From 05064ac269bbc7589947ba1cc3c880dec314aaba Mon Sep 17 00:00:00 2001
From: David Hendriks <davidhendriks93@gmail.com>
Date: Thu, 27 Feb 2020 01:12:04 +0000
Subject: [PATCH] fixed bug in hdf5 writer. updated example population script
---
binarycpython/utils/functions.py | 4 +-
examples/example_population.py | 128 +++++++++++++++++++++++--------
2 files changed, 100 insertions(+), 32 deletions(-)
diff --git a/binarycpython/utils/functions.py b/binarycpython/utils/functions.py
index da2c5bb5e..127772da6 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")
diff --git a/examples/example_population.py b/examples/example_population.py
index 4ee06d7d7..bfac41b69 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 about which stars go supernova when.
+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']
+ 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
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\\n",
+ //
+ stardata->model.time, // 1
+ stardata->star[0].mass, //2
+ stardata->star[0].pms_mass, //4
+ stardata->model.probability //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': 10}
-# 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 +144,17 @@ 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
--
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