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Merge pull request #153 from ReactionMechanismGenerator/shared_libraries
Allow users to use a shared RMG library between different T3 projects
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,189 @@ | ||
| """ | ||
| t3 utils libraries module | ||
| for working with RMG thermo and kinetics libraries | ||
| """ | ||
|
|
||
| import datetime | ||
| import os | ||
| import shutil | ||
| import time | ||
|
|
||
| from typing import Dict, TYPE_CHECKING | ||
|
|
||
| from rmgpy.data.kinetics import KineticsLibrary | ||
| from rmgpy.data.thermo import ThermoLibrary | ||
| from rmgpy.kinetics import Arrhenius, KineticsData | ||
| from rmgpy.reaction import Reaction | ||
| from rmgpy.thermo import NASAPolynomial, NASA, ThermoData, Wilhoit | ||
| from rmgpy.species import Species | ||
|
|
||
| if TYPE_CHECKING: | ||
| from t3.logger import Logger | ||
|
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||
|
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| def add_to_rmg_libraries(library_name: str, | ||
| shared_library_name: str, | ||
| paths: Dict[str, str], | ||
| logger: 'Logger', | ||
| ): | ||
| """ | ||
| Creates RMG libraries in the RMG database repository if they don't already exist, | ||
| and appends with the respective entries from the libraries generated by ARC. | ||
| Args: | ||
| library_name (str): The name of the RMG library. | ||
| shared_library_name (str): The name of an RMG database library shared between T3 projects. | ||
| paths (Dict[str, str]): T3's dictionary of paths. | ||
| logger (Logger): Instance of T3's Logger class. | ||
| """ | ||
| for token in ['thermo', 'kinetics']: | ||
| arc_lib_path, t3_lib_path, shared_lib_path = \ | ||
| paths[f'ARC {token} lib'], paths[f'T3 {token} lib'], paths[f'shared T3 {token} lib'] | ||
| if token == 'thermo': | ||
| local_context = { | ||
| 'ThermoData': ThermoData, | ||
| 'Wilhoit': Wilhoit, | ||
| 'NASAPolynomial': NASAPolynomial, | ||
| 'NASA': NASA, | ||
| } | ||
| else: | ||
| local_context = { | ||
| 'KineticsData': KineticsData, | ||
| 'Arrhenius': Arrhenius, | ||
| } | ||
| for to_lib_path, lib_name, race in zip([shared_lib_path, t3_lib_path], | ||
| [library_name, shared_library_name], | ||
| [True, False]): | ||
| if os.path.isfile(arc_lib_path) and to_lib_path is not None and os.path.isfile(to_lib_path): | ||
| append_to_rmg_library(library_name=lib_name, | ||
| from_lib_path=arc_lib_path, | ||
| to_lib_path=to_lib_path, | ||
| local_context=local_context, | ||
| lib_type=token, | ||
| logger=logger, | ||
| race=race, | ||
| ) | ||
| else: | ||
| # The destination library (T3's or the shared) doesn't exist. Just copy the library generated by ARC. | ||
| if os.path.isfile(arc_lib_path) and to_lib_path is not None: | ||
| if not os.path.isdir(os.path.dirname(to_lib_path)): | ||
| os.makedirs(os.path.dirname(to_lib_path)) | ||
| shutil.copy(arc_lib_path, to_lib_path) | ||
|
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||
|
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| def append_to_rmg_library(library_name: str, | ||
| from_lib_path: str, | ||
| to_lib_path: str, | ||
| local_context: dict, | ||
| lib_type: str, | ||
| logger: 'Logger', | ||
| race: bool = False, | ||
| ): | ||
| """ | ||
| Append the entries from the ARC-generated library to an RMG library. | ||
| Args: | ||
| library_name (str): The name of the RMG library. | ||
| from_lib_path (str): The path to the ARC-generated library. | ||
| to_lib_path (str): The path to the RMG library to append to. | ||
| local_context (dict): The local context to use when loading the libraries. | ||
| lib_type (str): The type of the library (either 'thermo' or 'kinetics'). | ||
| logger (Logger): Instance of T3's Logger class. | ||
| race (bool, optional): Whether to take measures to avoid a race condition when appending to the library. | ||
| """ | ||
| race_path = os.path.join(os.path.dirname(to_lib_path), f'{library_name}.race') | ||
| if race: | ||
| race_free = check_race_condition(race_path) | ||
| if not race_free: | ||
| logger.error(f'Could not write to library {to_lib_path} due to a race condition.\n' | ||
| f'Check whether it is safe to delete the {race_path} file to continue.') | ||
| return | ||
| from_lib, to_lib = (ThermoLibrary(), ThermoLibrary()) if lib_type == 'thermo' \ | ||
| else (KineticsLibrary(), KineticsLibrary()) | ||
| to_lib.load(path=to_lib_path, local_context=local_context, global_context=dict()) | ||
| from_lib.load(path=from_lib_path, local_context=local_context, global_context=dict()) | ||
| from_description = from_lib.long_desc | ||
| description_to_append = '\n' | ||
| append = False | ||
| for line in from_description.splitlines(): | ||
| if 'Overall time since project initiation' in line: | ||
| append = False | ||
| if append: | ||
| description_to_append += line + '\n' | ||
| if 'Considered the following' in line: | ||
| append = True | ||
| to_lib.long_desc += description_to_append | ||
| for entry in from_lib.entries.values(): | ||
| skip_entry = False | ||
| if lib_type == 'thermo': | ||
| entry_species = Species(molecule=[entry.item]) | ||
| entry_species.generate_resonance_structures(keep_isomorphic=False, filter_structures=True) | ||
| for existing_entry in to_lib.entries.values(): | ||
| if entry_species.is_isomorphic(existing_entry.item): | ||
| if entry.label != existing_entry.label: | ||
| logger.warning(f"Not adding species {entry.label} to the {library_name} thermo library, " | ||
| f"the species seems to already exist under the label {existing_entry.label}.") | ||
| skip_entry = True | ||
| break | ||
| elif lib_type == 'kinetics': | ||
| entry_reaction = Reaction(reactants=entry.item.reactants[:], | ||
| products=entry.item.products[:], | ||
| specific_collider=entry.item.specific_collider, | ||
| kinetics=entry.data, | ||
| duplicate=entry.item.duplicate, | ||
| reversible=entry.item.reversible, | ||
| allow_pdep_route=entry.item.allow_pdep_route, | ||
| elementary_high_p=entry.item.elementary_high_p, | ||
| ) | ||
| for existing_entry in to_lib.entries.values(): | ||
| if entry_reaction.is_isomorphic(existing_entry.item): | ||
| logger.warning(f"Not adding reaction {entry.label} to the {library_name} kinetics library, " | ||
| f"the reaction seems to already exist under the label {existing_entry.label}.") | ||
| skip_entry = True | ||
| break | ||
| if not skip_entry: | ||
| to_lib.entries[entry.label] = entry | ||
| to_lib.save(path=to_lib_path) | ||
| lift_race_condition(race_path) | ||
|
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| def check_race_condition(race_path: str, | ||
| ) -> bool: | ||
| """ | ||
| Check for a race condition and avoid one by creating a race holder file. | ||
| Args: | ||
| race_path (str): The path to the race file to check. | ||
| Returns: | ||
| bool: Whether there is no race condition and T3 may continue (True) or an unavoidable race exists (False). | ||
| """ | ||
| counter = 0 | ||
| while os.path.isfile(race_path): | ||
| with open(race_path, 'r') as f: | ||
| content = f.read() | ||
| if content: | ||
| creation_date = content.split(' ')[-1] | ||
| creation_datetime = datetime.datetime.strptime(creation_date, "%H%M%S_%b%d_%Y") | ||
| time_delta = datetime.datetime.now() - creation_datetime | ||
| if time_delta.total_seconds() > 1000: | ||
| lift_race_condition(race_path) | ||
| return True | ||
| counter += 1 | ||
| time.sleep(10) | ||
| if counter > 1000: | ||
| return False | ||
| with open(race_path, 'w') as f: | ||
| f.write(f'Race created at {datetime.datetime.now().strftime("%H%M%S_%b%d_%Y")}') | ||
| return True | ||
|
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||
|
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| def lift_race_condition(race_path: str) -> None: | ||
| """ | ||
| Lift the race condition by deleting the race holder file. | ||
| Args: | ||
| race_path (str): The path to the race file to check. | ||
| """ | ||
| if os.path.isfile(race_path): | ||
| os.remove(race_path) |
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