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 loadOld(self, path):
"""
Load an old-style RMG kinetics library from the location `path`.
"""
path = os.path.abspath(path)
self.loadOldDictionary(os.path.join(path, 'species.txt'),
pattern=False)
species = dict([(label, Species(label=label, molecule=[entry.item]))
for label, entry in self.entries.iteritems()])
# Add common bath gases (Ar, Ne, He, N2) if not already present
for label, smiles in [('AR', '[Ar]'), ('HE', '[He]'), ('NE', '[Ne]'),
('N2', 'N#N')]:
if label not in species:
molecule = Molecule().fromSMILES(smiles)
spec = Species(label=label, molecule=[molecule])
species[label] = spec
reactions = []
reactions.extend(
self.__loadOldReactions(os.path.join(path, 'reactions.txt'),
species))
if os.path.exists(os.path.join(path, 'pdepreactions.txt')):
pdep_reactions = self.__loadOldReactions(
os.path.join(path, 'pdepreactions.txt'), species)
# RMG-Py likes otherwise equivalent PDep and non-pdep reactions to be marked as duplicates
self.markValidDuplicates(reactions, pdep_reactions)
reactions.extend(pdep_reactions)
self.entries = {}
for index, reaction in enumerate(reactions):
entry = Entry(
index=index + 1,
item=reaction,
data=reaction.kinetics,
)
entry.longDesc = reaction.kinetics.comment
reaction.kinetics.comment = ''
self.entries[index + 1] = entry
reaction.kinetics = None
self.checkForDuplicates()
self.convertDuplicatesToMulti()
def loadOld(self, path):
"""
Load an old-style RMG kinetics library from the location `path`.
"""
path = os.path.abspath(path)
self.loadOldDictionary(
os.path.join(path, 'species.txt'), pattern=False)
species = dict([(label, Species(label=label, molecule=[entry.item]))
for label, entry in self.entries.iteritems()])
# Add common bath gases (Ar, Ne, He, N2) if not already present
for label, smiles in [('Ar', '[Ar]'), ('He', '[He]'), ('Ne', '[Ne]'),
('N2', 'N#N')]:
if label not in species:
molecule = Molecule().fromSMILES(smiles)
spec = Species(label=label, molecule=[molecule])
species[label] = spec
reactions = []
reactions.extend(
self.__loadOldReactions(
os.path.join(path, 'reactions.txt'), species))
if os.path.exists(os.path.join(path, 'pdepreactions.txt')):
pdep_reactions = self.__loadOldReactions(
os.path.join(path, 'pdepreactions.txt'), species)
# RMG-Py likes otherwise equivalent PDep and non-pdep reactions to be marked as duplicates
self.markValidDuplicates(reactions, pdep_reactions)
reactions.extend(pdep_reactions)
self.entries = {}
for index, reaction in enumerate(reactions):
entry = Entry(
index=index + 1,
item=reaction,
data=reaction.kinetics,
)
entry.longDesc = reaction.kinetics.comment
reaction.kinetics.comment = ''
self.entries[index + 1] = entry
reaction.kinetics = None
self.checkForDuplicates()
self.convertDuplicatesToMulti()
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()
kineticsLibrary.entries = {}
for i in range(len(reactionList)):
reaction = reactionList[i]
entry = Entry(
index = i+1,
item = reaction,
data = reaction.kinetics,
)
entry.longDesc = reaction.kinetics.comment
kineticsLibrary.entries[i+1] = entry
kineticsLibrary.checkForDuplicates()
kineticsLibrary.convertDuplicatesToMulti()
# Assign history to all entries
user = getUsername() # Pulls username from current git repository
#user = '******'.format(name, email) # If not in git repository, then enter user information manually
event = [time.asctime(),user,'action','{0} imported this entry from the old RMG database.'.format(user)]
for label, entry in thermoLibrary.entries.iteritems():
entry.history.append(event)
for label, entry in kineticsLibrary.entries.iteritems():
entry.history.append(event)
# Save in Py format
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
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
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)
kineticsLibrary.entries = {}
for i in range(len(reactionList)):
reaction = reactionList[i]
entry = Entry(
index = i+1,
label = str(reaction),
item = reaction,
data = reaction.kinetics,
)
try:
entry.longDesc = 'Originally from reaction library: ' + reaction.library + "\n" + reaction.kinetics.comment
except AttributeError:
entry.longDesc = reaction.kinetics.comment
kineticsLibrary.entries[i+1] = entry
# Mark as duplicates where there are mixed pressure dependent and non-pressure dependent duplicate kinetics
# Even though CHEMKIN does not require a duplicate flag, RMG needs it.
# Using flag markDuplicates = True
kineticsLibrary.checkForDuplicates(markDuplicates=True)
kineticsLibrary.convertDuplicatesToMulti()
# Save in Py format
databaseDirectory = settings['database.directory']
try:
os.makedirs(os.path.join(databaseDirectory, 'kinetics', 'libraries',name))
except:
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()
kineticsLibrary.entries = {}
for i in range(len(reactionList)):
reaction = reactionList[i]
entry = Entry(
index=i + 1,
item=reaction,
data=reaction.kinetics,
)
entry.longDesc = reaction.kinetics.comment
kineticsLibrary.entries[i + 1] = entry
kineticsLibrary.checkForDuplicates()
kineticsLibrary.convertDuplicatesToMulti()
# Assign history to all entries
user = getUsername() # Pulls username from current git repository
#user = '******'.format(name, email) # If not in git repository, then enter user information manually
event = [
time.asctime(), user, 'action',
'{0} imported this entry from the old RMG database.'.format(user)
]
for label, entry in thermoLibrary.entries.iteritems():
entry.history.append(event)
for label, entry in kineticsLibrary.entries.iteritems():
