arc.processor

Processor module for computing thermodynamic properties and rate coefficients using statistical mechanics.

arc.processor.clean_output_directory(project_directory: str) → None

A helper function to organize the output directory.

• remove redundant rotor.txt files (from kinetics jobs)

• move remaining rotor files to the rotor directory

• move the Arkane YAML file from the species directory to the base directory, and delete species

Parameters:

project_directory (str) – The path to the ARC project directory.

arc.processor.compare_rates(rxns_for_kinetics_lib: list, rmg_database: Type[RMGDatabase], output_directory: str, T_min: Optional[tuple] = None, T_max: Optional[tuple] = None, T_count: int = 50) → None

Compare the calculates rates with RMG’s estimations.

Parameters:

• rxns_for_kinetics_lib (list) – Reactions for which rate coefficients were computed.

• rmg_database (RMGDatabase, optional) – The RMG database object.

• output_directory (str) – The path to the project’s output folder.

• T_min (tuple, optional) – The minimum temperature for kinetics computations, e.g., (500, ‘K’).

• T_max (tuple, optional) – The maximum temperature for kinetics computations, e.g., (3000, ‘K’).

• T_count (int, optional) – The number of temperature points between T_min and T_max.

arc.processor.compare_thermo(species_for_thermo_lib: list, rmg_database: Type[RMGDatabase], output_directory: str) → None

Compare the calculates thermo with RMG’s estimations.

Parameters:

• species_for_thermo_lib (list) – Species for which thermochemical properties were computed.

• rmg_database (RMGDatabase, optional) – The RMG database object.

• output_directory (str) – The path to the project’s output folder.

arc.processor.compare_transport(species_for_transport_lib: list, rmg_database: Type[RMGDatabase], output_directory: str) → None

Compare the calculates transport data with RMG’s estimations.

Parameters:

• species_for_transport_lib (list) – Species for which thermochemical properties were computed.

• rmg_database (RMGDatabase, optional) – The RMG database object.

• output_directory (str) – The path to the project’s output folder.

arc.processor.load_rmg_database(rmg_database: Optional[Type[RMGDatabase]], species_dict: dict, output_dict: dict) → None

Load the RMG database.

Parameters:

• rmg_database (RMGDatabase, optional) – The RMG database object.

• species_dict (dict) – Keys are labels, values are ARCSpecies objects.

• output_dict (dict) – Keys are labels, values are output file paths. See Scheduler for a description of this dictionary.

arc.processor.process_arc_project(thermo_adapter: str, kinetics_adapter: str, project: str, project_directory: str, species_dict: dict, reactions: list, output_dict: dict, bac_type: Optional[str] = None, sp_level: Optional[Level] = None, freq_scale_factor: float = 1.0, compute_thermo: bool = True, compute_rates: bool = True, compute_transport: bool = False, T_min: Optional[tuple] = None, T_max: Optional[tuple] = None, T_count: int = 50, lib_long_desc: str = '', rmg_database: Optional[RMGDatabase] = None, compare_to_rmg: bool = True, three_params: bool = True, skip_nmd: bool = False) → None

Process an ARC project, generate thermo and rate coefficients using statistical mechanics (statmech).

Parameters:

• thermo_adapter (str) – The software to use for calculating thermodynamic data.

• kinetics_adapter (str) – The software to use for calculating rate coefficients.

• project (str) – The ARC project name.

• project_directory (str) – The path to the ARC project directory.

• species_dict (dict) – Keys are labels, values are ARCSpecies objects.

• reactions (list) – Entries are ARCReaction objects.

• output_dict (dict) – Keys are labels, values are output file paths. See Scheduler for a description of this dictionary.

• bac_type (str, optional) – The bond additivity correction type. ‘p’ for Petersson- or ‘m’ for Melius-type BAC. None to not use BAC.

• sp_level (Level, optional) – The level of theory used for energy corrections.

• freq_scale_factor (float, optional) – The harmonic frequencies scaling factor.

• compute_thermo (bool, optional) – Whether to compute thermodynamic properties for the provided species.

• compute_rates (bool, optional) – Whether to compute high pressure limit rate coefficients.

• compute_transport (bool, optional) – Whether to compute transport properties.

• T_min (tuple, optional) – The minimum temperature for kinetics computations, e.g., (500, ‘K’).

• T_max (tuple, optional) – The maximum temperature for kinetics computations, e.g., (3000, ‘K’).

• T_count (int, optional) – The number of temperature points between T_min and T_max.

• lib_long_desc (str, optional) – A multiline description of levels of theory for the resulting RMG libraries.

• rmg_database (RMGDatabase, optional) – The RMG database object.

• compare_to_rmg (bool, optional) – If True, ARC’s calculations will be compared against estimations from RMG’s database.

• three_params (bool, optional) – Compute rate coefficients using the modified three-parameter Arrhenius equation format (True, default) or classical two-parameter Arrhenius equation format (False).

• skip_nmd (bool, optional) – Whether to skip the normal mode displacement check analysis. Defaults to False.

arc.processor.process_bdes(label: str, species_dict: dict) → dict

Process bond dissociation energies for a single parent species represented by label.

Parameters:

• label (str) – The species label.

• species_dict (dict) – Keys are labels, values are ARCSpecies objects.

Returns:

The BDE report for a single species. Keys are pivots, values are energies in kJ/mol.

Return type:

dict

arc.processor.write_unconverged_log(unconverged_species: list, unconverged_rxns: list, log_file_path: str) → None

Write a log file of unconverged species and reactions.

Parameters:

• unconverged_species (list) – List of unconverged species to report.

• unconverged_rxns (list) – List of unconverged reactions to report.

• log_file_path (str) – The path to the log file to write.