</p>
</div>
-
-
-
- Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a
-
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+
<br><br>
-Generated on binarycpython git branch: master git revision 0886cd4f1d7f43222aac21d6ed91e917b67b20fc url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/tree/master">git url</a>.
+Generated on binarycpython git branch: auto_resolution git revision be7bd630af892a785312affc34d87c57eb337fd3 url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/tree/auto_resolution">git url</a>.
<br><br>
-Using binary_c with bit branch newmaster: git revision: "6185:20210910:1621c23a5" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/newmaster">git url</a>.
+Using binary_c with bit branch master: git revision: "6209:20211006:c4a4c332e" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/master">git url</a>.
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diff --git a/docs/build/html/notebook_population.ipynb b/docs/build/html/notebook_population.ipynb
index a24638c0bd3a15a57bbf611fccb71b2100c75945..1ec2f94d3b03db0bccabe6ea2d2c100946add611 100644
--- a/docs/build/html/notebook_population.ipynb
+++ b/docs/build/html/notebook_population.ipynb
@@ -62,7 +62,7 @@
"adding: orbital_period=45000000080 to BSE_options\n",
"adding: max_evolution_time=15000 to BSE_options\n",
"adding: eccentricity=0.02 to BSE_options\n",
- "adding: amt_cores=2 to grid_options\n",
+ "adding: num_cores=2 to grid_options\n",
"adding: tmp_dir=/tmp/binary_c_python/notebooks/notebook_population to grid_options\n",
"<<<< Warning: Key does not match previously known parameter: adding: data_dir=/tmp/binary_c_python/notebooks/notebook_population/example_python_population_result to custom_options >>>>\n",
"<<<< Warning: Key does not match previously known parameter: adding: base_filename=example_pop.dat to custom_options >>>>\n",
@@ -92,7 +92,7 @@
"\n",
"\n",
" # grid_options\n",
- " amt_cores=2,\n",
+ " num_cores=2,\n",
" tmp_dir=TMP_DIR,\n",
" \n",
" # Custom options # TODO: need to be set in grid_options probably\n",
@@ -219,7 +219,7 @@
" Examples:\n",
" range = [math.log(m_min), math.log(m_max)]\n",
" resolution:\n",
- " Resolution of the sampled range (amount of samples).\n",
+ " Resolution of the sampled range (number of samples).\n",
" TODO: check if this is used anywhere\n",
" \n",
" Examples:\n",
@@ -496,7 +496,7 @@
" print(line)\n",
" \n",
" if not len(parameters) == len(values):\n",
- " print(\"Amount of column names isnt equal to amount of columns\")\n",
+ " print(\"Number of column names isnt equal to number of columns\")\n",
" raise ValueError\n",
"\n",
" if not os.path.exists(outfilename):\n",
@@ -520,7 +520,7 @@
"## Evolving the grid\n",
"Now that we configured all the main parts of the population object, we can actually run the population! Doing this is straightforward: `example_pop.evolve()`\n",
"\n",
- "This will start up the processing of all the systems. We can control how many cores are used by settings `amt_cores`. By setting the `verbosity` of the population object to a higher value we can get a lot of verbose information about the run, but for now we will set it to 0.\n",
+ "This will start up the processing of all the systems. We can control how many cores are used by settings `num_cores`. By setting the `verbosity` of the population object to a higher value we can get a lot of verbose information about the run, but for now we will set it to 0.\n",
"\n",
"There are many grid_options that can lead to different behaviour of the evolution of the grid. Please do have a look at those: [grid options docs](https://ri0005.pages.surrey.ac.uk/binary_c-python/grid_options_descriptions.html), and try "
]
@@ -770,7 +770,7 @@
" values = el.split()[1:]\n",
"\n",
" if not len(parameters) == len(values):\n",
- " print(\"Amount of column names isnt equal to amount of columns\")\n",
+ " print(\"Number of column names isnt equal to number of columns\")\n",
" raise ValueError\n",
"\n",
" if not os.path.exists(outfilename):\n",
@@ -797,7 +797,7 @@
" eccentricity=0.02, # bse_options\n",
" \n",
" # grid_options\n",
- " amt_cores=2,\n",
+ " num_cores=2,\n",
" tmp_dir=TMP_DIR,\n",
"\n",
" # Custom options: the data directory and the output filename\n",
@@ -963,7 +963,7 @@
" values = el.split()[1:]\n",
"\n",
" if not len(parameters) == len(values):\n",
- " print(\"Amount of column names isnt equal to amount of columns\")\n",
+ " print(\"Number of column names isnt equal to number of columns\")\n",
" raise ValueError\n",
"\n",
" if not os.path.exists(outfilename):\n",
@@ -990,7 +990,7 @@
" eccentricity=0.02, # bse_options\n",
" \n",
" # grid_options\n",
- " amt_cores=2, # grid_options\n",
+ " num_cores=2, # grid_options\n",
" tmp_dir=TMP_DIR,\n",
"\n",
" # Custom options: the data directory and the output filename\n",
diff --git a/docs/build/html/objects.inv b/docs/build/html/objects.inv
index 8708d9045129d5de91f91d108c5287531956a6c4..35c080a007bb1f137e363cdaf2d854bbac2bd709 100644
Binary files a/docs/build/html/objects.inv and b/docs/build/html/objects.inv differ
diff --git a/docs/build/html/plot_functions.html b/docs/build/html/plot_functions.html
index 77f66e48c2062fb51262e6b7e28a04e939d7d275..b06bf97c1970988c9e098f02f7bf418859b4d64c 100644
--- a/docs/build/html/plot_functions.html
+++ b/docs/build/html/plot_functions.html
@@ -1,71 +1,35 @@
-
-
<!DOCTYPE html>
<html class="writer-html5" lang="en" >
<head>
- <meta charset="utf-8">
-
- <meta name="viewport" content="width=device-width, initial-scale=1.0">
-
- <title>plot_functions module — binary_c-python documentation</title>
-
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- <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
- <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+ <meta charset="utf-8" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
-
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-
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+ <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+ <title>plot_functions module — binary_c-python documentation</title>
+ <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+ <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
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-
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+ <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
<script src="_static/jquery.js"></script>
<script src="_static/underscore.js"></script>
<script src="_static/doctools.js"></script>
- <script src="_static/language_data.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
- <script async="async" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.7/latest.js?config=TeX-AMS-MML_HTMLorMML"></script>
- <script type="text/x-mathjax-config">MathJax.Hub.Config({"tex2jax": {"inlineMath": [["$", "$"], ["\\(", "\\)"]], "processEscapes": true, "ignoreClass": "document", "processClass": "math|output_area"}})</script>
-
- <script type="text/javascript" src="_static/js/theme.js"></script>
-
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+ <script src="_static/js/theme.js"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="next" title="run_system_wrapper module" href="run_system_wrapper.html" />
<link rel="prev" title="hpc_functions module" href="hpc_functions.html" />
</head>
-<body class="wy-body-for-nav">
-
-
+<body class="wy-body-for-nav">
<div class="wy-grid-for-nav">
-
<nav data-toggle="wy-nav-shift" class="wy-nav-side">
<div class="wy-side-scroll">
<div class="wy-side-nav-search" >
-
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- <a href="index.html" class="icon icon-home" alt="Documentation Home"> binary_c-python
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+ <a href="index.html" class="icon icon-home"> binary_c-python
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<div role="search">
<form id="rtd-search-form" class="wy-form" action="search.html" method="get">
<input type="text" name="q" placeholder="Search docs" />
@@ -73,19 +37,8 @@
<input type="hidden" name="area" value="default" />
</form>
</div>
-
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- </div>
-
-
- <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
-
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+ </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
+ <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
<ul class="current">
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<li class="toctree-l1 current"><a class="reference internal" href="modules.html">Binarycpython code</a><ul class="current">
@@ -109,71 +62,31 @@
<li class="toctree-l1"><a class="reference external" href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/issues/new">Submit an issue</a></li>
</ul>
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-<div role="navigation" aria-label="breadcrumbs navigation">
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+ <div role="navigation" aria-label="Page navigation">
<ul class="wy-breadcrumbs">
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<li><a href="index.html" class="icon icon-home"></a> »</li>
-
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-
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-
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<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
-
+
<style>
/* CSS overrides for sphinx_rtd_theme */
@@ -198,8 +111,8 @@
text-align: unset;
}
</style>
-<div class="section" id="module-binarycpython.utils.plot_functions">
-<span id="plot-functions-module"></span><h1>plot_functions module<a class="headerlink" href="#module-binarycpython.utils.plot_functions" title="Permalink to this headline">¶</a></h1>
+<section id="module-binarycpython.utils.plot_functions">
+<span id="plot-functions-module"></span><h1>plot_functions module<a class="headerlink" href="#module-binarycpython.utils.plot_functions" title="Permalink to this headline">ïƒ</a></h1>
<p>Module that contains functionality to plot some properties of (binary) systems.</p>
<p>Different routines are defined here to plot orbits, masses, angular momenta etc.</p>
<dl class="simple">
@@ -221,20 +134,20 @@ TODO: Put all the plotting functions in here</p>
</dd>
</dl>
<dl class="py function">
-<dt id="binarycpython.utils.plot_functions.color_by_index">
-<code class="sig-prename descclassname">binarycpython.utils.plot_functions.</code><code class="sig-name descname">color_by_index</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">row</span></em>, <em class="sig-param"><span class="n">column</span></em>, <em class="sig-param"><span class="n">colors</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/plot_functions.html#color_by_index"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.plot_functions.color_by_index" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.plot_functions.color_by_index">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.plot_functions.</span></span><span class="sig-name descname"><span class="pre">color_by_index</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">row</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">column</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">colors</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/plot_functions.html#color_by_index"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.plot_functions.color_by_index" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function that returns a color based on row and column information. Used to color the stellar types</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.plot_functions.dummy">
-<code class="sig-prename descclassname">binarycpython.utils.plot_functions.</code><code class="sig-name descname">dummy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/plot_functions.html#dummy"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.plot_functions.dummy" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.plot_functions.dummy">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.plot_functions.</span></span><span class="sig-name descname"><span class="pre">dummy</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/plot_functions.html#dummy"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.plot_functions.dummy" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Placeholder</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.plot_functions.parse_function_hr_diagram">
-<code class="sig-prename descclassname">binarycpython.utils.plot_functions.</code><code class="sig-name descname">parse_function_hr_diagram</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">output</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/plot_functions.html#parse_function_hr_diagram"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.plot_functions.parse_function_hr_diagram" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.plot_functions.parse_function_hr_diagram">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.plot_functions.</span></span><span class="sig-name descname"><span class="pre">parse_function_hr_diagram</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">output</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/plot_functions.html#parse_function_hr_diagram"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.plot_functions.parse_function_hr_diagram" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Parsing function for the HR plotting routine</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
@@ -247,8 +160,8 @@ TODO: Put all the plotting functions in here</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.plot_functions.parse_function_masses">
-<code class="sig-prename descclassname">binarycpython.utils.plot_functions.</code><code class="sig-name descname">parse_function_masses</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">output</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/plot_functions.html#parse_function_masses"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.plot_functions.parse_function_masses" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.plot_functions.parse_function_masses">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.plot_functions.</span></span><span class="sig-name descname"><span class="pre">parse_function_masses</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">output</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/plot_functions.html#parse_function_masses"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.plot_functions.parse_function_masses" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Parsing function for the orbit plotting routine</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
@@ -261,8 +174,8 @@ TODO: Put all the plotting functions in here</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.plot_functions.parse_function_orbit">
-<code class="sig-prename descclassname">binarycpython.utils.plot_functions.</code><code class="sig-name descname">parse_function_orbit</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">output</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/plot_functions.html#parse_function_orbit"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.plot_functions.parse_function_orbit" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.plot_functions.parse_function_orbit">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.plot_functions.</span></span><span class="sig-name descname"><span class="pre">parse_function_orbit</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">output</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/plot_functions.html#parse_function_orbit"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.plot_functions.parse_function_orbit" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Parsing function for the orbit plotting routine</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
@@ -275,8 +188,8 @@ TODO: Put all the plotting functions in here</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.plot_functions.plot_HR_diagram">
-<code class="sig-prename descclassname">binarycpython.utils.plot_functions.</code><code class="sig-name descname">plot_HR_diagram</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">df</span></em>, <em class="sig-param"><span class="n">show_stellar_types</span><span class="o">=</span><span class="default_value">False</span></em>, <em class="sig-param"><span class="n">show_plot</span><span class="o">=</span><span class="default_value">True</span></em>, <em class="sig-param"><span class="n">use_astropy_values</span><span class="o">=</span><span class="default_value">True</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/plot_functions.html#plot_HR_diagram"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.plot_functions.plot_HR_diagram" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.plot_functions.plot_HR_diagram">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.plot_functions.</span></span><span class="sig-name descname"><span class="pre">plot_HR_diagram</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">df</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">show_stellar_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">show_plot</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_astropy_values</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/plot_functions.html#plot_HR_diagram"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.plot_functions.plot_HR_diagram" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function to plot the HR diagram evolution of the system. Assumes its a binary system.</p>
<p>For a single star see plot_HR_diagram_single</p>
<p>Plot shows Log luminosity on y axis,
@@ -320,8 +233,8 @@ log temperature on x axis (reversed)</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.plot_functions.plot_masses">
-<code class="sig-prename descclassname">binarycpython.utils.plot_functions.</code><code class="sig-name descname">plot_masses</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">df</span></em>, <em class="sig-param"><span class="n">show_stellar_types</span><span class="o">=</span><span class="default_value">False</span></em>, <em class="sig-param"><span class="n">show_plot</span><span class="o">=</span><span class="default_value">True</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/plot_functions.html#plot_masses"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.plot_functions.plot_masses" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.plot_functions.plot_masses">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.plot_functions.</span></span><span class="sig-name descname"><span class="pre">plot_masses</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">df</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">show_stellar_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">show_plot</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/plot_functions.html#plot_masses"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.plot_functions.plot_masses" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function to plot the masses of the system.</p>
<dl class="simple">
<dt>Function requires the following keys:</dt><dd><ul class="simple">
@@ -360,8 +273,8 @@ log temperature on x axis (reversed)</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.plot_functions.plot_orbit">
-<code class="sig-prename descclassname">binarycpython.utils.plot_functions.</code><code class="sig-name descname">plot_orbit</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">df</span></em>, <em class="sig-param"><span class="n">show_stellar_types</span><span class="o">=</span><span class="default_value">False</span></em>, <em class="sig-param"><span class="n">show_plot</span><span class="o">=</span><span class="default_value">True</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/plot_functions.html#plot_orbit"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.plot_functions.plot_orbit" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.plot_functions.plot_orbit">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.plot_functions.</span></span><span class="sig-name descname"><span class="pre">plot_orbit</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">df</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">show_stellar_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">show_plot</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/plot_functions.html#plot_orbit"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.plot_functions.plot_orbit" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function to plot the orbital elements of the system</p>
<dl class="simple">
<dt>Plots the following quantities:</dt><dd><ul class="simple">
@@ -388,8 +301,8 @@ log temperature on x axis (reversed)</p>
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.plot_functions.plot_system">
-<code class="sig-prename descclassname">binarycpython.utils.plot_functions.</code><code class="sig-name descname">plot_system</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">plot_type</span></em>, <em class="sig-param"><span class="o">**</span><span class="n">kwargs</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/plot_functions.html#plot_system"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.plot_functions.plot_system" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.plot_functions.plot_system">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.plot_functions.</span></span><span class="sig-name descname"><span class="pre">plot_system</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">plot_type</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/plot_functions.html#plot_system"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.plot_functions.plot_system" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function to plot the different quantities of a system.</p>
<dl class="simple">
<dt>This goes (in general) via the following steps:</dt><dd><ul class="simple">
@@ -437,68 +350,43 @@ This is not included in all the plotting routines.</p></li>
</dl>
</dd></dl>
-</div>
+</section>
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-
</div>
- <footer>
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- <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
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-
- </p>
+ <p>© Copyright 2021, David Hendriks, Robert Izzard.</p>
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+
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-Generated on binarycpython git branch: master git revision 0886cd4f1d7f43222aac21d6ed91e917b67b20fc url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/tree/master">git url</a>.
+Generated on binarycpython git branch: auto_resolution git revision be7bd630af892a785312affc34d87c57eb337fd3 url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/tree/auto_resolution">git url</a>.
<br><br>
-Using binary_c with bit branch newmaster: git revision: "6185:20210910:1621c23a5" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/newmaster">git url</a>.
+Using binary_c with bit branch master: git revision: "6209:20211006:c4a4c332e" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/master">git url</a>.
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--- a/docs/build/html/py-modindex.html
+++ b/docs/build/html/py-modindex.html
@@ -1,42 +1,21 @@
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@@ -44,29 +23,13 @@
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<li class="toctree-l1"><a class="reference internal" href="modules.html">Binarycpython code</a></li>
@@ -97,65 +49,29 @@
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@@ -232,55 +148,36 @@
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<footer>
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<hr/>
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- <p>
-
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-
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+ <p>© Copyright 2021, David Hendriks, Robert Izzard.</p>
</div>
-
-
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- Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a
-
- <a href="https://github.com/rtfd/sphinx_rtd_theme">theme</a>
-
+
+ Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
+ <a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
provided by <a href="https://readthedocs.org">Read the Docs</a>.
+
<br><br>
-Generated on binarycpython git branch: master git revision 0886cd4f1d7f43222aac21d6ed91e917b67b20fc url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/tree/master">git url</a>.
+Generated on binarycpython git branch: auto_resolution git revision be7bd630af892a785312affc34d87c57eb337fd3 url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/tree/auto_resolution">git url</a>.
<br><br>
-Using binary_c with bit branch newmaster: git revision: "6185:20210910:1621c23a5" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/newmaster">git url</a>.
+Using binary_c with bit branch master: git revision: "6209:20211006:c4a4c332e" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/master">git url</a>.
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diff --git a/docs/build/html/readme_link.html b/docs/build/html/readme_link.html
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--- a/docs/build/html/readme_link.html
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+ <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
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<li class="toctree-l1 current"><a class="current reference internal" href="#">Python module for binary_c</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#requirements">Requirements</a></li>
@@ -112,69 +65,30 @@
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/* CSS overrides for sphinx_rtd_theme */
@@ -199,16 +113,16 @@
text-align: unset;
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</style>
-<div class="section" id="python-module-for-binary-c">
-<h1>Python module for binary_c<a class="headerlink" href="#python-module-for-binary-c" title="Permalink to this headline">¶</a></h1>
+<section id="python-module-for-binary-c">
+<h1>Python module for binary_c<a class="headerlink" href="#python-module-for-binary-c" title="Permalink to this headline">ïƒ</a></h1>
<p>Docstring coverage:</p>
<a class="reference external image-reference" href="./badges/docstring_coverage.svg"><img alt="docstring coverage" src="_images/docstring_coverage.svg" /></a>
<p>Test coverage:</p>
<a class="reference external image-reference" href="./badges/test_coverage.svg"><img alt="test coverage" src="_images/test_coverage.svg" /></a>
<p>Binary population synthesis code that interfaces with binary_c. Based on a original work by Jeff Andrews (can be found in old_solution/ directory). Updated and extended for Python3 by David Hendriks, Robert Izzard.</p>
<p>The current release is version 0.9.1, make sure to use that version number when installing!</p>
-<div class="section" id="requirements">
-<h2>Requirements<a class="headerlink" href="#requirements" title="Permalink to this headline">¶</a></h2>
+<section id="requirements">
+<h2>Requirements<a class="headerlink" href="#requirements" title="Permalink to this headline">ïƒ</a></h2>
<p>To run this code you need to at least have installations of:</p>
<ul class="simple">
<li><p>Python 3.6 or higher</p></li>
@@ -225,9 +139,9 @@
<li><p>matplotlib</p></li>
<li><p>py_rinterpolate</p></li>
</ul>
-</div>
-<div class="section" id="environment-variables">
-<h2>Environment variables<a class="headerlink" href="#environment-variables" title="Permalink to this headline">¶</a></h2>
+</section>
+<section id="environment-variables">
+<h2>Environment variables<a class="headerlink" href="#environment-variables" title="Permalink to this headline">ïƒ</a></h2>
<p>Before compilation you need to have certain environment variables:</p>
<p>Required:</p>
<ul class="simple">
@@ -236,51 +150,50 @@
<li><p><code class="docutils literal notranslate"><span class="pre">LIBRARY_PATH</span></code> should include whatever directories are required to build binary_c (e.g. locations of libgsl, libmemoize, librinterpolate, etc.)</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">GSL_DIR</span></code> should point to the root location where you installed GSL to. This root dir should contain <code class="docutils literal notranslate"><span class="pre">bin/</span></code>, <code class="docutils literal notranslate"><span class="pre">lib/</span></code> etc</p></li>
</ul>
-</div>
-<div class="section" id="build-instructions">
-<h2>Build instructions<a class="headerlink" href="#build-instructions" title="Permalink to this headline">¶</a></h2>
+</section>
+<section id="build-instructions">
+<h2>Build instructions<a class="headerlink" href="#build-instructions" title="Permalink to this headline">ïƒ</a></h2>
<p>First, make sure you have built binary_c (See <code class="docutils literal notranslate"><span class="pre">$BINARY_C/doc/binary_c2.pdf</span></code> section: installation for all the installation instructions for <code class="docutils literal notranslate"><span class="pre">binary_c</span></code>)) and that it functions correctly.</p>
-<div class="section" id="installation-via-pip">
-<h3>Installation via PIP:<a class="headerlink" href="#installation-via-pip" title="Permalink to this headline">¶</a></h3>
+<section id="installation-via-pip">
+<h3>Installation via PIP:<a class="headerlink" href="#installation-via-pip" title="Permalink to this headline">ïƒ</a></h3>
<p>To install this package via pip:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">pip</span> <span class="n">install</span> <span class="n">binarycpython</span>
</pre></div>
</div>
-</div>
-<div class="section" id="installation-from-source">
-<h3>Installation from source:<a class="headerlink" href="#installation-from-source" title="Permalink to this headline">¶</a></h3>
+</section>
+<section id="installation-from-source">
+<h3>Installation from source:<a class="headerlink" href="#installation-from-source" title="Permalink to this headline">ïƒ</a></h3>
<p>For this it is best to set up a virtual environment. Activate the virtualenvironment and enter the cloned version of the repo.</p>
<p>Then run:</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">python</span> <span class="n">setup</span><span class="o">.</span><span class="n">py</span> <span class="n">clean</span> <span class="o">&&</span> <span class="n">python</span> <span class="n">setup</span><span class="o">.</span><span class="n">py</span> <span class="n">build</span> <span class="o">--</span><span class="n">force</span> <span class="o">&&</span> <span class="n">python</span> <span class="n">setup</span><span class="o">.</span><span class="n">py</span> <span class="n">sdist</span> <span class="o">&&</span> <span class="n">pip</span> <span class="n">install</span> <span class="o">-</span><span class="n">v</span> <span class="n">dist</span><span class="o">/</span><span class="n">binarycpython</span><span class="o">-<</span><span class="n">version</span> <span class="n">of</span> <span class="n">this</span> <span class="n">package</span><span class="o">>.</span><span class="n">tar</span><span class="o">.</span><span class="n">gz</span>
-<span class="n">python</span> <span class="n">setup</span><span class="o">.</span><span class="n">py</span> <span class="n">clean</span> <span class="o">&&</span> <span class="n">pip</span> <span class="n">uninstall</span> <span class="n">binarycpython</span> <span class="o">&&</span> <span class="n">rm</span> <span class="n">dist</span><span class="o">/*</span> <span class="o">&&</span> <span class="n">python</span> <span class="n">setup</span><span class="o">.</span><span class="n">py</span> <span class="n">build</span> <span class="o">--</span><span class="n">force</span> <span class="o">&&</span> <span class="n">python</span> <span class="n">setup</span><span class="o">.</span><span class="n">py</span> <span class="n">sdist</span> <span class="o">&&</span> <span class="n">pip</span> <span class="n">install</span> <span class="o">-</span><span class="n">v</span> <span class="n">dist</span><span class="o">/</span><span class="n">binarycpython</span><span class="o">-<</span><span class="n">version</span> <span class="n">of</span> <span class="n">this</span> <span class="n">package</span><span class="o">>.</span><span class="n">tar</span><span class="o">.</span><span class="n">gz</span>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">python</span> <span class="n">setup</span><span class="o">.</span><span class="n">py</span> <span class="n">clean</span> <span class="o">&&</span> <span class="n">pip</span> <span class="n">uninstall</span> <span class="n">binarycpython</span> <span class="o">&&</span> <span class="n">python</span> <span class="n">setup</span><span class="o">.</span><span class="n">py</span> <span class="n">build</span> <span class="o">--</span><span class="n">force</span> <span class="o">&&</span> <span class="n">python</span> <span class="n">setup</span><span class="o">.</span><span class="n">py</span> <span class="n">sdist</span> <span class="o">&&</span> <span class="n">pip</span> <span class="n">install</span> <span class="o">-</span><span class="n">v</span> <span class="n">dist</span><span class="o">/</span><span class="n">binarycpython</span><span class="o">-<</span><span class="n">version</span> <span class="n">of</span> <span class="n">this</span> <span class="n">package</span><span class="o">>.</span><span class="n">tar</span><span class="o">.</span><span class="n">gz</span>
</pre></div>
</div>
<p>This will clean the build directory, remove binarycpython from the venv, remove the dist packages, and then rebuilding and reinstalling the package. You can find the version of this package in setup.py.</p>
<p>This will install this package into the virtual environment. Making changes to the sourcecode can be “installed†into the virtual env with the same command.</p>
<p>If this is not the first time you install the package, but rather rebuild it because you make changes in either binary_c or binarycpython, you should ignore the currently installed version, and also skip installing the dependencies again, by executing the following command:</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">python</span> <span class="n">setup</span><span class="o">.</span><span class="n">py</span> <span class="n">clean</span> <span class="o">&&</span> <span class="n">pip</span> <span class="n">uninstall</span> <span class="n">binarycpython</span> <span class="o">&&</span> <span class="n">rm</span> <span class="n">dist</span><span class="o">/*</span> <span class="o">&&</span> <span class="n">python</span> <span class="n">setup</span><span class="o">.</span><span class="n">py</span> <span class="n">build</span> <span class="o">--</span><span class="n">force</span> <span class="o">&&</span> <span class="n">python</span> <span class="n">setup</span><span class="o">.</span><span class="n">py</span> <span class="n">sdist</span> <span class="o">&&</span> <span class="n">pip</span> <span class="n">install</span> <span class="o">--</span><span class="n">ignore</span><span class="o">-</span><span class="n">installed</span> <span class="o">--</span><span class="n">no</span><span class="o">-</span><span class="n">dependencies</span> <span class="o">-</span><span class="n">v</span> <span class="n">dist</span><span class="o">/</span><span class="n">binarycpython</span><span class="o">-<</span><span class="n">version</span> <span class="n">of</span> <span class="n">this</span> <span class="n">package</span><span class="o">>.</span><span class="n">tar</span><span class="o">.</span><span class="n">gz</span>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">python</span> <span class="n">setup</span><span class="o">.</span><span class="n">py</span> <span class="n">clean</span> <span class="o">&&</span> <span class="n">pip</span> <span class="n">uninstall</span> <span class="n">binarycpython</span> <span class="o">&&</span> <span class="n">python</span> <span class="n">setup</span><span class="o">.</span><span class="n">py</span> <span class="n">build</span> <span class="o">--</span><span class="n">force</span> <span class="o">&&</span> <span class="n">python</span> <span class="n">setup</span><span class="o">.</span><span class="n">py</span> <span class="n">sdist</span> <span class="o">&&</span> <span class="n">pip</span> <span class="n">install</span> <span class="o">--</span><span class="n">ignore</span><span class="o">-</span><span class="n">installed</span> <span class="o">--</span><span class="n">no</span><span class="o">-</span><span class="n">dependencies</span> <span class="o">-</span><span class="n">v</span> <span class="n">dist</span><span class="o">/</span><span class="n">binarycpython</span><span class="o">-<</span><span class="n">version</span> <span class="n">of</span> <span class="n">this</span> <span class="n">package</span><span class="o">>.</span><span class="n">tar</span><span class="o">.</span><span class="n">gz</span>
</pre></div>
</div>
-<div class="section" id="after-installation">
-<h4>After installation<a class="headerlink" href="#after-installation" title="Permalink to this headline">¶</a></h4>
+<section id="after-installation">
+<h4>After installation<a class="headerlink" href="#after-installation" title="Permalink to this headline">ïƒ</a></h4>
<p>After installing the code via source it is useful to run the test suite before doing any programming with it. The test suite is stored in <code class="docutils literal notranslate"><span class="pre">binarycpython/tests</span></code> and running <code class="docutils literal notranslate"><span class="pre">python</span> <span class="pre">main.py</span></code> in there will run all the tests.</p>
-</div>
-</div>
-</div>
-<div class="section" id="examples">
-<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
+</section>
+</section>
+</section>
+<section id="examples">
+<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">ïƒ</a></h2>
<p>See the examples/ directory for example scripts and notebooks. The documentation contains example pages as well.</p>
-</div>
-<div class="section" id="usage-notes">
-<h2>Usage notes<a class="headerlink" href="#usage-notes" title="Permalink to this headline">¶</a></h2>
+</section>
+<section id="usage-notes">
+<h2>Usage notes<a class="headerlink" href="#usage-notes" title="Permalink to this headline">ïƒ</a></h2>
<p>Make sure that with every change/recompilation you make in <code class="docutils literal notranslate"><span class="pre">binary_c</span></code>, you also rebuild this package. Whenever you change the sourcecode of this package, you need to reinstall it into your virtualenvironment as well</p>
-</div>
-<div class="section" id="documentation">
-<h2>Documentation<a class="headerlink" href="#documentation" title="Permalink to this headline">¶</a></h2>
+</section>
+<section id="documentation">
+<h2>Documentation<a class="headerlink" href="#documentation" title="Permalink to this headline">ïƒ</a></h2>
<p>Look in the docs/ directory. Within the build/html/ there is the html version of the documentation. The</p>
-</div>
-<div class="section" id="faq-issues">
-<h2>FAQ/Issues:<a class="headerlink" href="#faq-issues" title="Permalink to this headline">¶</a></h2>
+</section>
+<section id="faq-issues">
+<h2>FAQ/Issues:<a class="headerlink" href="#faq-issues" title="Permalink to this headline">ïƒ</a></h2>
<p>Building issues with binary_c itself:</p>
<ul class="simple">
<li><p>see the documentation of binary_c (in doc/).</p></li>
@@ -298,69 +211,44 @@
<li><p>When running jupyter notebooks, make sure you are running the jupyter installation from the same virtual environment.</p></li>
<li><p>When the output of binary_c seems to be different than expected, you might need to rebuild this python package. Everytime binary_c is compiled, this package needs to be rebuilt too.</p></li>
</ul>
-</div>
-</div>
+</section>
+</section>
</div>
-
</div>
- <footer>
-
- <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
-
- <a href="modules.html" class="btn btn-neutral float-right" title="Binarycpython code" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
-
-
- <a href="index.html" class="btn btn-neutral float-left" title="Welcome to binary_c-python’s documentation!" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
-
+ <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
+ <a href="index.html" class="btn btn-neutral float-left" title="Welcome to binary_c-python’s documentation!" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
+ <a href="modules.html" class="btn btn-neutral float-right" title="Binarycpython code" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
</div>
-
<hr/>
<div role="contentinfo">
- <p>
-
- © Copyright 2021, David Hendriks, Robert Izzard
-
- </p>
+ <p>© Copyright 2021, David Hendriks, Robert Izzard.</p>
</div>
-
-
-
- Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a
-
- <a href="https://github.com/rtfd/sphinx_rtd_theme">theme</a>
-
+
+ Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
+ <a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
provided by <a href="https://readthedocs.org">Read the Docs</a>.
+
<br><br>
-Generated on binarycpython git branch: master git revision 0886cd4f1d7f43222aac21d6ed91e917b67b20fc url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/tree/master">git url</a>.
+Generated on binarycpython git branch: auto_resolution git revision be7bd630af892a785312affc34d87c57eb337fd3 url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/tree/auto_resolution">git url</a>.
<br><br>
-Using binary_c with bit branch newmaster: git revision: "6185:20210910:1621c23a5" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/newmaster">git url</a>.
+Using binary_c with bit branch master: git revision: "6209:20211006:c4a4c332e" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/master">git url</a>.
</footer>
-
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-
</section>
-
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-
-
- <script type="text/javascript">
+ <script>
jQuery(function () {
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});
- </script>
-
-
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-
-
+ </script>
</body>
</html>
\ No newline at end of file
diff --git a/docs/build/html/run_system_wrapper.html b/docs/build/html/run_system_wrapper.html
index 02408d8e7a9620f8f624644c5262ded959c80737..6cd8f2a10a2259c4e087e8388a5047f00f53ca33 100644
--- a/docs/build/html/run_system_wrapper.html
+++ b/docs/build/html/run_system_wrapper.html
@@ -1,71 +1,35 @@
-
-
<!DOCTYPE html>
<html class="writer-html5" lang="en" >
<head>
- <meta charset="utf-8">
-
- <meta name="viewport" content="width=device-width, initial-scale=1.0">
-
- <title>run_system_wrapper module — binary_c-python documentation</title>
-
-
-
- <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
- <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+ <meta charset="utf-8" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
-
-
-
-
-
-
+ <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+ <title>run_system_wrapper module — binary_c-python documentation</title>
+ <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+ <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
<!--[if lt IE 9]>
<script src="_static/js/html5shiv.min.js"></script>
<![endif]-->
-
- <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
+ <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
<script src="_static/jquery.js"></script>
<script src="_static/underscore.js"></script>
<script src="_static/doctools.js"></script>
- <script src="_static/language_data.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
- <script async="async" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.7/latest.js?config=TeX-AMS-MML_HTMLorMML"></script>
- <script type="text/x-mathjax-config">MathJax.Hub.Config({"tex2jax": {"inlineMath": [["$", "$"], ["\\(", "\\)"]], "processEscapes": true, "ignoreClass": "document", "processClass": "math|output_area"}})</script>
-
- <script type="text/javascript" src="_static/js/theme.js"></script>
-
-
+ <script src="_static/js/theme.js"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="next" title="spacing_functions module" href="spacing_functions.html" />
<link rel="prev" title="plot_functions module" href="plot_functions.html" />
</head>
-<body class="wy-body-for-nav">
-
-
+<body class="wy-body-for-nav">
<div class="wy-grid-for-nav">
-
<nav data-toggle="wy-nav-shift" class="wy-nav-side">
<div class="wy-side-scroll">
<div class="wy-side-nav-search" >
-
-
-
- <a href="index.html" class="icon icon-home" alt="Documentation Home"> binary_c-python
-
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+ <a href="index.html" class="icon icon-home"> binary_c-python
</a>
-
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-
-
-
<div role="search">
<form id="rtd-search-form" class="wy-form" action="search.html" method="get">
<input type="text" name="q" placeholder="Search docs" />
@@ -73,19 +37,8 @@
<input type="hidden" name="area" value="default" />
</form>
</div>
-
-
- </div>
-
-
- <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
-
-
-
-
-
-
- <p class="caption"><span class="caption-text">Contents:</span></p>
+ </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
+ <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="readme_link.html">Python module for binary_c</a></li>
<li class="toctree-l1 current"><a class="reference internal" href="modules.html">Binarycpython code</a><ul class="current">
@@ -109,71 +62,31 @@
<li class="toctree-l1"><a class="reference external" href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/issues/new">Submit an issue</a></li>
</ul>
-
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-
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</nav>
- <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap">
-
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- <nav class="wy-nav-top" aria-label="top navigation">
-
+ <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
<i data-toggle="wy-nav-top" class="fa fa-bars"></i>
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-
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-
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-<div role="navigation" aria-label="breadcrumbs navigation">
-
+ <div role="navigation" aria-label="Page navigation">
<ul class="wy-breadcrumbs">
-
<li><a href="index.html" class="icon icon-home"></a> »</li>
-
<li><a href="modules.html">Binarycpython code</a> »</li>
-
<li>run_system_wrapper module</li>
-
-
<li class="wy-breadcrumbs-aside">
-
-
<a href="_sources/run_system_wrapper.rst.txt" rel="nofollow"> View page source</a>
-
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-
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<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
-
+
<style>
/* CSS overrides for sphinx_rtd_theme */
@@ -198,13 +111,13 @@
text-align: unset;
}
</style>
-<div class="section" id="module-binarycpython.utils.run_system_wrapper">
-<span id="run-system-wrapper-module"></span><h1>run_system_wrapper module<a class="headerlink" href="#module-binarycpython.utils.run_system_wrapper" title="Permalink to this headline">¶</a></h1>
+<section id="module-binarycpython.utils.run_system_wrapper">
+<span id="run-system-wrapper-module"></span><h1>run_system_wrapper module<a class="headerlink" href="#module-binarycpython.utils.run_system_wrapper" title="Permalink to this headline">ïƒ</a></h1>
<p>Module containing the utility function run_system,
which handles a lot of things by analysing the passed kwargs</p>
<dl class="py function">
-<dt id="binarycpython.utils.run_system_wrapper.run_system">
-<code class="sig-prename descclassname">binarycpython.utils.run_system_wrapper.</code><code class="sig-name descname">run_system</code><span class="sig-paren">(</span><em class="sig-param"><span class="o">**</span><span class="n">kwargs</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/run_system_wrapper.html#run_system"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.run_system_wrapper.run_system" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.run_system_wrapper.run_system">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.run_system_wrapper.</span></span><span class="sig-name descname"><span class="pre">run_system</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/run_system_wrapper.html#run_system"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.run_system_wrapper.run_system" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function that runs a system.
Mostly as a useful utility function that handles all the setup of argument lists etc.</p>
<p class="rubric">Examples</p>
@@ -247,68 +160,43 @@ and returns what the parse_function returns</p>
</dl>
</dd></dl>
-</div>
+</section>
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- <footer>
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-
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+ <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
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-
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- <p>
-
- © Copyright 2021, David Hendriks, Robert Izzard
-
- </p>
+ <p>© Copyright 2021, David Hendriks, Robert Izzard.</p>
</div>
-
-
-
- Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a
-
- <a href="https://github.com/rtfd/sphinx_rtd_theme">theme</a>
-
+
+ Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
+ <a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
provided by <a href="https://readthedocs.org">Read the Docs</a>.
+
<br><br>
-Generated on binarycpython git branch: master git revision 0886cd4f1d7f43222aac21d6ed91e917b67b20fc url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/tree/master">git url</a>.
+Generated on binarycpython git branch: auto_resolution git revision be7bd630af892a785312affc34d87c57eb337fd3 url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/tree/auto_resolution">git url</a>.
<br><br>
-Using binary_c with bit branch newmaster: git revision: "6185:20210910:1621c23a5" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/newmaster">git url</a>.
+Using binary_c with bit branch master: git revision: "6209:20211006:c4a4c332e" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/master">git url</a>.
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-<div class="section" id="module-binarycpython.utils.spacing_functions">
-<span id="spacing-functions-module"></span><h1>spacing_functions module<a class="headerlink" href="#module-binarycpython.utils.spacing_functions" title="Permalink to this headline">¶</a></h1>
+<section id="module-binarycpython.utils.spacing_functions">
+<span id="spacing-functions-module"></span><h1>spacing_functions module<a class="headerlink" href="#module-binarycpython.utils.spacing_functions" title="Permalink to this headline">ïƒ</a></h1>
<p>Module containing the spacing functions for the binarycpython package. Very under-populated at the moment, but more are likely to come soon</p>
<dl class="simple">
<dt>Tasks:</dt><dd><p>TODO: add more spacing functions to this module.</p>
</dd>
</dl>
<dl class="py function">
-<dt id="binarycpython.utils.spacing_functions.const">
-<code class="sig-prename descclassname">binarycpython.utils.spacing_functions.</code><code class="sig-name descname">const</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">min_bound</span></em>, <em class="sig-param"><span class="n">max_bound</span></em>, <em class="sig-param"><span class="n">steps</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/spacing_functions.html#const"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.spacing_functions.const" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.spacing_functions.const">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.spacing_functions.</span></span><span class="sig-name descname"><span class="pre">const</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">min_bound</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_bound</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">steps</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/spacing_functions.html#const"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.spacing_functions.const" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Samples a range linearly. Uses numpy linspace.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>min_bound</strong> (<code class="xref py py-data docutils literal notranslate"><span class="pre">Union</span></code>[<code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code>, <code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code>]) – lower bound of range</p></li>
<li><p><strong>max_bound</strong> (<code class="xref py py-data docutils literal notranslate"><span class="pre">Union</span></code>[<code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code>, <code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code>]) – upper bound of range</p></li>
-<li><p><strong>steps</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code>) – amount of segments between min_bound and max_bound</p></li>
+<li><p><strong>steps</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code>) – number of segments between min_bound and max_bound</p></li>
</ul>
</dd>
<dt class="field-even">Return type</dt>
@@ -226,68 +139,153 @@
</dl>
</dd></dl>
-</div>
+<dl class="py function">
+<dt class="sig sig-object py" id="binarycpython.utils.spacing_functions.const_dt">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.spacing_functions.</span></span><span class="sig-name descname"><span class="pre">const_dt</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dt</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1000.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dlogt</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mmin</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.07</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mmax</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">100.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nres</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1000</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">logspacing</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tmin</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">3.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tmax</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mindm</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">maxdm</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">((0.07,</span> <span class="pre">1.0,</span> <span class="pre">0.1),</span> <span class="pre">(1.0,</span> <span class="pre">300.0,</span> <span class="pre">1.0))</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fsample</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">factor</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">showtable</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/spacing_functions.html#const_dt"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.spacing_functions.const_dt" title="Permalink to this definition">ïƒ</a></dt>
+<dd><p>const_dt returns a list of masses spaced at a constant age difference</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>dt</strong> – the time difference between the masses (1000.0 Myr, used when logspacing==False)</p></li>
+<li><p><strong>dlogt</strong> – the delta log10(time) difference between masses (0.1 dex, used when logspacing==True)</p></li>
+<li><p><strong>mmin</strong> – the minimum mass to be considered in the stellar lifetime interpolation table (0.07 Msun)</p></li>
+<li><p><strong>mmax</strong> – the maximum mass to be considered in the stellar lifetime interpolation table (100.0 Msun)</p></li>
+<li><p><strong>nres</strong> – the resolution of the stellar lifetime interpolation table (100)</p></li>
+<li><p><strong>logspacing</strong> – whether to use log-spaced time, in which case dt is actually d(log10(t))</p></li>
+<li><p><strong>tmin</strong> – the minimum time to consider (Myr, default 3.0 Myr)</p></li>
+<li><p><strong>tmax</strong> – the maximum time to consider (Myr, default None which means we use the grid option ‘max_evolution_time’)</p></li>
+<li><p><strong>mindm</strong> – a tuple of tuples containing a mass range and minimum mass spacing in that range. The default is ((0.07,1.0,0.1),(1.0,300.0,1.0)) allocated a minimum dm of 0.1Msun in the mass range 0.07 to 1.0 Msun and 1.0Msun in the range 1.0 to 300.0 Msun. Anything you set overrides this.</p></li>
+<li><p><strong>maxdm</strong> – a list of tuples similar to mindm but specifying a maximum mass spacing. (None)</p></li>
+<li><p><strong>fsample</strong> – a global sampling (Shannon-like) factor (<1) to improve resolution (default 1.0, set to smaller to improve resolution)</p></li>
+<li><p><strong>factor</strong> – all masses generated are multiplied by this after generation</p></li>
+<li><p><strong>showtable</strong> – if True, the mass list and times are shown to stdout after generation</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>Array of masses.</p>
+</dd>
+</dl>
+<p>Example:
+# these are lines set as options to Population.add_grid_value(…)</p>
+<p># linear time bins of 1Gyr
+spacingfunc=â€const_dt(self,dt=1000,nres=100,mmin=0.07,mmax=2.0,showtable=True)â€</p>
+<p># logarithmic spacing in time, generally suitable for Galactic
+# chemical evolution yield grids.
+spacingfunc=â€const_dt(self,dlogt=0.1,nres=100,mmin=0.07,mmax=80.0,maxdm=((0.07,1.0,0.1),(1.0,10.0,1.0),(10.0,80.0,2.0)),showtable=True,logspacing=True,fsample=1.0/4.0)â€</p>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="binarycpython.utils.spacing_functions.const_ranges">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.spacing_functions.</span></span><span class="sig-name descname"><span class="pre">const_ranges</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ranges</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/spacing_functions.html#const_ranges"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.spacing_functions.const_ranges" title="Permalink to this definition">ïƒ</a></dt>
+<dd><p>Samples a series of ranges linearly.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>ranges</strong> – a tuple of tuples passed to the const() spacing function.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></p>
+</dd>
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>numpy array of masses</p>
+</dd>
+</dl>
+<p class="rubric">Example</p>
+<p>The following allocates 10 stars between 0.1 and 0.65, 20 stars between 0.65
+and 0.85, and 10 stars between 0.85 and 10.0 Msun.</p>
+<dl class="simple">
+<dt>spacingfunc=â€const_ranges((({},{},{}),({},{},{}),({},{},{})))â€.format(</dt><dd><p>0.1,0.65,10,
+0.65,0.85,20,
+0.85,10.0,10</p>
+</dd>
+</dl>
+<p>),</p>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="binarycpython.utils.spacing_functions.gaussian_zoom">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.spacing_functions.</span></span><span class="sig-name descname"><span class="pre">gaussian_zoom</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">min_bound</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_bound</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">zoom_mean</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">zoom_dispersion</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">zoom_magnitude</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">steps</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/spacing_functions.html#gaussian_zoom"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.spacing_functions.gaussian_zoom" title="Permalink to this definition">ïƒ</a></dt>
+<dd><p>Samples such that a region is zoomed in according to a 1-Gaussian function</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>min_bound</strong> (<code class="xref py py-data docutils literal notranslate"><span class="pre">Union</span></code>[<code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code>, <code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code>]) – lower bound of range</p></li>
+<li><p><strong>max_bound</strong> (<code class="xref py py-data docutils literal notranslate"><span class="pre">Union</span></code>[<code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code>, <code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code>]) – upper bound of range</p></li>
+<li><p><strong>zoom_mean</strong> (<code class="xref py py-data docutils literal notranslate"><span class="pre">Union</span></code>[<code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code>, <code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code>]) – mean of the Gaussian zoom location</p></li>
+<li><p><strong>zoom_dispersion</strong> (<code class="xref py py-data docutils literal notranslate"><span class="pre">Union</span></code>[<code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code>, <code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code>]) – dispersion of the Gaussian</p></li>
+<li><p><strong>zoom_magnitude</strong> (<code class="xref py py-data docutils literal notranslate"><span class="pre">Union</span></code>[<code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code>, <code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code>]) – depth of the Gaussian (should be 0<= zoom_magntiude <1)</p></li>
+<li><p><strong>steps</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code>) – number of segments between min_bound and max_bound assuming a linear step
+this is what you’d normally call “resolutionâ€</p></li>
+</ul>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></p>
+</dd>
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Numpy array of sample values</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="binarycpython.utils.spacing_functions.peak_normalized_gaussian_func">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.spacing_functions.</span></span><span class="sig-name descname"><span class="pre">peak_normalized_gaussian_func</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">x</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mean</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sigma</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/spacing_functions.html#peak_normalized_gaussian_func"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.spacing_functions.peak_normalized_gaussian_func" title="Permalink to this definition">ïƒ</a></dt>
+<dd><p>Function to evaluate a Gaussian at a given point, note
+that the normalization is such that the peak is always 1.0,
+not that the integral is 1.0</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>x</strong> (<code class="xref py py-data docutils literal notranslate"><span class="pre">Union</span></code>[<code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code>, <code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code>]) – location at which to evaluate the distribution</p></li>
+<li><p><strong>mean</strong> (<code class="xref py py-data docutils literal notranslate"><span class="pre">Union</span></code>[<code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code>, <code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code>]) – mean of the Gaussian</p></li>
+<li><p><strong>sigma</strong> (<code class="xref py py-data docutils literal notranslate"><span class="pre">Union</span></code>[<code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code>, <code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code>]) – standard deviation of the Gaussian</p></li>
+</ul>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><code class="xref py py-data docutils literal notranslate"><span class="pre">Union</span></code>[<code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code>, <code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code>]</p>
+</dd>
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>value of the Gaussian at x</p>
+</dd>
+</dl>
+</dd></dl>
+
+</section>
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-Generated on binarycpython git branch: master git revision 0886cd4f1d7f43222aac21d6ed91e917b67b20fc url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/tree/master">git url</a>.
+Generated on binarycpython git branch: auto_resolution git revision be7bd630af892a785312affc34d87c57eb337fd3 url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/tree/auto_resolution">git url</a>.
<br><br>
-Using binary_c with bit branch newmaster: git revision: "6185:20210910:1621c23a5" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/newmaster">git url</a>.
+Using binary_c with bit branch master: git revision: "6209:20211006:c4a4c332e" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/master">git url</a>.
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index c31a11e0d20a28510c2e2c06485f5f472aaa6072..696a32f9138dbcb16d3c3da02a8021316444d5c2 100644
--- a/docs/build/html/stellar_types.html
+++ b/docs/build/html/stellar_types.html
@@ -1,71 +1,35 @@
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+ </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
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<li class="toctree-l1 current"><a class="reference internal" href="modules.html">Binarycpython code</a><ul class="current">
@@ -109,71 +62,31 @@
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/* CSS overrides for sphinx_rtd_theme */
@@ -198,8 +111,8 @@
text-align: unset;
}
</style>
-<div class="section" id="module-binarycpython.utils.stellar_types">
-<span id="stellar-types-module"></span><h1>stellar_types module<a class="headerlink" href="#module-binarycpython.utils.stellar_types" title="Permalink to this headline">¶</a></h1>
+<section id="module-binarycpython.utils.stellar_types">
+<span id="stellar-types-module"></span><h1>stellar_types module<a class="headerlink" href="#module-binarycpython.utils.stellar_types" title="Permalink to this headline">ïƒ</a></h1>
<dl class="simple">
<dt>Module containing two stellar type dicts:</dt><dd><ul class="simple">
<li><p>STELLAR_TYPE_DICT: dictionary with long names</p></li>
@@ -207,68 +120,43 @@
</ul>
</dd>
</dl>
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+</section>
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+ <p>© Copyright 2021, David Hendriks, Robert Izzard.</p>
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+Generated on binarycpython git branch: auto_resolution git revision be7bd630af892a785312affc34d87c57eb337fd3 url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/tree/auto_resolution">git url</a>.
<br><br>
-Using binary_c with bit branch newmaster: git revision: "6185:20210910:1621c23a5" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/newmaster">git url</a>.
+Using binary_c with bit branch master: git revision: "6209:20211006:c4a4c332e" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/master">git url</a>.
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diff --git a/docs/build/html/useful_funcs.html b/docs/build/html/useful_funcs.html
index a123310d9429a3a25f964bc783c337c9d96a7c46..33aecc3e855675bdb6ebcf213bde54b2352a2418 100644
--- a/docs/build/html/useful_funcs.html
+++ b/docs/build/html/useful_funcs.html
@@ -1,71 +1,35 @@
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+ </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
+ <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
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<li class="toctree-l1 current"><a class="reference internal" href="modules.html">Binarycpython code</a><ul class="current">
@@ -109,71 +62,31 @@
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/* CSS overrides for sphinx_rtd_theme */
@@ -198,8 +111,8 @@
text-align: unset;
}
</style>
-<div class="section" id="module-binarycpython.utils.useful_funcs">
-<span id="useful-funcs-module"></span><h1>useful_funcs module<a class="headerlink" href="#module-binarycpython.utils.useful_funcs" title="Permalink to this headline">¶</a></h1>
+<section id="module-binarycpython.utils.useful_funcs">
+<span id="useful-funcs-module"></span><h1>useful_funcs module<a class="headerlink" href="#module-binarycpython.utils.useful_funcs" title="Permalink to this headline">ïƒ</a></h1>
<p>Collection of useful functions.</p>
<p>Part of this is copied/inspired by Rob’s binary_stars module</p>
<dl class="simple">
@@ -222,8 +135,8 @@
</dd>
</dl>
<dl class="py function">
-<dt id="binarycpython.utils.useful_funcs.calc_period_from_sep">
-<code class="sig-prename descclassname">binarycpython.utils.useful_funcs.</code><code class="sig-name descname">calc_period_from_sep</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">M1</span></em>, <em class="sig-param"><span class="n">M2</span></em>, <em class="sig-param"><span class="n">sep</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/useful_funcs.html#calc_period_from_sep"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.useful_funcs.calc_period_from_sep" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.useful_funcs.calc_period_from_sep">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.useful_funcs.</span></span><span class="sig-name descname"><span class="pre">calc_period_from_sep</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">M1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">M2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sep</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/useful_funcs.html#calc_period_from_sep"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.useful_funcs.calc_period_from_sep" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>calculate period from separation</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
@@ -243,8 +156,8 @@
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.useful_funcs.calc_sep_from_period">
-<code class="sig-prename descclassname">binarycpython.utils.useful_funcs.</code><code class="sig-name descname">calc_sep_from_period</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">M1</span></em>, <em class="sig-param"><span class="n">M2</span></em>, <em class="sig-param"><span class="n">period</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/useful_funcs.html#calc_sep_from_period"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.useful_funcs.calc_sep_from_period" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.useful_funcs.calc_sep_from_period">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.useful_funcs.</span></span><span class="sig-name descname"><span class="pre">calc_sep_from_period</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">M1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">M2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">period</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/useful_funcs.html#calc_sep_from_period"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.useful_funcs.calc_sep_from_period" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Calculate separation from period.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
@@ -264,8 +177,8 @@
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.useful_funcs.maximum_mass_ratio_for_RLOF">
-<code class="sig-prename descclassname">binarycpython.utils.useful_funcs.</code><code class="sig-name descname">maximum_mass_ratio_for_RLOF</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">M1</span></em>, <em class="sig-param"><span class="n">orbital_period</span></em>, <em class="sig-param"><span class="n">metallicity</span><span class="o">=</span><span class="default_value">0.02</span></em>, <em class="sig-param"><span class="n">store_memaddr</span><span class="o">=</span><span class="default_value">None</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/useful_funcs.html#maximum_mass_ratio_for_RLOF"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.useful_funcs.maximum_mass_ratio_for_RLOF" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.useful_funcs.maximum_mass_ratio_for_RLOF">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.useful_funcs.</span></span><span class="sig-name descname"><span class="pre">maximum_mass_ratio_for_RLOF</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">M1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">orbital_period</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">metallicity</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.02</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">store_memaddr</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/useful_funcs.html#maximum_mass_ratio_for_RLOF"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.useful_funcs.maximum_mass_ratio_for_RLOF" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Wrapper function for _binary_c_bindings.return_maximum_mass_ratio_for_RLOF</p>
<p>Handles the output and returns the maximum mass ratio at which RLOF just does not occur at ZAMS</p>
<dl class="field-list simple">
@@ -284,8 +197,8 @@
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.useful_funcs.minimum_period_for_RLOF">
-<code class="sig-prename descclassname">binarycpython.utils.useful_funcs.</code><code class="sig-name descname">minimum_period_for_RLOF</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">M1</span></em>, <em class="sig-param"><span class="n">M2</span></em>, <em class="sig-param"><span class="n">metallicity</span></em>, <em class="sig-param"><span class="n">store_memaddr</span><span class="o">=</span><span class="default_value">- 1</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/useful_funcs.html#minimum_period_for_RLOF"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.useful_funcs.minimum_period_for_RLOF" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.useful_funcs.minimum_period_for_RLOF">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.useful_funcs.</span></span><span class="sig-name descname"><span class="pre">minimum_period_for_RLOF</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">M1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">M2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">metallicity</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">store_memaddr</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">-</span> <span class="pre">1</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/useful_funcs.html#minimum_period_for_RLOF"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.useful_funcs.minimum_period_for_RLOF" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Wrapper function for _binary_c_bindings.return_minimum_orbit_for_RLOF</p>
<p>Handles the output and returns the minimum orbital period at which RLOF just does not occur at ZAMS</p>
<dl class="field-list simple">
@@ -304,8 +217,8 @@
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.useful_funcs.minimum_separation_for_RLOF">
-<code class="sig-prename descclassname">binarycpython.utils.useful_funcs.</code><code class="sig-name descname">minimum_separation_for_RLOF</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">M1</span></em>, <em class="sig-param"><span class="n">M2</span></em>, <em class="sig-param"><span class="n">metallicity</span></em>, <em class="sig-param"><span class="n">store_memaddr</span><span class="o">=</span><span class="default_value">- 1</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/useful_funcs.html#minimum_separation_for_RLOF"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.useful_funcs.minimum_separation_for_RLOF" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.useful_funcs.minimum_separation_for_RLOF">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.useful_funcs.</span></span><span class="sig-name descname"><span class="pre">minimum_separation_for_RLOF</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">M1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">M2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">metallicity</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">store_memaddr</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">-</span> <span class="pre">1</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/useful_funcs.html#minimum_separation_for_RLOF"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.useful_funcs.minimum_separation_for_RLOF" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Wrapper function for _binary_c_bindings.return_minimum_orbit_for_RLOF</p>
<p>Handles the output and returns the minimum separation at which RLOF just does not occur at ZAMS</p>
<dl class="field-list simple">
@@ -324,8 +237,8 @@
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.useful_funcs.ragb">
-<code class="sig-prename descclassname">binarycpython.utils.useful_funcs.</code><code class="sig-name descname">ragb</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">m</span></em>, <em class="sig-param"><span class="n">z</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/useful_funcs.html#ragb"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.useful_funcs.ragb" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.useful_funcs.ragb">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.useful_funcs.</span></span><span class="sig-name descname"><span class="pre">ragb</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">m</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">z</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/useful_funcs.html#ragb"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.useful_funcs.ragb" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function to calculate radius of a star in units of solar radii at first thermal pulse as a function of mass (Z=0.02 only, but also good for Z=0.0001)</p>
<p>TODO: ask rob about this function</p>
<dl class="field-list simple">
@@ -345,8 +258,8 @@
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.useful_funcs.roche_lobe">
-<code class="sig-prename descclassname">binarycpython.utils.useful_funcs.</code><code class="sig-name descname">roche_lobe</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">q</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/useful_funcs.html#roche_lobe"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.useful_funcs.roche_lobe" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.useful_funcs.roche_lobe">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.useful_funcs.</span></span><span class="sig-name descname"><span class="pre">roche_lobe</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">q</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/useful_funcs.html#roche_lobe"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.useful_funcs.roche_lobe" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>A function to evaluate R_L/a(q), Eggleton 1983.</p>
<p># TODO: check the definition of the mass ratio
# TODO: check whether the logs are correct</p>
@@ -364,8 +277,8 @@
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.useful_funcs.rzams">
-<code class="sig-prename descclassname">binarycpython.utils.useful_funcs.</code><code class="sig-name descname">rzams</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">m</span></em>, <em class="sig-param"><span class="n">z</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/useful_funcs.html#rzams"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.useful_funcs.rzams" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.useful_funcs.rzams">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.useful_funcs.</span></span><span class="sig-name descname"><span class="pre">rzams</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">m</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">z</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/useful_funcs.html#rzams"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.useful_funcs.rzams" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Function to determine the radius of a ZAMS star as a function of m and z:</p>
<p>Based on the fits of Tout et al., 1996, MNRAS, 281, 257</p>
<dl class="field-list simple">
@@ -382,8 +295,8 @@
</dd></dl>
<dl class="py function">
-<dt id="binarycpython.utils.useful_funcs.zams_collision">
-<code class="sig-prename descclassname">binarycpython.utils.useful_funcs.</code><code class="sig-name descname">zams_collision</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">m1</span></em>, <em class="sig-param"><span class="n">m2</span></em>, <em class="sig-param"><span class="n">sep</span></em>, <em class="sig-param"><span class="n">e</span></em>, <em class="sig-param"><span class="n">z</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/useful_funcs.html#zams_collision"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.useful_funcs.zams_collision" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="binarycpython.utils.useful_funcs.zams_collision">
+<span class="sig-prename descclassname"><span class="pre">binarycpython.utils.useful_funcs.</span></span><span class="sig-name descname"><span class="pre">zams_collision</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">m1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">m2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sep</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">e</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">z</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/useful_funcs.html#zams_collision"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.useful_funcs.zams_collision" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>given m1,m2, separation and eccentricity (and metallicity)
determine if two stars collide on the ZAMS</p>
<dl class="field-list simple">
@@ -405,68 +318,43 @@ determine if two stars collide on the ZAMS</p>
</dl>
</dd></dl>
-</div>
+</section>
</div>
-
</div>
- <footer>
-
- <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
-
- <a href="example_notebooks.html" class="btn btn-neutral float-right" title="Example notebooks" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
-
-
- <a href="stellar_types.html" class="btn btn-neutral float-left" title="stellar_types module" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
-
+ <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
+ <a href="stellar_types.html" class="btn btn-neutral float-left" title="stellar_types module" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
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- <p>
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- © Copyright 2021, David Hendriks, Robert Izzard
-
- </p>
+ <p>© Copyright 2021, David Hendriks, Robert Izzard.</p>
</div>
-
-
-
- Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a
-
- <a href="https://github.com/rtfd/sphinx_rtd_theme">theme</a>
-
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+ Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
+ <a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
provided by <a href="https://readthedocs.org">Read the Docs</a>.
+
<br><br>
-Generated on binarycpython git branch: master git revision 0886cd4f1d7f43222aac21d6ed91e917b67b20fc url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/tree/master">git url</a>.
+Generated on binarycpython git branch: auto_resolution git revision be7bd630af892a785312affc34d87c57eb337fd3 url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/tree/auto_resolution">git url</a>.
<br><br>
-Using binary_c with bit branch newmaster: git revision: "6185:20210910:1621c23a5" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/newmaster">git url</a>.
+Using binary_c with bit branch master: git revision: "6209:20211006:c4a4c332e" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/master">git url</a>.
</footer>
-
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-
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-
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-
-
- <script type="text/javascript">
+ <script>
jQuery(function () {
SphinxRtdTheme.Navigation.enable(true);
});
- </script>
-
-
-
-
-
+ </script>
</body>
</html>
\ No newline at end of file
diff --git a/docs/source/_templates/footer.html b/docs/source/_templates/footer.html
index 5ce2068330b83eb6854c4df9e437e480fd83b1ef..b0a4817f8cdabd3c6e655d5e7ca239411d8d1c7a 100644
--- a/docs/source/_templates/footer.html
+++ b/docs/source/_templates/footer.html
@@ -2,8 +2,8 @@
{%- block extrafooter %}
<br><br>
-Generated on binarycpython git branch: master git revision 0886cd4f1d7f43222aac21d6ed91e917b67b20fc url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/tree/master">git url</a>.
+Generated on binarycpython git branch: auto_resolution git revision be7bd630af892a785312affc34d87c57eb337fd3 url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/tree/auto_resolution">git url</a>.
<br><br>
-Using binary_c with bit branch newmaster: git revision: "6185:20210910:1621c23a5" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/newmaster">git url</a>.
+Using binary_c with bit branch master: git revision: "6209:20211006:c4a4c332e" url: <a href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/tree/master">git url</a>.
{% endblock %}
\ No newline at end of file
diff --git a/docs/source/binary_c_parameters.rst b/docs/source/binary_c_parameters.rst
index cdce51580c9e3478b29c356fadc3e11bb84ac62b..a47b428512a8495e31b1c6224fec98e3c4ffd247 100644
--- a/docs/source/binary_c_parameters.rst
+++ b/docs/source/binary_c_parameters.rst
@@ -4,7 +4,7 @@ The following chapter contains all the parameters that the current version of bi
This information was obtained by the following binary_c build:
- **binary_c git branch**: newmaster **binary_c git revision**: 6185:20210910:1621c23a5 **Built on**: Sep 10 2021 15:05:46
+ **binary_c git branch**: master **binary_c git revision**: 6209:20211006:c4a4c332e **Built on**: Oct 6 2021 08:31:27
Section: stars
@@ -2537,6 +2537,12 @@ Section: output
| **Default value**: NULL
| **Extra**: Ignore
+| **Parameter**: tides_diagnosis_log
+| **Description**: Enable logging to test MINT tides. Requires MINT. Choices are: 0 disabled, 1 enable lambda test.
+| **Parameter input type**: Integer
+| **Default value**: 0
+| **Extra**: Ignore
+
Section: input
--------------
diff --git a/docs/source/grid_options_descriptions.rst b/docs/source/grid_options_descriptions.rst
index 84538e2c4a51e19e6c1e6299dcea91c1c5e2d5f2..21095484f9b57a46dc4b825c59c2ac450bacb08f 100644
--- a/docs/source/grid_options_descriptions.rst
+++ b/docs/source/grid_options_descriptions.rst
@@ -1,7 +1,7 @@
Population grid code options
============================
The following chapter contains all grid code options, along with their descriptions
-There are 2 options that are not described yet.
+There are 4 options that are not described yet.
Public options
@@ -13,8 +13,6 @@ The following options are meant to be changed by the user.
| **C_logging_code**: Variable to store the exact code that is used for the custom_logging. In this way the user can do more complex logging, as well as putting these logging strings in files.
-| **amt_cores**: The amount of cores that the population grid will use. The multiprocessing is useful but make sure to figure out how many logical cores the machine has. The core is multi processed, not multi threaded, and will gain no extra speed when amt_cores exceeds the amount of logical cores. Input: int
-
| **combine_ensemble_with_thread_joining**: Boolean flag on whether to combine everything and return it to the user or if false: write it to data_dir/ensemble_output_{population_id}_{thread_id}.json
| **condor**: Int flag whether to use a condor type population evolution. Not implemented yet.
@@ -27,7 +25,9 @@ The following options are meant to be changed by the user.
| **evolution_type**: Variable containing the type of evolution used of the grid. Multiprocessing or linear processing
-| **failed_systems_threshold**: Variable storing the maximum amount of systems that are allowed to fail before logging their command line arguments to failed_systems log files
+| **exit_after_dry_run**: No description available yet
+
+| **failed_systems_threshold**: Variable storing the maximum number of systems that are allowed to fail before logging their command line arguments to failed_systems log files
| **gridcode_filename**: Filename for the grid code. Set and used by the population object. TODO: allow the user to provide their own function, rather than only a generated function.
@@ -49,6 +49,10 @@ The following options are meant to be changed by the user.
| **multiplicity_fraction_function**: Which multiplicity fraction function to use. 0: None, 1: Arenou 2010, 2: Rhagavan 2010, 3: M&S 2017
+| **n_logging_stats**: No description available yet
+
+| **num_cores**: The number of cores that the population grid will use. The multiprocessing is useful but make sure to figure out how many logical cores the machine has (use e.g. psutil.cpu_count(logical=False) to find the true number of cores, psutil.cpu_count(logical=True) to find the number of logical cores). The core is multi processed, not multi threaded, and will gain no extra speed when num_cores exceeds the number of logical cores. Input: int
+
| **parse_function**: Function that the user can provide to handle the output the binary_c. This function has to take the arguments (self, output). Its best not to return anything in this function, and just store stuff in the self.grid_results dictionary, or just output results to a file
| **repeat**: Factor of how many times a system should be repeated. Consider the evolution splitting binary_c argument for supernovae kick repeating.
@@ -164,13 +168,13 @@ The following options are not meant to be changed by the user, as these options
| **_end_time_evolution**: Variable storing the end timestamp of the population evolution. Set by the object itself
-| **_errors_exceeded**: Variable storing a Boolean flag whether the amount of errors was higher than the set threshold (failed_systems_threshold). If True, then the command line arguments of the failing systems will not be stored in the failed_system_log files.
+| **_errors_exceeded**: Variable storing a Boolean flag whether the number of errors was higher than the set threshold (failed_systems_threshold). If True, then the command line arguments of the failing systems will not be stored in the failed_system_log files.
| **_errors_found**: Variable storing a Boolean flag whether errors by binary_c are encountered.
| **_evolution_type_options**: List containing the evolution type options.
-| **_failed_count**: Variable storing the amount of failed systems.
+| **_failed_count**: Variable storing the number of failed systems.
| **_failed_prob**: Variable storing the total probability of all the failed systems
@@ -198,7 +202,7 @@ The following options are not meant to be changed by the user, as these options
| **_total_probability_weighted_mass_run**: To count the total mass * probability for each system that thread/process has ran
-| **_total_starcount**: Variable storing the total amount of systems in the generator. Used and set by the population object.
+| **_total_starcount**: Variable storing the total number of systems in the generator. Used and set by the population object.
| **_zero_prob_stars_skipped**: Internal counter to track how many systems are skipped because they have 0 probability
diff --git a/docs/source/notebook_HRD.ipynb b/docs/source/notebook_HRD.ipynb
index 52590f8a2a6abc7245e9ea0c08d274432cd2a1ad..bf95d554d2125de449ec4b8404550132e06091f7 100644
--- a/docs/source/notebook_HRD.ipynb
+++ b/docs/source/notebook_HRD.ipynb
@@ -264,7 +264,7 @@
"## Evolving the grid\n",
"Now that we configured all the main parts of the population object, we can actually run the population! Doing this is straightforward: `population.evolve()`\n",
"\n",
- "This will start up the processing of all the systems. We can control how many cores are used by settings `amt_cores`. By setting the `verbosity` of the population object to a higher value we can get a lot of verbose information about the run, but for now we will set it to 0.\n",
+ "This will start up the processing of all the systems. We can control how many cores are used by settings `num_cores`. By setting the `verbosity` of the population object to a higher value we can get a lot of verbose information about the run, but for now we will set it to 0.\n",
"\n",
"There are many grid_options that can lead to different behaviour of the evolution of the grid. Please do have a look at those: [grid options docs](https://ri0005.pages.surrey.ac.uk/binary_c-python/grid_options_descriptions.html), and try "
]
@@ -300,7 +300,7 @@
" # verbose output is not required \n",
" verbosity=0,\n",
" # set number of threads (i.e. number of CPU cores we use)\n",
- " amt_cores=4,\n",
+ " num_cores=4,\n",
" )\n",
"\n",
"# Evolve the population - this is the slow, number-crunching step\n",
@@ -796,7 +796,7 @@
],
"metadata": {
"kernelspec": {
- "display_name": "Python 3",
+ "display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
@@ -810,7 +810,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
- "version": "3.6.4"
+ "version": "3.9.5"
}
},
"nbformat": 4,
diff --git a/docs/source/notebook_common_envelope_evolution.ipynb b/docs/source/notebook_common_envelope_evolution.ipynb
index 526320ccf954c1ed86c6d5c641204c4a9345bbe5..feb6b18e6a264b08eab1e52d639106123f494cf5 100644
--- a/docs/source/notebook_common_envelope_evolution.ipynb
+++ b/docs/source/notebook_common_envelope_evolution.ipynb
@@ -363,7 +363,7 @@
"metadata": {},
"source": [
"## Evolving the grid\n",
- "Now we actually run the population. This may take a little while. You can set amt_cores higher if you have a powerful machine."
+ "Now we actually run the population. This may take a little while. You can set num_cores higher if you have a powerful machine."
]
},
{
@@ -378,7 +378,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "adding: amt_cores=4 to grid_options\n",
+ "adding: num_cores=4 to grid_options\n",
"Creating and loading custom logging functionality\n",
"Generating grid code\n",
"Generating grid code\n",
@@ -540,7 +540,7 @@
"# set number of threads\n",
"population.set(\n",
" # set number of threads (i.e. number of CPU cores we use)\n",
- " amt_cores=4,\n",
+ " num_cores=4,\n",
" )\n",
"\n",
"# Evolve the population - this is the slow, number-crunching step\n",
@@ -686,7 +686,7 @@
],
"metadata": {
"kernelspec": {
- "display_name": "Python 3",
+ "display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
@@ -700,7 +700,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
- "version": "3.6.4"
+ "version": "3.9.5"
}
},
"nbformat": 4,
diff --git a/docs/source/notebook_individual_systems.ipynb b/docs/source/notebook_individual_systems.ipynb
index 85aef1e3962a1626f37a9ef36bf5e16f479eb68e..50c604385e0365b3404fb8d6427b9b9f0c0f7fbf 100644
--- a/docs/source/notebook_individual_systems.ipynb
+++ b/docs/source/notebook_individual_systems.ipynb
@@ -8,19 +8,22 @@
"# Tutorial: Running individual systems with binary_c-python\n",
"This notebook will show you how to run single systems and analyze their results.\n",
"\n",
- "It can be useful to have some functions to quickly run a single system to e.g. inspect what evolutionary steps a specific system goes through, to plot the mass loss evolution of a single star, etc. "
+ "It can be useful to have some functions to quickly run a single system to, for example, inspect what evolutionary steps a specific system goes through, to plot the mass loss evolution of a single system, etc. "
]
},
{
"cell_type": "markdown",
"id": "dd5d9ec7-5791-45f1-afbd-225947e2a583",
- "metadata": {},
+ "metadata": {
+ "tags": []
+ },
"source": [
- "## Single system with run_wrapper\n",
+ "## Single system with run_system_wrapper\n",
+ "\n",
"The simplest method to run a single system is to use the run_system wrapper. This function deals with setting up the argument string, makes sure all the required parameters are included and handles setting and cleaning up the custom logging functionality (see notebook_custom_logging).\n",
"\n",
"As arguments to this function we can add any of the parameters that binary_c itself actually knows, as well as:\n",
- "- custom_logging_code: string containing a print statement that binary_c can use to print information\n",
+ "- custom_logging_code: string containing a Printf statement that binary_c can use to print information\n",
"- log_filename: path of the logfile that binary_c generates\n",
"- parse_function: function that handles parsing the output of binary-c"
]
@@ -86,7 +89,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- " TIME M1 M2 K1 K2 SEP PER ECC R1/ROL1 R2/ROL2 TYPE RANDOM_SEED=17089 RANDOM_COUNT=0\n",
+ " TIME M1 M2 K1 K2 SEP PER ECC R1/ROL1 R2/ROL2 TYPE RANDOM_SEED=12122 RANDOM_COUNT=0\n",
" 0.0000 1.000 0.000 1 15 -1 -1 -1.00 0.000 0.000 \"INITIAL \"\n",
" 11003.1302 1.000 0.000 2 15 -1 -1 -1.00 0.000 0.000 \"OFF_MS\"\n",
" 11003.1302 1.000 0.000 2 15 -1 -1 -1.00 0.000 0.000 \"TYPE_CHNGE\"\n",
@@ -225,18 +228,18 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "0 time mass initial_mass stellar_type\n",
- "1 0 1 1 1\n",
- "2 0 1 1 1\n",
- "3 1e-06 1 1 1\n",
- "4 2e-06 1 1 1\n",
- "5 3e-06 1 1 1\n",
- "... ... ... ... ...\n",
- "1617 12461.8 0.546683 1 6\n",
- "1618 12461.9 0.517749 1 11\n",
- "1619 13461.9 0.517749 1 11\n",
- "1620 14461.9 0.517749 1 11\n",
- "1621 15000 0.517749 1 11\n",
+ "0 time mass initial_mass stellar_type\n",
+ "1 0.0 1.0 1.0 1.0\n",
+ "2 0.0 1.0 1.0 1.0\n",
+ "3 0.000001 1.0 1.0 1.0\n",
+ "4 0.000002 1.0 1.0 1.0\n",
+ "5 0.000003 1.0 1.0 1.0\n",
+ "... ... ... ... ...\n",
+ "1617 12461.819616 0.546683 1.0 6.0\n",
+ "1618 12461.945773 0.517749 1.0 11.0\n",
+ "1619 13461.945773 0.517749 1.0 11.0\n",
+ "1620 14461.945773 0.517749 1.0 11.0\n",
+ "1621 15000.0 0.517749 1.0 11.0\n",
"\n",
"[1621 rows x 4 columns]\n"
]
@@ -358,7 +361,7 @@
"Creating and loading custom logging functionality\n",
"Running binary_c M_1 10 api_log_filename_prefix /tmp/binary_c_python/notebooks/notebook_individual_systems\n",
"Cleaning up the custom logging stuff. type: single\n",
- "Removed /tmp/binary_c_python/custom_logging/libcustom_logging_8967553693ac4e11a49c42d4eef773e8.so\n",
+ "Removed /tmp/binary_c_python/custom_logging/libcustom_logging_6d4ed30fa6684630885c08523336d45f.so\n",
"EXAMPLE_MASSLOSS 0.000000000000e+00 10 0 10 1\n",
"EXAMPLE_MASSLOSS 0.000000000000e+00 10 10 10 1\n",
"EXAMPLE_MASSLOSS 1.000000000000e-06 10 10 10 1\n",
@@ -460,13 +463,13 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "adding: parse_function=<function object_parse_function at 0x7fb4d41ebbf8> to grid_options\n",
+ "adding: parse_function=<function object_parse_function at 0x14938275de50> to grid_options\n",
"<<<< Warning: Key does not match previously known parameter: adding: output_dir=/tmp/binary_c_python/notebooks/notebook_individual_systems to custom_options >>>>\n",
"adding: api_log_filename_prefix=/tmp/binary_c_python/notebooks/notebook_individual_systems to BSE_options\n",
"Creating and loading custom logging functionality\n",
"Running binary_c M_1 10 api_log_filename_prefix /tmp/binary_c_python/notebooks/notebook_individual_systems\n",
"Cleaning up the custom logging stuff. type: single\n",
- "Removed /tmp/binary_c_python/custom_logging/libcustom_logging_5d7779e8190e4b79b10c7e6a44cb0e7e.so\n",
+ "Removed /tmp/binary_c_python/custom_logging/libcustom_logging_3bc2f679982a4df6a2b83d382e83d724.so\n",
"[['time', 'mass', 'initial_mass', 'stellar_type'], [0.0, 10.0, 0.0, 10.0, 1.0], [0.0, 10.0, 10.0, 10.0, 1.0], [1e-06, 10.0, 10.0, 10.0, 1.0]]\n",
"dict_keys(['time', 'mass', 'initial_mass', 'stellar_type'])\n"
]
@@ -496,7 +499,7 @@
"## Single system via API functionality\n",
"It is possible to construct your own functionality to run a single system by directly calling the API function to run a system. Under the hood all the other functions and wrappers actually use this API.\n",
"\n",
- "There are less failsafes for this method, so this make sure the input is correct and binary_c knows all the arguments you pass in.\n",
+ "There are fewer failsafes for this method, so this make sure the input is correct and binary_c knows all the arguments you pass in.\n",
"\n",
"for more details on this API function see `notebook_api_functions`"
]
@@ -519,7 +522,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "SINGLE_STAR_LIFETIME 15 14.9947\n",
+ "SINGLE_STAR_LIFETIME 15 14.9927\n",
"\n"
]
}
diff --git a/docs/source/notebook_luminosity_function_binaries.ipynb b/docs/source/notebook_luminosity_function_binaries.ipynb
index c6b5f1e64cc36c684fdf5cefe0fae4b450a1c936..f054310a62ea8a37e55df724be75879dababbe38 100644
--- a/docs/source/notebook_luminosity_function_binaries.ipynb
+++ b/docs/source/notebook_luminosity_function_binaries.ipynb
@@ -5,7 +5,7 @@
"id": "bbbaafbb-fd7d-4b73-a970-93506ba35d71",
"metadata": {},
"source": [
- "# Zero-age stellar luminosity function in binaries\n",
+ "# Example use case: Zero-age stellar luminosity function in binaries\n",
"\n",
"In this notebook we compute the luminosity function of the zero-age main-sequence by running a population of binary stars using binary_c. \n",
"\n",
@@ -369,7 +369,7 @@
"## Evolving the grid\n",
"Now that we configured all the main parts of the population object, we can actually run the population! Doing this is straightforward: `population.evolve()`\n",
"\n",
- "This will start up the processing of all the systems. We can control how many cores are used by settings `amt_cores`. By setting the `verbosity` of the population object to a higher value we can get a lot of verbose information about the run, but for now we will set it to 0.\n",
+ "This will start up the processing of all the systems. We can control how many cores are used by settings `num_cores`. By setting the `verbosity` of the population object to a higher value we can get a lot of verbose information about the run, but for now we will set it to 0.\n",
"\n",
"There are many grid_options that can lead to different behaviour of the evolution of the grid. Please do have a look at those: [grid options docs](https://ri0005.pages.surrey.ac.uk/binary_c-python/grid_options_descriptions.html), and try "
]
@@ -386,7 +386,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "adding: amt_cores=4 to grid_options\n",
+ "adding: num_cores=4 to grid_options\n",
"Running the population now, this may take a little while...\n",
"Creating and loading custom logging functionality\n",
"Generating grid code\n",
@@ -547,7 +547,7 @@
" # verbose output is not required \n",
" verbosity=1,\n",
" # set number of threads (i.e. number of CPU cores we use)\n",
- " amt_cores=4,\n",
+ " num_cores=4,\n",
" )\n",
"\n",
"# Evolve the population - this is the slow, number-crunching step\n",
diff --git a/docs/source/notebook_luminosity_function_single.ipynb b/docs/source/notebook_luminosity_function_single.ipynb
index cdae316f90802fe46611ea17732506c0410aef55..09af8acc59f26e909901c0649e02a0d0864b789a 100644
--- a/docs/source/notebook_luminosity_function_single.ipynb
+++ b/docs/source/notebook_luminosity_function_single.ipynb
@@ -297,7 +297,7 @@
"## Evolving the grid\n",
"Now that we configured all the main parts of the population object, we can actually run the population! Doing this is straightforward: `population.evolve()`\n",
"\n",
- "This will start up the processing of all the systems. We can control how many cores are used by settings `amt_cores`. By setting the `verbosity` of the population object to a higher value we can get a lot of verbose information about the run, but for now we will set it to 0.\n",
+ "This will start up the processing of all the systems. We can control how many cores are used by settings `num_cores`. By setting the `verbosity` of the population object to a higher value we can get a lot of verbose information about the run, but for now we will set it to 0.\n",
"\n",
"There are many grid_options that can lead to different behaviour of the evolution of the grid. Please do have a look at those: [grid options docs](https://ri0005.pages.surrey.ac.uk/binary_c-python/grid_options_descriptions.html), and try "
]
@@ -332,7 +332,7 @@
" # verbose output is not required \n",
" verbosity=0,\n",
" # set number of threads (i.e. number of CPU cores we use)\n",
- " amt_cores=2,\n",
+ " num_cores=2,\n",
" )\n",
"\n",
"# Evolve the population - this is the slow, number-crunching step\n",
@@ -703,7 +703,7 @@
],
"metadata": {
"kernelspec": {
- "display_name": "Python 3",
+ "display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
@@ -717,7 +717,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
- "version": "3.6.4"
+ "version": "3.9.5"
}
},
"nbformat": 4,
diff --git a/docs/source/notebook_population.ipynb b/docs/source/notebook_population.ipynb
index a24638c0bd3a15a57bbf611fccb71b2100c75945..1ec2f94d3b03db0bccabe6ea2d2c100946add611 100644
--- a/docs/source/notebook_population.ipynb
+++ b/docs/source/notebook_population.ipynb
@@ -62,7 +62,7 @@
"adding: orbital_period=45000000080 to BSE_options\n",
"adding: max_evolution_time=15000 to BSE_options\n",
"adding: eccentricity=0.02 to BSE_options\n",
- "adding: amt_cores=2 to grid_options\n",
+ "adding: num_cores=2 to grid_options\n",
"adding: tmp_dir=/tmp/binary_c_python/notebooks/notebook_population to grid_options\n",
"<<<< Warning: Key does not match previously known parameter: adding: data_dir=/tmp/binary_c_python/notebooks/notebook_population/example_python_population_result to custom_options >>>>\n",
"<<<< Warning: Key does not match previously known parameter: adding: base_filename=example_pop.dat to custom_options >>>>\n",
@@ -92,7 +92,7 @@
"\n",
"\n",
" # grid_options\n",
- " amt_cores=2,\n",
+ " num_cores=2,\n",
" tmp_dir=TMP_DIR,\n",
" \n",
" # Custom options # TODO: need to be set in grid_options probably\n",
@@ -219,7 +219,7 @@
" Examples:\n",
" range = [math.log(m_min), math.log(m_max)]\n",
" resolution:\n",
- " Resolution of the sampled range (amount of samples).\n",
+ " Resolution of the sampled range (number of samples).\n",
" TODO: check if this is used anywhere\n",
" \n",
" Examples:\n",
@@ -496,7 +496,7 @@
" print(line)\n",
" \n",
" if not len(parameters) == len(values):\n",
- " print(\"Amount of column names isnt equal to amount of columns\")\n",
+ " print(\"Number of column names isnt equal to number of columns\")\n",
" raise ValueError\n",
"\n",
" if not os.path.exists(outfilename):\n",
@@ -520,7 +520,7 @@
"## Evolving the grid\n",
"Now that we configured all the main parts of the population object, we can actually run the population! Doing this is straightforward: `example_pop.evolve()`\n",
"\n",
- "This will start up the processing of all the systems. We can control how many cores are used by settings `amt_cores`. By setting the `verbosity` of the population object to a higher value we can get a lot of verbose information about the run, but for now we will set it to 0.\n",
+ "This will start up the processing of all the systems. We can control how many cores are used by settings `num_cores`. By setting the `verbosity` of the population object to a higher value we can get a lot of verbose information about the run, but for now we will set it to 0.\n",
"\n",
"There are many grid_options that can lead to different behaviour of the evolution of the grid. Please do have a look at those: [grid options docs](https://ri0005.pages.surrey.ac.uk/binary_c-python/grid_options_descriptions.html), and try "
]
@@ -770,7 +770,7 @@
" values = el.split()[1:]\n",
"\n",
" if not len(parameters) == len(values):\n",
- " print(\"Amount of column names isnt equal to amount of columns\")\n",
+ " print(\"Number of column names isnt equal to number of columns\")\n",
" raise ValueError\n",
"\n",
" if not os.path.exists(outfilename):\n",
@@ -797,7 +797,7 @@
" eccentricity=0.02, # bse_options\n",
" \n",
" # grid_options\n",
- " amt_cores=2,\n",
+ " num_cores=2,\n",
" tmp_dir=TMP_DIR,\n",
"\n",
" # Custom options: the data directory and the output filename\n",
@@ -963,7 +963,7 @@
" values = el.split()[1:]\n",
"\n",
" if not len(parameters) == len(values):\n",
- " print(\"Amount of column names isnt equal to amount of columns\")\n",
+ " print(\"Number of column names isnt equal to number of columns\")\n",
" raise ValueError\n",
"\n",
" if not os.path.exists(outfilename):\n",
@@ -990,7 +990,7 @@
" eccentricity=0.02, # bse_options\n",
" \n",
" # grid_options\n",
- " amt_cores=2, # grid_options\n",
+ " num_cores=2, # grid_options\n",
" tmp_dir=TMP_DIR,\n",
"\n",
" # Custom options: the data directory and the output filename\n",
diff --git a/examples/notebook_HRD.ipynb b/examples/notebook_HRD.ipynb
index 23202ff3a1af319f4a7c3d9e99e925cc24e10466..bf95d554d2125de449ec4b8404550132e06091f7 100644
--- a/examples/notebook_HRD.ipynb
+++ b/examples/notebook_HRD.ipynb
@@ -264,7 +264,7 @@
"## Evolving the grid\n",
"Now that we configured all the main parts of the population object, we can actually run the population! Doing this is straightforward: `population.evolve()`\n",
"\n",
- "This will start up the processing of all the systems. We can control how many cores are used by settings `amt_cores`. By setting the `verbosity` of the population object to a higher value we can get a lot of verbose information about the run, but for now we will set it to 0.\n",
+ "This will start up the processing of all the systems. We can control how many cores are used by settings `num_cores`. By setting the `verbosity` of the population object to a higher value we can get a lot of verbose information about the run, but for now we will set it to 0.\n",
"\n",
"There are many grid_options that can lead to different behaviour of the evolution of the grid. Please do have a look at those: [grid options docs](https://ri0005.pages.surrey.ac.uk/binary_c-python/grid_options_descriptions.html), and try "
]
@@ -300,7 +300,7 @@
" # verbose output is not required \n",
" verbosity=0,\n",
" # set number of threads (i.e. number of CPU cores we use)\n",
- " amt_cores=4,\n",
+ " num_cores=4,\n",
" )\n",
"\n",
"# Evolve the population - this is the slow, number-crunching step\n",
diff --git a/examples/notebook_common_envelope_evolution.ipynb b/examples/notebook_common_envelope_evolution.ipynb
index 580dbcfbaa9c5358f10f897c6aa9496d1e2a952f..feb6b18e6a264b08eab1e52d639106123f494cf5 100644
--- a/examples/notebook_common_envelope_evolution.ipynb
+++ b/examples/notebook_common_envelope_evolution.ipynb
@@ -363,7 +363,7 @@
"metadata": {},
"source": [
"## Evolving the grid\n",
- "Now we actually run the population. This may take a little while. You can set amt_cores higher if you have a powerful machine."
+ "Now we actually run the population. This may take a little while. You can set num_cores higher if you have a powerful machine."
]
},
{
@@ -378,7 +378,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "adding: amt_cores=4 to grid_options\n",
+ "adding: num_cores=4 to grid_options\n",
"Creating and loading custom logging functionality\n",
"Generating grid code\n",
"Generating grid code\n",
@@ -540,7 +540,7 @@
"# set number of threads\n",
"population.set(\n",
" # set number of threads (i.e. number of CPU cores we use)\n",
- " amt_cores=4,\n",
+ " num_cores=4,\n",
" )\n",
"\n",
"# Evolve the population - this is the slow, number-crunching step\n",
diff --git a/examples/notebook_luminosity_function_binaries.ipynb b/examples/notebook_luminosity_function_binaries.ipynb
index 51f8660853f181f1d7704717aae95f923c826427..f054310a62ea8a37e55df724be75879dababbe38 100644
--- a/examples/notebook_luminosity_function_binaries.ipynb
+++ b/examples/notebook_luminosity_function_binaries.ipynb
@@ -369,7 +369,7 @@
"## Evolving the grid\n",
"Now that we configured all the main parts of the population object, we can actually run the population! Doing this is straightforward: `population.evolve()`\n",
"\n",
- "This will start up the processing of all the systems. We can control how many cores are used by settings `amt_cores`. By setting the `verbosity` of the population object to a higher value we can get a lot of verbose information about the run, but for now we will set it to 0.\n",
+ "This will start up the processing of all the systems. We can control how many cores are used by settings `num_cores`. By setting the `verbosity` of the population object to a higher value we can get a lot of verbose information about the run, but for now we will set it to 0.\n",
"\n",
"There are many grid_options that can lead to different behaviour of the evolution of the grid. Please do have a look at those: [grid options docs](https://ri0005.pages.surrey.ac.uk/binary_c-python/grid_options_descriptions.html), and try "
]
@@ -386,7 +386,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "adding: amt_cores=4 to grid_options\n",
+ "adding: num_cores=4 to grid_options\n",
"Running the population now, this may take a little while...\n",
"Creating and loading custom logging functionality\n",
"Generating grid code\n",
@@ -547,7 +547,7 @@
" # verbose output is not required \n",
" verbosity=1,\n",
" # set number of threads (i.e. number of CPU cores we use)\n",
- " amt_cores=4,\n",
+ " num_cores=4,\n",
" )\n",
"\n",
"# Evolve the population - this is the slow, number-crunching step\n",
diff --git a/examples/notebook_luminosity_function_single.ipynb b/examples/notebook_luminosity_function_single.ipynb
index acab6b2d0fdbf914eaae70a47b9250c8b6b0977f..09af8acc59f26e909901c0649e02a0d0864b789a 100644
--- a/examples/notebook_luminosity_function_single.ipynb
+++ b/examples/notebook_luminosity_function_single.ipynb
@@ -297,7 +297,7 @@
"## Evolving the grid\n",
"Now that we configured all the main parts of the population object, we can actually run the population! Doing this is straightforward: `population.evolve()`\n",
"\n",
- "This will start up the processing of all the systems. We can control how many cores are used by settings `amt_cores`. By setting the `verbosity` of the population object to a higher value we can get a lot of verbose information about the run, but for now we will set it to 0.\n",
+ "This will start up the processing of all the systems. We can control how many cores are used by settings `num_cores`. By setting the `verbosity` of the population object to a higher value we can get a lot of verbose information about the run, but for now we will set it to 0.\n",
"\n",
"There are many grid_options that can lead to different behaviour of the evolution of the grid. Please do have a look at those: [grid options docs](https://ri0005.pages.surrey.ac.uk/binary_c-python/grid_options_descriptions.html), and try "
]
@@ -332,7 +332,7 @@
" # verbose output is not required \n",
" verbosity=0,\n",
" # set number of threads (i.e. number of CPU cores we use)\n",
- " amt_cores=2,\n",
+ " num_cores=2,\n",
" )\n",
"\n",
"# Evolve the population - this is the slow, number-crunching step\n",
diff --git a/examples/notebook_population.ipynb b/examples/notebook_population.ipynb
index a24638c0bd3a15a57bbf611fccb71b2100c75945..1ec2f94d3b03db0bccabe6ea2d2c100946add611 100644
--- a/examples/notebook_population.ipynb
+++ b/examples/notebook_population.ipynb
@@ -62,7 +62,7 @@
"adding: orbital_period=45000000080 to BSE_options\n",
"adding: max_evolution_time=15000 to BSE_options\n",
"adding: eccentricity=0.02 to BSE_options\n",
- "adding: amt_cores=2 to grid_options\n",
+ "adding: num_cores=2 to grid_options\n",
"adding: tmp_dir=/tmp/binary_c_python/notebooks/notebook_population to grid_options\n",
"<<<< Warning: Key does not match previously known parameter: adding: data_dir=/tmp/binary_c_python/notebooks/notebook_population/example_python_population_result to custom_options >>>>\n",
"<<<< Warning: Key does not match previously known parameter: adding: base_filename=example_pop.dat to custom_options >>>>\n",
@@ -92,7 +92,7 @@
"\n",
"\n",
" # grid_options\n",
- " amt_cores=2,\n",
+ " num_cores=2,\n",
" tmp_dir=TMP_DIR,\n",
" \n",
" # Custom options # TODO: need to be set in grid_options probably\n",
@@ -219,7 +219,7 @@
" Examples:\n",
" range = [math.log(m_min), math.log(m_max)]\n",
" resolution:\n",
- " Resolution of the sampled range (amount of samples).\n",
+ " Resolution of the sampled range (number of samples).\n",
" TODO: check if this is used anywhere\n",
" \n",
" Examples:\n",
@@ -496,7 +496,7 @@
" print(line)\n",
" \n",
" if not len(parameters) == len(values):\n",
- " print(\"Amount of column names isnt equal to amount of columns\")\n",
+ " print(\"Number of column names isnt equal to number of columns\")\n",
" raise ValueError\n",
"\n",
" if not os.path.exists(outfilename):\n",
@@ -520,7 +520,7 @@
"## Evolving the grid\n",
"Now that we configured all the main parts of the population object, we can actually run the population! Doing this is straightforward: `example_pop.evolve()`\n",
"\n",
- "This will start up the processing of all the systems. We can control how many cores are used by settings `amt_cores`. By setting the `verbosity` of the population object to a higher value we can get a lot of verbose information about the run, but for now we will set it to 0.\n",
+ "This will start up the processing of all the systems. We can control how many cores are used by settings `num_cores`. By setting the `verbosity` of the population object to a higher value we can get a lot of verbose information about the run, but for now we will set it to 0.\n",
"\n",
"There are many grid_options that can lead to different behaviour of the evolution of the grid. Please do have a look at those: [grid options docs](https://ri0005.pages.surrey.ac.uk/binary_c-python/grid_options_descriptions.html), and try "
]
@@ -770,7 +770,7 @@
" values = el.split()[1:]\n",
"\n",
" if not len(parameters) == len(values):\n",
- " print(\"Amount of column names isnt equal to amount of columns\")\n",
+ " print(\"Number of column names isnt equal to number of columns\")\n",
" raise ValueError\n",
"\n",
" if not os.path.exists(outfilename):\n",
@@ -797,7 +797,7 @@
" eccentricity=0.02, # bse_options\n",
" \n",
" # grid_options\n",
- " amt_cores=2,\n",
+ " num_cores=2,\n",
" tmp_dir=TMP_DIR,\n",
"\n",
" # Custom options: the data directory and the output filename\n",
@@ -963,7 +963,7 @@
" values = el.split()[1:]\n",
"\n",
" if not len(parameters) == len(values):\n",
- " print(\"Amount of column names isnt equal to amount of columns\")\n",
+ " print(\"Number of column names isnt equal to number of columns\")\n",
" raise ValueError\n",
"\n",
" if not os.path.exists(outfilename):\n",
@@ -990,7 +990,7 @@
" eccentricity=0.02, # bse_options\n",
" \n",
" # grid_options\n",
- " amt_cores=2, # grid_options\n",
+ " num_cores=2, # grid_options\n",
" tmp_dir=TMP_DIR,\n",
"\n",
" # Custom options: the data directory and the output filename\n",