Run one binary on your laptop for debugging
For debugging purposes you might want to run a single binary on your laptop to test a quick modification of the inlists, run_star_extras.f or run_binary_extras.f. Assume we want to run the same binary as in the previous tutorial. To use the POSYDON API to run a single binary, you can use the following command:
posydon-setup-grid --grid-type fixed --inifile HMS-HMS_yggdrasil.ini --submission-type shell
Similar to before, in our directorty we have:
[1]:
!ls
binary grid_test.csv laptop.ipynb star1
grid_command.sh HMS-HMS_yggdrasil.ini mk star2
We now export the SLURM_ARRAY_TASK_ID enviroment variable corresponding to the csv index of the grid_test.csv we want to run, 0 in this case in the temrinal:
export $SLURM_ARRAY_TASK_ID=0
We can now run the MESA binary simulation in the terminal with the following command:
chmod +x grid_command.sh
./grid_command.sh
The terminal will not display an output, the screen output is saved to an out.txt file in the simulation directory.
[6]:
!ls
binary
grid_command.sh
grid_test.csv
HMS-HMS_yggdrasil.ini
laptop.ipynb
mk
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
[7]:
!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_star1_binary_controls
binary_history.data inlist_grid_star2_binary_controls
history_columns.list LOGS1
initial_star1.mod LOGS2
initial_star2.mod out.txt
inlist profile_columns.list
inlist_grid_points tmp.hdf5
[10]:
!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_on_laptop/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!