def fillRulesByAveragingUp(self, rootTemplate, alreadyDone, verbose=False):
"""
Fill in gaps in the kinetics rate rules by averaging child nodes.
If verbose is set to True, then exact sources of kinetics are saved in the kinetics comments
(warning: this uses up a lot of memory due to the extensively long comments)
"""
rootLabel = ';'.join([g.label for g in rootTemplate])
if rootLabel in alreadyDone:
return alreadyDone[rootLabel]
# Generate the distance 1 pairings which must be averaged for this root template.
# The distance 1 template is created by taking the parent node from one or more trees
# and creating the combinations with children from a single remaining tree.
# i.e. for some node (A,B), we want to fetch all combinations for the pairing of (A,B's children) and
# (A's children, B). For node (A,B,C), we would retrieve all combinations of (A,B,C's children)
# (A,B's children,C) etc...
# If a particular node has no children, it is skipped from the children expansion altogether.
childrenList = []
distanceList = []
for i, parent in enumerate(rootTemplate):
# Start with the root template, and replace the ith member with its children
if parent.children:
childrenSet = [[group] for group in rootTemplate]
childrenSet[i] = parent.children
childrenList.extend(getAllCombinations(childrenSet))
distanceList.extend([k.nodalDistance for k in parent.children])
if distanceList != []: #average the minimum distance neighbors
minDist = min(distanceList)
closeChildrenList = [
childrenList[i] for i in xrange(len(childrenList))
if distanceList[i] == minDist
]
else:
closeChildrenList = []
kineticsList = []
for template in childrenList:
label = ';'.join([g.label for g in template])
if label in alreadyDone:
kinetics = alreadyDone[label]
else:
kinetics = self.fillRulesByAveragingUp(template, alreadyDone,
verbose)
if template in closeChildrenList and kinetics is not None:
kineticsList.append([kinetics, template])
# See if we already have a rate rule for this exact template instead
# and return it now that we have finished searching its children
entry = self.getRule(rootTemplate)
if entry is not None and entry.rank > 0:
# We already have a rate rule for this exact template
# If the entry has rank of zero, then we have so little faith
# in it that we'd rather use an averaged value if possible
# Since this entry does not have a rank of zero, we keep its
# value
alreadyDone[rootLabel] = entry.data
return entry.data
if len(kineticsList) > 0:
if len(kineticsList) > 1:
# We found one or more results! Let's average them together
kinetics = self.__getAverageKinetics(
[k for k, t in kineticsList])
if verbose:
kinetics.comment = 'Average of [{0}]'.format(' + '.join(
k.comment if k.comment != '' else ';'.join(g.label
for g in t)
for k, t in kineticsList))
else:
kinetics.comment = 'Average of [{0}]'.format(' + '.join(
';'.join(g.label for g in t) for k, t in kineticsList))
else:
k, t = kineticsList[0]
kinetics = deepcopy(k)
# Even though we are using just a single set of kinetics, it's still considered
# an average. It just happens that the other distance 1 children had no data.
if verbose:
kinetics.comment = 'Average of [{0}]'.format(
k.comment if k.comment != '' else ';'.join(g.label
for g in t))
else:
kinetics.comment = 'Average of [{0}]'.format(';'.join(
g.label for g in t))
entry = Entry(
index=0,
label=rootLabel,
item=rootTemplate,
data=kinetics,
rank=10, # Indicates this is an averaged estimate
)
self.entries[entry.label] = [entry]
alreadyDone[rootLabel] = entry.data
return entry.data
alreadyDone[rootLabel] = None
return None
molecule=species.molecule[0].to_adjacency_list(),
thermo=species.thermo,
)
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)
kinetics_library.entries = {}
for i in range(len(reaction_list)):
reaction = reaction_list[i]
entry = Entry(
index=i + 1,
label=reaction.to_labeled_str(),
item=reaction,
data=reaction.kinetics,
)
try:
entry.long_desc = 'Originally from reaction library: ' + reaction.library + "\n" + reaction.kinetics.comment
except AttributeError:
entry.long_desc = reaction.kinetics.comment
kinetics_library.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 mark_duplicates = True
kinetics_library.check_for_duplicates(mark_duplicates=True)
kinetics_library.convert_duplicates_to_multi()
# Save in Py format
def generateRules(family, database):
"""
For a given reaction `family` label, generate additional rate rules from
the corresponding depository training set. This function does automatically
what users used to do by hand to construct a rate rule from reaction
kinetics found in the literature, i.e. determine the groups involved,
adjust to a per-site basis, etc.
"""
# Load rules and determine starting index
rules = family.rules
index = max([entry.index for entry in rules.entries.values()] or [0]) + 1
# Load training entries
for depository in family.depositories:
if 'training' in depository.name:
entries = sorted(depository.entries.values(),
key=lambda entry: (entry.index, entry.label))
break
# Generate a rate rule for each training entry
for entry in entries:
# Load entry's reaction, template, and kinetics
reaction, template = database.kinetics.getForwardReactionForFamilyEntry(
entry=entry, family=family.name, thermoDatabase=database.thermo)
kinetics = reaction.kinetics
# Convert KineticsData to Arrhenius
if isinstance(kinetics, KineticsData):
kinetics = Arrhenius().fitToData(Tdata=kinetics.Tdata.values,
kdata=kinetics.kdata.values,
kunits=kinetics.kdata.units,
T0=1)
# Ignore other kinetics types
if not isinstance(kinetics, Arrhenius):
continue
# Change reference temperature to 1 K if necessary
if kinetics.T0.value != 1:
kinetics = kinetics.changeT0(1)
# Convert kinetics to a per-site basis
kinetics.A.value /= reaction.degeneracy
# Convert to ArrheniusEP
kinetics = ArrheniusEP(A=kinetics.A,
n=kinetics.n,
alpha=0,
E0=kinetics.Ea,
Tmin=kinetics.Tmin,
Tmax=kinetics.Tmax)
# Add new rate rule
rules.entries[index] = Entry(index=index,
label=';'.join(
[group.label for group in template]),
item=Reaction(reactants=template[:],
products=None),
data=kinetics,
reference=entry.reference,
rank=entry.rank,
shortDesc=entry.shortDesc,
longDesc=entry.longDesc,
history=entry.history)
index += 1
molecule=species.molecule[0].toAdjacencyList(removeH=removeH),
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()
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)
]
def getLibraries(self):
"""Get RMG kinetics and thermo libraries"""
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
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)
kineticsLibrary.entries = {}
for i in range(len(reactionList)):
reaction = reactionList[i]
entry = Entry(
index=i + 1,
label=str(reaction),
item=reaction,
data=reaction.kinetics,
)
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(
def getKinetics(self):
"""
Extracts the kinetic data from the chemkin file for plotting purposes.
"""
from rmgpy.chemkin import loadChemkinFile
from rmgpy.kinetics import ArrheniusEP, Chebyshev
from rmgpy.reaction import Reaction
from rmgpy.data.base import Entry
kineticsDataList = []
chemkinPath = self.path + '/chemkin/chem.inp'
dictionaryPath = self.path + 'RMG_Dictionary.txt'
if self.Foreign:
readComments = False
else:
readComments = True
if os.path.exists(dictionaryPath):
speciesList, reactionList = loadChemkinFile(
chemkinPath, dictionaryPath, readComments=readComments)
else:
speciesList, reactionList = loadChemkinFile(
chemkinPath, readComments=readComments)
for reaction in reactionList:
# If the kinetics are ArrheniusEP, replace them with Arrhenius
if isinstance(reaction.kinetics, ArrheniusEP):
reaction.kinetics = reaction.kinetics.toArrhenius(
reaction.getEnthalpyOfReaction(298))
if os.path.exists(dictionaryPath):
reactants = ' + '.join([
moleculeToInfo(reactant) for reactant in reaction.reactants
])
arrow = '⇔' if reaction.reversible else '→'
products = ' + '.join(
[moleculeToInfo(product) for product in reaction.products])
href = reaction.getURL()
else:
reactants = ' + '.join(
[reactant.label for reactant in reaction.reactants])
arrow = '⇔' if reaction.reversible else '→'
products = ' + '.join(
[product.label for product in reaction.products])
href = ''
source = str(reaction).replace('<=>', '=')
entry = Entry()
entry.result = reactionList.index(reaction) + 1
forwardKinetics = reaction.kinetics
forward = True
chemkin = reaction.toChemkin(speciesList)
reverseKinetics = reaction.generateReverseRateCoefficient()
reverseKinetics.comment = 'Fitted reverse reaction. ' + reaction.kinetics.comment
rev_reaction = Reaction(reactants=reaction.products,
products=reaction.reactants,
kinetics=reverseKinetics)
chemkin_rev = rev_reaction.toChemkin(speciesList)
kineticsDataList.append([
reactants, arrow, products, entry, forwardKinetics, source,
href, forward, chemkin, reverseKinetics, chemkin_rev
])
return kineticsDataList
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:
logger.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'))