def save_kinetics_lib(rxn_list, path, name, lib_long_desc):
"""
Save an RMG kinetics library.
Args:
rxn_list (list): Entries are Reaction object instances for which kinetics will be saved.
path (str): The base folder in which the kinetic library will be saved.
name (str): The library name.
lib_long_desc (str): A multiline string with relevant description.
"""
entries = dict()
if rxn_list:
for i, rxn in enumerate(rxn_list):
if rxn.kinetics is not None:
entry = Entry(index=i,
item=rxn,
data=rxn.kinetics,
label=rxn.label)
entries[i + 1] = entry
else:
logging.warning(
f'Reaction {rxn.label} did not contain any kinetic data and was omitted from the '
f'kinetics library.')
kinetics_library = KineticsLibrary(name=name,
long_desc=lib_long_desc,
auto_generated=True)
kinetics_library.entries = entries
if os.path.exists(path):
shutil.rmtree(path)
try:
os.makedirs(path)
except OSError:
pass
kinetics_library.save(os.path.join(path, 'reactions.py'))
kinetics_library.save_dictionary(os.path.join(path, 'dictionary.txt'))
def save_kinetics_lib(rxn_list, path, name, lib_long_desc):
"""
Save an RMG kinetics library of all reactions in `rxn_list` in the supplied `path`
`rxn_list` is a list of ARCReaction objects
`name` is the library's name (or project's name)
`long_desc` is a multiline string with level of theory description
"""
entries = dict()
if rxn_list:
for i, rxn in enumerate(rxn_list):
if rxn.kinetics is not None:
if len(rxn.rmg_reaction.reactants):
reactants = rxn.rmg_reaction.reactants
products = rxn.rmg_reaction.products
elif rxn.r_species.mol_list is not None:
reactants = [Species(molecule=arc_spc.mol_list) for arc_spc in rxn.r_species]
products = [Species(molecule=arc_spc.mol_list) for arc_spc in rxn.p_species]
elif rxn.r_species.mol is not None:
reactants = [Species(molecule=[arc_spc.mol]) for arc_spc in rxn.r_species]
products = [Species(molecule=[arc_spc.mol]) for arc_spc in rxn.p_species]
else:
reactants = [Species(molecule=[arc_spc.xyz_mol]) for arc_spc in rxn.r_species]
products = [Species(molecule=[arc_spc.xyz_mol]) for arc_spc in rxn.p_species]
rxn.rmg_reaction.reactants = reactants
rxn.rmg_reaction.products = products
entry = Entry(
index=i,
item=rxn.rmg_reaction,
data=rxn.kinetics,
label=rxn.label)
rxn.ts_species.make_ts_report()
entry.longDesc = rxn.ts_species.ts_report + '\n\nOptimized TS geometry:\n' + rxn.ts_species.final_xyz
rxn.rmg_reaction.kinetics = rxn.kinetics
rxn.rmg_reaction.kinetics.comment = str('')
entries[i+1] = entry
else:
logging.warning('Reaction {0} did not contain any kinetic data and was omitted from the kinetics'
' library.'.format(rxn.label))
kinetics_library = KineticsLibrary(name=name, longDesc=lib_long_desc, autoGenerated=True)
kinetics_library.entries = entries
lib_path = os.path.join(path, 'kinetics', '')
if os.path.exists(lib_path):
shutil.rmtree(lib_path)
try:
os.makedirs(lib_path)
except OSError:
pass
kinetics_library.save(os.path.join(lib_path, 'reactions.py'))
kinetics_library.saveDictionary(os.path.join(lib_path, 'dictionary.txt'))
def get_libraries(self):
"""Get RMG kinetics and thermo libraries"""
name = 'kineticsjobs'
species_list = list(self.species_dict.values())
reaction_list = list(self.reaction_dict.values())
# remove duplicate species
for rxn in reaction_list:
for i, rspc in enumerate(rxn.reactants):
for spc in species_list:
if spc.is_isomorphic(rspc):
rxn.reactants[i] = spc
break
for i, rspc in enumerate(rxn.products):
for spc in species_list:
if spc.is_isomorphic(rspc):
rxn.products[i] = spc
break
del_inds = []
for i, spc1 in enumerate(species_list):
for j, spc2 in enumerate(species_list):
if j > i and spc1.is_isomorphic(spc2):
del_inds.append(j)
for j in sorted(del_inds)[::-1]:
del species_list[j]
thermo_library = ThermoLibrary(name=name)
for i, species in enumerate(species_list):
if species.thermo:
thermo_library.load_entry(
index=i + 1,
label=species.label,
molecule=species.molecule[0].to_adjacency_list(),
thermo=species.thermo,
shortDesc=species.thermo.comment)
else:
logging.warning(
'Species {0} did not contain any thermo data and was omitted from the thermo library.'
.format(str(species)))
# load kinetics library entries
kinetics_library = KineticsLibrary(name=name, auto_generated=True)
kinetics_library.entries = {}
for i, reaction in enumerate(reaction_list):
entry = Entry(index=i + 1,
label=reaction.to_labeled_str(),
item=reaction,
data=reaction.kinetics)
if reaction.kinetics is not None:
if hasattr(reaction, 'library') and reaction.library:
entry.long_desc = 'Originally from reaction library: ' + \
reaction.library + "\n" + reaction.kinetics.comment
else:
entry.long_desc = reaction.kinetics.comment
kinetics_library.entries[i + 1] = entry
kinetics_library.label = name
return thermo_library, kinetics_library, species_list
def getLibraries(self):
name = 'kineticsjobs'
speciesList = self.speciesDict.values()
reactionList = self.reactionDict.values()
# remove duplicate species
for rxn in reactionList:
for i,rspc in enumerate(rxn.reactants):
for spc in speciesList:
if spc.isIsomorphic(rspc):
rxn.reactants[i] = spc
break
for i,rspc in enumerate(rxn.products):
for spc in speciesList:
if spc.isIsomorphic(rspc):
rxn.products[i] = spc
break
del_inds = []
for i,spc1 in enumerate(speciesList):
for j,spc2 in enumerate(speciesList):
if j>i and spc1.isIsomorphic(spc2):
del_inds.append(j)
for j in sorted(del_inds)[::-1]:
del speciesList[j]
thermoLibrary = ThermoLibrary(name=name)
for i,species in enumerate(speciesList):
if species.thermo:
thermoLibrary.loadEntry(index = i + 1,
label = species.label,
molecule = species.molecule[0].toAdjacencyList(),
thermo = species.thermo,
shortDesc = species.thermo.comment
)
else:
logging.warning('Species {0} did not contain any thermo data and was omitted from the thermo library.'.format(str(species)))
# load kinetics library entries
kineticsLibrary = KineticsLibrary(name=name,autoGenerated=True)
kineticsLibrary.entries = {}
for i,reaction in enumerate(reactionList):
entry = Entry(
index = i+1,
label = reaction.toLabeledStr(),
item = reaction,
data = reaction.kinetics,
)
if reaction.kinetics is not None:
if hasattr(reaction,'library') and reaction.library:
entry.longDesc = 'Originally from reaction library: ' +\
reaction.library + "\n" + reaction.kinetics.comment
else:
entry.longDesc = reaction.kinetics.comment
kineticsLibrary.entries[i+1] = entry
kineticsLibrary.label = name
return thermoLibrary,kineticsLibrary,speciesList