def set_e0_with_thermo(self):
"""
Helper method that sets species' E0 using the species' thermo data
"""
if self.get_thermo_data().E0 is not None:
self.conformer.E0 = self.get_thermo_data().E0
else:
if not self.thermo.Cp0 or not self.thermo.CpInf:
# set Cp0 and CpInf
from rmgpy.data.thermo import find_cp0_and_cpinf
find_cp0_and_cpinf(self, self.thermo)
self.conformer.E0 = self.get_thermo_data().to_wilhoit().E0
def run(input_file,
output_directory,
original=None,
maximum_isotopic_atoms=1,
use_original_reactions=False,
kinetic_isotope_effect=None):
"""
Accepts one input file with the RMG-Py model to generate.
Firstly, generates the RMG model for the first input file. Takes the core species of that mechanism
and generates all isotopomers of those core species. Next, generates all reactions between the
generated pool of isotopomers, and writes it to file.
"""
logging.info("isotope: Starting the RMG isotope generation method 'run'")
if not original:
logging.info(
"isotope: original model not found, generating new one in directory `rmg`"
)
logging.info(
"isotope: check `rmg/RMG.log` for the rest of the logging info.")
outputdir_rmg = os.path.join(output_directory, 'rmg')
os.mkdir(outputdir_rmg)
rmg = generate_rmg_model(input_file, outputdir_rmg)
else:
logging.info(
"isotope: original model being copied from previous RMG job in folder {}"
.format(original))
outputdir_rmg = original
chemkin_file = os.path.join(outputdir_rmg, 'chemkin',
'chem_annotated.inp')
dict_file = os.path.join(outputdir_rmg, 'chemkin',
'species_dictionary.txt')
rmg = load_rmg_job(input_file,
chemkin_file,
dict_file,
generate_images=False,
use_chemkin_names=True)
logging.info("isotope: generating isotope model")
logging.info('Generating isotopomers for the core species in {}'.format(
outputdir_rmg))
isotopes = []
logging.info("isotope: adding all the new and old isotopomers")
for spc in rmg.reaction_model.core.species:
find_cp0_and_cpinf(spc, spc.thermo)
isotopes.append([spc] +
generate_isotopomers(spc, maximum_isotopic_atoms))
logging.info('isotope: number of isotopomers: {}'.format(
sum([len(isotopomer) for isotopomer in isotopes if isotopomer])))
outputdir_iso = os.path.join(output_directory, 'iso')
os.mkdir(outputdir_iso)
logging.info(
'isotope: Generating RMG isotope model in {}'.format(outputdir_iso))
generate_isotope_model(outputdir_iso,
rmg,
isotopes,
use_original_reactions=use_original_reactions,
kinetic_isotope_effect=kinetic_isotope_effect)
def reconstruct_kinetics_from_source(self,
reaction,
source,
fix_barrier_height=False,
force_positive_barrier=False):
"""
Reaction is the original reaction with original kinetics.
Note that for Library and PDep reactions this function does not do anything other than return the original kinetics...
You must enter source data in the appropriate format such as returned from returned from self.extract_source_from_comments,
self-constructed.
fix_barrier_height and force_positive_barrier will change the kinetics based on the Reaction.fix_barrier_height function.
Return Arrhenius form kinetics if the source is from training reaction or rate rules.
"""
from rmgpy.data.thermo import find_cp0_and_cpinf
from rmgpy.thermo import Wilhoit
if 'Library' in source:
return reaction.kinetics
elif 'PDep' in source:
return reaction.kinetics
else:
rxn_copy = deepcopy(reaction)
if 'Training' in source:
training_entry = source['Training'][1]
reverse = source['Training'][2]
if reverse:
reverse_kinetics = training_entry.data
rxn_copy.kinetics = reverse_kinetics
forward_kinetics = rxn_copy.generate_reverse_rate_coefficient(
)
kinetics = forward_kinetics
else:
kinetics = training_entry.data
elif 'Rate Rules' in source:
source_dict = source['Rate Rules'][1]
rules = source_dict['rules']
training = source_dict['training']
degeneracy = source_dict['degeneracy']
log_a = 0
n = 0
alpha = 0
E0 = 0
for rule_entry, weight in rules:
log_a += np.log10(rule_entry.data.A.value_si) * weight
n += rule_entry.data.n.value_si * weight
alpha += rule_entry.data.alpha.value_si * weight
E0 += rule_entry.data.E0.value_si * weight
for rule_entry, training_entry, weight in training:
log_a += np.log10(rule_entry.data.A.value_si) * weight
n += rule_entry.data.n.value_si * weight
alpha += rule_entry.data.alpha.value_si * weight
E0 += rule_entry.data.E0.value_si * weight
a_units = rule_entry.data.A.units
if a_units == 'cm^3/(mol*s)' or a_units == 'cm^3/(molecule*s)' or a_units == 'm^3/(molecule*s)':
a_units = 'm^3/(mol*s)'
elif a_units == 'cm^6/(mol^2*s)' or a_units == 'cm^6/(molecule^2*s)' or a_units == 'm^6/(molecule^2*s)':
a_units = 'm^6/(mol^2*s)'
elif a_units == 's^-1' or a_units == 'm^3/(mol*s)' or a_units == 'm^6/(mol^2*s)':
pass
else:
raise ValueError(
'Invalid units {0} for averaging kinetics.'.format(
a_units))
kinetics = ArrheniusEP(
A=(degeneracy * 10**log_a, a_units),
n=n,
alpha=alpha,
E0=(E0 * 0.001, "kJ/mol"),
)
else:
raise ValueError(
"Source data must be either 'Library', 'PDep','Training', or 'Rate Rules'."
)
# Convert ArrheniusEP to Arrhenius
if fix_barrier_height:
for spc in rxn_copy.reactants + rxn_copy.products:
# Need wilhoit to do this
if not isinstance(spc.thermo, Wilhoit):
find_cp0_and_cpinf(spc, spc.thermo)
wilhoit = spc.thermo.to_wilhoit()
spc.thermo = wilhoit
rxn_copy.kinetics = kinetics
rxn_copy.fix_barrier_height(
force_positive=force_positive_barrier)
return rxn_copy.kinetics
else:
h298 = rxn_copy.get_enthalpy_of_reaction(298)
if isinstance(kinetics, (ArrheniusEP, ArrheniusBM)):
kinetics = kinetics.to_arrhenius(h298)
return kinetics