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"
speciesList, reactionList = loadChemkinFile(chemkinPath, dictionaryPath)
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))
reactants = " + ".join([moleculeToInfo(reactant) for reactant in reaction.reactants])
arrow = "⇔" if reaction.reversible else "→"
products = " + ".join([moleculeToInfo(reactant) for reactant in reaction.products])
source = str(reaction).replace("<=>", "=")
href = reaction.getURL()
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 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 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()
label = species.label,
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)]
for label, entry in thermoLibrary.entries.iteritems():
entry.history.append(event)
for label, entry in kineticsLibrary.entries.iteritems():
def kineticsGroupEstimateEntry(
request, family, reactant1, product1, reactant2="", reactant3="", product2="", product3=""
):
"""
View a kinetics group estimate as an entry.
"""
# Load the kinetics database if necessary
loadDatabase("kinetics", "families")
# Also load the thermo database so we can generate reverse kinetics if necessary
loadDatabase("thermo")
# we need 'database' to reference the top level object that we pass to generateReactions
from tools import database
# check the family exists
try:
getKineticsDatabase("families", family + "/groups")
except ValueError:
raise Http404
reactantList = []
reactantList.append(moleculeFromURL(reactant1))
if reactant2 != "":
reactantList.append(moleculeFromURL(reactant2))
if reactant3 != "":
reactantList.append(moleculeFromURL(reactant3))
productList = []
productList.append(moleculeFromURL(product1))
if product2 != "":
productList.append(moleculeFromURL(product2))
if product3 != "":
productList.append(moleculeFromURL(product3))
# Search for the corresponding reaction(s)
reactionList, empty_list = generateReactions(database, reactantList, productList, only_families=[family])
kineticsDataList = []
# discard all the rates from depositories and rules
reactionList = [reaction for reaction in reactionList if isinstance(reaction, TemplateReaction)]
# if there are still two, only keep the forward direction
if len(reactionList) == 2:
reactionList = [reaction for reaction in reactionList if reactionHasReactants(reaction, reactantList)]
assert len(reactionList) == 1, "Was expecting one group estimate rate, not {0}".format(len(reactionList))
reaction = reactionList[0]
# Generate the thermo data for the species involved
for reactant in reaction.reactants:
generateSpeciesThermo(reactant, database)
for product in reaction.products:
generateSpeciesThermo(product, database)
# If the kinetics are ArrheniusEP, replace them with Arrhenius
if isinstance(reaction.kinetics, ArrheniusEP):
reaction.kinetics = reaction.kinetics.toArrhenius(reaction.getEnthalpyOfReaction(298))
reactants = " + ".join([moleculeToInfo(reactant) for reactant in reaction.reactants])
arrow = "⇔" if reaction.reversible else "→"
products = " + ".join([moleculeToInfo(reactant) for reactant in reaction.products])
assert isinstance(reaction, TemplateReaction), "Expected group additive kinetics to be a TemplateReaction"
source = "%s (RMG-Py Group additivity)" % (reaction.family.name)
entry = Entry(
item=reaction,
data=reaction.kinetics,
longDesc=reaction.kinetics.comment,
shortDesc="Estimated by RMG-Py Group Additivity",
)
# Get the entry as a entry_string, to populate the New Entry form
# first, replace the kinetics with a fitted arrhenius form with no comment
entry.data = reaction.kinetics.toArrhenius()
entry.data.comment = ""
entry_buffer = StringIO.StringIO(u"")
rmgpy.data.kinetics.saveEntry(entry_buffer, entry)
entry_string = entry_buffer.getvalue()
entry_buffer.close()
# replace the kinetics with the original ones
entry.data = reaction.kinetics
entry_string = re.sub("^entry\(\n", "", entry_string) # remove leading entry(
entry_string = re.sub("\s*index = -?\d+,\n", "", entry_string) # remove the 'index = 23,' (or -1)line
entry_string = re.sub(
"\s+history = \[.*", "", entry_string, flags=re.DOTALL
) # remove the history and everything after it (including the final ')' )
new_entry_form = KineticsEntryEditForm(initial={"entry": entry_string})
forwardKinetics = reaction.kinetics
reverseKinetics = reaction.generateReverseRateCoefficient()
forward = reactionHasReactants(reaction, reactantList) # boolean: true if template reaction in forward direction
reactants = " + ".join([moleculeToInfo(reactant) for reactant in reaction.reactants])
products = " + ".join([moleculeToInfo(reactant) for reactant in reaction.products])
reference = rmgpy.data.reference.Reference(
url=request.build_absolute_uri(
reverse(kinetics, kwargs={"section": "families", "subsection": family + "/groups"})
)
)
referenceType = ""
entry.index = -1
reactionUrl = getReactionUrl(reaction)
return render_to_response(
"kineticsEntry.html",
{
"section": "families",
"subsection": family,
"databaseName": family,
"entry": entry,
"reactants": reactants,
"arrow": arrow,
"products": products,
"reference": reference,
"referenceType": referenceType,
"kinetics": reaction.kinetics,
"reactionUrl": reactionUrl,
"reaction": reaction,
"new_entry_form": new_entry_form,
},
context_instance=RequestContext(request),
)
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 loadEntry(
self,
index,
group1=None,
group2=None,
group3=None,
group4=None,
kinetics=None,
degeneracy=1,
label='',
duplicate=False,
reversible=True,
reference=None,
referenceType='',
shortDesc='',
longDesc='',
rank=None,
):
reactants = []
if group1[0:3].upper() == 'OR{' or group1[0:4].upper(
) == 'AND{' or group1[0:7].upper() == 'NOT OR{' or group1[0:8].upper(
) == 'NOT AND{':
reactants.append(makeLogicNode(group1))
else:
reactants.append(Group().fromAdjacencyList(group1))
if group2 is not None:
if group2[0:3].upper() == 'OR{' or group2[0:4].upper(
) == 'AND{' or group2[0:7].upper(
) == 'NOT OR{' or group2[0:8].upper() == 'NOT AND{':
reactants.append(makeLogicNode(group2))
else:
reactants.append(Group().fromAdjacencyList(group2))
if group3 is not None:
if group3[0:3].upper() == 'OR{' or group3[0:4].upper(
) == 'AND{' or group3[0:7].upper(
) == 'NOT OR{' or group3[0:8].upper() == 'NOT AND{':
reactants.append(makeLogicNode(group3))
else:
reactants.append(Group().fromAdjacencyList(group3))
if group4 is not None:
if group4[0:3].upper() == 'OR{' or group4[0:4].upper(
) == 'AND{' or group4[0:7].upper(
) == 'NOT OR{' or group4[0:8].upper() == 'NOT AND{':
reactants.append(makeLogicNode(group4))
else:
reactants.append(Group().fromAdjacencyList(group4))
reaction = Reaction(reactants=reactants, products=[])
entry = Entry(
index=index,
label=label,
item=reaction,
data=kinetics,
reference=reference,
referenceType=referenceType,
shortDesc=shortDesc,
longDesc=longDesc.strip(),
rank=rank,
)
try:
self.entries[label].append(entry)
except KeyError:
self.entries[label] = [entry]
return entry
def fillRulesByAveragingUp(self, rootTemplate, alreadyDone):
"""
Fill in gaps in the kinetics rate rules by averaging child nodes.
"""
rootLabel = ';'.join([g.label for g in rootTemplate])
if rootLabel in alreadyDone:
return alreadyDone[rootLabel]
# See if we already have a rate rule for this exact template
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
# Recursively descend to the child nodes
childrenList = [[group] for group in rootTemplate]
for group in childrenList:
parent = group.pop(0)
if len(parent.children) > 0:
group.extend(parent.children)
else:
group.append(parent)
childrenList = getAllCombinations(childrenList)
kineticsList = []
for template in childrenList:
label = ';'.join([g.label for g in template])
if template == rootTemplate:
continue
if label in alreadyDone:
kinetics = alreadyDone[label]
else:
kinetics = self.fillRulesByAveragingUp(template, alreadyDone)
if kinetics is not None:
kineticsList.append([kinetics, template])
if len(kineticsList) > 0:
# We found one or more results! Let's average them together
kinetics = self.__getAverageKinetics([k for k, t in kineticsList])
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
]), )
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
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)
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
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'))
def generateAdditionalRateRules(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.
"""
# Find the database components we will need
rules = database.kinetics.depository['{0}/rules'.format(family)]
groups = database.kinetics.groups[family]
index = max([entry.index for entry in rules.entries.values()]) + 1
for depositoryLabel in ['training']:
depository = database.kinetics.depository['{0}/{1}'.format(family, depositoryLabel)]
entries = depository.entries.values()
entries.sort(key=lambda x: (x.index, x.label))
for entry0 in entries:
reaction, template = database.kinetics.getForwardReactionForFamilyEntry(entry=entry0, family=family, thermoDatabase=database.thermo)
# We must convert the kinetics to ArrheniusEP to finish our rate rule
kinetics = reaction.kinetics
# If kinetics are KineticsData, then first convert to Arrhenius
if isinstance(kinetics, KineticsData):
kinetics = Arrhenius().fitToData(
Tdata=kinetics.Tdata.values,
kdata=kinetics.kdata.values,
kunits=kinetics.kdata.units,
T0=1,
)
# Now convert from Arrhenius to ArrheniusEP
# If not Arrhenius (or KineticsData), then skip this entry
if isinstance(kinetics, Arrhenius):
if kinetics.T0.value != 1:
kinetics.changeT0(1)
kinetics = ArrheniusEP(
A = kinetics.A,
n = kinetics.n,
alpha = 0,
E0 = kinetics.Ea,
Tmin = kinetics.Tmin,
Tmax = kinetics.Tmax,
)
else:
break
# Put the kinetics on a per-site basis
kinetics.A.value /= reaction.degeneracy
# Construct a new entry for the new rate rule
label = ';'.join([group.label for group in template])
item = Reaction(
reactants = template[:],
products = None,
)
entry = Entry(
index = index,
label = label,
item = item,
data = kinetics,
reference = entry0.reference,
rank = entry0.rank,
shortDesc = entry0.shortDesc,
longDesc = entry0.longDesc,
history = entry0.history,
)
# Add the new rate rule to the depository of rate rules
rules.entries[entry.index] = entry
index += 1
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 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
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 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
