{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Processing Single Stars with POSYDON" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "This tutorial shows you how to process the single stellar models into a PSyGrid object.\n", "\n", "WARNING: Unfortunatly, the software to resample the raw MESA histories into equivalent evolutionary points (EEPs) is not available in POSYDON yet, but we are using the standalone Fortran code of Aaron Dotter, see http://adsabs.harvard.edu/abs/2016ApJS..222....8D . This tutorial will be updated as soon as they are available.\n", "\n", "If you are a POSYDON developer, then you should know that you can find the EEP code we used to export the v2.0.0 single star grids on Yggdrasil HPC in `/srv/beegfs/scratch/shares/astro/posydon/POSYDON_GRIDS_v2/single_HMS/eep_code`.\n", "\n", "The steps are the following:\n", "1. You should create a work directory, say `eeps` where you will create two directories `grid_name` where you will copy the raw MESA history files from all your MESA single stellar models and `eeps_grid_name` where the code will export the resample EEP histories.\n", "2. You should create a `input.grid_name` file in the `eep_code` directory that will run the EEP code to resample the histories." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Generating the EEP history files" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "The following cell shows you how to copy the histories in ``./eeps/grid`` where we use the 10 single HMS models we run in the step 3 tutorial (step 1)." ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "10\n", "Zbase_0.0014_initial_mass_26.4098_initial_z_1.4200e-03_grid_index_5.data\n", "Zbase_0.0014_initial_mass_9.7294_initial_z_1.4200e-03_grid_index_2.data\n", "Zbase_0.0014_initial_mass_13.5721_initial_z_1.4200e-03_grid_index_3.data\n", "Zbase_0.0014_initial_mass_71.6871_initial_z_1.4200e-03_grid_index_8.data\n", "Zbase_0.0014_initial_mass_18.9324_initial_z_1.4200e-03_grid_index_4.data\n", "Zbase_0.0014_initial_mass_36.8403_initial_z_1.4200e-03_grid_index_6.data\n", "Zbase_0.0014_initial_mass_5.0000_initial_z_1.4200e-03_grid_index_0.data\n", "Zbase_0.0014_initial_mass_51.3904_initial_z_1.4200e-03_grid_index_7.data\n", "Zbase_0.0014_initial_mass_100.0000_initial_z_1.4200e-03_grid_index_9.data\n", "Zbase_0.0014_initial_mass_6.9748_initial_z_1.4200e-03_grid_index_1.data\n" ] } ], "source": [ "import numpy as np\n", "import csv\n", "import os\n", "import shutil\n", "\n", "grid_name = 'single_hms_1e-01_Zsun'\n", "dirs = [ d for d in os.listdir('../'+grid_name) if 'initial_mass' in d]\n", "missing = []\n", "print(len(dirs))\n", "for i in range(len(dirs)):\n", " filename = '../'+grid_name+'/'+dirs[i]+'/LOGS1/history.data'\n", " if os.path.exists(filename):\n", " shutil.copy(filename,'./eeps/'+grid_name+'/'+dirs[i]+'.data')\n", " print(dirs[i]+'.data')\n", " else:\n", " missing += [filename]\n", "if len(missing)>0:\n", " print(len(dirs)-len(missing))\n", " for f in missing:\n", " print(f)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Copy the above list of file names in the `input` file below." ] }, { "cell_type": "code", "execution_count": 5, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Writing input.single_hms_1e-01_Zsun\n" ] } ], "source": [ "%%writefile input.single_hms_1e-01_Zsun\n", "#version string, max 8 characters\n", "POSYDON\n", "#initial Y, initial Z, [Fe/H], [alpha/Fe], v/vcrit\n", "0.2703 0.0142 -1.0 0.0 0.0\n", "#data directories: 1) history files, 2) eeps, 3) isochrones\n", "/srv/beegfs/scratch/shares/astro/posydon/simone/documentation/running_mesa/processing_single_hms/eeps/single_hms_1e-01_Zsun\n", "/srv/beegfs/scratch/shares/astro/posydon/simone/documentation/running_mesa/processing_single_hms/eeps/eeps_single_hms_1e-01_Zsun\n", "/dev/null\n", "# read history_columns\n", "/srv/beegfs/scratch/shares/astro/posydon/POSYDON_GRIDS_v2/single_HMS/eep_code/posydon_history_columns.list\n", "#tracks 10\n", "10\n", "Zbase_0.0014_initial_mass_26.4098_initial_z_1.4200e-03_grid_index_5.data\n", "Zbase_0.0014_initial_mass_9.7294_initial_z_1.4200e-03_grid_index_2.data\n", "Zbase_0.0014_initial_mass_13.5721_initial_z_1.4200e-03_grid_index_3.data\n", "Zbase_0.0014_initial_mass_71.6871_initial_z_1.4200e-03_grid_index_8.data\n", "Zbase_0.0014_initial_mass_18.9324_initial_z_1.4200e-03_grid_index_4.data\n", "Zbase_0.0014_initial_mass_36.8403_initial_z_1.4200e-03_grid_index_6.data\n", "Zbase_0.0014_initial_mass_5.0000_initial_z_1.4200e-03_grid_index_0.data\n", "Zbase_0.0014_initial_mass_51.3904_initial_z_1.4200e-03_grid_index_7.data\n", "Zbase_0.0014_initial_mass_100.0000_initial_z_1.4200e-03_grid_index_9.data\n", "Zbase_0.0014_initial_mass_6.9748_initial_z_1.4200e-03_grid_index_1.data" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Now run the eep code as follows." ] }, { "cell_type": "code", "execution_count": 12, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 1 1 surface_mu 10\n", " 1 2 star_age 8\n", " 1 3 star_mass 9\n", " 1 4 star_mdot 9\n", " 1 5 log_abs_mdot 12\n", " 1 6 log_dt 6\n", " 1 7 log_total_angular_momentum 26\n", " 1 8 mass_conv_core 14\n", " 1 9 conv_mx1_top 12\n", " 1 10 conv_mx1_bot 12\n", " 1 11 conv_mx2_top 12\n", " 1 12 conv_mx2_bot 12\n", " 1 13 conv_mx1_top_r 14\n", " 1 14 conv_mx1_bot_r 14\n", " 1 15 conv_mx2_top_r 14\n", " 1 16 conv_mx2_bot_r 14\n", " 1 17 he_core_mass 12\n", " 1 18 he_core_radius 14\n", " 1 19 c_core_mass 11\n", " 1 20 c_core_radius 13\n", " 1 21 o_core_mass 11\n", " 1 22 o_core_radius 13\n", " 1 23 envelope_mass 13\n", " 1 24 log_LH 6\n", " 1 25 log_LHe 7\n", " 1 26 log_LZ 6\n", " 1 27 log_Lnuc 8\n", " 1 28 log_Lneu 8\n", " 1 29 log_abs_Lgrav 13\n", " 1 30 log_Teff 8\n", " 1 31 photosphere_r 13\n", " 1 32 photosphere_cell_density 24\n", " 1 33 log_L 5\n", " 1 34 log_R 5\n", " 1 35 log_g 5\n", " 1 36 log_L_div_Ledd 14\n", " 1 37 surf_avg_j_rot 14\n", " 1 38 surf_avg_omega 14\n", " 1 39 surf_avg_omega_crit 19\n", " 1 40 surf_avg_omega_div_omega_crit 29\n", " 1 41 surf_avg_v_rot 14\n", " 1 42 surf_avg_v_crit 15\n", " 1 43 surf_avg_Lrad_div_Ledd 22\n", " 1 44 rotational_mdot_boost 21\n", " 1 45 surf_r_equatorial_div_r_polar 29\n", " 1 46 surf_r_equatorial_div_r 23\n", " 1 47 surf_r_polar_div_r 18\n", " 1 48 log_center_T 12\n", " 1 49 log_center_Rho 14\n", " 1 50 log_center_P 12\n", " 1 51 center_degeneracy 17\n", " 1 52 center_gamma 12\n", " 1 53 center_mu 9\n", " 1 54 center_ye 9\n", " 1 55 center_omega 12\n", " 1 56 center_h1 9\n", " 1 57 center_he3 10\n", " 1 58 center_he4 10\n", " 1 59 center_c12 10\n", " 1 60 center_n14 10\n", " 1 61 center_o16 10\n", " 1 62 center_ne20 11\n", " 1 63 center_si28 11\n", " 1 64 center_s32 10\n", " 1 65 center_ca40 11\n", " 1 66 center_ti44 11\n", " 1 67 center_fe56 11\n", " 1 68 surface_h1 10\n", " 1 69 surface_he3 11\n", " 1 70 surface_he4 11\n", " 1 71 surface_c12 11\n", " 1 72 surface_n14 11\n", " 1 73 surface_o16 11\n", " 1 74 surface_ne20 12\n", " 1 75 surface_si28 12\n", " 1 76 surface_s32 11\n", " 1 77 surface_ca40 12\n", " 1 78 surface_ti44 12\n", " 1 79 surface_fe56 12\n", " 1 80 total_mass_h1 13\n", " 1 81 total_mass_he4 14\n", " 1 82 pp 2\n", " 1 83 cno 3\n", " 1 84 tri_alfa 8\n", " 1 85 burn_c 6\n", " 1 86 burn_n 6\n", " 1 87 burn_o 6\n", " 1 88 burn_ne 7\n", " 1 89 c12_c12 7\n", " 1 90 delta_nu 8\n", " 1 91 delta_Pg 8\n", " 1 92 nu_max 6\n", " 1 93 acoustic_cutoff 15\n", " 1 94 v_div_csound_surf 17\n", " 1 95 e_thermal 9\n", " 1 96 max_conv_vel_div_csound 23\n", " 1 97 max_gradT_div_grada 19\n", " 1 98 surf_c12_minus_o16 18\n", " 1 99 min_Pgas_div_P 14\n", " 1 100 total_internal_energy 21\n", " 1 101 total_gravitational_energy 26\n", " 1 102 total_radial_kinetic_energy 27\n", " 1 103 total_rotational_kinetic_energy 31\n", " 1 104 total_energy 12\n", " 1 105 total_eps_grav 14\n", " 1 106 conv_env_top_mass 17\n", " 1 107 conv_env_bot_mass 17\n", " 1 108 conv_env_top_radius 19\n", " 1 109 conv_env_bot_radius 19\n", " 1 110 conv_env_turnover_time_g 24\n", " 1 111 conv_env_turnover_time_l_b 26\n", " 1 112 conv_env_turnover_time_l_t 26\n", " 1 113 envelope_binding_energy 23\n", " 1 114 total_moment_of_inertia 23\n", " 1 115 spin_parameter 14\n", " 1 116 avg_c_in_c_core 15\n", " 1 117 mass_conv_reg_fortides 22\n", " 1 118 thickness_conv_reg_fortides 27\n", " 1 119 radius_conv_reg_fortides 24\n", " 1 120 lambda_CE_1cent 15\n", " 1 121 lambda_CE_10cent 16\n", " 1 122 lambda_CE_30cent 16\n", " 1 123 co_core_mass 12\n", " 1 124 co_core_radius 14\n", " 1 125 lambda_CE_pure_He_star_10cent 29\n", " 1 126 he_core_mass_1cent 18\n", " 1 127 he_core_mass_10cent 19\n", " 1 128 he_core_mass_30cent 19\n", " 1 129 he_core_radius_1cent 20\n", " 1 130 he_core_radius_10cent 21\n", " 1 131 he_core_radius_30cent 21\n", " 2 1 surface_mu 10\n", " 2 2 star_age 8\n", " 2 3 star_mass 9\n", " 2 4 star_mdot 9\n", " 2 5 log_abs_mdot 12\n", " 2 6 log_dt 6\n", " 2 7 log_total_angular_momentum 26\n", " 2 8 mass_conv_core 14\n", " 2 9 conv_mx1_top 12\n", " 2 10 conv_mx1_bot 12\n", " 2 11 conv_mx2_top 12\n", " 2 12 conv_mx2_bot 12\n", " 2 13 conv_mx1_top_r 14\n", " 2 14 conv_mx1_bot_r 14\n", " 2 15 conv_mx2_top_r 14\n", " 2 16 conv_mx2_bot_r 14\n", " 2 17 he_core_mass 12\n", " 2 18 he_core_radius 14\n", " 2 19 c_core_mass 11\n", " 2 20 c_core_radius 13\n", " 2 21 o_core_mass 11\n", " 2 22 o_core_radius 13\n", " 2 23 envelope_mass 13\n", " 2 24 log_LH 6\n", " 2 25 log_LHe 7\n", " 2 26 log_LZ 6\n", " 2 27 log_Lnuc 8\n", " 2 28 log_Lneu 8\n", " 2 29 log_abs_Lgrav 13\n", " 2 30 log_Teff 8\n", " 2 31 photosphere_r 13\n", " 2 32 photosphere_cell_density 24\n", " 2 33 log_L 5\n", " 2 34 log_R 5\n", " 2 35 log_g 5\n", " 2 36 log_L_div_Ledd 14\n", " 2 37 surf_avg_j_rot 14\n", " 2 38 surf_avg_omega 14\n", " 2 39 surf_avg_omega_crit 19\n", " 2 40 surf_avg_omega_div_omega_crit 29\n", " 2 41 surf_avg_v_rot 14\n", " 2 42 surf_avg_v_crit 15\n", " 2 43 surf_avg_Lrad_div_Ledd 22\n", " 2 44 rotational_mdot_boost 21\n", " 2 45 surf_r_equatorial_div_r_polar 29\n", " 2 46 surf_r_equatorial_div_r 23\n", " 2 47 surf_r_polar_div_r 18\n", " 2 48 log_center_T 12\n", " 2 49 log_center_Rho 14\n", " 2 50 log_center_P 12\n", " 2 51 center_degeneracy 17\n", " 2 52 center_gamma 12\n", " 2 53 center_mu 9\n", " 2 54 center_ye 9\n", " 2 55 center_omega 12\n", " 2 56 center_h1 9\n", " 2 57 center_he3 10\n", " 2 58 center_he4 10\n", " 2 59 center_c12 10\n", " 2 60 center_n14 10\n", " 2 61 center_o16 10\n", " 2 62 center_ne20 11\n", " 2 63 center_si28 11\n", " 2 64 center_s32 10\n", " 2 65 center_ca40 11\n", " 2 66 center_ti44 11\n", " 2 67 center_fe56 11\n", " 2 68 surface_h1 10\n", " 2 69 surface_he3 11\n", " 2 70 surface_he4 11\n", " 2 71 surface_c12 11\n", " 2 72 surface_n14 11\n", " 2 73 surface_o16 11\n", " 2 74 surface_ne20 12\n", " 2 75 surface_si28 12\n", " 2 76 surface_s32 11\n", " 2 77 surface_ca40 12\n", " 2 78 surface_ti44 12\n", " 2 79 surface_fe56 12\n", " 2 80 total_mass_h1 13\n", " 2 81 total_mass_he4 14\n", " 2 82 pp 2\n", " 2 83 cno 3\n", " 2 84 tri_alfa 8\n", " 2 85 burn_c 6\n", " 2 86 burn_n 6\n", " 2 87 burn_o 6\n", " 2 88 burn_ne 7\n", " 2 89 c12_c12 7\n", " 2 90 delta_nu 8\n", " 2 91 delta_Pg 8\n", " 2 92 nu_max 6\n", " 2 93 acoustic_cutoff 15\n", " 2 94 v_div_csound_surf 17\n", " 2 95 e_thermal 9\n", " 2 96 max_conv_vel_div_csound 23\n", " 2 97 max_gradT_div_grada 19\n", " 2 98 surf_c12_minus_o16 18\n", " 2 99 min_Pgas_div_P 14\n", " 2 100 total_internal_energy 21\n", " 2 101 total_gravitational_energy 26\n", " 2 102 total_radial_kinetic_energy 27\n", " 2 103 total_rotational_kinetic_energy 31\n", " 2 104 total_energy 12\n", " 2 105 total_eps_grav 14\n", " 2 106 conv_env_top_mass 17\n", " 2 107 conv_env_bot_mass 17\n", " 2 108 conv_env_top_radius 19\n", " 2 109 conv_env_bot_radius 19\n", " 2 110 conv_env_turnover_time_g 24\n", " 2 111 conv_env_turnover_time_l_b 26\n", " 2 112 conv_env_turnover_time_l_t 26\n", " 2 113 envelope_binding_energy 23\n", " 2 114 total_moment_of_inertia 23\n", " 2 115 spin_parameter 14\n", " 2 116 avg_c_in_c_core 15\n", " 2 117 mass_conv_reg_fortides 22\n", " 2 118 thickness_conv_reg_fortides 27\n", " 2 119 radius_conv_reg_fortides 24\n", " 2 120 lambda_CE_1cent 15\n", " 2 121 lambda_CE_10cent 16\n", " 2 122 lambda_CE_30cent 16\n", " 2 123 co_core_mass 12\n", " 2 124 co_core_radius 14\n", " 2 125 lambda_CE_pure_He_star_10cent 29\n", " 2 126 he_core_mass_1cent 18\n", " 2 127 he_core_mass_10cent 19\n", " 2 128 he_core_mass_30cent 19\n", " 2 129 he_core_radius_1cent 20\n", " 2 130 he_core_radius_10cent 21\n", " 2 131 he_core_radius_30cent 21\n", " process_history_columns: ncol = 131\n", " number of history columns = 131\n", " star_age column = 2\n", " star_mass column= 3\n", " main = 32\n", " head = 28\n", " xtra = 1\n", " Zbase_0.0014_initial_mass_26.4098_initial_z_1.4200e-03_grid_index_5.data 0.0000000000000000 11701\n", " number of columns: 131\n", " do not have surface_mu\n", " do not have photosphere_cell_density\n", " Zbase_0.0014_initial_mass_26.4098_initial_z_1.4200e-03_grid_index_5.data 9 11701\n", " guess = 194\n", " my_guess = 194\n", " ntrack = 1134\n", " 21 117 193 301 321 920 1134 0 0\n", " track, number of p, s eeps = 0 7 700\n", " 6277.9927750097913 \n", " 5287405.0672792234 \n", " 7457780.3353313934 \n", " 7469035.5533669619 \n", " 7481078.8974012667 \n", " 7967779.7210960779 \n", " 7973760.0214983337 \n", " main = 32\n", " head = 28\n", " xtra = 1\n", " Zbase_0.0014_initial_mass_9.7294_initial_z_1.4200e-03_grid_index_2.data 26.409758771088889 11701\n", " number of columns: 131\n", " do not have surface_mu\n", " do not have photosphere_cell_density\n", " Zbase_0.0014_initial_mass_9.7294_initial_z_1.4200e-03_grid_index_2.data 9 11701\n", " guess = 187\n", " my_guess = 187\n", " ntrack = 1199\n", " 15 111 186 286 301 892 1199 0 0\n", " track, number of p, s eeps = 0 7 700\n", " 24396.344533808904 \n", " 21042522.104845978 \n", " 28037631.964223422 \n", " 28079495.980469674 \n", " 28136942.251048498 \n", " 29667168.542051919 \n", " 29700034.195994429 \n", " main = 32\n", " head = 28\n", " xtra = 1\n", " Zbase_0.0014_initial_mass_13.5721_initial_z_1.4200e-03_grid_index_3.data 9.7294385594764741 11701\n", " number of columns: 131\n", " do not have surface_mu\n", " do not have photosphere_cell_density\n", " Zbase_0.0014_initial_mass_13.5721_initial_z_1.4200e-03_grid_index_3.data 9 11701\n", " guess = 196\n", " my_guess = 196\n", " ntrack = 1179\n", " 17 112 195 312 327 912 1179 0 0\n", " track, number of p, s eeps = 0 7 700\n", " 15610.060101129055 \n", " 12218224.667538654 \n", " 16588094.368652388 \n", " 16612520.250515623 \n", " 16641397.545344574 \n", " 17585086.263796750 \n", " 17601144.656836938 \n", " main = 32\n", " head = 28\n", " xtra = 1\n", " Zbase_0.0014_initial_mass_71.6871_initial_z_1.4200e-03_grid_index_8.data 13.572087956491831 11701\n", " number of columns: 131\n", " do not have surface_mu\n", " do not have photosphere_cell_density\n", " Zbase_0.0014_initial_mass_71.6871_initial_z_1.4200e-03_grid_index_8.data 9 11701\n", " guess = 219\n", " my_guess = 219\n", " ntrack = 1017\n", " 28 126 218 254 262 847 1017 0 0\n", " track, number of p, s eeps = 0 7 700\n", " 1882.7797692549086 \n", " 2433136.2664018041 \n", " 3657144.1286053685 \n", " 3662905.7394964132 \n", " 3666937.2754223552 \n", " 3968981.8990034591 \n", " 3972461.2129875328 \n", " main = 32\n", " head = 28\n", " xtra = 1\n", " Zbase_0.0014_initial_mass_18.9324_initial_z_1.4200e-03_grid_index_4.data 71.687115078083323 11701\n", " number of columns: 131\n", " do not have surface_mu\n", " do not have photosphere_cell_density\n", " Zbase_0.0014_initial_mass_18.9324_initial_z_1.4200e-03_grid_index_4.data 9 11701\n", " guess = 190\n", " my_guess = 190\n", " ntrack = 1125\n", " 19 115 189 295 311 907 1125 0 0\n", " track, number of p, s eeps = 0 7 700\n", " 9921.7595238775411 \n", " 7739637.6514137154 \n", " 10685722.442352418 \n", " 10700524.445156630 \n", " 10718291.466290537 \n", " 11364471.722192684 \n", " 11373601.929193445 \n", " main = 32\n", " head = 28\n", " xtra = 1\n", " Zbase_0.0014_initial_mass_36.8403_initial_z_1.4200e-03_grid_index_6.data 18.932394689168561 11701\n", " number of columns: 131\n", " do not have surface_mu\n", " do not have photosphere_cell_density\n", " Zbase_0.0014_initial_mass_36.8403_initial_z_1.4200e-03_grid_index_6.data 9 11701\n", " guess = 193\n", " my_guess = 193\n", " ntrack = 986\n", " 23 119 192 222 229 854 986 0 0\n", " track, number of p, s eeps = 0 7 700\n", " 3960.2690882564220 \n", " 3851575.8069463656 \n", " 5582710.4292462571 \n", " 5588591.1389014870 \n", " 5589612.3684672052 \n", " 5991126.2522320682 \n", " 5995772.7040485023 \n", " main = 32\n", " head = 28\n", " xtra = 1\n", " Zbase_0.0014_initial_mass_5.0000_initial_z_1.4200e-03_grid_index_0.data 36.840313846957606 11701\n", " number of columns: 131\n", " do not have surface_mu\n", " do not have photosphere_cell_density\n", " Zbase_0.0014_initial_mass_5.0000_initial_z_1.4200e-03_grid_index_0.data 9 11701\n", " guess = 181\n", " my_guess = 181\n", " ntrack = 3913\n", " 13 108 180 269 290 888 1020 3681 3913\n", " track, number of p, s eeps = 0 9 900\n", " 86753.360233281302 \n", " 64319463.355284028 \n", " 86185376.573872104 \n", " 86633375.415914938 \n", " 87099149.826188803 \n", " 96055736.197538793 \n", " 96465309.995612055 \n", " 96499955.970155716 \n", " 96512030.582908586 \n", " main = 32\n", " head = 28\n", " xtra = 1\n", " Zbase_0.0014_initial_mass_51.3904_initial_z_1.4200e-03_grid_index_7.data 4.9999999804196547 11701\n", " number of columns: 131\n", " do not have surface_mu\n", " do not have photosphere_cell_density\n", " Zbase_0.0014_initial_mass_51.3904_initial_z_1.4200e-03_grid_index_7.data 9 11701\n", " guess = 212\n", " my_guess = 212\n", " ntrack = 985\n", " 26 123 211 231 306 912 985 0 0\n", " track, number of p, s eeps = 0 7 700\n", " 2996.8596073236631 \n", " 3010166.5713262074 \n", " 4416981.4144611228 \n", " 4418486.3517615385 \n", " 4425592.2093049819 \n", " 4768141.7818553476 \n", " 4772090.7663751869 \n", " main = 32\n", " head = 28\n", " xtra = 1\n", " Zbase_0.0014_initial_mass_100.0000_initial_z_1.4200e-03_grid_index_9.data 51.390425259010733 11701\n", " number of columns: 131\n", " do not have surface_mu\n", " do not have photosphere_cell_density\n", " Zbase_0.0014_initial_mass_100.0000_initial_z_1.4200e-03_grid_index_9.data 9 11701\n", " guess = 218\n", " my_guess = 218\n", " ntrack = 975\n", " 1 113 217 219 234 806 975 0 0\n", " track, number of p, s eeps = 0 7 700\n", " 100.00000000000000 \n", " 2056224.0174175713 \n", " 3136810.0982837169 \n", " 3138943.4469665275 \n", " 3145922.3057053299 \n", " 3420158.4876993480 \n", " 3423291.9848860670 \n", " main = 32\n", " head = 28\n", " xtra = 1\n", " Zbase_0.0014_initial_mass_6.9748_initial_z_1.4200e-03_grid_index_1.data 99.999899139008136 11701\n", " number of columns: 131\n", " do not have surface_mu\n", " do not have photosphere_cell_density\n", " Zbase_0.0014_initial_mass_6.9748_initial_z_1.4200e-03_grid_index_1.data 9 11701\n", " guess = 186\n", " my_guess = 186\n", " ntrack = 1209\n", " 14 109 185 286 302 893 1209 0 0\n", " track, number of p, s eeps = 0 7 700\n", " 46075.447975750540 \n", " 37892525.232744850 \n", " 50239784.193855718 \n", " 50340442.508530043 \n", " 50473179.666073054 \n", " 53361156.397665329 \n", " 53451365.900661089 \n" ] } ], "source": [ "!cd /srv/beegfs/scratch/shares/astro/posydon/POSYDON_GRIDS_v2/single_HMS/eep_code/ && ./make_eep /srv/beegfs/scratch/shares/astro/posydon/simone/documentation/running_mesa/processing_single_hms/input.single_hms_1e-01_Zsun" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Great! Now that we have the EEPs files we can create the PSyGrid object and compute the processed quantities with the following code. " ] }, { "cell_type": "code", "execution_count": 15, "metadata": {}, "outputs": [], "source": [ "# NOTE: to load slurm_magic commands you need to first install them with pip install git+https://github.com/NERSC/slurm-magic.git\n", "%load_ext slurm_magic" ] }, { "cell_type": "code", "execution_count": 17, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/srv/beegfs/scratch/shares/astro/posydon/simone/documentation/running_mesa/processing_single_hms\n" ] } ], "source": [ "!pwd" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Creating the PSyGrid Object and Computing the Processed Quantities" ] }, { "cell_type": "code", "execution_count": 25, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Overwriting ./script.py\n" ] } ], "source": [ "%%writefile ./script.py\n", "import os\n", "import sys\n", "from shutil import copyfile\n", "from posydon.grids.psygrid import PSyGrid\n", "from posydon.grids.post_processing import post_process_grid, add_post_processed_quantities\n", "\n", "if __name__ == \"__main__\":\n", "\n", " i = int(sys.argv[1])\n", " print('Job array index:',i)\n", " names = ['single_hms_1e-01_Zsun']\n", " name = names[i]\n", " inpath = \"../%s/\"%name\n", " eep_path = \"./eeps/eeps_%s/\"%name\n", " outpath = \"./\"\n", " grid_name = \"%s.h5\"%name\n", "\n", " grid = PSyGrid(verbose=False)\n", " grid.create(inpath, outpath+grid_name, binary=False, overwrite=True, compression=\"gzip9\", max_number_of_runs=None, eep=eep_path,\n", " **{'star1_history_saved_columns' : ['star_mdot','conv_mx1_top_r', 'conv_mx1_bot_r','mass_conv_reg_fortides', \n", " 'thickness_conv_reg_fortides', 'radius_conv_reg_fortides', 'surface_he3',\n", " #'photosphere_cell_density', 'surface_mu'\n", " ]})\n", " grid.close()\n", " print('Done creating grid!')\n", " \n", " path = outpath\n", " grid_name_processed = 'processed_'+grid_name\n", " # copy file, it will be overwritten when we add columns\n", " if os.path.exists(path+grid_name_processed):\n", " print('Post processed grid file alredy exist, removing it...')\n", " os.remove(path+grid_name_processed)\n", " copyfile(path+grid_name, path+grid_name_processed)\n", "\n", " grid = PSyGrid()\n", " grid.load(path+grid_name_processed)\n", " MESA_dirs_EXTRA_COLUMNS, EXTRA_COLUMNS = post_process_grid(grid, index=None, star_2_CO=False, single_star=True, verbose=False)\n", " add_post_processed_quantities(grid, MESA_dirs_EXTRA_COLUMNS, EXTRA_COLUMNS, verbose=False)\n", " grid.close()\n", " del MESA_dirs_EXTRA_COLUMNS\n", " del EXTRA_COLUMNS\n", " print('Done appending columns!')" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Run the job array, in this case we only have one grid, so the array will go from index 0 to 0." ] }, { "cell_type": "code", "execution_count": 26, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "'Submitted batch job 28474201\\n'" ] }, "execution_count": 26, "metadata": {}, "output_type": "execute_result" } ], "source": [ "%%sbatch\n", "#!/bin/bash\n", "#SBATCH --account=meynet\n", "#SBATCH --partition=private-astro-cpu\n", "#SBATCH -N 1\n", "#SBATCH --array=0-0\n", "#SBATCH --cpus-per-task 1\n", "#SBATCH --ntasks-per-node 1\n", "#SBATCH --time=06:00:00\n", "#SBATCH --job-name=\"psygrid_\\${SLURM_ARRAY_TASK_ID}\"\n", "#SBATCH --output=./log.out\n", "#SBATCH --mail-type=ALL\n", "#SBATCH --mail-user=simone.bavera@unige.ch\n", "#SBATCH --mem-per-cpu=8G\n", "\n", "srun python ./script.py $SLURM_ARRAY_TASK_ID" ] }, { "cell_type": "code", "execution_count": 28, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)\n", " 28474201_0 private-a psygrid_ bavera R 0:04 1 cpu147\n" ] } ], "source": [ "!squeue -u bavera -j 28474201" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Once the job is done we can check that the grid has been created and that the data are contained in the PSyGrid object:" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Exploring the PSyGrid obejct" ] }, { "cell_type": "code", "execution_count": 32, "metadata": {}, "outputs": [], "source": [ "from posydon.grids.psygrid import PSyGrid\n", "\n", "grid = PSyGrid('./processed_single_hms_1e-01_Zsun.h5')\n", "grid.load()" ] }, { "cell_type": "code", "execution_count": 35, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "array([( 6277.99277501, 26.4097595 , 0., 0., 0., 0., 0., 0., 0.74661422, 0.25194858, 4.37299425e-06, 0.00052925, 0.00041712, 0.74748, 0.25107328, 0.00025117, 7.35752498e-05, 0.00060884, -71.17175117, 0.01046428, 0., 0., 0., 4.95159897, -23.39844565, 1.49499256, 4.95175071, 4.63860306, 4.93996484, 0.71603514, 7.64091423, 0.80568409, 6.59702886e+56, 0., -99., 0. , 0. , 0. , 0. , 0.00000000e+00, 0.e+00, 0.e+00, -2.76560315e+50, 0.00000000e+00, 0. , 0. , 1.83454693, 1.83454693, 1.83454693, 0., 0., 1.83454693, -0.47392652, -2.74056706e-08, 1.82720354, 0.00768976, 2.67220936e-05, 0.74748, 0.2511, 0.00142),\n", " (24396.34453381, 9.72943859, 0., 0., 0., 0., 0., 0., 0.74674423, 0.25181197, 3.20475486e-06, 0.00048611, 0.00046799, 0.74748, 0.25107328, 0.00025117, 7.35752498e-05, 0.00060884, -77.4560927 , 0.01688819, 0., 0., 0., 3.775321 , -26.64516867, 0.31740152, 3.77547228, 4.47302913, 3.75932537, 0.45686326, 7.56813577, 1.21103236, 6.61911701e+55, 0., -99., 9.72943487, 9.72943487, 2.86147412, 2.85865442, -1.00000000e+99, -1.e+99, -1.e+99, -8.16891431e+49, 3.24145284e-10, 0.0028197 , 2.86006427, 1.5298747 , 1.5298747 , 1.5298747 , 0., 0., 1.5298747 , -0.76841313, -1.26697530e-10, 0.76372292, 0.00403775, 2.67220936e-05, 0.74748, 0.2511, 0.00142),\n", " (15610.06010113, 13.57208808, 0., 0., 0., 0., 0., 0., 0.74663148, 0.25192828, 3.64972826e-06, 0.00050979, 0.00044032, 0.74748, 0.25107328, 0.00025117, 7.35752498e-05, 0.00060884, -75.14930055, 0.01414088, 0., 0., 0., 4.19391627, -25.44798894, 0.73873336, 4.19406851, 4.53347181, 4.18011152, 0.54637099, 7.59450858, 1.05877441, 1.45734769e+56, 0., -99., 13.57206965, 13.57206965, 3.51730941, 3.51503286, -1.00000000e+99, -1.e+99, -1.e+99, -1.23079422e+50, 2.49233206e-10, 0.00227656, 3.51617113, 1.60828807, 1.60828807, 1.60828807, 0., 0., 1.60828807, -0.65191396, -1.04325683e-09, 1.02329832, 0.00507219, 2.67220936e-05, 0.74748, 0.2511, 0.00142),\n", " ( 1882.77976925, 71.68711644, 0., 0., 0., 0., 0., 0., 0.74667952, 0.25188536, 5.20460986e-06, 0.00054179, 0.00040168, 0.74748, 0.25107328, 0.00025117, 7.35752498e-05, 0.00060884, -66.78075539, 0.00747133, 0., 0., 0., 5.86040847, -21.18461477, 2.39959949, 5.86055875, 4.74585427, 5.85082109, 0.95696085, 7.69323666, 0.52375113, 5.60217239e+57, 0., -99., 71.68602562, 71.68602562, 9.0565095 , 9.05126109, 3.41948936e+06, -1.e+99, -1.e+99, -8.77155713e+50, 3.17655845e-07, 0.04622897, 8.98425941, 2.44823508, 2.44823508, 2.44823508, 0., 0., 2.44823508, -0.23839679, -5.65977861e-07, 4.11840915, 0.01332546, 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0., -99., 0. , 0. , 0. , 0. , 0.00000000e+00, 0.e+00, 0.e+00, -4.10055250e+50, 0.00000000e+00, 0. , 0. , 1.99792468, 1.99792468, 1.99792468, 0., 0., 1.99792468, -0.38865155, -9.20733750e-08, 2.41769015, 0.00930852, 2.67220936e-05, 0.74748, 0.2511, 0.00142),\n", " (86753.36023328, 5. , 0., 0., 0., 0., 0., 0., 0.7466874 , 0.25186564, 2.50626676e-06, 0.00046705, 0.0004907 , 0.74748, 0.25107328, 0.00025117, 7.35752498e-05, 0.00060884, -82.96464122, 0.02522663, 0., 0., 0., 2.86412353, -29.64322718, -0.62787222, 2.8642634 , 4.33588796, 2.84606574, 0.27451579, 7.50579968, 1.54682129, 1.31885098e+55, 0., -99., 4.99999777, 4.99999777, 1.87849103, 1.8762103 , -1.00000000e+99, -1.e+99, -1.e+99, -3.56658133e+49, 2.90680305e-10, 0.00228073, 1.87735066, 1.40732829, 1.40732829, 1.40732829, 0., 0., 1.40732829, -1.18564104, -2.00383522e-11, 0.43011231, 0.00249988, 2.67220936e-05, 0.74748, 0.2511, 0.00142),\n", " ( 2996.85960732, 51.39042664, 0., 0., 0., 0., 0., 0., 0.74665424, 0.25191017, 4.95851149e-06, 0.00053913, 0.00040505, 0.74748, 0.25107328, 0.00025117, 7.35752498e-05, 0.00060884, -68.06323402, 0.00825675, 0., 0., 0., 5.58586557, -21.82537327, 2.12654 , 5.58601637, 4.71695579, 5.57516733, 0.87693093, 7.67784561, 0.60779877, 2.77775974e+57, 0., -99., 0. , 0. , 0. , 0. , 0.00000000e+00, 0.e+00, 0.e+00, -6.02443780e+50, 1.62812825e-07, 0.02388221, 7.46957392, 2.20229762, 2.20229762, 2.20229762, 0., 0., 2.20229762, -0.30888975, -2.47247483e-07, 3.17362128, 0.01117727, 2.67220936e-05, 0.74748, 0.2511, 0.00142),\n", " ( 100. , 100. , 0., 0., 0., 0., 0., 0., 0.74673088, 0.25183447, 6.38102280e-06, 0.00054251, 0.00039929, 0.74748, 0.25107328, 0.00025117, 7.35752498e-05, 0.00060884, -60.8579449 , 0.00682707, 0., 0., 0., 7.08396649, -17.84621136, 3.61347829, 7.08411345, 4.80210852, 6.11186526, 0.97497443, 7.76754605, 0.62921669, 8.45792890e+57, 0., -99., 99.99989914, 99.99989914, 9.44005298, 9.43531656, 1.08267993e+06, -1.e+99, -1.e+99, -1.45410256e+51, 3.49167598e-09, 0.00473642, 9.43768477, 2.75824057, 2.75824057, 2.75824057, 0., 0., 2.75824057, -0.15968088, -1.00860992e-06, 4.20260728, 0.01373076, 2.67220936e-05, 0.74748, 0.2511, 0.00142),\n", " (46075.44797575, 6.97475397, 0., 0., 0., 0., 0., 0., 0.74672054, 0.25183431, 2.85789437e-06, 0.00047798, 0.00047774, 0.74748, 0.25107328, 0.00025117, 7.35752498e-05, 0.00060884, -80.07947648, 0.02050378, 0., 0., 0., 3.32814369, -28.06079619, -0.13793693, 3.32829216, 4.40681953, 3.31272289, 0.36598123, 7.53818226, 1.37391117, 2.97021072e+55, 0., -99., 6.97475328, 6.97475328, 2.32013167, 2.31753894, -1.00000000e+99, -1.e+99, -1.e+99, -5.40027262e+49, 3.14431346e-10, 0.00259273, 2.3188353 , 1.46566002, 1.46566002, 1.46566002, 0., 0., 1.46566002, -0.96075345, -1.04179328e-11, 0.57282062, 0.00318963, 2.67220936e-05, 0.74748, 0.2511, 0.00142)],\n", " dtype=[('S1_star_age', '