.. _inifile:
#########################################
.ini file documentation for POSYDON GRIDS
#########################################
How to write a configuration file
==================================
The `posydon-setup-grid` command-line executable cannot run without a
configuration file. This inifile is meant to specify all aspects of the MESA
simulation that is static, i.e. those parts that are shared amongst every MESA
simulation in your grid. The design of the inifile file is such that it will
start with the MESA defaults for every possible MESA parameter, stack on top of
that the POSYDON suggested defaults, and then finally, if supplied, stack user
specific parameters on top of both the MESA defaults and the POSYDON defaults.
This scheme requires a high-performance computing environment with SLURM
installed.
Below we describe each section of the inifile and what each value corresponds
to. In general, lines with capitalized quantities surrounded by {} are
quantities that need to be adjusted for your specific case.
Here is a link to the most recent stable release version of the default inifile
for POSYDON:
`Stable Version INIFILE <https://github.com/POSYDON-code/POSYDON/blob/main/grid_params/grid_params.ini>`_
Here is a link to the unstable development version of the default inifile for
POSYDON:
`Development Version INIFILE <https://github.com/POSYDON-code/POSYDON/blob/development/grid_params/grid_params.ini>`_
.. _inifile_slurm:
[slurm]
-------
This section designates all the SLURM-related parameters.
.. code-block:: ini
[slurm]
; Number of nodes you would like to request
number_of_nodes=1
; This is the number of processes that will be running MESA simulations
number_of_mpi_tasks=1
; This is the number of cores you will let each MESA simulation use
number_of_cpus_per_task=4
; run as job array
; cannot be false if running with --run-type sample
job_array=True
; user name
user={USERNAME}
; partition
partition={PARTITION}
; account
; If running on geneva cluster set this to "default"
account={ACCOUNT}
; wall-time
walltime='2-00:00:00'
; work-directory: place, where MESA writes during runtime
work_dir={WORK_DIRECTORY}
;email
email={YOUR_EMAIL_ADDRESS}
; new group to be set with write permission
; if empty string no changes on group and permission
; group on yggdrasil: GL_S_Astro_POSYDON
; group on Quest: b1119
newgroup=''
.. table:: general settings
======================= ===========
Setting name Description
======================= ===========
number_of_nodes The number of nodes each job will request
number_of_mpi_tasks (outdated) The number of parallel processes ganerates by MPI (recommended to not change)
number_of_cpus_per_task The number of CPUs each job will request (in best this should align with the number of threads set for MESA)
job_array Set to `True` to run a SLURM job array
user User name
partition SLURM partition to run the jobs on
account SLURM account to run the jobs on
walltime Maximum time for each run, otherwise it will get cancelled by SLURM to avoid never ending MESA runs going on too short time steps
work_dir The path to the place, where the data will be writting during runtime (it is recommended to use fast local node storage here), afterwards the data will be copied/moved to the current directory (uncommend this line to write always to the final location)
email Your email address to receive notifications from SLURM
newgroup The name of the owning group all the files should get (leave empty if no changes are needed here)
======================= ===========
[mesa_inlists]
--------------
This section designates all the basic MESA-specific parameters.
.. code-block:: ini
[mesa_inlists]
; inlist types: binary_control,binary_job,star_job,star_control
; Please leave MESA defaults lines alone, please fill in the path to
; you local clone of POSYDON
posydon_github_root={PATH_TO_POSYDON_DIRECTORY}
; There are a number of ways to build the physics of your MESA grid
; the first way is to point the sections below to your own MESA inlists,
; and/or the POSYDON default inlists (versions of which can be found in the
; following repo: https://github.com/POSYDON-code/POSYDON-MESA-INLISTS)
; you can also supply a scenario using syntax such as below, and the setup script
; will automatically find the inlists from POSYDON
; you want to use based on the git tag/commit and the scenario
; (in this case you are simulating MS-MS binaries)
; NOTE: You can use the scenario logic below and *still* supply your own local
; user mesa inlists that will overwrite or tweak some of the physics associated
; with the scenario.
scenario = ['posydon', 'master-9ddb61bb0c482399fa5a41dd22fde41ccd8175d9', 'CO-H_star']
; zams_filename if a zams_filename is supplied this supercedes any star1 or star2 formation inlists
; and skips to running the binary with this pre-computed zams model.
zams_filename = ${posydon_github_root}/grid_params/POSYDON-MESA-INLISTS/r11701/ZAMS_models/zams_z0.0142m2_y0.2703.data
; single_star_grid, this boolean, when True, will take the inlist1 from the binary mesa inlist section
; and run in a single star grid configuration
single_star_grid = False
; Star1 formation - star1_job
; star1_formation_job_mesa_defaults = ${posydon_github_root}/grid_params/defaults/r11701/star/star_job.defaults
; star1_formation_job_posydon_defaults = ${user_template_root}/inlist1
; star1_formation_job_user = None
; Star2 formation - star2_job
; star2_formation_job_mesa_defaults = ${posydon_github_root}/grid_params/defaults/r11701/star/star_job.defaults
; star2_formation_job_posydon_defaults = ${user_template_root}/inlist2
; star2_formation_job_user = None
; Star1 formation - star1_control
; star1_formation_controls_mesa_defaults = ${posydon_github_root}/grid_params/defaults/r11701/star/controls.defaults
; star1_formation_controls_posydon_defaults = ${user_template_root}/inlist1
; star1_formation_controls_user = None
; Star2 formation - star2_control
; star2_formation_controls_mesa_defaults = ${posydon_github_root}/grid_params/defaults/r11701/star/controls.defaults
; star2_formation_controls_posydon_defaults = ${user_template_root}/inlist2
; star2_formation_controls_user = None
; binary_control
binary_controls_mesa_defaults = ${posydon_github_root}/grid_params/defaults/r11701/binary/binary_controls.defaults
; binary_controls_posydon_defaults = ${posydon_github_root}/grid_params/POSYDON-MESA-INLISTS/r11701/default_common_inlists/binary/inlist_project
; binary_controls_user = ${user_template_root}/binary/inlist_project
; binary_job
binary_job_mesa_defaults = ${posydon_github_root}/grid_params/defaults/r11701/binary/binary_job.defaults
; binary_job_posydon_defaults = ${posydon_github_root}/grid_params/POSYDON-MESA-INLISTS/r11701/default_common_inlists/binary/inlist_project
; binary_job_user = ${user_template_root}/binary/inlist_project
; star1_job
star1_job_mesa_defaults = ${posydon_github_root}/grid_params/defaults/r11701/star/star_job.defaults
; star1_job_posydon_defaults = ${posydon_github_root}/grid_params/POSYDON-MESA-INLISTS/r11701/default_common_inlists/binary/inlist1
; star1_job_user = ${user_template_root}/binary/inlist1
; star1_control
star1_controls_mesa_defaults = ${posydon_github_root}/grid_params/defaults/r11701/star/controls.defaults
; star1_controls_posydon_defaults = ${posydon_github_root}/grid_params/POSYDON-MESA-INLISTS/r11701/default_common_inlists/binary/inlist1
; star1_controls_user = ${user_template_root}/binary/inlist1
; star2_job
star2_job_mesa_defaults = ${posydon_github_root}/grid_params/defaults/r11701/star/star_job.defaults
; star2_job_posydon_defaults = ${user_template_root}/binary/inlist2
; star2_job_user = None
; star2_control
star2_controls_mesa_defaults = ${posydon_github_root}/grid_params/defaults/r11701/star/controls.defaults
; star2_controls_posydon_defaults = ${user_template_root}/binary/inlist2
; star2_controls_user = None
; star history columns
star_history_columns = ${posydon_github_root}/grid_params/POSYDON-MESA-INLISTS/r11701/default_common_inlists/history_columns.list
; binary history columns
binary_history_columns = ${posydon_github_root}/grid_params/POSYDON-MESA-INLISTS/r11701/default_common_inlists/binary_history_columns.list
; profile columns
profile_columns = ${posydon_github_root}/grid_params/POSYDON-MESA-INLISTS/r11701/default_common_inlists/profile_columns.list
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;;;;; MESA OUTPUT CONTROLS ;;;;;;;
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
; controls how often MESA prints out the history of the evolution
history_interval = 1
; Save binary history (history file will be named: )
binary_history = True
; save history of star1
history_star1 = True
;save final profile of star1
final_profile_star1 = False
; save final model of star1
final_model_star1 = True
; save history of star2
history_star2 = False
; save profile of star2
final_profile_star2 = False
; save final model of star2
final_model_star2 = False
.. table:: settings for the MESA inlist
========================================= ===========
Setting name Description
========================================= ===========
posydon_github_root The path to your used POSYDON version
scenario List containing multiple information: 1) the source ('posydon' or 'user'(for future use)), 2) the git commit (the branch and full git hash for the inlist submodule separated by a dash), 3) the systems type ('HMS-HMS', 'CO-H_star', 'CO-He_star')
zams_filename The location of the file containing the ZAMS models
single_star_grid Flag to indicate single star or binary evolution
star1_formation_job_mesa_defaults (outdated) Path to the MESA job section defaults to form star 1
star1_formation_job_posydon_defaults (outdated) Path to the MESA job section inlist of POSYDON to form star 1
star1_formation_job_user (outdated) Path to the MESA job section inlist of the user to form star 1
star2_formation_job_mesa_defaults (outdated) Path to the MESA job section defaults to form star 2
star2_formation_job_posydon_defaults (outdated) Path to the MESA job section inlist of POSYDON to form star 2
star2_formation_job_user (outdated) Path to the MESA job section inlist of the user to form star 2
star1_formation_controls_mesa_defaults (outdated) Path to the MESA controls section defaults to form star 1
star1_formation_controls_posydon_defaults (outdated) Path to the MESA controls section inlist of POSYDON to form star 1
star1_formation_controls_user (outdated) Path to the MESA controls section inlist of the user to form star 1
star2_formation_controls_mesa_defaults (outdated) Path to the MESA controls section defaults to form star 2
star2_formation_controls_posydon_defaults (outdated) Path to the MESA controls section inlist of POSYDON to form star 2
star2_formation_controls_user (outdated) Path to the MESA controls section inlist of the user to form star 2
binary_controls_mesa_defaults (outdated) Path to the MESA controls section defaults to evolve the binary
binary_controls_posydon_defaults (outdated) Path to the MESA controls section inlist of POSYDON to evolve the binary
binary_controls_user (outdated) Path to the MESA controls section inlist of the user to evolve the binary
binary_job_mesa_defaults (outdated) Path to the MESA job section defaults to evolve the binary
binary_job_posydon_defaults (outdated) Path to the MESA job section inlist of POSYDON to evolve the binary
binary_job_user (outdated) Path to the MESA job section inlist of the user to evolve the binary
star1_job_mesa_defaults (outdated) Path to the MESA job section defaults to evolve star 1
star1_job_posydon_defaults (outdated) Path to the MESA job section inlist of POSYDON to evolve star 1
star1_job_user (outdated) Path to the MESA job section inlist of the user to evolve star 1
star1_controls_mesa_defaults (outdated) Path to the MESA controls section defaults to evolve star 1
star1_controls_posydon_defaults (outdated) Path to the MESA controls section inlist of POSYDON to evolve star 1
star1_controls_user (outdated) Path to the MESA controls section inlist of the user to evolve star 1
star2_job_mesa_defaults (outdated) Path to the MESA job section defaults to evolve star 2
star2_job_posydon_defaults (outdated) Path to the MESA job section inlist of POSYDON to evolve star 2
star2_job_user (outdated) Path to the MESA job section inlist of the user to evolve star 2
star2_controls_mesa_defaults (outdated) Path to the MESA controls section defaults to evolve star 2
star2_controls_posydon_defaults (outdated) Path to the MESA controls section inlist of POSYDON to evolve star 2
star2_controls_user (outdated) Path to the MESA controls section inlist of the user to evolve star 2
star_history_columns (outdated) Path to the history columns list of the stars
binary_history_columns (outdated) Path to the history columns list of the binary
profile_columns (outdated) Path to the profile columns list to write the final stellar profile
history_interval Interval how often MESA will add a model to the star's histories
binary_history Interval how often MESA will add a model to the binary history
history_star1 Flag, whether the history of star 1 should be saved
final_profile_star1 (outdated, done in :samp:`run_star_extras.f`) Flag, whether the final profil of star 1 should be saved
final_model_star1 Flag, whether the final model of star 1 should be saved
history_star2 Flag, whether the history of star 2 should be saved
final_profile_star2 (outdated, done in :samp:`run_star_extras.f`) Flag, whether the final profil of star 2 should be saved
final_model_star2 Flag, whether the final model of star 2 should be saved
========================================= ===========
[mesa_extras]
-------------
This section designates all the parameters for MESA makefiles and fortran files.
.. code-block:: ini
[mesa_extras]
; path to MESA makefile for executable binary and star
makefile_binary = ${MESA_DIR}/binary/work/make/makefile
makefile_star = ${MESA_DIR}/star/work/make/makefile
; N.B. Normally system_type will determine which extras file gets used.
; posydon has a set of approved extras files for given types of systems
; and it will use these extra files by default but you may supply your own
; if you wish.
; user specified binary extra
mesa_binary_extras = ${MESA_DIR}/binary/work/src/run_binary_extras.f
; user_binary_extras = ${mesa_inlists:posydon_github_root}/grid_params/POSYDON-MESA-INLISTS/r11701/default_common_inlists/binary/src/run_binary_extras.f
; user specified star extra - these go into the binary/src/ directory
mesa_star_binary_extras = ${MESA_DIR}/binary/work/src/run_star_extras.f
; user_star_binary_extras =${mesa_inlists:posydon_github_root}/grid_params/POSYDON-MESA-INLISTS/r11701/default_common_inlists/binary/src/run_star_extras.f
; user specified star extras - these are for single star formation (e.g., pre-MS evolution)
mesa_star1_extras = ${MESA_DIR}/star/work/src/run_star_extras.f
; user_star1_extras = ${mesa_inlists:posydon_github_root}/grid_params/POSYDON-MESA-INLISTS/r11701/default_common_inlists/binary/src/run_star_extras.f
mesa_star2_extras = ${MESA_DIR}/star/work/src/run_star_extras.f
; user_star2_extras = ${mesa_inlists:posydon_github_root}/grid_params/POSYDON-MESA-INLISTS/r11701/default_common_inlists/binary/src/run_star_extras.f
; binary_run.f
binary_run = ${MESA_DIR}/binary/work/src/binary_run.f
; star_run.f
star_run = ${MESA_DIR}/star/work/src/run.f
.. table:: settings for the MESA extras
======================= ===========
Setting name Description
======================= ===========
makefile_binary Path to the make file of MESA's binary module
makefile_star Path to the make file of MESA's star module
mesa_binary_extras Path to MESA's binary module default :samp:`run_binary_extras.f`
user_binary_extras Path to the users/POSYDON :samp:`run_binary_extras.f`
mesa_star_binary_extras Path to MESA's binary module default :samp:`run_star_extras.f`
user_star_binary_extras Path to the users/POSYDON :samp:`run_star_extras.f`
mesa_star1_extras Path to MESA's star module default :samp:`run_star_extras.f`
user_star1_extras Path to the users/POSYDON :samp:`run_star_extras.f`
mesa_star2_extras Path to MESA's star module default :samp:`run_star_extras.f`
user_star2_extras Path to the users/POSYDON :samp:`run_star_extras.f`
binary_run Path to MESA's binary module :samp:`binary_run.f`
star_run Path to MESA's star module :samp:`run.f`
======================= ===========
[run_parameters]
----------------
This section designates the run parameters for a grid.
.. code-block:: ini
[run_parameters]
; If running posydon-run-grid with option --grid-type fixed
; then the grid is a file with all the different samples you would like to
; run MESA on.
; If posydon-make-grid is run with --grid-type dynamic, then grid is
; a file of pre-run MESA simulations from which you will generate new samples to
; run MESA on (i.e. generate grid points on the fly).
grid = {PATH_TO_GRID}
The :samp:`grid` specifies where to find the csv file to read the runs from.