wsssss.inlists package

Submodules

wsssss.inlists.create_grid module

class wsssss.inlists.create_grid.MesaGrid(mesa_dir='', inlist_filename='inlist', inlists_index=5, starjob_filename='inlist_project', controls_filename='inlist_project', eos_filename='inlist_project', kap_filename='inlist_project', pgstar_filename='inlist_project', add_base_workdir=False)

Bases: object

__init__(mesa_dir='', inlist_filename='inlist', inlists_index=5, starjob_filename='inlist_project', controls_filename='inlist_project', eos_filename='inlist_project', kap_filename='inlist_project', pgstar_filename='inlist_project', add_base_workdir=False)

MesaGrid class which contains all inlist settings for a grid. When the create_grid method is called, a copy of the script which called it is copied into the grid directory.

Parameters:

mesa_dir (str) – $MESA_DIR root directory to be used with this grid.
inlist_filename (str, optional) – Defaults to ‘inlist’.
inlists_index (int, optional) – Which read_extra_*_inlist(inlists_index) to use. Defaults to 5.
starjob_filename (str, optional) – Cannot be the same as inlist_filename. Defaults to ‘inlist_project’.
controls_filename (str, optional) – Cannot be the same as inlist_filename. Defaults to ‘inlist_project’.
eos_filename (str, optional) – Cannot be the same as inlist_filename. Defaults to ‘inlist_project’.
kap_filename (str, optional) – Cannot be the same as inlist_filename. Defaults to ‘inlist_project’.
pgstar_filename (str, optional) – Cannot be the same as inlist_filename. Defaults to ‘inlist_project’.
add_base_workdir (bool, optional) – Add minimum required files from $MESA_DIR/star/work to each run directory (make/, src/, mk, re, rn, clean).

star_job

Options for star_job.

Type:: dict

controls

Options for controls.

Type:: dict

pgstar

Options for pgstar.

Type:: dict

kap

Options for kap. Only exists if mesa_dir version is later than or equal to 15140.

Type:: dict

eos

Options for eos. Only exists if mesa_dir version is later than or equal to 15140.

Type:: dict

Examples

Creating a grid of MESA runs with initial masses of 1 and 2 Msol.

>>> import os
>>> from wsssss.inlists import create_grid as cg
>>> grid = cg.MesaGrid()
>>> grid.controls['initial_mass'] = [1, 2]
>>> grid.create_grid('path/to/grid')
>>> os.listdir('path/to/grid')
['0000', '0001]

add_file(path)

Add a file which will be copied into each run directory. Will raise a FileNotFoundError if the file at path does not exist.

Parameters:: path (str) – Path to file to be added to every run directory.

Examples

Copy the file at path/to/file to each run directory when the grid is created.

>>> from wsssss.inlists import create_grid as cg
>>> grid = cg.MesaGrid()
>>> grid.add_file('path/to/file')

add_dir(path)

Add a directory which will be copied into each run directory.

Parameters:: path (str) – Path to directory to be added to every run directory.

Examples

Copy the directory at path/to/directory to each run directory when the grid is created.

>>> from wsssss.inlists import create_grid as cg
>>> grid = cg.MesaGrid()
>>> grid.add_dir('path/to/directory')

add_inlist_option_file_check(namelist, option)

Add a check that the file specified in the namelist[option] must exist in each run directory, e.g. controls[‘history_columns_filename’], which is included by default as well as profile_columns_filename.

Parameters:

namelist (str)
option (str)

Examples

>>> from wsssss.inlists import create_grid as cg
>>> grid = cg.MesaGrid()
>>> grid.add_inlist_option_file_check('controls', 'history_columns_file')

add_no_expand_key(namelist, key)

Add a key which will not be expanded. For example &kap’s user_kap_Xs :param namelist: Which namelist the key is part of. E.g. ‘kap’. :type namelist: str :param key: Name of parameter. E.g. ‘user_kap_Xs’. :type key: str

Examples

>>> from wsssss.inlists import create_grid as cg
>>> grid = cg.MesaGrid()
>>> grid.add_no_expand_key('kap', f'user_kap_Xs')

add_non_mesa_key(namelist, key): Add a key which is not in MESA’s keys and expand it. For example including a parameter which is used in inlist_finalize_function. :param namelist: Which namelist the key is part of. E.g. controls. :type namelist: str :param key: Name of parameter. Must start with '!PY_KEY_'. :type key: str

set_inlist_finalize_function(function)

Set the function which is applied to all unpacked inlists.

The function must accept a single inlist and return a single inlist.

Parameters:: function (function)

Examples

Change an option in star_job depending on initial_mass in controls. This could also be accomplished using the f'{non_mesa_key_start}group_unpack' key.

>>> import numpy as np
>>> from wsssss.inlists import create_grid as cg
>>> grid = cg.MesaGrid()
>>> grid.star_job['change_initial_net'] = True
>>> grid.star_job['new_net_name'] = 'pp_extras.net'
>>> grid.controls['initial_mass'] = np.linspace(1, 2, 6)
>>> def finalize_function(unpacked_inlist):
...     if unpacked_inlist['controls']['initial_mass'] > 1.3:
...         unpacked_inlist['star_job']['new_net_name'] = 'pp_cno_extras.net'
...     return unpacked_inlist
>>> grid.set_inlist_finalize_function(finalize_function)
>>> grid.unpack_inlists()
>>> grid.unpacked[0]['star_job']['new_net_name']
'pp_extras.net'
>>> grid.unpacked[-1]['star_job']['new_net_name']
'pp_cno_extras.net'

set_griddir_finalize_function(function)

Set the function which is called in each grid directory. The arguments to the function are a MesaGrid object and the run index.

Parameters:: function (function)

Examples

>>> import os
>>> from wsssss.inlists import create_grid as cg
>>> grid = cg.MesaGrid()
>>> grid.controls['initial_mass'] = [1, 2]
>>> def griddir_finalize_function(grid, i):
...     os.system("pwd")
>>> grid.set_griddir_finalize_function(griddir_finalize_function)
>>> grid.create_grid('path/to/grid')
/home/walter/Github/wsssss/path/to/grid/0000
/home/walter/Github/wsssss/path/to/grid/0001

set_name_function(function)

Set the function which is used to generate the name of each run directory. It recieves a fully unpacked inlist (dict of dicts) or grid index and unpacked inlist and returns a string. It should generate a unique name for each inlist.

Parameters:: function (function)

Examples

>>> import os
>>> from wsssss.inlists import create_grid as cg
>>> grid = cg.MesaGrid()
>>> grid.controls['initial_mass'] = [1, 2]
>>> def name_function(unpacked_inlist):
...     return f'm{unpacked_inlist["controls"]["initial_mass"]:.3f}'
>>> grid.set_name_function(name_function)
>>> grid.create_grid('path/to/grid')
>>> os.listdir('path/to/grid')
['m1.000', 'm2.000']

create_grid(grid_path, rm_dir=True)

Create the MESA grid in grid_path. The inlist options are validated and extra files and directories copied to each run directory. :param grid_path: Path to grid directory. :param rmdir: Remove grid directory if it exists. Defaults to True. :type rmdir: bool, optional

Examples

>>> import os
>>> from wsssss.inlists import create_grid as cg
>>> grid = cg.MesaGrid()
>>> grid.controls['initial_mass'] = [1, 2]
>>> grid.create_grid('path/to/grid')
>>> os.listdir('path/to/grid')
['0000', '0001']

validate_inlists(mesa_dir=None)

Check if all options in the inlists are valid MESA keys.

Parameters:: mesa_dir (str, optional) – MESA root directory to check against. Defaults to None, which will use $MESA_DIR.

Examples

>>> from wsssss.inlists import create_grid as cg
>>> grid = cg.MesaGrid()
>>> grid.controls['this_option_does_not_exist'] = 1
KeyError: 'Option(s) not in available controls keys: this_option_does_not_exist.'

_validate_files(grid_path): Check if all specified files are accounted for. :param grid_path: Grid directory. :type grid_path: str

_get_available_options(path)

TODO: Replace with inlists.get_mesa_defaults :param path:

Returns:

check_copy(): Check if all files and directories which are to be copied exist.

unpack_inlists(): Unpack all inlists. Will place them in the unpacked attribute as a tuple.

_make_inlist_generator(inlist_dict)

Create a generator which yields all unique inlists with all combinations of any lists, tuples, or numpy arrays of length greater than 1. Can handle groups of variables which must change together by appending a list of dict`s in the `group_unpack key. If multiple lists of `dict`s are appended, they are treated as separate variables. :param inlist_dict: :type inlist_dict: dict

Yields:: dict – Unpacked inlist.

_setup_directories(grid_path, rm_dir)

Create the directory structure for a grid at grid_path.

Parameters:

grid_path (str) – Path which will contain the grid.
rm_dir (bool) – If it exists, first remove the grid directory.

_write_inlists(grid_path)

Write the unpacked inlists to grid_path in their respective directories.

Parameters:: grid_path (str) – Path which will contain the grid.

_generate_inlist_string(inlist_dict)

Generates an inlist string from inlist_dict. Which is an unpacked controls etc dict.

Parameters:: inlist_dict (dict) – Dictionary containing a set of inlist options.
Returns:: A string representation of inlist_dict readable by MESA.
Return type:: inlist_str (str)

_copy_extra_files_and_dirs(grid_path)

Copy extra files and directories specified in MesaGrid.extra_files and MesaGrid.extra_dirs to each run directory.

Parameters:: grid_path

summary(): Print a summary of which variables change.

wsssss.inlists.inlists module

wsssss.inlists.inlists.inlist_diff(dict1, dict2)

Compare two inlists and show which items change or remain the same.

Parameters:

dict1 (dict)
dict2 (dict)

Returns:

Items which remain the same are in result['same'],: and those which changed in result['changed'].

Return type:

dict

wsssss.inlists.inlists.evaluate_inlist_str(inlist_str, inlist_dir)

Fully evaluate inlist_str as if it were written in inlist_dir, following all read_extra_*_inlist if they are .true...

Parameters:

inlist_str (str) – str form of an inlist.
inlist_dir (str) – Reference directory for reading other files.

Returns:

Evaluated inlist.

Return type:

dict

wsssss.inlists.inlists.evaluate_inlist(path)

Fully evaluate the inlist at path, following all read_extra_*_inlist if they are .true... :param path: Path to inlist. :type path: str

Returns:: Evaluated inlist.
Return type:: dict

wsssss.inlists.inlists.get_inlist_type(inlist)

wsssss.inlists.inlists._evaluate_inlist(inlist, inlist_dir)

Fully evaluate inlist as if it were written in inlist_dir, following all read_extra_*_inlist if they are .true...

Parameters:

inlist (dict) – Inlist dictionary.
inlist_dir (str) – Directory which contains inlist.

Returns:

Evaluated inlist.

Return type:

dict

wsssss.inlists.inlists.variable_to_string(value)

Convert value to a fortran-compatible string. Can be a string, bool, int, or float.

Parameters:: value (str, bool, int, or float) – Value to convert.
Returns:: Fortran-compatible string.
Return type:: str

wsssss.inlists.inlists.write_inlist(inlist, path, header='', mode='w')

Write the inlist to path. header is prepended to the string which is written. mode is passed to open.

Parameters:

inlist (dict)
path (str) – Inlist file path.
header (str)
mode (str) – File mode passed to open.

wsssss.inlists.inlists.print_dict(to_print)

Print the dict to_print with a key and value on every line.

Parameters:: to_print (dict)

wsssss.inlists.inlists.load_MESA_defaults(mesa_dir)

wsssss.inlists.inlists.compare_inlist(path1, path2, show_same=False)

wsssss.inlists.inlists.get_mesa_defaults(mesa_dir)

Get the available MESA inlist options for the version of MESA installed in mesa_dir.

Parameters:: mesa_dir (str) – $``MESA_DIR root directory.
Returns:: List of keys for each inlist type (e.g. star_job, controls, etc.).
Return type:: dict

wsssss.inlists.inlists.check_inlist(path, mesa_dir)

Check whether the options in the inlist at path are available in the version of mesa specified in mesa_dir. Will try to detect if the options have been moved to eos or kap from star_job or controls.

Parameters:

path (str) – Path to an inlist.
mesa_dir (str) – $``MESA_DIR root directory.

Returns:

For each inlist option, states whether it is available in the version of mesa specified in mesa_dir.

Return type:

dict

wsssss.inlists package

Submodules

wsssss.inlists.create_grid module

wsssss.inlists.inlists module

Module contents