Run your first MESA HMS-HMS binary simulation with POSYDON
If you haven’t done it already, export all the relevan POSYDON and MESA enviroment variables.
Tip: create a file called .bash_posydon with the following content:
export PATH_TO_POSYDON=/srv/beegfs/scratch/shares/astro/posydon/simone/documentation/POSYDON/
export PATH_TO_POSYDON_DATA=/srv/beegfs/scratch/shares/astro/posydon/POSYDON_GRIDS_v2/POSYDON_data/230914/
export MESA_DIR=/srv/beegfs/scratch/shares/astro/posydon/software/mesa-r11701-posydon-v2-fiximplicit
export OMP_NUM_THREADS=4
export MESASDK_ROOT=/srv/beegfs/scratch/shares/astro/posydon/software/mesasdk-r11701
source $MESASDK_ROOT/bin/mesasdk_init.sh
so that every time you open a new terminal you can just run:
source .bash_posydon
If you haven’t done it already, please download the development branch of the POSYDON-MESA-INLISTS submodule. This is the branch that contains the simulation properties of all POSYDON MESA grids.
Creating the Initialization File for the POSYDON MESA Submission Script
From the submodule, you can now copy in your working directory the API ini file configuration of HMS-HMS binaries: $PATH_TO_POSYDON/grid_params/POSYDON-MESA-INLISTS/r11701/running_scripts/HMS-HMS_yggdrasil.ini.
For each grid we support two ini file configured to the Northwestern and UNIGE HPC clusters.
[5]:
import os
import shutil
from posydon.config import PATH_TO_POSYDON
path_to_ini = os.path.join(PATH_TO_POSYDON, "grid_params/POSYDON-MESA-INLISTS/r11701/running_scripts/HMS-HMS_yggdrasil.ini")
shutil.copyfile(path_to_ini, './HMS-HMS_yggdrasil.ini')
[5]:
'./HMS-HMS_yggdrasil.ini'
Open the file and edit the following parameters: - user=your_username - account=your_account - email=your_email - posydon_github_root=your_path_to_POSYDON
The scanrio parameter of the ini file is where the magic happens. This parameter let’s us decide which simulation we want to run. The syntax is the following: - the first argument is the name of the submodule posydon which points to the POSYDON-MESA-INLISTS submodule (other options are avaialble, e.g. user which points to a private submodule) - the second argument is the name of the branch and commit of the submodule we want to use connected by a dash -. In this case we want to
use the development branch of the submodule and it’s latest commit, so we write development-c4f90ce2d93595f66751011d2002fc3ab3d090ec - the third argument is the name of the simulation grid we want to run, in this case we want to run a HMS-HMS grid. The name of the grid is HMS-HMS.
To summarize, you should have scenario = ['posydon', 'development-c4f90ce2d93595f66751011d2002fc3ab3d090ec', 'HMS-HMS']
The zams_file points to the ZAMS model used to generate the HMS stars in the binary system. POSYDON v2.0.0 supports 8 different metallicities, here we use the default value that points to the 0.1Zsun POSYDON MESA ZAMS model $PATH_TO_POSYDON/grid_params/POSYDON-MESA-INLISTS/r11701/ZAMS_models/zams_z1.42m3_y0.2511.data
The last parameter of this file is grid and points to the csv file containing the initial coditions of the grid. In this case we want to run a HMS-HMS grid consisting of one system, so we keep grid = grid_test.csv and generate such file specifying the metallicity, the two star masses and the initial orbital period.
Craeting the Initial Simulation Points CSV File
Note: a notebook showing you how all the grid points of v2.0.0 are generated is available in the POSYDON-MESA-INLISTS submodule at $PATH_TO_POSYDON/grid_params/POSYDON-MESA-INLISTS/r11701/running_scripts/parameter_space_v2/create_csv.ipynb
[7]:
import csv
import numpy as np
import pandas as pd
with open('./grid_test.csv', 'w', newline='') as file:
writer = csv.writer(file)
writer.writerow(['initial_z','Zbase','m1','m2','initial_period_in_days'])
writer.writerow([0.00142, 0.00142, 30., 21., 10.])
You should now have the following files in your working directory:
[8]:
!ls
1_hms_hms.ipynb grid_test.csv HMS-HMS_yggdrasil.ini
Let’s now use the magic of POSYDON to set up the MESA simulation. In your termianal run
posydon-setup-grid --grid-type fixed --inifile HMS-HMS_yggdrasil.ini --submission-type slurm
The following files will be created:
[11]:
!ls
1_hms_hms.ipynb grid_test.csv mk star1
binary HMS-HMS_yggdrasil.ini slurm_job_array_grid_submit.sh star2
Running the MESA Model and Exploring the Simulaiton Output
You are now ready to submit the simulation to the cluster with the following command:
[12]:
!sbatch slurm_job_array_grid_submit.sh
Submitted batch job 28453658
[15]:
!squeue -u bavera
JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
28453658_[0] private-a mesa_gri bavera PD 0:00 1 (Priority)
After the job is finished, we can check the output files:
[1]:
!ls
1_hms_hms.ipynb
binary
grid_test.csv
HMS-HMS_yggdrasil.ini
mesa_grid.28453658_0.out
mk
slurm_job_array_grid_submit.sh
star1
star2
Zbase_0.0014_m1_30.0000_m2_21.0000_initial_z_1.4200e-03_initial_period_in_days_1.0000e+01_grid_index_0
[2]:
!ls Zbase_0.0014_m1_30.0000_m2_21.0000_initial_z_1.4200e-03_initial_period_in_days_1.0000e+01_grid_index_0
binary_history_columns.list inlist_grid_points
binary_history.data inlist_grid_star1_binary_controls
final_star1.mod inlist_grid_star2_binary_controls
final_star2.mod LOGS1
history_columns.list LOGS2
initial_star1.mod out.txt
initial_star2.mod profile_columns.list
inlist tmp.hdf5
[4]:
!head -n 200 Zbase_0.0014_m1_30.0000_m2_21.0000_initial_z_1.4200e-03_initial_period_in_days_1.0000e+01_grid_index_0/out.txt
read /srv/beegfs/scratch/shares/astro/posydon/simone/documentation/running_mesa/running_1_hms_hms/binary/inlist_project
read inlist_grid_points
version_number 11701
read inlist_grid_star1_binary_controls
set_eos_PC_parameters
mass_fraction_limit_for_PC 1.0000000000000000D-03
logRho1_PC_limit 2.9990000000000001D+00
logRho2_PC_limit 2.7999999999999998D+00
log_Gamma_all_HELM 1.0000000000000000D+00
log_Gamma_all_PC 1.3010299956000000D+00
PC_Gamma_start_crystal 1.5000000000000000D+02
PC_Gamma_full_crystal 1.7500000000000000D+02
PC_min_Z 9.9900000000000000D-01
change rates preference to 2
set_initial_age 0.0000000000000000D+00
set_initial_model_number 0
change to "approx21.net"
number of species 21
new_rotation_flag T
new_surface_rotation_v 0 0.0000000000000000D+00 0.0000000000000000D+00
net name approx21.net
rotation_flag T
species
1 neut
2 h1
3 prot
4 he3
5 he4
6 c12
7 n14
8 o16
9 ne20
10 mg24
11 si28
12 s32
13 ar36
14 ca40
15 ti44
16 cr48
17 cr56
18 fe52
19 fe54
20 fe56
21 ni56
kappa_file_prefix gs98
kappa_lowT_prefix lowT_fa05_gs98
OMP_NUM_THREADS 4
read inlist_grid_star2_binary_controls
set_eos_PC_parameters
mass_fraction_limit_for_PC 1.0000000000000000D-03
logRho1_PC_limit 2.9990000000000001D+00
logRho2_PC_limit 2.7999999999999998D+00
log_Gamma_all_HELM 1.0000000000000000D+00
log_Gamma_all_PC 1.3010299956000000D+00
PC_Gamma_start_crystal 1.5000000000000000D+02
PC_Gamma_full_crystal 1.7500000000000000D+02
PC_min_Z 9.9900000000000000D-01
change rates preference to 2
set_initial_age 0.0000000000000000D+00
set_initial_model_number 0
change to "approx21.net"
number of species 21
new_rotation_flag T
new_surface_rotation_v 0 0.0000000000000000D+00 0.0000000000000000D+00
net name approx21.net
rotation_flag T
species
1 neut
2 h1
3 prot
4 he3
5 he4
6 c12
7 n14
8 o16
9 ne20
10 mg24
11 si28
12 s32
13 ar36
14 ca40
15 ti44
16 cr48
17 cr56
18 fe52
19 fe54
20 fe56
21 ni56
kappa_file_prefix gs98
kappa_lowT_prefix lowT_fa05_gs98
OMP_NUM_THREADS 4
m2 2.1000000000000000D+01
m1 3.0000000000000000D+01
initial_period_in_days 1.0000000000000000D+01
initial_separation_in_Rsun 7.2417496333000003D+01
jdot_multiplier 1.0000000000000000D+00
fr 1.0000000000000000D-02
The binary terminal output contains the following information
'step' is the number of steps since the start of the run,
'lg_dt' is log10 timestep in years,
'age_yr' is the simulated years since the start run,
'M1+M2' is the total mass of the system (Msun),
'M1' is the mass of the primary (Msun)
'M2' is the mass of the secondary (Msun)
'separ' is the semi-major axis of the orbit (Rsun),
'R1' is the radius of the primary (Rsun)
'R2' is the radius of the secondary (Rsun)
'Porb' is the orbital period (days),
'P1' is the rotation period of star 1 (days, zero if not modeling rotation),
'P2' is the rotation period of star 2 (days, zero if not modeling rotation),
'e' orbital eccentricity,
'dot_e' time derivative of e (1/yr),
'Eorb' orbital energy G*M1*M2/2*separation (ergs),
'M2/M1' mass ratio,
'vorb1' orbital velocity of star 1 (km/s),
'vorb2' orbital velocity of star 2 (km/s),
'pm_i' index of star evolved as point mass, zero if both stars are modeled,
'RL1' Roche lobe radius of star 1 (Rsun),
'Rl2' Roche lobe radius of star 2 (Rsun),
'donor_i' index of star taken as donor,
'RL_gap1' (R1-Rl1)/Rl1,
'RL_gap2' (R2-Rl2)/Rl2,
'dot_Mmt', mass transfer rate (Msun/yr),
'dot_M1', time derivative for the mass of star 1 (Msun/yr),
'dot_M2', time derivative for the mass of star 2 (Msun/yr),
'eff', mass transfer efficiency, computed as -dot_M2/dot_M1 (zero if dot_M1=0),
'dot_Medd', Eddington accretion rate (Msun/yr),
'L_acc', accretion luminosity when accreting to a point mass (ergs/s),
'Jorb', orbital angular momentum (g*cm^2/s)
'spin1', spin angular momentum of star 1 (g*cm^2/s),
'spin2', spin angular momentum of star 2 (g*cm^2/s),
'dot_J', time derivative of Jorb (g*cm^2/s^2),
'dot_Jgr', time derivative of Jorb due to gravitational waves (g*cm^2/s^2),
'dot_Jml', time derivative of Jorb due to mass loss (g*cm^2/s^2),
'dot_Jmb', time derivative of Jorb due to magnetic braking (g*cm^2/s^2),
'dot_Jls', time derivative of Jorb due to spin-orbit coupling (g*cm^2/s^2),
'rlo_iters', number of iterations for implicit calculation of mass transfer,
All this and more can be saved in binary_history.data during the run.
num_steps_to_relax_rotation 50
relax to omega: wanted-current, current, wanted 1 7.2722052166430393D-06 0.0000000000000000D+00 7.2722052166430393D-06
relax to omega: wanted-current, current, wanted 2 7.1239371671217664D-06 1.4826804952127298D-07 7.2722052166430393D-06
relax to omega: wanted-current, current, wanted 3 6.9775031537422630D-06 2.9470206290077610D-07 7.2722052166430393D-06
relax to omega: wanted-current, current, wanted 4 6.8325228134160023D-06 4.3968240322703724D-07 7.2722052166430393D-06
relax to omega: wanted-current, current, wanted 5 6.6880335934326623D-06 5.8417162321037739D-07 7.2722052166430393D-06
relax to omega: wanted-current, current, wanted 6 6.5429720944820478D-06 7.2923312216099155D-07 7.2722052166430393D-06
relax to omega: wanted-current, current, wanted 7 6.3960414376057951D-06 8.7616377903724423D-07 7.2722052166430393D-06
relax to omega: wanted-current, current, wanted 8 6.2481185101766360D-06 1.0240867064664032D-06 7.2722052166430393D-06
relax to omega: wanted-current, current, wanted 9 6.0988144371784416D-06 1.1733907794645978D-06 7.2722052166430393D-06
10 7.649681 4.541E+04 5.083637 5.083787 30.000000 30.000000 0.746765 0.000508 0.251100 0.747141 -6.159624 2598 0
3.021836 0.768039 0.749893 -23.011309 3.935137 -99.000000 0.000000 0.251795 0.000441 0.001420 0.251427 0.009963 3 0
2.3543E+03 16.667399 5.081908 1.622938 4.361599 -8.707435 0.000000 0.000004 0.000133 0.000071 1.432E-03 0.000E+00 max increase
relax to omega: wanted-current, current, wanted 10 5.9494923842667907D-06 1.3227128323762491D-06 7.2722052166430393D-06
relax to omega: wanted-current, current, wanted 11 5.8047902383525235D-06 1.4674149782905158D-06 7.2722052166430393D-06
relax to omega: wanted-current, current, wanted 12 5.6656472219130140D-06 1.6065579947300258D-06 7.2722052166430393D-06
relax to omega: wanted-current, current, wanted 13 5.5253850379006039D-06 1.7468201787424357D-06 7.2722052166430393D-06
relax to omega: wanted-current, current, wanted 14 5.3813998139082310D-06 1.8908054027348084D-06 7.2722052166430393D-06
relax to omega: wanted-current, current, wanted 15 5.2360332812183832D-06 2.0361719354246558D-06 7.2722052166430393D-06
relax to omega: wanted-current, current, wanted 16 5.0905569484589031D-06 2.1816482681841367D-06 7.2722052166430393D-06
relax to omega: wanted-current, current, wanted 17 4.9451036922867509D-06 2.3271015243562889D-06 7.2722052166430393D-06
relax to omega: wanted-current, current, wanted 18 4.7996593421142631D-06 2.4725458745287766D-06 7.2722052166430393D-06
relax to omega: wanted-current, current, wanted 19 4.6542152662843934D-06 2.6179899503586464D-06 7.2722052166430393D-06
20 7.648797 4.525E+04 5.069089 5.069239 30.000000 30.000000 0.746765 0.000508 0.251100 0.747141 -6.164975 2613 0
6.032136 0.764405 0.746596 -23.057888 3.920548 -99.000000 0.000000 0.251795 0.000441 0.001420 0.251427 0.009955 2 0
2.1539E+06 16.663052 5.069239 1.607921 4.359365 -8.704639 0.000000 0.000004 0.000133 0.000071 1.432E-03 0.000E+00 max increase
relax to omega: wanted-current, current, wanted 20 4.5087711728839026D-06 2.7634340437591372D-06 7.2722052166430393D-06
relax to omega: wanted-current, current, wanted 21 4.3633267819036798D-06 2.9088784347393599D-06 7.2722052166430393D-06
relax to omega: wanted-current, current, wanted 22 4.2178823225008446D-06 3.0543228941421948D-06 7.2722052166430393D-06
relax to omega: wanted-current, current, wanted 23 4.0724377789053992D-06 3.1997674377376405D-06 7.2722052166430393D-06
relax to omega: wanted-current, current, wanted 24 3.9269931252400189D-06 3.3452120914030209D-06 7.2722052166430393D-06
relax to omega: wanted-current, current, wanted 25 3.7815483288686108D-06 3.4906568877744285D-06 7.2722052166430393D-06
relax to omega: wanted-current, current, wanted 26 3.6361034654341649D-06 3.6361017512088744D-06 7.2722052166430393D-06
relax to omega: wanted-current, current, wanted 27 3.4906587737615971D-06 3.7815464428814422D-06 7.2722052166430393D-06
relax to omega: wanted-current, current, wanted 28 3.3452144110082463D-06 3.9269908056347930D-06 7.2722052166430393D-06
relax to omega: wanted-current, current, wanted 29 3.1997702456217982D-06 4.0724349710212411D-06 7.2722052166430393D-06
30 7.648797 4.525E+04 5.069078 5.069228 30.000000 30.000000 0.746765 0.000508 0.251100 0.747141 -6.164960 2610 0
9.042435 0.764409 0.746606 -23.057923 3.920536 -99.000000 0.000000 0.251795 0.000441 0.001420 0.251427 0.009955 2 0
2.2053E+09 16.663054 5.069228 1.607910 4.359335 -8.704658 0.000000 0.000004 0.000133 0.000071 1.432E-03 0.000E+00 max increase
relax to omega: wanted-current, current, wanted 30 3.0543261335993711D-06 4.2178790830436683D-06 7.2722052166430393D-06
relax to omega: wanted-current, current, wanted 31 2.9088820289801618D-06 4.3633231876628776D-06 7.2722052166430393D-06
Congratulation, you now know how to harvast the power of POSYDON to run a grid of simulations on a supercomputer!