diff --git a/binarycpython/utils/functions.py b/binarycpython/utils/functions.py
index da2c5bb5ec3888b441286e8b70c8ad4b60ed137f..675441579f7d9638ea3ed5e5a91f912bcc824d39 100644
--- a/binarycpython/utils/functions.py
+++ b/binarycpython/utils/functions.py
@@ -134,8 +134,8 @@ def create_hdf5(data_dir, name):
[file for file in content_data_dir if file.endswith("_settings.json")][0],
)
- with open(settings_file, "r") as f:
- settings_json = json.load(f)
+ with open(settings_file, "r") as settings_file:
+ settings_json = json.load(settings_file)
# Create settings group
settings_grp = f.create_group("settings")
@@ -380,7 +380,7 @@ def get_arg_keys():
return get_defaults().keys()
-def get_help(param_name, print_help=True, return_dict=False, fail_silently=False):
+def get_help(param_name="", print_help=True, return_dict=False, fail_silently=False):
"""
Function that returns the help info for a given parameter.
@@ -397,78 +397,82 @@ def get_help(param_name, print_help=True, return_dict=False, fail_silently=False
return_dict: wether to return the help info dictionary
"""
-
+
available_arg_keys = get_arg_keys()
- if param_name in available_arg_keys:
- help_info = binary_c_python_api.return_help(param_name)
- cleaned = [el for el in help_info.split("\n") if not el == ""]
-
- # Get line numbers
- did_you_mean_nr = [
- i for i, el in enumerate(cleaned) if el.startswith("Did you mean")
- ]
- parameter_line_nr = [
- i for i, el in enumerate(cleaned) if el.startswith("binary_c help")
- ]
- default_line_nr = [
- i for i, el in enumerate(cleaned) if el.startswith("Default")
- ]
- macros_line_nr = [
- i for i, el in enumerate(cleaned) if el.startswith("Available")
- ]
-
- help_info_dict = {}
-
- # Get alternatives
- if did_you_mean_nr:
- alternatives = cleaned[did_you_mean_nr[0] + 1 : parameter_line_nr[0]]
- alternatives = [el.strip() for el in alternatives]
- help_info_dict["alternatives"] = alternatives
-
- # Information about the parameter
- parameter_line = cleaned[parameter_line_nr[0]]
- parameter_name = parameter_line.split(":")[1].strip().split(" ")[0]
- parameter_value_input_type = (
- " ".join(parameter_line.split(":")[1].strip().split(" ")[1:])
- .replace("<", "")
- .replace(">", "")
- )
+ if not param_name:
+ print("Please set the param_name to any of the following:\n {}".format(sorted(available_arg_keys)))
+ return None
+ else:
+ if param_name in available_arg_keys:
+ help_info = binary_c_python_api.return_help(param_name)
+ cleaned = [el for el in help_info.split("\n") if not el == ""]
+
+ # Get line numbers
+ did_you_mean_nr = [
+ i for i, el in enumerate(cleaned) if el.startswith("Did you mean")
+ ]
+ parameter_line_nr = [
+ i for i, el in enumerate(cleaned) if el.startswith("binary_c help")
+ ]
+ default_line_nr = [
+ i for i, el in enumerate(cleaned) if el.startswith("Default")
+ ]
+ macros_line_nr = [
+ i for i, el in enumerate(cleaned) if el.startswith("Available")
+ ]
+
+ help_info_dict = {}
+
+ # Get alternatives
+ if did_you_mean_nr:
+ alternatives = cleaned[did_you_mean_nr[0] + 1 : parameter_line_nr[0]]
+ alternatives = [el.strip() for el in alternatives]
+ help_info_dict["alternatives"] = alternatives
+
+ # Information about the parameter
+ parameter_line = cleaned[parameter_line_nr[0]]
+ parameter_name = parameter_line.split(":")[1].strip().split(" ")[0]
+ parameter_value_input_type = (
+ " ".join(parameter_line.split(":")[1].strip().split(" ")[1:])
+ .replace("<", "")
+ .replace(">", "")
+ )
- help_info_dict["parameter_name"] = parameter_name
- help_info_dict["parameter_value_input_type"] = parameter_value_input_type
+ help_info_dict["parameter_name"] = parameter_name
+ help_info_dict["parameter_value_input_type"] = parameter_value_input_type
- description_line = " ".join(
- cleaned[parameter_line_nr[0] + 1 : default_line_nr[0]]
- )
- help_info_dict["description"] = description_line
+ description_line = " ".join(
+ cleaned[parameter_line_nr[0] + 1 : default_line_nr[0]]
+ )
+ help_info_dict["description"] = description_line
- # Default:
- default_line = cleaned[default_line_nr[0]]
- default_value = default_line.split(":")[-1].strip()
+ # Default:
+ default_line = cleaned[default_line_nr[0]]
+ default_value = default_line.split(":")[-1].strip()
- help_info_dict["default"] = default_value
+ help_info_dict["default"] = default_value
- # Get Macros:
- if macros_line_nr:
- macros = cleaned[macros_line_nr[0] + 1 :]
- help_info_dict["macros"] = macros
+ # Get Macros:
+ if macros_line_nr:
+ macros = cleaned[macros_line_nr[0] + 1 :]
+ help_info_dict["macros"] = macros
- if print_help:
- for key in help_info_dict.keys():
- print("{}:\n\t{}".format(key, help_info_dict[key]))
+ if print_help:
+ for key in help_info_dict.keys():
+ print("{}:\n\t{}".format(key, help_info_dict[key]))
- if return_dict:
- return help_info_dict
+ if return_dict:
+ return help_info_dict
- else:
- if not fail_silently:
- print(
- "{} is not a valid parameter name. Please choose from the following parameters:\n\t{}".format(
- param_name, list(available_arg_keys)
+ else:
+ if not fail_silently:
+ print(
+ "{} is not a valid parameter name. Please choose from the following parameters:\n\t{}".format(
+ param_name, list(available_arg_keys)
+ )
)
- )
- return None
+ return None
def run_system(**kwargs):
diff --git a/binarycpython/utils/grid.py b/binarycpython/utils/grid.py
index 7f9b6754a0dade92699ce4b78478f2dd6461b88c..3c3a9c4167b88eba3aab5735de55c650f5f74243 100644
--- a/binarycpython/utils/grid.py
+++ b/binarycpython/utils/grid.py
@@ -351,6 +351,16 @@ class Population(object):
include_binary_c_help_all=include_binary_c_help_all,
)
+ # Copy dict
+ all_info_cleaned = copy.deepcopy(all_info)
+
+
+ # Clean the all_info_dict: (i.e. transform the function objects to strings)
+ if all_info_cleaned.get('population_settings', None):
+ if all_info_cleaned['population_settings']['grid_options']['parse_function']:
+ all_info_cleaned['population_settings']['grid_options']['parse_function'] = str(all_info_cleaned['population_settings']['grid_options']['parse_function'])
+
+
if use_datadir:
base_name = os.path.splitext(self.custom_options["base_filename"])[0]
settings_name = base_name + "_settings.json"
@@ -366,14 +376,14 @@ class Population(object):
print("Writing settings to {}".format(settings_fullname))
# if not outfile.endswith('json'):
with open(settings_fullname, "w") as f:
- f.write(json.dumps(all_info, indent=4))
+ f.write(json.dumps(all_info_cleaned, indent=4))
else:
if self.grid_options["verbose"] > 0:
print("Writing settings to {}".format(outfile))
# if not outfile.endswith('json'):
with open(outfile, "w") as f:
- f.write(json.dumps(all_info, indent=4))
+ f.write(json.dumps(all_info_cleaned, indent=4))
def set_custom_logging(self):
"""
@@ -978,6 +988,7 @@ class Population(object):
code_string += "import numpy as np\n"
code_string += "from binarycpython.utils.distribution_functions import *\n"
code_string += "from binarycpython.utils.spacing_functions import *\n"
+ code_string += "from binarycpython.utils.useful_funcs import *\n"
code_string += "\n\n"
# Make the function
@@ -1123,7 +1134,7 @@ class Population(object):
code_string += (
indent * (depth + 1)
+ "{}".format(
- grid_variable["precode"].replace("\n", "\n" + indent * (depth + 1))
+ grid_variable["precode"].replace("\n", "\n" + indent * (depth))
)
+ "\n"
)
@@ -1440,9 +1451,9 @@ class Population(object):
# Define frequency
if self.grid_options['verbose'] == 1:
- print_freq = 10
- else:
print_freq = 1
+ else:
+ print_freq = 10
# Calculate amount of time left
diff --git a/examples/example_population.py b/examples/example_population.py
index 4ee06d7d7bd669dd4b9f19bb02a3180059597723..e3a9cab26203fdec33131e16cfaa895439c9f71a 100644
--- a/examples/example_population.py
+++ b/examples/example_population.py
@@ -6,13 +6,53 @@ import os
from binarycpython.utils.grid import Population
from binarycpython.utils.functions import get_help_all, get_help, create_hdf5
-
+from binarycpython.utils.custom_logging_functions import temp_dir
#########################################################
# This file serves as an example for running a population.
# The use of help(<function>) is a good way to inspect what parameters are there to use
#########################################################
+
+## Quick script to get some output
+def output_lines(output):
+ """
+ Function that outputs the lines that were recieved from the binary_c run.
+ """
+ return output.splitlines()
+
+def parse_function(self, output):
+ # extract info from the population instance
+ # TODO: think about whether this is smart. Passing around this object might be an overkill
+
+ # Get some information from the
+ data_dir = self.custom_options['data_dir']
+ base_filename = self.custom_options['base_filename']
+
+ # Check directory, make if necessary
+ os.makedirs(data_dir, exist_ok=True)
+
+ seperator = ' '
+
+ # Create filename
+ outfilename = os.path.join(data_dir, base_filename)
+
+ # Go over the output.
+ for el in output_lines(output):
+ headerline = el.split()[0]
+
+ # CHeck the header and act accordingly
+ if (headerline=='MY_STELLAR_DATA'):
+ parameters = ['time', 'mass', 'zams_mass', 'probability', 'radius']
+ values = el.split()[1:]
+
+ if not os.path.exists(outfilename):
+ with open(outfilename, 'w') as f:
+ f.write(seperator.join(parameters)+'\n')
+
+ with open(outfilename, 'a') as f:
+ f.write(seperator.join(values)+'\n')
+
# Create population object
example_pop = Population()
@@ -24,48 +64,72 @@ example_pop.set(verbose=1)
# Those that are present in the default grid_options are set in grid_options
# All other values that you set are put in a custom_options dict
example_pop.set(
- #
+ # binary_c physics options
M_1=10, # bse_options
separation=0, # bse_options
- orbital_period=4580, # bse_options
+ orbital_period=45000000080, # bse_options
max_evolution_time=15000, # bse_options
eccentricity=0.02, # bse_options
- #
+
+ # grid_options
amt_cores=1, # grid_options
- #
+ verbose=1, # verbosity. Not fully configured correctly yet but having it value of 1 prints alot of stuff
+ parse_function=parse_function, # Setting the parse function thats used in the evolve_population
+
+ # Custom options # TODO: need to be set in grid_options probably
data_dir=os.path.join(
- os.environ["BINARYC_DATA_ROOT"], "example_python"
+ temp_dir(), "example_python_population_result"
), # custom_options
base_filename="example_pop.dat", # custom_options
)
-# Custom logging
-# TODO: show different ways
-example_pop.set(
- C_auto_logging={
- "MY_HEADER_LINE": ["star[0].mass", "star[1].mass", "model.probability"]
- }
-)
+### Custom logging
+
+## Below example requires changing the parse function
+## very simple example of custom logging. Will work but need to change the parse function to handle that nicely.
+# example_pop.set(
+# C_auto_logging={
+# "MY_HEADER_LINE": ["star[0].mass", "star[1].mass", "model.probability"]
+# }
+# )
+
+
+# Log the moment when the star turns into a hertzsprung-gap
example_pop.set(
- C_logging_code='Printf("MY_STELLAR_DATA time=%g mass=%g radius=%g\\n", stardata->model.time, stardata->star[0].mass, stardata->star[0].radius);'
-)
+ C_logging_code="""
+if(stardata->star[0].stellar_type >= 2)
+{
+ if (stardata->model.time < stardata->model.max_evolution_time)
+ {
+ Printf("MY_STELLAR_DATA %30.12e %g %g %g %g\\n",
+ //
+ stardata->model.time, // 1
+ stardata->star[0].mass, //2
+ stardata->star[0].pms_mass, //4
+ stardata->model.probability, //5
+ stardata->star[0].radius // 6
+ );
+ };
+ /* Kill the simulation to save time */
+ stardata->model.max_evolution_time = stardata->model.time - stardata->model.dtm;
+};
+""")
-# TODO: show when reading from file
-example_pop.set_custom_logging() # TODO: remove this one
+# Add grid variables
+resolution = {'M_1': 100}
-# Adding grid variables:
+# Mass
example_pop.add_grid_variable(
name="lnm1",
- longname="log primary mass",
- valuerange=[10, 20],
- resolution="10",
- spacingfunc="np.linspace(0.213, 10.2, 10)",
+ longname="Primary mass",
+ valuerange=[2, 150],
+ resolution="{}".format(resolution['M_1']),
+ spacingfunc="const(math.log(2), math.log(150), {})".format(resolution['M_1']),
precode="M_1=math.exp(lnm1)",
- probdist="flat(M_1)",
- # probdist='self.custom_options["extra_prob_function"](M_1)',
- dphasevol="",
+ probdist="three_part_powerlaw(M_1, 0.1, 0.5, 1.0, 150, -1.3, -2.3, -2.3)*M_1",
+ dphasevol="dlnm1",
parameter_name="M_1",
- condition="",
+ condition="", # Impose a condition on this grid variable. Mostly for a check for yourself
)
# Exporting of all the settings can be done with .export_all_info()
@@ -80,13 +144,16 @@ example_pop.export_all_info()
# Creating a parsing function
# TODO: add example of setting up a parsing function
-# Executing a single system
-# TODO: add example of running a single system
+## Executing a single system
+## This uses the M_1 orbital period etc set with the set function
+# output = example_pop.evolve_single()
+# print(output)
-# Executing a population
-# TODO: add example of running a population
+## Executing a population
+## This uses the values generated by the grid_variables
+example_pop.evolve_population_mp_chunks() # TODO: update this function call
# Wrapping up the results to an hdf5 file can be done by using the create_hdf5(<directory containing data and settings>)
# This function takes the settings file (ending in _settings.json) and the data files (ending in .dat) from the data_dir
# and packing them into an hdf5 file, which is then written into the same data_dir directory
-create_hdf5(example_pop.custom_options["data_dir"])
+create_hdf5(data_dir=example_pop.custom_options["data_dir"], name='example_pop.hdf5')
\ No newline at end of file