.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
Here is a link to the unstable development version of the default inifile for POSYDON: Development Version INIFILE
[slurm]
This section designates all the SLURM-related parameters.
[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=''
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(outdated) The number of parallel processes ganerates by MPI (recommended to not change) |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) |
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.
[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
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 |
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 |
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.
[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
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 |
user_binary_extras |
Path to the users/POSYDON |
mesa_star_binary_extras |
Path to MESA’s binary module default |
user_star_binary_extras |
Path to the users/POSYDON |
mesa_star1_extras |
Path to MESA’s star module default |
user_star1_extras |
Path to the users/POSYDON |
mesa_star2_extras |
Path to MESA’s star module default |
user_star2_extras |
Path to the users/POSYDON |
binary_run |
Path to MESA’s binary module |
star_run |
Path to MESA’s star module |
[run_parameters]
This section designates the run parameters for a grid.
[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 grid specifies where to find the csv file to read the runs from.