def load_rmg_database(
rmg_database: Type[RMGDatabase],
species_dict: dict,
output_dict: dict,
) -> None:
"""
Load the RMG database.
Args:
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.
"""
load_thermo_libs, load_kinetic_libs = False, False
if any([
species.is_ts and output_dict[species.label]['convergence']
for species in species_dict.values()
]):
load_kinetic_libs = True
if any([
species.compute_thermo
and output_dict[species.label]['convergence']
for species in species_dict.values()
]):
load_thermo_libs = True
if rmg_database is not None and (load_kinetic_libs or load_thermo_libs):
rmgdb.load_rmg_database(rmgdb=rmg_database,
load_thermo_libs=load_thermo_libs,
load_kinetic_libs=load_kinetic_libs)
def __init__(self, project, project_directory, species_dict, rxn_list, output, use_bac, model_chemistry,
lib_long_desc, rmgdatabase, t_min=None, t_max=None, t_count=None, freq_scale_factor=None):
self.rmgdb = rmgdatabase
self.project = project
self.project_directory = project_directory
self.species_dict = species_dict
self.rxn_list = rxn_list
self.output = output
self.use_bac = use_bac
self.sp_level, self.freq_level = process_model_chemistry(model_chemistry)
self.freq_scale_factor = freq_scale_factor
self.lib_long_desc = lib_long_desc
load_thermo_libs, load_kinetic_libs = False, False
if any([species.is_ts and species.final_xyz for species in self.species_dict.values()])\
and any(['ALL converged' in out['status'] for out in output.values()]):
load_kinetic_libs = True
if any([species.generate_thermo for species in self.species_dict.values()])\
and any(['ALL converged' in out['status'] for out in output.values()]):
load_thermo_libs = True
if any(['ALL converged' in spc_output_dict['status'] for spc_output_dict in output.values()]):
rmgdb.load_rmg_database(rmgdb=self.rmgdb, load_thermo_libs=load_thermo_libs,
load_kinetic_libs=load_kinetic_libs)
t_min = t_min if t_min is not None else (300, 'K')
t_max = t_max if t_max is not None else (3000, 'K')
if isinstance(t_min, (int, float)):
t_min = (t_min, 'K')
if isinstance(t_max, (int, float)):
t_max = (t_max, 'K')
self.t_min = (t_min[0], str(t_min[1]))
self.t_max = (t_max[0], str(t_max[1]))
self.t_count = t_count if t_count is not None else 50
def __init__(self,
project,
project_directory,
species_dict,
rxn_list,
output,
use_bac,
model_chemistry,
lib_long_desc,
rmgdatabase,
t_min=None,
t_max=None,
t_count=None):
self.rmgdb = rmgdatabase
self.project = project
self.project_directory = project_directory
self.species_dict = species_dict
self.rxn_list = rxn_list
self.output = output
self.use_bac = use_bac
self.model_chemistry = model_chemistry
self.lib_long_desc = lib_long_desc
load_thermo_libs, load_kinetic_libs = True, True
if not any([
species.is_ts and species.final_xyz
for species in self.species_dict.values()
]):
load_kinetic_libs = False # don't load reaction libraries, not TS has converged
if not any([
species.generate_thermo
for species in self.species_dict.values()
]):
load_thermo_libs = False # don't load thermo libraries, not thermo requested
rmgdb.load_rmg_database(rmgdb=self.rmgdb,
load_thermo_libs=load_thermo_libs,
load_kinetic_libs=load_kinetic_libs)
t_min = t_min if t_min is not None else (300, 'K')
t_max = t_max if t_max is not None else (3000, 'K')
if isinstance(t_min, (int, float)):
t_min = (t_min, 'K')
if isinstance(t_max, (int, float)):
t_max = (t_max, 'K')
self.t_min = (t_min[0], str(t_min[1]))
self.t_max = (t_max[0], str(t_max[1]))
self.t_count = t_count if t_count is not None else 50
def setUpClass(cls):
"""
A method that is run before all unit tests in this class.
"""
cls.rmgdb = rmgdb.make_rmg_database_object()
rmgdb.load_rmg_database(rmgdb=cls.rmgdb)