Pynta calculate IRC in different mode by user's choice #44
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typo fixed (stupid uppercase)... typo fix delete empty IRC_obj_dict collect_firework() added again
fix typo (case sensitive)
indentation fix
typo fixed (stupid uppercase)... typo fix delete empty IRC_obj_dict collect_firework() added again if irc_mode is not defined, define irc_mode = skip define IRC_obj_dict key value in run_task fix typo (case sensitive) delete prints() and redundent info for logger add IRC_opj_dict in optional_params indentation fix
fix typo add irc_mode to ts_task typo fixed (stupid uppercase)... typo fix delete empty IRC_obj_dict collect_firework() added again define IRC_obj_dict key value in run_task fix typo (case sensitive) add IRC_opj_dict in optional_params indentation fix define IRC_obj_dict key value in run_task fix typo (case sensitive) add IRC_opj_dict in optional_params indentation fix make irc_obj_dict optional in MolecularTSEstimate fix typo add irc_mode to ts_task typo fixed (stupid uppercase)... typo fix delete empty IRC_obj_dict collect_firework() added again
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Summary of modification
I have updated the way of running IRC by user's choice.
In pynta class from main.py, the keyword
irc_modeis added. User can add this keyword in Pynta input script.If
irc_mode = "relaxed", irc is calculated with top half of the slab layers relaxed.irc_obj_dictupdated accordingly.If
irc_mode = "fixed", irc is calculated with all slab layers frozen.irc_obj_dictupdated accordingly.If
irc_mode, is not "relaxed" nor "fixed", IRC is not calculated. It will callMolecularTSEstimate_noIRCin tasks.pyUpdated comments (04/15/2024)
setup_transition_states(). This will generate pynta.log file and dump info, which file and module vialogging.info, firetasks are running. It is only implemented insetup_transition_states()at the moment as a test. But will be expanded throughout pynta. print() statement is still there to parse the output to job output file generated by slurm.IRC_obj_dictas optional keyword forMolecularTSEstimate