Restart option added in case of unexpected termination #64

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sakim8048 wants to merge 166 commits into

pynta-restart-updated

Commits on Mar 24, 2025

polaris mapping info added in polaris.py

rayhe88
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launch several Rockets in a parallel environment

rayhe88
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Commits on Mar 27, 2025

restart module update: copy traj file to destination directory for opt task and delete empty json file in vib folder for vib task
sakim8048
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Commits on Mar 25, 2026

Calculate IRC with fmaxirc not fmaxopt

mjohnson541
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correctly find index of the site in adslabmol to provide to add_coadsorbate_2D

mjohnson541
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fix naming issues in TSest task adaption

mjohnson541
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add safety ensuring Molecule updating in geometricanalysis

mjohnson541
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update Molecule objects after merge actions

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use copies of the 2D adslabmol when looping through possible sites

mjohnson541
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specify flask in environment.yml

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bugfixes for adsorbate guess generation, particularly for bidentates

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enable use of any ASE calculator for harmonically forced calculations within pynta

mjohnson541
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take harmonically forced software inputs

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adapt adsorbate guess generation to software flexibility

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adapt TSest to harmonically forced software flexibility

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rename functions to remove xtb specific names

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remove unnecessary import of HarmonicallyForcedXTB

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handle TBLite calculator import in name_to_ase_software

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handle XTB and TBLite the same for testing purposes

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add test for harmonically forced optimization

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add fischer-tropsch run for testing

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update split_adsorbed_structures

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add a reaction_adsorbate_bond_cutoff to generate_TS_2D

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add function validate_TS_geometry

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add function validate_TS_ircs to assess TS validity based on IRC information

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add function validate_TS to combine geometry/frequency information and IRC information when available to overall assess the validity of a TS

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add validate_TS_configs function

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add testGeometricanalysis.py file for testing geometricanalysis.py functions

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add automatic transition state validation information in the postprocessing notebook

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enable clean_pynta_path to handle not saving the initial guess

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rename Ntsmin to Nharmmin, remove fmaxopthard

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add construct_initial_guess_files function

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enable MoleculeCollect fireworks to either add new fireworks as detours or additions

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create MolecularAdsorbateEstimate Firetask

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adapt initial guess generation to occur through fireworks

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adapt TSest to change in adsorbate_fw_dict

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adapt execute to the new workflow

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remove initial guesses from the main test example

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adapt testMain.py to initial guess changes

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adapt map_harmonically_forced and move to calculator.py

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add and pass along the nprocs_harm attribute

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parallelize adsorbate guess generation

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parallelize HFSP optimizations

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run the test example using 4 processes for harmonic optimizations

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Function for generating minimum energy adsorbate db with all data required for thermochemistry

tdprice-858
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Made base thermochemistry class for Pynta

tdprice-858
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Adding method to thermochemistry class to calculate heats of formation referenced to gas phase adsorbates. Current code is intended for gas phase refs: H2O, CH4, H2, NH3

tdprice-858
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adding method to thermo class calculate translational thermo

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Added method to thermo class for calculating vibrational thermo

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Add method to thermoclass to fit NASA polynomial from thermochemistry data

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Add method to thermo class for formatting RMG library output

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Added method to thermochem class for generating RMG thermochem library header

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Added method to thermo class for calculating temperature corrections, calling subroutines for fitting NASA polynomials and formatting RMG output.

tdprice-858
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Update postprocessing.py

tdprice-858
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improve adsorbate guess generation logging

mjohnson541
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delete forces to avoid errors when constructing Atoms object

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update the slab used for the main test

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delete generated rmg libraries when cleaning pynta directory

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add to_dict function

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remove admol construction error logging for handled errors

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enable get_vibdata to handle gas phase species

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improve TS validation information

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fix get_cp function

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add GasConfiguration for handling statmech and energy calculations for Gas phase species

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create SurfaceConfiguration object

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tweak computation of heat of formation

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tweak translation thermo calculations for SurfaceConfigurations

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tweaks to vibrational thermo calculations

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use rmgmolecule to fit thermochemistry greatly simplifying fitting NASA polynomials

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improve RMG output/thermo commenting

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adapt thermochemistry calculations in SurfaceConfiguration

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add run function for running statmech calculations for SurfaceConfiguration

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add new Class Kinetics for running kinetics calculations

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add to_dict and calculate_barrier for Kinetics

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enable calculation of kinetic parameters in Kinetics objects

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enable generation of RMG reaction library entries

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add run function for Kinetics

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add functions for calculating reaction thermochemistry

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add get_species function for postprocessing species into configuration dictionaries

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add get_TS function for postprocessing TSs into configuration dictionaries

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add function get_kinetics for postprocessing TSs into Kinetics objects

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add get_reference_energies function for extracting reference energies from pynta run

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add postprocess function for postprocessing Pynta runs into Configuration and Kinetics objects

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add write_rmg_libraries function for writing RMG libraries for a pynta run

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add Postprocessing Firework for running postprocessing automatically during Pynta runs

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enable Collect fireworks to generate Postprocessing fireworks

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add postprocessing options to the adsorbate and TS guess fireworks

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enable automatic postprocessing to be requested

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check thermo and reaction libraries get made in the workflow test

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adapt the postprocessing notebook

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remove old slab_init

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enable input of individual species/adsorbates as "molecule"s in the input yaml

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update rxn_test.yaml to improve testing

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fix guess generation for gas phase species

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enable get_reference_energies to also return what atoms can be referenced from the available reference species

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fix configuration classes

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avoid outputting thermochemistry for species not properly referenced

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adapt Postprocessing firework to thermochemistry availability tracking

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add calculate_thermodynamic_references keyword

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adapt generate_pair_geometries to handle input sites and site_adjacency's

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adapt setup_pair_opts_for_rxns to handle input adsorbates and input sites/site_adjacency

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enable get_coadsorbate_information to pass imag_freq_max through to get_unique_adsorbate_geometries

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adapt get_configs_for_calculation to operate on multiple coadsorbates

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adapt CalculateConfigurationEnergiesTask to operate on distinct coadsorbates

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adapt train_covdep_model_firework to handle multiple coadsorbates

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adapt SelectCalculationsTask to handle multiple coadsorbates

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adapt CoverageDependence to handle adsorbates and multiple coadsorbates

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enable CoverageDependence to launch in execute

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adapt postprocessing notebook to thermochemistry changes

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add a full xtb pynta run for testing coverage dependence

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add fireworks configurations for covdep test

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this adds a set of pairs calculations for the covdep run

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directory setup and directory cleaning for covdep test

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add the covdep workflow test

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skip calculation of thermodynamic references in the Pynta workflow test

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handle missing frequency files in get_best_adsorbate_xyz

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upgrade get_best_adsorbate_xyz to compare 2D structures to target

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fix call of get_best_adsorbate_xyz

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fix/cleanup task.py imports

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remove tasks import from coveragedependence.py

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handle TooManyElectronsException errors when generating unstable pairs

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fix importing of place_adsorbate

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restore adsorbate placement handling for covdep

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Have git track test, but not launches in IPython

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error handling for get_best_adsorbate_xyz

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move get_best_adsorbate_xyz to geometricanalysis.py

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move mol_to_atoms to geometricanalysis.py

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add get_energy_correction_configuration for computing the covdep energy correction for a given configuration

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add functions for computing barrier and reaction energy covdep corrections

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add extract_covdep_data for extracting import information for covdep postprocessing

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add analyze_covdep_lowest_energy function for examining the lowest energy covdep structures of a configuration

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add analyze_covdep_sample_data for looking at covdep samples associated with a target configuration

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add coverage dependence postprocessing notebook

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automatically apply and enforce reaction indexing

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postprocessing exception handling

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fix bug related to Xv generation

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get adsorbate mappings directly from their info file

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use single bond comparisons to avoid issues with generating the map for ts

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throw error if reactant/product is missing in TSguess

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properly compute num_surf_sites in TSguess

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allow to keep vdW bonds if they exist in the starting adsorbate for the TSguess

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skip structures if we cannot find occupied sites matching the template

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overhaul bond order determination

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skip configurations that cannot be converted to 2D in HFSP

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skip 2D configurations that cannot be properly labeled from the template in HFSP

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handle ValueError in TS validation

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add additional print statements to HFSP logging

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improve missing reactant or product logging

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fix flipped boolean in fix_bond_orders

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handle desorption of vdW species when adding them as a coadsorbate

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compress the adjacency list identifier

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prefer HFSP directions that have fewer vdW bonded species

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increment to python 3.9

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turn off verbosity for GFN1-xTB

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use python 3.9 in CI

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tweak CI workflow

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handle versioning

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Get information of the workflow and restart Pynta for optimization restart job. Delete empty vibration cache file in vib folder for vibration restart job

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add machine keyword in firework task
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Function copyDataAndSave() is added to copy a file from a origin subdirectory to a destination subdirectory

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add machine keywords to optimization and vibration firework tasks
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