From 0b646fdfa9a45b4a707344eab1a63451d24680be Mon Sep 17 00:00:00 2001
From: David Hendriks <davidhendriks93@gmail.com>
Date: Sun, 8 Aug 2021 18:19:09 +0100
Subject: [PATCH] updated notebook for population
---
binarycpython/utils/grid.py | 41 ++-
examples/notebook_population.ipynb | 535 ++++++++++-------------------
2 files changed, 196 insertions(+), 380 deletions(-)
diff --git a/binarycpython/utils/grid.py b/binarycpython/utils/grid.py
index 0d35b58d5..42ef3cd49 100644
--- a/binarycpython/utils/grid.py
+++ b/binarycpython/utils/grid.py
@@ -240,6 +240,7 @@ class Population:
1,
)
self.custom_options[key] = kwargs[key]
+
def parse_cmdline(self) -> None:
"""
Function to handle settings values via the command line.
@@ -347,7 +348,7 @@ class Population:
argline = argline.strip()
return argline
- def last_grid_variable(self):
+ def _last_grid_variable(self):
"""
Function that returns the last grid variable
(i.e. the one with the highest grid_variable_number)
@@ -362,6 +363,7 @@ class Population:
== number - 1
):
return grid_variable
+
def add_grid_variable(
self,
name: str,
@@ -498,7 +500,7 @@ class Population:
return options
- def _return_binary_c_version_info(self, parsed=False):
+ def return_binary_c_version_info(self, parsed=False):
"""
Function that returns the version information of binary_c
"""
@@ -507,7 +509,7 @@ class Population:
return version_info
- def _return_binary_c_defaults(self):
+ def return_binary_c_defaults(self):
"""
Function that returns the defaults of the binary_c version that is used.
"""
@@ -551,7 +553,7 @@ class Population:
#
if include_binary_c_defaults:
- binary_c_defaults = self._return_binary_c_defaults()
+ binary_c_defaults = self.return_binary_c_defaults()
all_info["binary_c_defaults"] = binary_c_defaults
if include_binary_c_version_info:
@@ -765,7 +767,7 @@ class Population:
self._condor_grid()
else:
# Execute population evolution subroutines
- self.evolve_population()
+ self._evolve_population()
# Put all interesting stuff in a variable and output that afterwards, as analytics of the run.
analytics_dict = {
@@ -796,7 +798,7 @@ class Population:
return analytics_dict
- def evolve_population(self):
+ def _evolve_population(self):
"""
Function to evolve populations. This handles the setting up, evolving
and cleaning up of a population of stars.
@@ -887,7 +889,7 @@ class Population:
0,
)
- def get_stream_logger(self, level=logging.DEBUG):
+ def _get_stream_logger(self, level=logging.DEBUG):
"""Return logger with configured StreamHandler."""
stream_logger = logging.getLogger("stream_logger")
stream_logger.handlers = []
@@ -901,7 +903,7 @@ class Population:
return stream_logger
- def system_queue_filler(self, job_queue, amt_cores):
+ def _system_queue_filler(self, job_queue, amt_cores):
"""
Function that is responsible for keeping the queue filled.
@@ -909,7 +911,7 @@ class Population:
Will have to play with the size of this.
"""
- stream_logger = self.get_stream_logger()
+ stream_logger = self._get_stream_logger()
if self.grid_options['verbosity'] >= _LOGGER_VERBOSITY_LEVEL:
stream_logger.debug(f"setting up the system_queue_filler now")
@@ -1025,7 +1027,7 @@ 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, amt_cores=self.grid_options["amt_cores"])
# Join the processes
for p in processes:
@@ -1095,6 +1097,7 @@ class Population:
"_total_probability_weighted_mass_run"
] = combined_output_dict["_total_probability_weighted_mass_run"]
self.grid_options['_zero_prob_stars_skipped'] = combined_output_dict['_zero_prob_stars_skipped']
+
def _evolve_system_mp(self, full_system_dict):
"""
Function that the multiprocessing evolution method calls to evolve a system
@@ -1147,7 +1150,7 @@ class Population:
ID # Store the ID as a object property again, lets see if that works.
)
- stream_logger = self.get_stream_logger()
+ stream_logger = self._get_stream_logger()
if self.grid_options['verbosity'] >= _LOGGER_VERBOSITY_LEVEL:
stream_logger.debug(f"Setting up processor: process-{self.process_ID}")
@@ -3015,6 +3018,9 @@ class Population:
output_dir: (optional, default = None) directory where to write the file to. If custom_options['data_dir'] is present, then that one will be used first, and then the output_dir
output_filename: (optional, default = None) filename of the output. If not set it will be called "binary_c_calls.txt"
include_defaults: (optional, default = None) whether to include the defaults of binary_c in the lines that are written. Beware that this will result in very long lines, and it might be better to just export the binary_c defaults and keep them in a separate file.
+
+ Returns:
+ filename: filename that was used to write the calls to
"""
# Check if there is no compiled grid yet. If not, lets try to build it first.
@@ -3089,6 +3095,10 @@ class Population:
print("Error. No grid function found!")
raise ValueError
+
+ return binary_c_calls_full_filename
+
+
def _cleanup_defaults(self):
"""
Function to clean up the default values:
@@ -3103,7 +3113,7 @@ class Population:
TODO: Rethink this functionality. seems a bit double, could also be just outside of the class
"""
- binary_c_defaults = self._return_binary_c_defaults().copy()
+ binary_c_defaults = self.return_binary_c_defaults().copy()
cleaned_dict = filter_arg_dict(binary_c_defaults)
return cleaned_dict
@@ -3901,15 +3911,10 @@ eccentricity3=0
)
# and finally the probability calculator
- self.grid_options["_grid_variables"][self.last_grid_variable()][
+ self.grid_options["_grid_variables"][self._last_grid_variable()][
"probdist"
] = probdist_addition
- # Add the options to the grid
- # self.grid_options["_grid_variables"][self.last_grid_variable()][
- # "precode"
- # ] += "; self.grid_options['m&s_ensemble_options'] = {}".format(o)
-
verbose_print(
"\tMoe_di_Stefano_2017: Added final call to the pdf function",
self.grid_options["verbosity"],
diff --git a/examples/notebook_population.ipynb b/examples/notebook_population.ipynb
index 1e21fe3a8..47a43d442 100644
--- a/examples/notebook_population.ipynb
+++ b/examples/notebook_population.ipynb
@@ -15,7 +15,7 @@
},
{
"cell_type": "code",
- "execution_count": 36,
+ "execution_count": 1,
"id": "bf6b8673-a2b5-4b50-ad1b-e90671f57470",
"metadata": {},
"outputs": [],
@@ -32,9 +32,6 @@
"id": "a081ab23-7822-4971-aa82-991548534714",
"metadata": {},
"source": [
- "- adding custom logging\n",
- "- setting up a parse function\n",
- "\n",
"- running ensemble\n",
"- using the output\n",
"- using M&S grid"
@@ -49,16 +46,16 @@
"To set up and configure the population object we need to make an object instance of the `Population` object, and add configuration via the `.set()` function.\n",
"\n",
"There are three categories of options that the Population object can set:\n",
- "- 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 `binary_c parameters` in the documentation. You can access these through `population.bse_options['<bse option name>']` after you have set them. \n",
+ "- 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 [`binary_c parameters` in the documentation](https://ri0005.pages.surrey.ac.uk/binary_c-python/binary_c_parameters.html). You can access these through `population.bse_options['<bse option name>']` after you have set them. \n",
"\n",
- "- Grid options: these options will be used to configure the behaviour of the Population object. To see which options are available, see section `Population grid code options` in the documentation. They can be accessed via `population.grid_options['<grid option name>']` after you have set them. \n",
+ "- Grid options: these options will be used to configure the behaviour of the Population object. To see which options are available, see section [`Population grid code options` in the documentation](https://ri0005.pages.surrey.ac.uk/binary_c-python/grid_options_descriptions.html). They can be accessed via `population.grid_options['<grid option name>']` after you have set them. \n",
"\n",
"- 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 `population.custom_options['<custom option name>']`"
]
},
{
"cell_type": "code",
- "execution_count": 37,
+ "execution_count": 2,
"id": "79ab50b7-591f-4883-af09-116d1835a751",
"metadata": {},
"outputs": [
@@ -136,7 +133,7 @@
},
{
"cell_type": "code",
- "execution_count": 38,
+ "execution_count": 3,
"id": "b9c2471a-a5b0-48b7-a50b-2f0d22100926",
"metadata": {},
"outputs": [
@@ -153,7 +150,7 @@
"'/tmp/binary_c_python/example_python_population_result/example_pop_settings.json'"
]
},
- "execution_count": 38,
+ "execution_count": 3,
"metadata": {},
"output_type": "execute_result"
}
@@ -182,7 +179,7 @@
},
{
"cell_type": "code",
- "execution_count": 39,
+ "execution_count": 4,
"id": "68c84521-9ae8-4020-af7a-5334173db969",
"metadata": {},
"outputs": [
@@ -280,7 +277,7 @@
},
{
"cell_type": "code",
- "execution_count": 40,
+ "execution_count": 5,
"id": "47979841-2c26-4b26-8945-603d013dc93a",
"metadata": {},
"outputs": [
@@ -373,7 +370,7 @@
},
{
"cell_type": "code",
- "execution_count": 41,
+ "execution_count": 6,
"id": "0c986215-93b1-4e30-ad79-f7c397e9ff7d",
"metadata": {},
"outputs": [
@@ -438,7 +435,7 @@
},
{
"cell_type": "code",
- "execution_count": 42,
+ "execution_count": 7,
"id": "fd197154-a8ce-4865-8929-008d3483101a",
"metadata": {},
"outputs": [
@@ -446,7 +443,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "adding: parse_function=<function parse_function at 0x7f1ef99d1f28> to grid_options\n"
+ "adding: parse_function=<function parse_function at 0x7f54b3a21a60> to grid_options\n"
]
}
],
@@ -471,7 +468,7 @@
" parameters = [\"time\", \"mass\", \"zams_mass\", \"probability\", \"stellar_type\"]\n",
"\n",
" # Go over the output.\n",
- " for line in output_lines(output):\n",
+ " for line in output.splitlines():\n",
" headerline = line.split()[0]\n",
"\n",
" # CHeck the header and act accordingly\n",
@@ -504,12 +501,14 @@
"## 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."
+ "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",
+ "\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 "
]
},
{
"cell_type": "code",
- "execution_count": 43,
+ "execution_count": 8,
"id": "8ea376c1-1e92-45af-8cab-9d7fdca564eb",
"metadata": {
"tags": []
@@ -524,25 +523,7 @@
"Constructing/adding: lnm1\n",
"Grid has handled 20 stars\n",
"with a total probability of 0.05150046619238192\n",
- "Total starcount for this run will be: 20\n"
- ]
- },
- {
- "name": "stderr",
- "output_type": "stream",
- "text": [
- "[2021-08-08 17:48:00,496 DEBUG MainProcess] --- setting up the system_queue_filler now\n",
- "[2021-08-08 17:48:00,498 DEBUG Process-38] --- Setting up processor: process-0[2021-08-08 17:48:00,499 DEBUG Process-39] --- Setting up processor: process-1\n",
- "[2021-08-08 17:48:00,505 DEBUG MainProcess] --- Signaling stop to processes\n",
- "\n"
- ]
- },
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "Process 1 started at 2021-08-08T17:48:00.506077.\tUsing store memaddr <capsule object \"STORE\" at 0x7f1efb31cd20>\n",
- "Process 0 started at 2021-08-08T17:48:00.516098.\tUsing store memaddr <capsule object \"STORE\" at 0x7f1efb31ce70>\n",
+ "Total starcount for this run will be: 20\n",
"Generating grid code\n",
"Constructing/adding: lnm1\n",
"EXAMPLE_COMPACT_OBJECT 2.867655467480e+01 1.33079 9.81391 0.00167028 13\n",
@@ -557,71 +538,9 @@
"EXAMPLE_COMPACT_OBJECT 4.337250536639e+00 2.35209 60.4424 0.000157195 14\n",
"EXAMPLE_COMPACT_OBJECT 3.862081089332e+00 2.56776 75.8628 0.000116989 14\n",
"EXAMPLE_COMPACT_OBJECT 3.449960890183e+00 2.80457 95.2174 8.70668e-05 14\n",
- "EXAMPLE_COMPACT_OBJECT 3.172196856333e+00 3.05193 119.51 6.47976e-05 14\n"
- ]
- },
- {
- "name": "stderr",
- "output_type": "stream",
- "text": [
- "[2021-08-08 17:48:01,097 DEBUG Process-39] --- Process-1 is finishing.\n"
- ]
- },
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "Process 1 finished:\n",
- "\tgenerator started at 2021-08-08T17:48:00.499672, done at 2021-08-08T17:48:01.114081 (total: 0.614409s of which 0.5701460838317871s interfacing with binary_c).\n",
- "\tRan 10 systems with a total probability of 0.026044641717704063.\n",
- "\tThis thread had 0 failing systems with a total probability of 0.\n",
- "\tSkipped a total of 0 systems because they had 0 probability\n"
- ]
- },
- {
- "name": "stderr",
- "output_type": "stream",
- "text": [
- "[2021-08-08 17:48:01,127 DEBUG Process-39] --- Process-1 is finished.\n"
- ]
- },
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "EXAMPLE_COMPACT_OBJECT 3.069627290216e+00 3.27563 150 4.82242e-05 14\n"
- ]
- },
- {
- "name": "stderr",
- "output_type": "stream",
- "text": [
- "[2021-08-08 17:48:01,152 DEBUG Process-38] --- Process-0 is finishing.\n"
- ]
- },
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "Process 0 finished:\n",
- "\tgenerator started at 2021-08-08T17:48:00.498331, done at 2021-08-08T17:48:01.161255 (total: 0.662924s of which 0.6246497631072998s interfacing with binary_c).\n",
- "\tRan 10 systems with a total probability of 0.025455824474677844.\n",
- "\tThis thread had 0 failing systems with a total probability of 0.\n",
- "\tSkipped a total of 0 systems because they had 0 probability\n"
- ]
- },
- {
- "name": "stderr",
- "output_type": "stream",
- "text": [
- "[2021-08-08 17:48:01,170 DEBUG Process-38] --- Process-0 is finished.\n"
- ]
- },
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "Population-4f23670fd94b48cbb6590a4e503782ca finished! The total probability was: 0.05150046619238191. It took a total of 0.864509105682373s to run 20 systems on 2 cores\n",
+ "EXAMPLE_COMPACT_OBJECT 3.172196856333e+00 3.05193 119.51 6.47976e-05 14\n",
+ "EXAMPLE_COMPACT_OBJECT 3.069627290216e+00 3.27563 150 4.82242e-05 14\n",
+ "Population-c8a5c8285f6047bfa420a68ccc89a04f finished! The total probability was: 0.05150046619238191. It took a total of 0.8319869041442871s to run 20 systems on 2 cores\n",
"There were no errors found in this run.\n"
]
}
@@ -645,7 +564,7 @@
},
{
"cell_type": "code",
- "execution_count": 44,
+ "execution_count": 9,
"id": "e1f0464b-0424-4022-b34b-5b744bc2c59d",
"metadata": {},
"outputs": [
@@ -653,7 +572,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "{'population_name': '4f23670fd94b48cbb6590a4e503782ca', 'evolution_type': 'grid', 'failed_count': 0, 'failed_prob': 0, 'failed_systems_error_codes': [], 'errors_exceeded': False, 'errors_found': False, 'total_probability': 0.05150046619238191, 'total_count': 20, 'start_timestamp': 1628441280.4808269, 'end_timestamp': 1628441281.345336, 'total_mass_run': 730.1048014407227, 'total_probability_weighted_mass_run': 0.2983275843337705, 'zero_prob_stars_skipped': 0}\n"
+ "{'population_name': 'c8a5c8285f6047bfa420a68ccc89a04f', 'evolution_type': 'grid', 'failed_count': 0, 'failed_prob': 0, 'failed_systems_error_codes': [], 'errors_exceeded': False, 'errors_found': False, 'total_probability': 0.05150046619238191, 'total_count': 20, 'start_timestamp': 1628442540.4302576, 'end_timestamp': 1628442541.2622445, 'total_mass_run': 730.1048014407228, 'total_probability_weighted_mass_run': 0.2983275843337705, 'zero_prob_stars_skipped': 0}\n"
]
}
],
@@ -661,286 +580,107 @@
"print(analytics)"
]
},
- {
- "cell_type": "code",
- "execution_count": null,
- "id": "1a10760f-f94e-496f-923c-89dbd450b65c",
- "metadata": {},
- "outputs": [],
- "source": []
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "id": "a6108170-2055-48ba-9732-d39f46baf16a",
- "metadata": {},
- "outputs": [],
- "source": []
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "id": "348ba1d2-4cea-47b8-a94c-677e43c9247a",
- "metadata": {},
- "outputs": [],
- "source": []
- },
{
"cell_type": "markdown",
- "id": "ce937b07-7292-4bb1-b2e7-d69e51bdff6e",
- "metadata": {
- "tags": []
- },
+ "id": "6460df56-9fba-4817-9a1e-593ef15d98c1",
+ "metadata": {},
"source": [
- "Wrapping up the results to an hdf5 file can be done by using the create_hdf5\n",
- "(<directory containing data and settings>) This function takes the settings file\n",
- "(ending in _settings.json) and the data files (ending in .dat) from the data_dir\n",
- "and packing them into an hdf5 file, which is then written into the same data_dir directory"
+ "## Noteworthy functionality\n",
+ "Some extra features that are available from via the population object are:\n",
+ "- write_binary_c_calls_to_file: Function to write the calls that would be passed to binary_c to a file"
]
},
{
"cell_type": "code",
- "execution_count": 45,
- "id": "ad444138-f854-4fdb-8e18-49e35ac9c7e2",
+ "execution_count": 10,
+ "id": "83f8e519-4f7c-474a-ad95-f175a34fae81",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
- "Creating /tmp/binary_c_python/example_python_population_result/example_pop.hdf5\n",
- "Adding settings to HDF5 file\n",
- "Adding data to HDF5 file\n"
- ]
- },
- {
- "ename": "ValueError",
- "evalue": "Wrong number of columns at line 17",
- "output_type": "error",
- "traceback": [
- "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
- "\u001b[0;31mValueError\u001b[0m Traceback (most recent call last)",
- "\u001b[0;32m<ipython-input-45-9734fbb7432e>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mcreate_hdf5\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdata_dir\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mexample_pop\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcustom_options\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m\"data_dir\"\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mname\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m\"example_pop.hdf5\"\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
- "\u001b[0;32m~/.pyenv/versions/3.6.4/envs/dev-binarycpython3.6.4/lib/python3.6/site-packages/binarycpython/utils/functions.py\u001b[0m in \u001b[0;36mcreate_hdf5\u001b[0;34m(data_dir, name)\u001b[0m\n\u001b[1;32m 482\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 483\u001b[0m \u001b[0;31m# Add data\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 484\u001b[0;31m \u001b[0mdata\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mnp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mloadtxt\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfull_path\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mskiprows\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 485\u001b[0m \u001b[0mdata_grp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcreate_dataset\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mbase_name\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mdata\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mdata\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 486\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
- "\u001b[0;32m~/.pyenv/versions/3.6.4/envs/dev-binarycpython3.6.4/lib/python3.6/site-packages/numpy/lib/npyio.py\u001b[0m in \u001b[0;36mloadtxt\u001b[0;34m(fname, dtype, comments, delimiter, converters, skiprows, usecols, unpack, ndmin, encoding, max_rows)\u001b[0m\n\u001b[1;32m 1137\u001b[0m \u001b[0;31m# converting the data\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1138\u001b[0m \u001b[0mX\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1139\u001b[0;31m \u001b[0;32mfor\u001b[0m \u001b[0mx\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mread_data\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0m_loadtxt_chunksize\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 1140\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mX\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1141\u001b[0m \u001b[0mX\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mnp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0marray\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mx\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mdtype\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
- "\u001b[0;32m~/.pyenv/versions/3.6.4/envs/dev-binarycpython3.6.4/lib/python3.6/site-packages/numpy/lib/npyio.py\u001b[0m in \u001b[0;36mread_data\u001b[0;34m(chunk_size)\u001b[0m\n\u001b[1;32m 1062\u001b[0m \u001b[0mline_num\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mi\u001b[0m \u001b[0;34m+\u001b[0m \u001b[0mskiprows\u001b[0m \u001b[0;34m+\u001b[0m \u001b[0;36m1\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1063\u001b[0m raise ValueError(\"Wrong number of columns at line %d\"\n\u001b[0;32m-> 1064\u001b[0;31m % line_num)\n\u001b[0m\u001b[1;32m 1065\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1066\u001b[0m \u001b[0;31m# Convert each value according to its column and store\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
- "\u001b[0;31mValueError\u001b[0m: Wrong number of columns at line 17"
+ "Help on method write_binary_c_calls_to_file in module binarycpython.utils.grid:\n",
+ "\n",
+ "write_binary_c_calls_to_file(output_dir:Union[str, NoneType]=None, output_filename:Union[str, NoneType]=None, include_defaults:bool=False) -> None method of binarycpython.utils.grid.Population instance\n",
+ " Function that loops over the grid code and writes the generated parameters to a file.\n",
+ " In the form of a command line call\n",
+ " \n",
+ " Only useful when you have a variable grid as system_generator. MC wouldn't be that useful\n",
+ " \n",
+ " Also, make sure that in this export there are the basic parameters\n",
+ " like m1,m2,sep, orb-per, ecc, probability etc.\n",
+ " \n",
+ " On default this will write to the datadir, if it exists\n",
+ " \n",
+ " Tasks:\n",
+ " - TODO: test this function\n",
+ " - TODO: make sure the binary_c_python .. output file has a unique name\n",
+ " \n",
+ " Args:\n",
+ " output_dir: (optional, default = None) directory where to write the file to. If custom_options['data_dir'] is present, then that one will be used first, and then the output_dir\n",
+ " output_filename: (optional, default = None) filename of the output. If not set it will be called \"binary_c_calls.txt\"\n",
+ " include_defaults: (optional, default = None) whether to include the defaults of binary_c in the lines that are written. Beware that this will result in very long lines, and it might be better to just export the binary_c defaults and keep them in a separate file.\n",
+ " \n",
+ " Returns:\n",
+ " filename: filename that was used to write the calls to\n",
+ "\n"
]
}
],
"source": [
- "create_hdf5(data_dir=example_pop.custom_options[\"data_dir\"], name=\"example_pop.hdf5\")"
+ "help(example_pop.write_binary_c_calls_to_file)"
]
},
{
"cell_type": "code",
- "execution_count": null,
- "id": "34da69bc-fe60-4a9d-b07a-f6cd2f216964",
+ "execution_count": 16,
+ "id": "dacfed75-dfe3-4afd-a0ff-a4be17746021",
"metadata": {},
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "adding: verbosity=10 to grid_options\n",
+ "Writing binary_c calls to /tmp/binary_c_python/example_python_population_result/binary_c_calls.txt\n",
+ "_calculate_multiplicity_fraction: Chosen not to use any multiplicity fraction.\n",
+ "_calculate_multiplicity_fraction: Chosen not to use any multiplicity fraction.\n",
+ "_calculate_multiplicity_fraction: Chosen not to use any multiplicity fraction.\n",
+ "_calculate_multiplicity_fraction: Chosen not to use any multiplicity fraction.\n",
+ "_calculate_multiplicity_fraction: Chosen not to use any multiplicity fraction.\n",
+ "_calculate_multiplicity_fraction: Chosen not to use any multiplicity fraction.\n",
+ "_calculate_multiplicity_fraction: Chosen not to use any multiplicity fraction.\n",
+ "_calculate_multiplicity_fraction: Chosen not to use any multiplicity fraction.\n",
+ "_calculate_multiplicity_fraction: Chosen not to use any multiplicity fraction.\n",
+ "_calculate_multiplicity_fraction: Chosen not to use any multiplicity fraction.\n",
+ "_calculate_multiplicity_fraction: Chosen not to use any multiplicity fraction.\n",
+ "_calculate_multiplicity_fraction: Chosen not to use any multiplicity fraction.\n",
+ "_calculate_multiplicity_fraction: Chosen not to use any multiplicity fraction.\n",
+ "_calculate_multiplicity_fraction: Chosen not to use any multiplicity fraction.\n",
+ "_calculate_multiplicity_fraction: Chosen not to use any multiplicity fraction.\n",
+ "_calculate_multiplicity_fraction: Chosen not to use any multiplicity fraction.\n",
+ "_calculate_multiplicity_fraction: Chosen not to use any multiplicity fraction.\n",
+ "_calculate_multiplicity_fraction: Chosen not to use any multiplicity fraction.\n",
+ "_calculate_multiplicity_fraction: Chosen not to use any multiplicity fraction.\n",
+ "_calculate_multiplicity_fraction: Chosen not to use any multiplicity fraction.\n",
+ "Grid has handled 20 stars\n",
+ "with a total probability of 0.25750233096190955\n",
+ "/tmp/binary_c_python/example_python_population_result/binary_c_calls.txt\n",
+ "binary_c M_1 2.0 eccentricity 0.02 max_evolution_time 15000 orbital_period 45000000080 phasevol 0.22723621650191106 probability 0.013208238029791246 separation 0\n",
+ "binary_c M_1 2.5102526289471614 eccentricity 0.02 max_evolution_time 15000 orbital_period 45000000080 phasevol 0.22723621650191106 probability 0.009829948023831718 separation 0\n",
+ "binary_c M_1 3.1506841305680684 eccentricity 0.02 max_evolution_time 15000 orbital_period 45000000080 phasevol 0.22723621650191106 probability 0.0073157281034221516 separation 0\n",
+ "binary_c M_1 3.9545065608702976 eccentricity 0.02 max_evolution_time 15000 orbital_period 45000000080 phasevol 0.22723621650191106 probability 0.005444573822104362 separation 0\n"
+ ]
+ }
+ ],
"source": [
+ "example_pop.set(verbosity=10)\n",
+ "calls_filename = example_pop.write_binary_c_calls_to_file()\n",
+ "print(calls_filename)\n",
"\n",
- "\n",
- "import os\n",
- "from binarycpython.utils.grid import Population\n",
- "from binarycpython.utils.functions import (\n",
- " get_help_all,\n",
- " get_help,\n",
- " create_hdf5,\n",
- " output_lines,\n",
- ")\n",
- "from binarycpython.utils.custom_logging_functions import temp_dir\n",
- "\n",
- "#########################################################\n",
- "# This file serves as an example for running a population.\n",
- "# The use of help(<function>) is a good way to inspect what parameters are there to use\n",
- "#########################################################\n",
- "\n",
- "\n",
- "def parse_function(self, output):\n",
- " # EXAMPLE PARSE_FUNCTION\n",
- "\n",
- " # extract info from the population instance\n",
- "\n",
- " # Get some information from the\n",
- " data_dir = self.custom_options[\"data_dir\"]\n",
- " base_filename = self.custom_options[\"base_filename\"]\n",
- "\n",
- " # Check directory, make if necessary\n",
- " os.makedirs(data_dir, exist_ok=True)\n",
- "\n",
- " seperator = \" \"\n",
- "\n",
- " # Create filename\n",
- " outfilename = os.path.join(data_dir, base_filename)\n",
- "\n",
- " parameters = [\"time\", \"mass\", \"zams_mass\", \"probability\", \"radius\", \"stellar_type\"]\n",
- "\n",
- " # Go over the output.\n",
- " for el in output_lines(output):\n",
- " headerline = el.split()[0]\n",
- "\n",
- " # CHeck the header and act accordingly\n",
- " if headerline == \"MY_STELLAR_DATA\":\n",
- " values = el.split()[1:]\n",
- " print(values)\n",
- "\n",
- " if not len(parameters) == len(values):\n",
- " print(\"Amount of column names isnt equal to amount of columns\")\n",
- " raise ValueError\n",
- "\n",
- " if not os.path.exists(outfilename):\n",
- " with open(outfilename, \"w\") as f:\n",
- " f.write(seperator.join(parameters) + \"\\n\")\n",
- "\n",
- " with open(outfilename, \"a\") as f:\n",
- " f.write(seperator.join(values) + \"\\n\")\n",
- "\n",
- "\n",
- "# Create population object\n",
- "example_pop = Population()\n",
- "\n",
- "# If you want verbosity, set this before other things\n",
- "example_pop.set(verbose=1)\n",
- "\n",
- "# Setting values can be done via .set(<parameter_name>=<value>)\n",
- "# Values that are known to be binary_c_parameters are loaded into bse_options.\n",
- "# Those that are present in the default grid_options are set in grid_options\n",
- "# All other values that you set are put in a custom_options dict\n",
- "example_pop.set(\n",
- " # binary_c physics options\n",
- " M_1=10, # bse_options\n",
- " separation=0, # bse_options\n",
- " orbital_period=45000000080, # bse_options\n",
- " max_evolution_time=15000, # bse_options\n",
- " eccentricity=0.02, # bse_options\n",
- " # Set companion to low mass\n",
- " M_2=0.08, # Since in the example we run a single system, we should set the companion mass here. If we donm't do this, the code will complain.\n",
- " # grid_options\n",
- " amt_cores=2, # grid_options\n",
- " verbose=1, # verbosity. Not fully configured correctly yet but having it value of 1 prints alot of stuff\n",
- " # Custom options # TODO: need to be set in grid_options probably\n",
- " data_dir=os.path.join(\n",
- " temp_dir(), \"example_python_population_result\"\n",
- " ), # custom_options\n",
- " base_filename=\"example_pop.dat\", # custom_options\n",
- ")\n",
- "\n",
- "# Creating a parsing function\n",
- "example_pop.set(\n",
- " parse_function=parse_function, # Setting the parse function thats used in the evolve_population\n",
- ")\n",
- "\n",
- "### Custom logging\n",
- "\n",
- "## Below example requires changing the parse function\n",
- "## very simple example of custom logging. Will work but need to change the parse function to handle that nicely.\n",
- "# example_pop.set(\n",
- "# C_auto_logging={\n",
- "# \"MY_HEADER_LINE\": [\"star[0].mass\", \"star[1].mass\", \"model.probability\"]\n",
- "# }\n",
- "# )\n",
- "\n",
- "\n",
- "# Log the moment when the star turns into neutron\n",
- "example_pop.set(\n",
- " C_logging_code=\"\"\"\n",
- "if(stardata->star[0].stellar_type >= 13) \n",
- "{\n",
- " if (stardata->model.time < stardata->model.max_evolution_time)\n",
- " {\n",
- " Printf(\"MY_STELLAR_DATA %30.12e %g %g %g %g %d\\\\n\",\n",
- " // \n",
- " stardata->model.time, // 1\n",
- " stardata->star[0].mass, // 2\n",
- " stardata->common.zero_age.mass[0], // 4\n",
- " stardata->model.probability, // 5\n",
- " stardata->star[0].radius, // 6\n",
- " stardata->star[0].stellar_type // 7\n",
- " );\n",
- " };\n",
- " /* Kill the simulation to save time */\n",
- " stardata->model.max_evolution_time = stardata->model.time - stardata->model.dtm;\n",
- "};\n",
- "\"\"\"\n",
- ")\n",
- "\n",
- "# Add grid variables\n",
- "resolution = {\"M_1\": 20, \"q\": 20, \"per\": 40}\n",
- "\n",
- "# Mass\n",
- "example_pop.add_grid_variable(\n",
- " name=\"lnm1\",\n",
- " longname=\"Primary mass\",\n",
- " valuerange=[2, 150],\n",
- " resolution=\"{}\".format(resolution[\"M_1\"]),\n",
- " spacingfunc=\"const(math.log(2), math.log(150), {})\".format(resolution[\"M_1\"]),\n",
- " precode=\"M_1=math.exp(lnm1)\",\n",
- " probdist=\"three_part_powerlaw(M_1, 0.1, 0.5, 1.0, 150, -1.3, -2.3, -2.3)*M_1\",\n",
- " dphasevol=\"dlnm1\",\n",
- " parameter_name=\"M_1\",\n",
- " condition=\"\", # Impose a condition on this grid variable. Mostly for a check for yourself\n",
- ")\n",
- "\n",
- "# # Mass ratio\n",
- "# test_pop.add_grid_variable(\n",
- "# name=\"q\",\n",
- "# longname=\"Mass ratio\",\n",
- "# valuerange=[\"0.1/M_1\", 1],\n",
- "# resolution=\"{}\".format(resolution['q']),\n",
- "# spacingfunc=\"const(0.1/M_1, 1, {})\".format(resolution['q']),\n",
- "# probdist=\"flatsections(q, [{'min': 0.1/M_1, 'max': 1.0, 'height': 1}])\",\n",
- "# dphasevol=\"dq\",\n",
- "# precode=\"M_2 = q * M_1\",\n",
- "# parameter_name=\"M_2\",\n",
- "# condition=\"\", # Impose a condition on this grid variable. Mostly for a check for yourself\n",
- "# )\n",
- "\n",
- "# #\n",
- "# test_pop.add_grid_variable(\n",
- "# name=\"log10per\", # in days\n",
- "# longname=\"log10(Orbital_Period)\",\n",
- "# valuerange=[0.15, 5.5],\n",
- "# resolution=\"{}\".format(resolution[\"per\"]),\n",
- "# spacingfunc=\"const(0.15, 5.5, {})\".format(resolution[\"per\"]),\n",
- "# precode=\"\"\"orbital_period = 10** log10per\n",
- "# sep = calc_sep_from_period(M_1, M_2, orbital_period)\n",
- "# sep_min = calc_sep_from_period(M_1, M_2, 10**0.15)\n",
- "# sep_max = calc_sep_from_period(M_1, M_2, 10**5.5)\"\"\",\n",
- "# probdist=\"sana12(M_1, M_2, sep, orbital_period, sep_min, sep_max, math.log10(10**0.15), math.log10(10**5.5), -0.55)\",\n",
- "# parameter_name=\"orbital_period\",\n",
- "# dphasevol=\"dlog10per\",\n",
- "# )\n",
- "\n",
- "\n",
- "# Exporting of all the settings can be done with .export_all_info()\n",
- "# on default it exports everything, but can be supressed by turning it off:\n",
- "# population settings (bse_options, grid_options, custom_options), turn off with include_population\n",
- "# settings=False\n",
- "# binary_c_defaults (all the commandline arguments that binary c accepts, and their defaults).\n",
- "# turn off with include_binary_c_defaults=False\n",
- "# include_binary_c_version_info (all the compilation info, and information about the compiled\n",
- "# parameters), turn off with include_binary_c_version_info=False\n",
- "# include_binary_c_help_all (all the help information for all the binary_c parameters),\n",
- "# turn off with include_binary_c_help_all=Fase\n",
- "# On default it will write this to the custom_options['data_dir'], but that can be overriden by\n",
- "# setting use_datadir=False and providing an outfile=<>\n",
- "example_pop.export_all_info()\n",
- "\n",
- "## Executing a single system\n",
- "## This uses the M_1 orbital period etc set with the set function\n",
- "# output = example_pop.evolve_single()\n",
- "# print(output)\n",
- "\n",
- "## Executing a population\n",
- "## This uses the values generated by the grid_variables\n",
- "example_pop.evolve() # TODO: update this function call\n",
- "\n",
- "# Wrapping up the results to an hdf5 file can be done by using the create_hdf5\n",
- "# (<directory containing data and settings>) This function takes the settings file\n",
- "# (ending in _settings.json) and the data files (ending in .dat) from the data_dir\n",
- "# and packing them into an hdf5 file, which is then written into the same data_dir directory\n",
- "create_hdf5(data_dir=example_pop.custom_options[\"data_dir\"], name=\"example_pop.hdf5\")\n"
+ "with open(calls_filename, 'r') as f:\n",
+ " print('\\n'.join(f.read().splitlines()[:4]))"
]
},
{
@@ -954,10 +694,81 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 12,
"id": "7212b6be-9787-4122-a7f1-86538cf38179",
"metadata": {},
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Generating grid code\n",
+ "Constructing/adding: lnm1\n",
+ "Grid has handled 20 stars\n",
+ "with a total probability of 0.05150046619238192\n",
+ "Total starcount for this run will be: 20\n"
+ ]
+ },
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "Process Process-5:\n",
+ "Traceback (most recent call last):\n",
+ "Process Process-6:\n",
+ "Traceback (most recent call last):\n",
+ " File \"/home/david/.pyenv/versions/3.6.4/lib/python3.6/multiprocessing/process.py\", line 258, in _bootstrap\n",
+ " self.run()\n",
+ " File \"/home/david/.pyenv/versions/3.6.4/lib/python3.6/multiprocessing/process.py\", line 93, in run\n",
+ " self._target(*self._args, **self._kwargs)\n",
+ " File \"/home/david/.pyenv/versions/3.6.4/lib/python3.6/multiprocessing/process.py\", line 258, in _bootstrap\n",
+ " self.run()\n",
+ " File \"/home/david/.pyenv/versions/3.6.4/envs/dev-binarycpython3.6.4/lib/python3.6/site-packages/binarycpython/utils/grid.py\", line 1312, in _process_run_population_grid\n",
+ " self._evolve_system_mp(full_system_dict)\n",
+ " File \"/home/david/.pyenv/versions/3.6.4/lib/python3.6/multiprocessing/process.py\", line 93, in run\n",
+ " self._target(*self._args, **self._kwargs)\n",
+ " File \"/home/david/.pyenv/versions/3.6.4/envs/dev-binarycpython3.6.4/lib/python3.6/site-packages/binarycpython/utils/grid.py\", line 1312, in _process_run_population_grid\n",
+ " self._evolve_system_mp(full_system_dict)\n",
+ " File \"/home/david/.pyenv/versions/3.6.4/envs/dev-binarycpython3.6.4/lib/python3.6/site-packages/binarycpython/utils/grid.py\", line 1128, in _evolve_system_mp\n",
+ " self.grid_options[\"parse_function\"](self, out)\n",
+ " File \"<ipython-input-12-6a22064fcbfb>\", line 30, in parse_function\n",
+ " for el in output_lines(output):\n",
+ "NameError: name 'output_lines' is not defined\n",
+ " File \"/home/david/.pyenv/versions/3.6.4/envs/dev-binarycpython3.6.4/lib/python3.6/site-packages/binarycpython/utils/grid.py\", line 1128, in _evolve_system_mp\n",
+ " self.grid_options[\"parse_function\"](self, out)\n",
+ " File \"<ipython-input-12-6a22064fcbfb>\", line 30, in parse_function\n",
+ " for el in output_lines(output):\n",
+ "NameError: name 'output_lines' is not defined\n"
+ ]
+ },
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Generating grid code\n",
+ "Constructing/adding: lnm1\n"
+ ]
+ },
+ {
+ "ename": "KeyboardInterrupt",
+ "evalue": "",
+ "output_type": "error",
+ "traceback": [
+ "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+ "\u001b[0;31mKeyboardInterrupt\u001b[0m Traceback (most recent call last)",
+ "\u001b[0;32m<ipython-input-12-6a22064fcbfb>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m 127\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 128\u001b[0m \u001b[0;31m# Evolve the population\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 129\u001b[0;31m \u001b[0mexample_pop\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mevolve\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 130\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 131\u001b[0m \u001b[0;31m#\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+ "\u001b[0;32m~/.pyenv/versions/3.6.4/envs/dev-binarycpython3.6.4/lib/python3.6/site-packages/binarycpython/utils/grid.py\u001b[0m in \u001b[0;36mevolve\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 766\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 767\u001b[0m \u001b[0;31m# Execute population evolution subroutines\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 768\u001b[0;31m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mevolve_population\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 769\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 770\u001b[0m \u001b[0;31m# Put all interesting stuff in a variable and output that afterwards, as analytics of the run.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+ "\u001b[0;32m~/.pyenv/versions/3.6.4/envs/dev-binarycpython3.6.4/lib/python3.6/site-packages/binarycpython/utils/grid.py\u001b[0m in \u001b[0;36mevolve_population\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 826\u001b[0m ):\n\u001b[1;32m 827\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mgrid_options\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m\"evolution_type\"\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;34m\"grid\"\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 828\u001b[0;31m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_evolve_population_grid\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 829\u001b[0m \u001b[0;31m# elif self.grid_options[\"evolution_type\"] == \"mc\":\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 830\u001b[0m \u001b[0;31m# # TODO: add MC option\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+ "\u001b[0;32m~/.pyenv/versions/3.6.4/envs/dev-binarycpython3.6.4/lib/python3.6/site-packages/binarycpython/utils/grid.py\u001b[0m in \u001b[0;36m_evolve_population_grid\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 1037\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1038\u001b[0m \u001b[0msentinel\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mobject\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1039\u001b[0;31m \u001b[0;32mfor\u001b[0m \u001b[0moutput_dict\u001b[0m \u001b[0;32min\u001b[0m \u001b[0miter\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mresult_queue\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mget\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0msentinel\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 1040\u001b[0m \u001b[0mcombined_output_dict\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mmerge_dicts\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mcombined_output_dict\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0moutput_dict\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1041\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mresult_queue\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mempty\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+ "\u001b[0;32m<string>\u001b[0m in \u001b[0;36mget\u001b[0;34m(self, *args, **kwds)\u001b[0m\n",
+ "\u001b[0;32m~/.pyenv/versions/3.6.4/lib/python3.6/multiprocessing/managers.py\u001b[0m in \u001b[0;36m_callmethod\u001b[0;34m(self, methodname, args, kwds)\u001b[0m\n\u001b[1;32m 755\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 756\u001b[0m \u001b[0mconn\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msend\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_id\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmethodname\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mkwds\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 757\u001b[0;31m \u001b[0mkind\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mresult\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mconn\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrecv\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 758\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 759\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mkind\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;34m'#RETURN'\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+ "\u001b[0;32m~/.pyenv/versions/3.6.4/lib/python3.6/multiprocessing/connection.py\u001b[0m in \u001b[0;36mrecv\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 248\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_check_closed\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 249\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_check_readable\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 250\u001b[0;31m \u001b[0mbuf\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_recv_bytes\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 251\u001b[0m \u001b[0;32mreturn\u001b[0m \u001b[0m_ForkingPickler\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mloads\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mbuf\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mgetbuffer\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 252\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
+ "\u001b[0;32m~/.pyenv/versions/3.6.4/lib/python3.6/multiprocessing/connection.py\u001b[0m in \u001b[0;36m_recv_bytes\u001b[0;34m(self, maxsize)\u001b[0m\n\u001b[1;32m 405\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 406\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0m_recv_bytes\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmaxsize\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mNone\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 407\u001b[0;31m \u001b[0mbuf\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_recv\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;36m4\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 408\u001b[0m \u001b[0msize\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mstruct\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0munpack\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"!i\"\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mbuf\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mgetvalue\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 409\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mmaxsize\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0;32mNone\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0msize\u001b[0m \u001b[0;34m>\u001b[0m \u001b[0mmaxsize\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+ "\u001b[0;32m~/.pyenv/versions/3.6.4/lib/python3.6/multiprocessing/connection.py\u001b[0m in \u001b[0;36m_recv\u001b[0;34m(self, size, read)\u001b[0m\n\u001b[1;32m 377\u001b[0m \u001b[0mremaining\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0msize\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 378\u001b[0m \u001b[0;32mwhile\u001b[0m \u001b[0mremaining\u001b[0m \u001b[0;34m>\u001b[0m \u001b[0;36m0\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 379\u001b[0;31m \u001b[0mchunk\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mread\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mhandle\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mremaining\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 380\u001b[0m \u001b[0mn\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mlen\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mchunk\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 381\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mn\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;36m0\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+ "\u001b[0;31mKeyboardInterrupt\u001b[0m: "
+ ]
+ }
+ ],
"source": [
"import os\n",
"\n",
@@ -988,7 +799,7 @@
" parameters = [\"time\", \"mass\", \"zams_mass\", \"probability\", \"radius\", \"stellar_type\"]\n",
"\n",
" # Go over the output.\n",
- " for el in output_lines(output):\n",
+ " for el in output.splitlines():\n",
" headerline = el.split()[0]\n",
"\n",
" # CHeck the header and act accordingly\n",
--
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