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* Add initial_z to be read from directory name Add initial_z to be read from directory name, which is the case for v2 and newer versions. * Try to get metallicity form directory name Try to get the metallicity value from the directory name in case, there is no history file. * Correct typo step_7 -> step_6 * Add to reset DISPLAY for plotting Add to reset DISPLAY for plotting step on a cluster to avoid problems when logged in with window mode on ssh. * Check for initial RLO in join_grids Check for initial RLO in join_grids, too. Use a joint initial RLO boundary. * Debug Flush output for debugging * Fix bug in adding too many boundary systems Fix bug in adding too many boundary systems * Remove debugging Remove debugging * Fix list entry replacement (psygrid.py) Fix list entry replacement in psygrid.py * Fix list entry replacement (termination_flags.py) Fix list entry replacement in termination_flags.py * Add STEPID Add the number of the step to the slurm job-name * Update last developement changes (#62) * Fixed more dict syntax for kwargs in docs (#53) In SingleStar object docs * Fixed dict syntax for kwargs1, kwargs2 definitions (#52) --------- Co-authored-by: Camille Liotine <cliotine@u.northwestern.edu> * account for suggestions - add else (nevertheless it will raise an error message later; I thought I predefined STEPID, but it looks like I put it out/or missed to put it in; using job_name here as content of the STEPID is a bad idea, because it is expected to be a single character and not a string) - add the check for the length after the split (again, this would cause an error message later nevertheless) * rename variable e -> exists_already * rename e -> exists_already --------- Co-authored-by: Camille Liotine <cliotine@u.northwestern.edu>
* Add initial_z to be read from directory name Add initial_z to be read from directory name, which is the case for v2 and newer versions. * Try to get metallicity form directory name Try to get the metallicity value from the directory name in case, there is no history file. * Correct typo step_7 -> step_6 * Add to reset DISPLAY for plotting Add to reset DISPLAY for plotting step on a cluster to avoid problems when logged in with window mode on ssh. * Check for initial RLO in join_grids Check for initial RLO in join_grids, too. Use a joint initial RLO boundary. * Debug Flush output for debugging * Fix bug in adding too many boundary systems Fix bug in adding too many boundary systems * Remove debugging Remove debugging * Fix list entry replacement (psygrid.py) Fix list entry replacement in psygrid.py * Fix list entry replacement (termination_flags.py) Fix list entry replacement in termination_flags.py * Add STEPID Add the number of the step to the slurm job-name * Update last developement changes (#62) * Fixed more dict syntax for kwargs in docs (#53) In SingleStar object docs * Fixed dict syntax for kwargs1, kwargs2 definitions (#52) --------- Co-authored-by: Camille Liotine <cliotine@u.northwestern.edu> * account for suggestions - add else (nevertheless it will raise an error message later; I thought I predefined STEPID, but it looks like I put it out/or missed to put it in; using job_name here as content of the STEPID is a bad idea, because it is expected to be a single character and not a string) - add the check for the length after the split (again, this would cause an error message later nevertheless) * rename variable e -> exists_already * rename e -> exists_already * Add run_pipeline.sh - create the bash script "run_pipeline.sh", which starts all the setup steps with dependency * Automatic kill on failure set option to kill pending jobs, where the depended job failed * Check all steps, which can run in parallel - allow step_5 to go in parallel to step_3, too --------- Co-authored-by: Camille Liotine <cliotine@u.northwestern.edu>
…ed step (#45) * Update common_functions.py * Update step_detached.py * Update step_mesa.py * Update step_detached.py
* Adding gzip support when reading MESA grids. * Adding GZIP support to psygrid metadata printing. * Adding GZIP support to grid points files. * Adding GZIP support to EEP files. * Clarifications for GZIP files inside the code. * Adding more clarification regarding support of GZIP files. * Adding GZIP support to function converting MESA output to table. * Adding GZIP support when inferring termination flag from MESA run output. * Adding GZIP support in EEP class. * Correcting types in io
* started the step_isolated files (2 is for superclass with detached) and first changes in detached and in flow * allowed for different psygrid for isoalted step, selected lists of stellar states, still need to solve absence of logR for mergers * deleted old step_isolated * made step_merging * integrated the step_merged correctly in the flow * before intorducing the option for not using log_R as a matching criteria, having the option do decide the parameters of the matching * added most merger cases, still need to solve logR avsence in matching * finished step_merged combinations * made the new disrupted_step * added spin of merged product * made step_initially_single too and changes of structure after discussion with Konstantinos * latest changes * Eirini's change,name of mist0 to match_to_single_star * making lists for each matching * changes in lambda minimize function to a more general function that can take an arbitrary list * typo * added the option of the different list of attributes in the step_merged * matching should work the same for all subclasses now * syntax errors prob fixed * fixing runtime errors in the new files * some more fixing * Some print statements * change the flowchart to not go to sterp_disurpted if one of the events is detached is called * prints * typo in flowchart * Friday's work * . * fix init orbit * disrupted bianry evolves until CC2 * step SN updated to expect a 2nd CC in an already disrupted system. Matching for postMS and maybe HeStars may still need work * matching fixing * slightly improved the verbose text of the matching * print errors * changes to match_to_single_star * generalized alternative matching * for this PR, step merged does nothing * matching happening only when needed (once) * step merged and intially single go to step end for now * testing cases of ZAMS stars not needed to match * binary fraction * minor changes in isolated or initially single * else statement, self.companion * typo * deleted the option of fidning ZAMS through logR * syntax error fixing * resolving merging issues * went back to grid_Hrich and grid_strippedHe * ini file * ini * surf_avg_omega_div_omega_crit is not always stored, so it is no longer called for and passed to solve_ivp. It is calculated in the Matt+2015 magnetic braking calculation from stellar properties now, as it is only needed there. * del grid from detached params * ini * Removed additional instances where interp1d_sec[surf_avg_omega_div_omega_crit](t - t_offset_sec) was called. * changing the random * removed superfluous commas in defining detached step properties * Adding step_isolated,step_disrupted in the STEP_NAMES_LOADING_GRIDS so the metallicity can propagate in ther kwargs * fix in ini file * I think I went the POSYDON-MESA-INLIST submodule back * changed class names according to CamelCase convention * time profiling * Corrections to the detached verbose with timestamp. * no matching for the CO star, using m0,t0 of the previously matched star * Giving additional option 1 in verbose to print only the matching parameters * Step 1 in cleaning detached step. * Step 2 in cleaing detached step. * Removing duplicate code in square difference function. * Deciding on which column are going to use relative distance during matching. * Deleting obsolete transform method in detached step. * Removing unnecessary transform when scaling columns in detached step. * Using stored scalers and removing some useless self.grid assignments * in the 3rd matching step, I added the change of htrack also for postMS stars * added htrack = star.htrack * commenting out the relative differences during matching for center_he4 * in the 3rd alternative matching we also change the parameters used for matching to the ones according to the new htrack * typo * htrack is updated outside match_to_single_star to be used in the rest of get_star_data * removed simulationproperties from CE folder... --------- Co-authored-by: Eirini Kasdagli <kasdaglie@login6.ufhpc> Co-authored-by: kasdaglie <kasdaglie@ufl.edu> Co-authored-by: sg <sethg45@gmail.com> Co-authored-by: kkovlakas <kkovla@gmail.com>
* updating modules to newest versions for python 3.11 * merge developmet and fix sintax warning in step_SN where is not was incorrectly used whencomparig strigs --------- Co-authored-by: ssbvr <sim.bavera@gmail.com>
…ted using grids of pre-calculated detection probabilities living at /projects/b1119/POSYDON_GRIDS/POSYDON_popsynth_data/v2/POSYDON_data/selection_effects/grids/pdet_grid.hdf5. This file contains pdets assuming a 3-detector HLV network operating at different sensitivities. (#82)
* add synthetic population parser * bug fixes * cleaning * get DCO population at formation as df_synthetic, add t_inspiral and underlying stellar mass for rate calculation * add method to compute merger efficiency * add intrinsic and detectable populations * define all class variables * add visualisation modules * small edit * add rate calculation and SFR * add docstrings and parser of oneline dataframe * update pdet calculation to POSYDON selection effects * update sensitivity docstring
* Update gridutils.py add a catch, if something goes wrong while reading files * Update psygrid.py Catch "None" in history_mod and history_age * Ignore runs with corrupted history Ignore runs with corrupted history * fix typo close an open bracket * Remove some ignore_data again Remove ignore_data on normal history read, to allow stars to not be included in the simulation, e.g. a CO * Update scrubbing.py Catch, that table might not be None, while model or age is. * catch None if (binary) history is None set length to 0
* adding profile interpolation * adding monotonicity enforcement to main class * fixing typo in learn_bounds and increase epochs/callbacks * remove default path, move IF interpolator argument to train method * changed some variable names * adding load interpolator arg to main class init function * changing arg name from interpolator to IF_interpolator to prevent confusion * adding docs for prof interpolation * fixed file format for docs * fix typo * removed extraneous line * addressing some stylistic issues * resolve various issues * changed name of finalmass to final_m1, added missing states to X_H class * fixed missing return in mono renorm * addressing Philipp's comments; changing a few argument/variable names, added arguments for model training parameters --------- Co-authored-by: Elizabeth Teng <elizabethteng@u.northwestern.edu>
* allow to remove slices from combining grids and only remove the combining if all slices are missing * Update setup-pipeline correct some typos * track previously created files * Update setup-pipeline fix typo * get files from step 1 * change range over df shape to instead use the index object * turn any to check on length * add check for no slurm tasks * account for larger length difference of histories * reuse columns from histories if possible, add warnings * bugfix * add open-mode, remove old file (make a copy first) * allow to ignore bad charaters in MESA log files * drop rows and columns
* Add function "keep_till_He_depletion" * Add option to stop at He depletion * Add option to pipeline (remove later) * correct not * Change threshold for He depletion * allow histories without age, add new flag * Check for history of 0 length * add C criterion for He depletion add C criterion for He depletion * Update psygrid.py use 0.08 carbon abundance * Update scrubbing.py where can't handle two arrays in parallel * Update psygrid.py change C limit to 0.1 * Update psygrid.py Add mass request to only apply stopping earlier to masses of 100Msun and above * Update run-pipeline remove "_He_depletion" extension for the file name of the hdf5 file containing the psygrid * rename function and flags * Update psygrid.py correct typo
* add synthetic population parser * bug fixes * cleaning * get DCO population at formation as df_synthetic, add t_inspiral and underlying stellar mass for rate calculation * add method to compute merger efficiency * add intrinsic and detectable populations * define all class variables * add visualisation modules * small edit * add rate calculation and SFR * add docstrings and parser of oneline dataframe * update pdet calculation to POSYDON selection effects * update sensitivity docstring * support arbitrary MODEL for rate calculation * fix
…models + introduce H envelope option to step_SN + v2 data pop synth debugged (#70) * Add function "keep_till_He_depletion" * Add option to stop at He depletion * Add option to pipeline (remove later) * correct not * Change threshold for He depletion * allow histories without age, add new flag * Check for history of 0 length * support BH formation above PISN gap and direct/Fryer collapse prescriptions now assume hydrogen envelope does not go into the BH * add C criterion for He depletion add C criterion for He depletion * Update psygrid.py use 0.08 carbon abundance * Update scrubbing.py where can't handle two arrays in parallel * Update psygrid.py change C limit to 0.1 * support the option to conserve the hydrogen envelope in BH formation * add MODEL var to post processing * update post processing script to support multiple core collapse models * Update psygrid.py Add mass request to only apply stopping earlier to masses of 100Msun and above * Update run-pipeline remove "_He_depletion" extension for the file name of the hdf5 file containing the psygrid * debug * rename function and flags * add support for BH disk mass * allow to remove slices from combining grids and only remove the combining if all slices are missing * fix small bug * Update setup-pipeline correct some typos * track previously created files * Update setup-pipeline fix typo * get files from step 1 * change range over df shape to instead use the index object * update step_6 run-pipeline * turn any to check on length * debug * add check for no slurm tasks * account for larger length difference of histories * reuse columns from histories if possible, add warnings * bugfix * propagate changes in step_SN and step_MESA * fix bug * debug plot2D * remove circular import * add open-mode, remove old file (make a copy first) * allow to ignore bad charaters in MESA log files * drop rows and columns * change import * import TF1 for post processing * fix bug * Update psygrid.py correct typo * debug * roll fix for single stars as well * debug * Matthias split grid rlo (#99) * fix in psygrid.py fix check of initial mass when cutting off carbon depletion * Update run-pipeline get start_at_RLO from compression type add flag to stop before carbon depletion (allow only for HMS grids) * Update setup-pipeline remove CO_HMS_GRID_START_AT_RLO add STOP_BEFORE_CARBON_DEPLETION * Update setup-pipeline get different directory for plotting if compression contains "RLO" * Update setup-pipeline correct typo * Update psygrid.py correct typo * Update psygrid.py debug * debug single interpolation * add support for other metallicities * update Z to Y conversion * SN_type not diclared in star properties * debug * update default params ini * increase len interp_class column * update params ini * add authorship to MODEL.py * Matthias split grid rlo (#100) * fix in psygrid.py fix check of initial mass when cutting off carbon depletion * Update run-pipeline get start_at_RLO from compression type add flag to stop before carbon depletion (allow only for HMS grids) * Update setup-pipeline remove CO_HMS_GRID_START_AT_RLO add STOP_BEFORE_CARBON_DEPLETION * Update setup-pipeline get different directory for plotting if compression contains "RLO" * Update setup-pipeline correct typo * Update psygrid.py correct typo * Update psygrid.py debug * Update setup-pipeline Add RLO to steps 6 and 7 * Update setup-pipeline Correct step 7 * Update run-pipeline don't interpolate no_MT for any grid starting at RLO * Update run-pipeline remove "_RLO" from method, which is read from the filename * Update setup-pipeline add "CO-HeMS_RLO" to export dirs * update spin orbit tilt name in rate calculation --------- Co-authored-by: mkruckow <122798003+mkruckow@users.noreply.github.com> Co-authored-by: mkruckow <Matthias.Kruckow@unige.ch>
* started the step_isolated files (2 is for superclass with detached) and first changes in detached and in flow * allowed for different psygrid for isoalted step, selected lists of stellar states, still need to solve absence of logR for mergers * deleted old step_isolated * made step_merging * integrated the step_merged correctly in the flow * before intorducing the option for not using log_R as a matching criteria, having the option do decide the parameters of the matching * added most merger cases, still need to solve logR avsence in matching * finished step_merged combinations * made the new disrupted_step * added spin of merged product * made step_initially_single too and changes of structure after discussion with Konstantinos * latest changes * Eirini's change,name of mist0 to match_to_single_star * making lists for each matching * changes in lambda minimize function to a more general function that can take an arbitrary list * typo * added the option of the different list of attributes in the step_merged * matching should work the same for all subclasses now * syntax errors prob fixed * fixing runtime errors in the new files * some more fixing * Some print statements * change the flowchart to not go to sterp_disurpted if one of the events is detached is called * prints * typo in flowchart * Friday's work * . * fix init orbit * disrupted bianry evolves until CC2 * step SN updated to expect a 2nd CC in an already disrupted system. Matching for postMS and maybe HeStars may still need work * matching fixing * slightly improved the verbose text of the matching * print errors * changes to match_to_single_star * generalized alternative matching * for this PR, step merged does nothing * matching happening only when needed (once) * step merged and intially single go to step end for now * testing cases of ZAMS stars not needed to match * binary fraction * minor changes in isolated or initially single * else statement, self.companion * typo * deleted the option of fidning ZAMS through logR * syntax error fixing * resolving merging issues * went back to grid_Hrich and grid_strippedHe * ini file * ini * surf_avg_omega_div_omega_crit is not always stored, so it is no longer called for and passed to solve_ivp. It is calculated in the Matt+2015 magnetic braking calculation from stellar properties now, as it is only needed there. * del grid from detached params * ini * Removed additional instances where interp1d_sec[surf_avg_omega_div_omega_crit](t - t_offset_sec) was called. * changing the random * removed superfluous commas in defining detached step properties * Adding step_isolated,step_disrupted in the STEP_NAMES_LOADING_GRIDS so the metallicity can propagate in ther kwargs * fix in ini file * I think I went the POSYDON-MESA-INLIST submodule back * changed class names according to CamelCase convention * time profiling * Corrections to the detached verbose with timestamp. * no matching for the CO star, using m0,t0 of the previously matched star * Giving additional option 1 in verbose to print only the matching parameters * printing of more timing profiling * Step 1 in cleaning detached step. * Step 2 in cleaing detached step. * Removing duplicate code in square difference function. * Deciding on which column are going to use relative distance during matching. * Deleting obsolete transform method in detached step. * Removing unnecessary transform when scaling columns in detached step. * Using stored scalers and removing some useless self.grid assignments * adding massless in the star states in flow chart * Adding massless_remant and a compact binary state list for the detached. Adding initially single stars in the step names for metallisity * fixing the primary.co in some elif * fixing the infite loop created by the flow chart * metallicity = 1 as default * in the flow, a CO+massless goes to step_end * going to step initially single only after ZAMS * pulled merged step from manos_merged_step * pulled the isolated step and the population defaults for all substeps (disrupted, initially_single, merged) * pulled step_SN, flow, and step_detached * added step_merged in steps that need a metallicity (in binarypopulations.py) * IsolatedStep changes * fixing the STAR_STATES_ALL in the flow_chart * properties_massless_remnant in common function * convert_massless_remenant in merged * properties massless in SingleStar class instead * corrected massless_remnant dictionary * fixing the state after CC1 in merged and single stars * set initial period and separation for single star equal to nan * deleting some unnecessary comments * deleting repeated dictionaries in detached * reverting the changes in MESA-INLISTS * Update step_detached.py * Update binarystar.py --------- Co-authored-by: ezapartas <ezapartas@gmail.com> Co-authored-by: Eirini Kasdagli <kasdaglie@login6.ufhpc> Co-authored-by: sg <sethg45@gmail.com> Co-authored-by: kkovlakas <kkovla@gmail.com>
* Fixing coordinate frame inconsistency in orbital_kick() * more documentation for orbital_kick fix * fixed issue with cos_psi being limited to >0 --------- Co-authored-by: Jeff Andrews <jeffrey.andrews@northwestern.edu>
* adding profile interpolation * adding monotonicity enforcement to main class * fixing typo in learn_bounds and increase epochs/callbacks * remove default path, move IF interpolator argument to train method * changed some variable names * adding load interpolator arg to main class init function * changing arg name from interpolator to IF_interpolator to prevent confusion * adding docs for prof interpolation * fixed file format for docs * fix typo * removed extraneous line * addressing some stylistic issues * resolve various issues * changed name of finalmass to final_m1, added missing states to X_H class * fixed missing return in mono renorm * addressing Philipp's comments; changing a few argument/variable names, added arguments for model training parameters * adding tensorflow to extras_require * fixed typo and added comment for tensorflow dependency * added helium profile interpolation, updated docs * update compiledata to include option for star 2, add MT class to dataframe * condensed a for loop * fixed a few bugs * moved some definitions around * make 80/20 split for validation data from training data * typos * allowed for star 2 in all classes * got rid of feature that would make predictions from untrained models for final star states with no training data * Update setup.py --------- Co-authored-by: Elizabeth Teng <elizabethteng@u.northwestern.edu> Co-authored-by: Jeff Andrews <jeffrey.andrews@ufl.edu>
* Added an agb_wind rerun type (to perform reruns that will have the Bloecker AGB wind enabled). * removed the initial mass < 10 Msol check * Update run-pipeline --------- Co-authored-by: Seth Shearer Gossage <ssg9761@quser32.quest.it.northwestern.edu> Co-authored-by: Seth Shearer Gossage <ssg9761@quser33.quest.it.northwestern.edu> Co-authored-by: Jeff Andrews <jeffrey.andrews@northwestern.edu>
Missing comment block
Adding a comma
set tpabg to False in case of a missing history, e.g. if there is a CO instead of a star
* Add function "keep_till_He_depletion" * Add option to stop at He depletion * Add option to pipeline (remove later) * correct not * Change threshold for He depletion * allow histories without age, add new flag * Check for history of 0 length * support BH formation above PISN gap and direct/Fryer collapse prescriptions now assume hydrogen envelope does not go into the BH * add C criterion for He depletion add C criterion for He depletion * Update psygrid.py use 0.08 carbon abundance * Update scrubbing.py where can't handle two arrays in parallel * Update psygrid.py change C limit to 0.1 * support the option to conserve the hydrogen envelope in BH formation * add MODEL var to post processing * update post processing script to support multiple core collapse models * Update psygrid.py Add mass request to only apply stopping earlier to masses of 100Msun and above * Update run-pipeline remove "_He_depletion" extension for the file name of the hdf5 file containing the psygrid * debug * rename function and flags * add support for BH disk mass * allow to remove slices from combining grids and only remove the combining if all slices are missing * fix small bug * Update setup-pipeline correct some typos * track previously created files * Update setup-pipeline fix typo * get files from step 1 * change range over df shape to instead use the index object * update step_6 run-pipeline * turn any to check on length * debug * add check for no slurm tasks * account for larger length difference of histories * reuse columns from histories if possible, add warnings * bugfix * propagate changes in step_SN and step_MESA * fix bug * debug plot2D * remove circular import * add open-mode, remove old file (make a copy first) * allow to ignore bad charaters in MESA log files * drop rows and columns * change import * import TF1 for post processing * fix bug * Update psygrid.py correct typo * debug * roll fix for single stars as well * debug * Matthias split grid rlo (#99) * fix in psygrid.py fix check of initial mass when cutting off carbon depletion * Update run-pipeline get start_at_RLO from compression type add flag to stop before carbon depletion (allow only for HMS grids) * Update setup-pipeline remove CO_HMS_GRID_START_AT_RLO add STOP_BEFORE_CARBON_DEPLETION * Update setup-pipeline get different directory for plotting if compression contains "RLO" * Update setup-pipeline correct typo * Update psygrid.py correct typo * Update psygrid.py debug * debug single interpolation * add support for other metallicities * update Z to Y conversion * SN_type not diclared in star properties * debug * update default params ini * increase len interp_class column * update params ini * add authorship to MODEL.py * Matthias split grid rlo (#100) * fix in psygrid.py fix check of initial mass when cutting off carbon depletion * Update run-pipeline get start_at_RLO from compression type add flag to stop before carbon depletion (allow only for HMS grids) * Update setup-pipeline remove CO_HMS_GRID_START_AT_RLO add STOP_BEFORE_CARBON_DEPLETION * Update setup-pipeline get different directory for plotting if compression contains "RLO" * Update setup-pipeline correct typo * Update psygrid.py correct typo * Update psygrid.py debug * Update setup-pipeline Add RLO to steps 6 and 7 * Update setup-pipeline Correct step 7 * Update run-pipeline don't interpolate no_MT for any grid starting at RLO * Update run-pipeline remove "_RLO" from method, which is read from the filename * Update setup-pipeline add "CO-HeMS_RLO" to export dirs * update spin orbit tilt name in rate calculation * adding function get_formation_channels * in parse function, shifting the binary_index * compute GRB properties * add channelwise merger efficiency calculation and plotting * add channelwise rate density * support channelwise histogram distributions * add file authorship * debug * cosistency change * add GRB rate calculation * fixing shift in binary index * minor bug * debug * debug * debug * address PR103 PR104 comments * remove bug introduced in previous comment * remove bug introduced in previous commit * debug --------- Co-authored-by: mkruckow <122798003+mkruckow@users.noreply.github.com> Co-authored-by: mkruckow <Matthias.Kruckow@unige.ch> Co-authored-by: Monica Gallegos-Garcia <monicagallegosgarcia2024@u.northwestern.edu>
* adding profile interpolation * adding monotonicity enforcement to main class * fixing typo in learn_bounds and increase epochs/callbacks * remove default path, move IF interpolator argument to train method * changed some variable names * adding load interpolator arg to main class init function * changing arg name from interpolator to IF_interpolator to prevent confusion * adding docs for prof interpolation * fixed file format for docs * fix typo * removed extraneous line * addressing some stylistic issues * resolve various issues * changed name of finalmass to final_m1, added missing states to X_H class * fixed missing return in mono renorm * addressing Philipp's comments; changing a few argument/variable names, added arguments for model training parameters * adding tensorflow to extras_require * fixed typo and added comment for tensorflow dependency * added helium profile interpolation, updated docs * update compiledata to include option for star 2, add MT class to dataframe * condensed a for loop * fixed a few bugs * moved some definitions around * make 80/20 split for validation data from training data * typos * allowed for star 2 in all classes * got rid of feature that would make predictions from untrained models for final star states with no training data * Update setup.py * testing branch * undo * Update ProfileInterpolator.rst * update comments and docstrings, fix star 1/star 2 stuff in composition class * adding missing argument name * fixed comment * update tensorflow version to 2.13 to avoid installation issues * added omega profiles normalized by omega/omega_crit --------- Co-authored-by: Elizabeth Teng <elizabethteng@u.northwestern.edu> Co-authored-by: Jeff Andrews <jeffrey.andrews@ufl.edu> Co-authored-by: Simone Bavera <32518238+ssbvr@users.noreply.github.com>
* Update gridutils.py * Update gridutils.py Use os functionalities instead * Update step_mesa.py Use os functionality * Update run-pipeline Use os functionalities * Update posydon-setup-grid Use os functionality correct bug (use file name instead of first directory name) * Update compress-mesa Use os functionality
…erbunt, and Joss 1983 prescription in step_detached (#114) The leading constant should have been 3.8e-30, not 3.8e30.
* Add function "keep_till_He_depletion" * Add option to stop at He depletion * Add option to pipeline (remove later) * correct not * Change threshold for He depletion * allow histories without age, add new flag * Check for history of 0 length * support BH formation above PISN gap and direct/Fryer collapse prescriptions now assume hydrogen envelope does not go into the BH * add C criterion for He depletion add C criterion for He depletion * Update psygrid.py use 0.08 carbon abundance * Update scrubbing.py where can't handle two arrays in parallel * Update psygrid.py change C limit to 0.1 * support the option to conserve the hydrogen envelope in BH formation * add MODEL var to post processing * update post processing script to support multiple core collapse models * Update psygrid.py Add mass request to only apply stopping earlier to masses of 100Msun and above * Update run-pipeline remove "_He_depletion" extension for the file name of the hdf5 file containing the psygrid * debug * rename function and flags * add support for BH disk mass * allow to remove slices from combining grids and only remove the combining if all slices are missing * fix small bug * Update setup-pipeline correct some typos * track previously created files * Update setup-pipeline fix typo * get files from step 1 * change range over df shape to instead use the index object * update step_6 run-pipeline * turn any to check on length * debug * add check for no slurm tasks * account for larger length difference of histories * reuse columns from histories if possible, add warnings * bugfix * propagate changes in step_SN and step_MESA * fix bug * debug plot2D * remove circular import * add open-mode, remove old file (make a copy first) * allow to ignore bad charaters in MESA log files * drop rows and columns * change import * import TF1 for post processing * fix bug * Update psygrid.py correct typo * debug * roll fix for single stars as well * debug * Matthias split grid rlo (#99) * fix in psygrid.py fix check of initial mass when cutting off carbon depletion * Update run-pipeline get start_at_RLO from compression type add flag to stop before carbon depletion (allow only for HMS grids) * Update setup-pipeline remove CO_HMS_GRID_START_AT_RLO add STOP_BEFORE_CARBON_DEPLETION * Update setup-pipeline get different directory for plotting if compression contains "RLO" * Update setup-pipeline correct typo * Update psygrid.py correct typo * Update psygrid.py debug * debug single interpolation * add support for other metallicities * update Z to Y conversion * SN_type not diclared in star properties * debug * update default params ini * increase len interp_class column * update params ini * add authorship to MODEL.py * Matthias split grid rlo (#100) * fix in psygrid.py fix check of initial mass when cutting off carbon depletion * Update run-pipeline get start_at_RLO from compression type add flag to stop before carbon depletion (allow only for HMS grids) * Update setup-pipeline remove CO_HMS_GRID_START_AT_RLO add STOP_BEFORE_CARBON_DEPLETION * Update setup-pipeline get different directory for plotting if compression contains "RLO" * Update setup-pipeline correct typo * Update psygrid.py correct typo * Update psygrid.py debug * Update setup-pipeline Add RLO to steps 6 and 7 * Update setup-pipeline Correct step 7 * Update run-pipeline don't interpolate no_MT for any grid starting at RLO * Update run-pipeline remove "_RLO" from method, which is read from the filename * Update setup-pipeline add "CO-HeMS_RLO" to export dirs * update spin orbit tilt name in rate calculation * adding function get_formation_channels * in parse function, shifting the binary_index * compute GRB properties * add channelwise merger efficiency calculation and plotting * add channelwise rate density * support channelwise histogram distributions * add file authorship * debug * cosistency change * add GRB rate calculation * debug * debug * debug * address PR103 PR104 comments * remove bug introduced in previous comment * remove bug introduced in previous commit * bug fix --------- Co-authored-by: mkruckow <122798003+mkruckow@users.noreply.github.com> Co-authored-by: mkruckow <Matthias.Kruckow@unige.ch> Co-authored-by: Monica Gallegos-Garcia <monicagallegosgarcia2024@u.northwestern.edu>
This fixes a bug in the logic. For `f_bin_simulated != 1`, the logic would result in the second if/else statement always being run, despite wanting to run the `f_bin_nature == 0`.
* implement Hendriks+23 SN prescription * Add commentedMODELS to train for Hendriks+23 with and without hydrogen envelope conservation * add additioanl PISN parameters in default population.ini file. Not necessary to include when running pops * add paper equation comment + limit metallicity to Z >= 1e-4 for equation. Lower values use 1e-4 PPI prescription * add new parameter for conserve_hydrogen_PPI * Add to default model * Allow CCSN to use conserve_hydrogen * define m_CO_core_PISN_min/max for easier understanding * Update the documentation with the new parameters
* Add BZ jet calculation option + restructure do_core_collapse_BH output * Update profile_collapse.py * fix verbose print statement * extend doc string + fix return on l 404 * remove ==BH statement * shift star.mass definition upwards before the check * remove double set of m_disk_x * Update posydon/binary_evol/SN/profile_collapse.py Co-authored-by: mkruckow <122798003+mkruckow@users.noreply.github.com> * typo fix --------- Co-authored-by: mkruckow <122798003+mkruckow@users.noreply.github.com>
…476) * split popsyn plotting into separate components for future modularity * swap m1 and m2 for CO grid plotting * additional comment * add small changes to doc strings * add value error + doc string * save file to add else
* use information about dominating star in infer_mass_transfer_case * Update profile_collapse.py correct typo * separate best_fit and new htrack * Update step_detached.py cleanup * cleanup blanks --------- Co-authored-by: Max Briel <max.briel@gmail.com>
sphinx at least 8.2.2
* change to v4 * add to CI for testing checkout and setup python versions * change other versions to 'latest'
* update first tutorial * add shell loop; make shell script executeable * add cleanup to shell run * reuse already loaded grid * tutorial2 * tutorial 4 * tutorial 3: changes before submission only * complete tutorial 3
* create data sets * add new functions * Update datasets.py * add command line interaction * add todos to not download full default always as soon as we have more datasets * add more error handling * use dataset name more in outputs * adpot documantation * Update data_download.py filename -> filepath in error * Update installation-guide.rst More info for the PATH* variables * correct typos and add more information * adjust line length --------- Co-authored-by: Jeff Andrews <jeffrey.andrews@ufl.edu>
* Update step_SN.py escape for ECSN in SN_MODELS * add check for ECSN to not use interpolated values * add warning for mismatching SN_type and reorder other warnings * replace np.isnan by pd.isna * attemped to overwrite ECSN in SN_MODEL * add ReplaceValueWarning * add warning if ECSN leads to BH * Update step_SN.py typo * Update step_SN.py typo * Update step_SN.py another typo * Update step_SN.py bug fix
* add WDs to infer_star_state, incl. testing and new limits * add references
change >3.10 to >=3.11
* create new pyproject.toml; try to reuse setup.py as much as possible * add refs
Update to give the correct usage for the engine if 'other' mechanisms are used
Contributor
Contributor
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This should be rebased or cherrypicked to merge into |
Contributor
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@philipp-rajah I linked Issue#86 to this PR. We stated back then that maybe we could resolve that issue and its sub-issues with this interpolator rewrite, so we should check that we can resolve them here. |
Contributor
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Linked Issue#419 to this PR. There it is suggested that we might find a solution to fix a possible classification issue that can lead HMS-HMS stars to result in RLO. An example there finds a system that entered unstable_MT during step_HMS_HMS, which should lead to step_CE, not step_detached (which would be valid as a result of stable MT). |
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Initial draft PR for the initial final interpolator rewrite which includes numerous improvements to the code, both at the preprocessing and the algorithmic levels.