def save(self, outputFile):
"""
Save the results of the kinetics job to the file located
at `path` on disk.
"""
reaction = self.reaction
logging.info("Saving kinetics for {0}...".format(reaction))
order = len(self.reaction.reactants)
factor = 1e6 ** (order - 1)
f = open(outputFile, "a")
f.write("# ======= =========== =========== =========== ===============\n")
f.write("# Temp. k (TST) Tunneling k (TST+T) Units\n")
f.write("# ======= =========== =========== =========== ===============\n")
for T in [300, 400, 500, 600, 800, 1000, 1500, 2000]:
tunneling = reaction.transitionState.tunneling
reaction.transitionState.tunneling = None
k0 = reaction.calculateTSTRateCoefficient(T) * factor
reaction.transitionState.tunneling = tunneling
k = reaction.calculateTSTRateCoefficient(T) * factor
tunneling = reaction.transitionState.tunneling
kappa = k / k0
f.write("# {0:4g} K {1:11.3e} {2:11g} {3:11.3e} {4}\n".format(T, k0, kappa, k, self.kunits))
f.write("# ======= =========== =========== =========== ===============\n")
# Reaction path degeneracy is INCLUDED in the kinetics itself!
string = "kinetics(label={0!r}, kinetics={1!r})".format(reaction.label, reaction.kinetics)
f.write("{0}\n\n".format(prettify(string)))
f.close()
def save(self, outputFile):
"""
Save the results of the kinetics job to the file located
at `path` on disk.
"""
reaction = self.reaction
logging.info('Saving kinetics for {0}...'.format(reaction))
order = len(self.reaction.reactants)
factor = 1e6**(order - 1)
f = open(outputFile, 'a')
f.write(
'# ======= =========== =========== =========== ===============\n'
)
f.write('# Temp. k (TST) Tunneling k (TST+T) Units\n')
f.write(
'# ======= =========== =========== =========== ===============\n'
)
for T in [300, 400, 500, 600, 800, 1000, 1500, 2000]:
tunneling = reaction.transitionState.tunneling
reaction.transitionState.tunneling = None
k0 = reaction.calculateTSTRateCoefficient(T) * factor
reaction.transitionState.tunneling = tunneling
k = reaction.calculateTSTRateCoefficient(T) * factor
tunneling = reaction.transitionState.tunneling
kappa = k / k0
f.write('# {0:4g} K {1:11.3e} {2:11g} {3:11.3e} {4}\n'.format(
T, k0, kappa, k, self.kunits))
f.write(
'# ======= =========== =========== =========== ===============\n'
)
# Reaction path degeneracy is INCLUDED in the kinetics itself!
string = 'kinetics(label={0!r}, kinetics={1!r})'.format(
reaction.label, reaction.kinetics)
f.write('{0}\n\n'.format(prettify(string)))
f.close()
# Also save the result to chem.inp
f = open(os.path.join(os.path.dirname(outputFile), 'chem.inp'), 'a')
reaction = self.reaction
kinetics = reaction.kinetics
string = '{0!s:51} {1:9.3e} {2:9.3f} {3:9.3f}\n'.format(
reaction,
kinetics.A.value_si * factor,
kinetics.n.value_si,
kinetics.Ea.value_si / 4184.,
)
f.write('{0}\n'.format(string))
f.close()
def save(self, outputFile):
"""
Save the results of the kinetics job to the file located
at `path` on disk.
"""
reaction = self.reaction
logging.info('Saving kinetics for {0}...'.format(reaction))
order = len(self.reaction.reactants)
factor = 1e6 ** (order-1)
f = open(outputFile, 'a')
f.write('# ======= =========== =========== =========== ===============\n')
f.write('# Temp. k (TST) Tunneling k (TST+T) Units\n')
f.write('# ======= =========== =========== =========== ===============\n')
if self.Tlist is None:
Tlist = [300,400,500,600,800,1000,1500,2000]
else:
Tlist =self.Tlist.value_si
for T in Tlist:
tunneling = reaction.transitionState.tunneling
reaction.transitionState.tunneling = None
k0 = reaction.calculateTSTRateCoefficient(T) * factor
reaction.transitionState.tunneling = tunneling
k = reaction.calculateTSTRateCoefficient(T) * factor
tunneling = reaction.transitionState.tunneling
kappa = k / k0
f.write('# {0:4g} K {1:11.3e} {2:11g} {3:11.3e} {4}\n'.format(T, k0, kappa, k, self.kunits))
f.write('# ======= =========== =========== =========== ===============\n')
# Reaction path degeneracy is INCLUDED in the kinetics itself!
string = 'kinetics(label={0!r}, kinetics={1!r})'.format(reaction.label, reaction.kinetics)
f.write('{0}\n\n'.format(prettify(string)))
f.close()
# Also save the result to chem.inp
f = open(os.path.join(os.path.dirname(outputFile), 'chem.inp'), 'a')
reaction = self.reaction
kinetics = reaction.kinetics
string = '{0!s:51} {1:9.3e} {2:9.3f} {3:9.3f}\n'.format(
reaction,
kinetics.A.value_si * factor,
kinetics.n.value_si,
kinetics.Ea.value_si / 4184.,
)
f.write('{0}\n'.format(string))
f.close()
def save(self, outputFile):
"""
Save the results of the thermodynamics job to the file located
at `path` on disk.
"""
species = self.species
logging.info('Saving thermo for {0}...'.format(species.label))
f = open(outputFile, 'a')
f.write('# Thermodynamics for {0}:\n'.format(species.label))
H298 = species.getThermoData().getEnthalpy(298) / 4184.
S298 = species.getThermoData().getEntropy(298) / 4.184
f.write(
'# Enthalpy of formation (298 K) = {0:9.3f} kcal/mol\n'.format(
H298))
f.write('# Entropy of formation (298 K) = {0:9.3f} cal/(mol*K)\n'.
format(S298))
f.write(
'# =========== =========== =========== =========== ===========\n'
)
f.write(
'# Temperature Heat cap. Enthalpy Entropy Free energy\n'
)
f.write(
'# (K) (cal/mol*K) (kcal/mol) (cal/mol*K) (kcal/mol)\n'
)
f.write(
'# =========== =========== =========== =========== ===========\n'
)
for T in [300, 400, 500, 600, 800, 1000, 1500, 2000, 2400]:
Cp = species.getThermoData().getHeatCapacity(T) / 4.184
H = species.getThermoData().getEnthalpy(T) / 4184.
S = species.getThermoData().getEntropy(T) / 4.184
G = species.getThermoData().getFreeEnergy(T) / 4184.
f.write('# {0:11g} {1:11.3f} {2:11.3f} {3:11.3f} {4:11.3f}\n'.
format(T, Cp, H, S, G))
f.write(
'# =========== =========== =========== =========== ===========\n'
)
string = 'thermo(label={0!r}, thermo={1!r})'.format(
species.label, species.getThermoData())
f.write('{0}\n\n'.format(prettify(string)))
f.close()
f = open(os.path.join(os.path.dirname(outputFile), 'chem.inp'), 'a')
string = writeThermoEntry(species,
elementCounts=species.props['elementCounts'],
verbose=False)
f.write(string)
f.close()
def save(self, outputFile):
"""
Save the results of the statistical mechanics job to the file located
at `path` on disk.
"""
logging.info(
'Saving statistical mechanics parameters for {0}...'.format(
self.species.label))
f = open(outputFile, 'a')
numbers = {
1: 'H',
6: 'C',
7: 'N',
8: 'O',
14: 'Si',
15: 'P',
16: 'S',
17: 'Cl'
}
conformer = self.species.conformer
coordinates = conformer.coordinates.value_si * 1e10
number = conformer.number.value_si
f.write('# Coordinates for {0} (angstroms):\n'.format(
self.species.label))
for i in range(coordinates.shape[0]):
x = coordinates[i, 0] - coordinates[0, 0]
y = coordinates[i, 1] - coordinates[0, 1]
z = coordinates[i, 2] - coordinates[0, 2]
f.write('# {0} {1:9.4f} {2:9.4f} {3:9.4f}\n'.format(
numbers[number[i]], x, y, z))
string = 'conformer(label={0!r}, E0={1!r}, modes={2!r}, spinMultiplicity={3:d}, opticalIsomers={4:d}'.format(
self.species.label,
conformer.E0,
conformer.modes,
conformer.spinMultiplicity,
conformer.opticalIsomers,
)
try:
string += ', frequency={0!r}'.format(self.species.frequency)
except AttributeError:
pass
string += ')'
f.write('{0}\n\n'.format(prettify(string)))
f.close()
def save(self, outputFile):
"""
Save the results of the thermodynamics job to the file located
at `path` on disk.
"""
species = self.species
logging.info('Saving thermo for {0}...'.format(species.label))
f = open(outputFile, 'a')
f.write('# Thermodynamics for {0}:\n'.format(species.label))
H298 = species.getThermoData().getEnthalpy(298) / 4184.
S298 = species.getThermoData().getEntropy(298) / 4.184
f.write('# Enthalpy of formation (298 K) = {0:9.3f} kcal/mol\n'.format(H298))
f.write('# Entropy of formation (298 K) = {0:9.3f} cal/(mol*K)\n'.format(S298))
f.write('# =========== =========== =========== =========== ===========\n')
f.write('# Temperature Heat cap. Enthalpy Entropy Free energy\n')
f.write('# (K) (cal/mol*K) (kcal/mol) (cal/mol*K) (kcal/mol)\n')
f.write('# =========== =========== =========== =========== ===========\n')
for T in [300,400,500,600,800,1000,1500,2000,2400]:
Cp = species.getThermoData().getHeatCapacity(T) / 4.184
H = species.getThermoData().getEnthalpy(T) / 4184.
S = species.getThermoData().getEntropy(T) / 4.184
G = species.getThermoData().getFreeEnergy(T) / 4184.
f.write('# {0:11g} {1:11.3f} {2:11.3f} {3:11.3f} {4:11.3f}\n'.format(T, Cp, H, S, G))
f.write('# =========== =========== =========== =========== ===========\n')
string = 'thermo(label={0!r}, thermo={1!r})'.format(species.label, species.getThermoData())
f.write('{0}\n\n'.format(prettify(string)))
f.close()
f = open(os.path.join(os.path.dirname(outputFile), 'chem.inp'), 'a')
if isinstance(species, Species):
if species.molecule and isinstance(species.molecule[0], Molecule):
elementCounts = retrieveElementCount(species.molecule[0])
else:
try:
elementCounts = species.props['elementCounts']
except KeyError:
elementCounts = {'C': 0, 'H': 0}
else:
elementCounts = {'C': 0, 'H': 0}
string = writeThermoEntry(species, elementCounts=elementCounts, verbose=False)
f.write('{0}\n'.format(string))
f.close()
def save(self, outputFile):
"""
Save the results of the statistical mechanics job to the file located
at `path` on disk.
"""
logging.info('Saving statistical mechanics parameters for {0}...'.format(self.species.label))
f = open(outputFile, 'a')
numbers = {1: 'H', 6: 'C', 7: 'N', 8: 'O', 14: 'Si', 15: 'P', 16: 'S', 17: 'Cl'}
conformer = self.species.conformer
coordinates = conformer.coordinates.value_si * 1e10
number = conformer.number.value_si
f.write('# Coordinates for {0} (angstroms):\n'.format(self.species.label))
for i in range(coordinates.shape[0]):
x = coordinates[i,0] - coordinates[0,0]
y = coordinates[i,1] - coordinates[0,1]
z = coordinates[i,2] - coordinates[0,2]
f.write('# {0} {1:9.4f} {2:9.4f} {3:9.4f}\n'.format(numbers[number[i]], x, y, z))
string = 'conformer(label={0!r}, E0={1!r}, modes={2!r}, spinMultiplicity={3:d}, opticalIsomers={4:d}'.format(
self.species.label,
conformer.E0,
conformer.modes,
conformer.spinMultiplicity,
conformer.opticalIsomers,
)
try:
string += ', frequency={0!r}'.format(self.species.frequency)
except AttributeError: pass
string += ')'
f.write('{0}\n\n'.format(prettify(string)))
f.close()
f.write('# Enthalpy of formation (298 K) = {0:9.3f} kcal/mol\n'.format(H298))
f.write('# Entropy of formation (298 K) = {0:9.3f} cal/(mol*K)\n'.format(S298))
f.write('# =========== =========== =========== =========== ===========\n')
f.write('# Temperature Heat cap. Enthalpy Entropy Free energy\n')
f.write('# (K) (cal/mol*K) (kcal/mol) (cal/mol*K) (kcal/mol)\n')
f.write('# =========== =========== =========== =========== ===========\n')
for T in T_list:
Cp = species.getThermoData().getHeatCapacity(T) / 4.184
H = species.getThermoData().getEnthalpy(T) / 4184.
S = species.getThermoData().getEntropy(T) / 4.184
G = species.getThermoData().getFreeEnergy(T) / 4184.
f.write('# {0:11g} {1:11.3f} {2:11.3f} {3:11.3f} {4:11.3f}\n'.format(T, Cp, H, S, G))
f.write('# =========== =========== =========== =========== ===========\n')
string = 'thermo(label={0!r}, thermo={1!r})'.format(species.label, species.getThermoData())
f.write('{0}\n\n'.format(prettify(string)))
f.close()
else:
print ('Species {0} did not contain any thermo data and was omitted from the output file.'.format(str(species)))
#Convert T_list into an array
T_list = numpy.asarray(T_list)
# Plot the thermo properties of each species at the specified T's and save as .pdf files
for i in range(len(speciesList)):
species = speciesList[i]
if species.thermo:
# Skip this step if matplotlib is not installed
try:
def save(self, outputFile):
"""
Save the results of the thermodynamics job to the file located
at `path` on disk.
"""
species = self.species
logging.info("Saving thermo for {0}...".format(species.label))
f = open(outputFile, "a")
f.write("# Thermodynamics for {0}:\n".format(species.label))
H298 = species.thermo.getEnthalpy(298) / 4184.0
S298 = species.thermo.getEntropy(298) / 4.184
f.write("# Enthalpy of formation (298 K) = {0:9.3f} kcal/mol\n".format(H298))
f.write("# Entropy of formation (298 K) = {0:9.3f} cal/(mol*K)\n".format(S298))
f.write("# =========== =========== =========== =========== ===========\n")
f.write("# Temperature Heat cap. Enthalpy Entropy Free energy\n")
f.write("# (K) (cal/mol*K) (kcal/mol) (cal/mol*K) (kcal/mol)\n")
f.write("# =========== =========== =========== =========== ===========\n")
for T in [300, 400, 500, 600, 800, 1000, 1500, 2000, 2400]:
Cp = species.thermo.getHeatCapacity(T) / 4.184
H = species.thermo.getEnthalpy(T) / 4184.0
S = species.thermo.getEntropy(T) / 4.184
G = species.thermo.getFreeEnergy(T) / 4184.0
f.write("# {0:11g} {1:11.3f} {2:11.3f} {3:11.3f} {4:11.3f}\n".format(T, Cp, H, S, G))
f.write("# =========== =========== =========== =========== ===========\n")
string = "thermo(label={0!r}, thermo={1!r})".format(species.label, species.thermo)
f.write("{0}\n\n".format(prettify(string)))
f.close()
f = open(os.path.join(os.path.dirname(outputFile), "chem.inp"), "w")
thermo = species.thermo
if isinstance(thermo, NASA):
poly_low = thermo.polynomials[0]
poly_high = thermo.polynomials[1]
# Determine the number of each type of element in the molecule
elements = ["C", "H", "N", "O"]
elementCounts = [0, 0, 0, 0]
# Remove elements with zero count
index = 2
while index < len(elementCounts):
if elementCounts[index] == 0:
del elements[index]
del elementCounts[index]
else:
index += 1
# Line 1
string = "{0:<16} ".format(species.label)
if len(elements) <= 4:
# Use the original Chemkin syntax for the element counts
for symbol, count in zip(elements, elementCounts):
string += "{0!s:<2}{1:<3d}".format(symbol, count)
string += " " * (4 - len(elements))
else:
string += " " * 4
string += "G{0:<10.3f}{1:<10.3f}{2:<8.2f} 1".format(
poly_low.Tmin.value_si, poly_high.Tmax.value_si, poly_low.Tmax.value_si
)
if len(elements) > 4:
string += "&\n"
# Use the new-style Chemkin syntax for the element counts
# This will only be recognized by Chemkin 4 or later
for symbol, count in zip(elements, elementCounts):
string += "{0!s:<2}{1:<3d}".format(symbol, count)
string += "\n"
# Line 2
string += "{0:< 15.8E}{1:< 15.8E}{2:< 15.8E}{3:< 15.8E}{4:< 15.8E} 2\n".format(
poly_high.c0, poly_high.c1, poly_high.c2, poly_high.c3, poly_high.c4
)
# Line 3
string += "{0:< 15.8E}{1:< 15.8E}{2:< 15.8E}{3:< 15.8E}{4:< 15.8E} 3\n".format(
poly_high.c5, poly_high.c6, poly_low.c0, poly_low.c1, poly_low.c2
)
# Line 4
string += "{0:< 15.8E}{1:< 15.8E}{2:< 15.8E}{3:< 15.8E} 4\n".format(
poly_low.c3, poly_low.c4, poly_low.c5, poly_low.c6
)
f.write(string)
f.close()
def save(self, outputFile):
logging.info(
'Saving pressure dependence results for {0} network...'.format(
self.network.label))
f = open(outputFile, 'a')
f_chemkin = open(os.path.join(os.path.dirname(outputFile), 'chem.inp'),
'a')
Nreac = self.network.Nisom + self.network.Nreac
Nprod = Nreac + self.network.Nprod
Tlist = self.Tlist.value_si
Plist = self.Plist.value_si
Tcount = Tlist.shape[0]
Pcount = Plist.shape[0]
count = 0
printed_reactions = [] # list of rxns already printed
for prod in range(Nprod):
for reac in range(Nreac):
if reac == prod: continue
reaction = self.network.netReactions[count]
count += 1
# make sure we aren't double counting any reactions
if not any([reaction.isIsomorphic(other_rxn,checkOnlyLabel=True) \
for other_rxn in printed_reactions]):
duplicate = False
# add reaction to printed reaction
printed_reactions.append(reaction)
else:
# comment out the extra reverse reaction
duplicate = True
# write chemkin output.
string = writeKineticsEntry(reaction,
speciesList=None,
verbose=False,
commented=duplicate)
f_chemkin.write('{0}\n'.format(string))
# write to 'output.py'
kdata = self.K[:, :, prod, reac].copy()
order = len(reaction.reactants)
kdata *= 1e6**(order - 1)
kunits = {
1: 's^-1',
2: 'cm^3/(mol*s)',
3: 'cm^6/(mol^2*s)'
}[order]
f.write('# =========== ')
f.write('=========== ' * Pcount)
f.write('\n')
f.write('# T \ P ')
f.write(' '.join(['{0:11.3e}'.format(P * 1e-5)
for P in Plist]))
f.write('\n')
f.write('# =========== ')
f.write('=========== ' * Pcount)
f.write('\n')
for t in range(Tcount):
f.write('# {0:11g}'.format(Tlist[t]))
for p in range(Pcount):
f.write(' {0:11.3e}'.format(kdata[t, p]))
f.write('\n')
f.write('# =========== ')
f.write('=========== ' * Pcount)
f.write('\n')
string = 'pdepreaction(reactants={0!r}, products={1!r}, kinetics={2!r})'.format(
[reactant.label for reactant in reaction.reactants],
[product.label for product in reaction.products],
reaction.kinetics,
)
pdep_function = '{0}\n\n'.format(prettify(string))
if duplicate:
# add comments to the start of the string
pdep_function = '# ' + pdep_function.replace(
'\n', '\n# ')
f.write(pdep_function)
f.close()
f_chemkin.close()
def saveEntry(f, entry):
"""
Save an `entry` in the kinetics database by writing a string to
the given file object `f`.
"""
from rmgpy.cantherm.output import prettify
def sortEfficiencies(efficiencies0):
efficiencies = {}
for mol, eff in efficiencies0.iteritems():
if isinstance(mol, str):
# already in SMILES string format
smiles = mol
else:
smiles = mol.toSMILES()
efficiencies[smiles] = eff
keys = efficiencies.keys()
keys.sort()
return [(key, efficiencies[key]) for key in keys]
f.write('entry(\n')
f.write(' index = {0:d},\n'.format(entry.index))
if entry.label != '':
f.write(' label = "{0}",\n'.format(entry.label))
#Entries for kinetic rules, libraries, training reactions
#and depositories will have an Reaction object for its item
if isinstance(entry.item, Reaction):
#Write out additional data if depository or library
#kinetic rules would have a Group object for its reactants instead of Species
if isinstance(entry.item.reactants[0], Species):
# Add degeneracy if the reaction is coming from a depository or kinetics library
f.write(' degeneracy = {0:.1f},\n'.format(entry.item.degeneracy))
if entry.item.duplicate:
f.write(' duplicate = {0!r},\n'.format(entry.item.duplicate))
if not entry.item.reversible:
f.write(' reversible = {0!r},\n'.format(entry.item.reversible))
#Entries for groups with have a group or logicNode for its item
elif isinstance(entry.item, Group):
f.write(' group = \n')
f.write('"""\n')
f.write(entry.item.toAdjacencyList())
f.write('""",\n')
elif isinstance(entry.item, LogicNode):
f.write(' group = "{0}",\n'.format(entry.item))
else:
raise DatabaseError("Encountered unexpected item of type {0} while saving database.".format(entry.item.__class__))
# Write kinetics
if isinstance(entry.data, str):
f.write(' kinetics = "{0}",\n'.format(entry.data))
elif entry.data is not None:
efficiencies = None
if hasattr(entry.data, 'efficiencies'):
efficiencies = entry.data.efficiencies
entry.data.efficiencies = dict(sortEfficiencies(entry.data.efficiencies))
kinetics = prettify(repr(entry.data))
kinetics = ' kinetics = {0},\n'.format(kinetics.replace('\n', '\n '))
f.write(kinetics)
if hasattr(entry.data, 'efficiencies'):
entry.data.efficiencies = efficiencies
else:
f.write(' kinetics = None,\n')
# Write reference
if entry.reference is not None:
reference = entry.reference.toPrettyRepr()
lines = reference.splitlines()
f.write(' reference = {0}\n'.format(lines[0]))
for line in lines[1:-1]:
f.write(' {0}\n'.format(line))
f.write(' ),\n'.format(lines[0]))
if entry.referenceType != "":
f.write(' referenceType = "{0}",\n'.format(entry.referenceType))
if entry.rank is not None:
f.write(' rank = {0},\n'.format(entry.rank))
if entry.shortDesc.strip() !='':
f.write(' shortDesc = u"""')
try:
f.write(entry.shortDesc.encode('utf-8'))
except:
f.write(entry.shortDesc.strip().encode('ascii', 'ignore')+ "\n")
f.write('""",\n')
if entry.longDesc.strip() !='':
f.write(' longDesc = \n')
f.write('u"""\n')
try:
f.write(entry.longDesc.strip().encode('utf-8') + "\n")
except:
f.write(entry.longDesc.strip().encode('ascii', 'ignore')+ "\n")
f.write('""",\n')
f.write(')\n\n')
def save(self, outputFile):
logging.info('Saving pressure dependence results for {0}...'.format(self.network))
f = open(outputFile, 'a')
Nreac = self.network.Nisom + self.network.Nreac
Nprod = Nreac + self.network.Nprod
Tlist = self.Tlist.value_si
Plist = self.Plist.value_si
Tcount = Tlist.shape[0]
Pcount = Plist.shape[0]
count = 0
for prod in range(Nprod):
for reac in range(Nreac):
if reac == prod: continue
reaction = self.network.netReactions[count]
count += 1
kdata = self.K[:,:,prod,reac].copy()
order = len(reaction.reactants)
kdata *= 1e6 ** (order-1)
kunits = {1: 's^-1', 2: 'cm^3/(mol*s)', 3: 'cm^6/(mol^2*s)'}[order]
f.write('# =========== ')
f.write('=========== ' * Pcount)
f.write('\n')
f.write('# T \ P ')
f.write(' '.join(['{0:11.3e}'.format(P*1e-5) for P in Plist]))
f.write('\n')
f.write('# =========== ')
f.write('=========== ' * Pcount)
f.write('\n')
for t in range(Tcount):
f.write('# {0:11g}'.format(Tlist[t]))
for p in range(Pcount):
f.write(' {0:11.3e}'.format(kdata[t,p]))
f.write('\n')
f.write('# =========== ')
f.write('=========== ' * Pcount)
f.write('\n')
string = 'pdepreaction(reactants={0!r}, products={1!r}, kinetics={2!r})'.format(
[reactant.label for reactant in reaction.reactants],
[product.label for product in reaction.products],
reaction.kinetics,
)
f.write('{0}\n\n'.format(prettify(string)))
f.close()
f = open(os.path.join(os.path.dirname(outputFile), 'chem.inp'), 'w')
count = 0
for prod in range(Nprod):
for reac in range(Nreac):
if reac == prod: continue
reaction = self.network.netReactions[count]
kinetics = reaction.kinetics
count += 1
string = '{0!s} 1.0 0.0 0.0 0.0 0.0 0.0\n'.format(reaction)
if isinstance(kinetics, PDepArrhenius):
for P, arrhenius in zip(kinetics.pressures.value_si, kinetics.arrhenius):
string += 'PLOG/ {0:<9.3f} {1:<11.3e} {2:<8.2f} {3:<8.2f}/\n'.format(P / 101325.,
arrhenius.A.value_si / (arrhenius.T0.value_si ** arrhenius.n) * 1e6 ** (len(reaction.reactants) - 1),
arrhenius.n,
arrhenius.Ea.value_si / 4184.
)
elif isinstance(kinetics, Chebyshev):
coeffs = kinetics.coeffs.value_si.copy()
coeffs[0,0] += 6 * (len(reaction.reactants) - 1)
string += 'TCHEB/ {0:<9.3f} {1:<9.3f}/\n'.format(kinetics.Tmin.value_si, kinetics.Tmax.value_si)
string += 'PCHEB/ {0:<9.3f} {1:<9.3f}/\n'.format(kinetics.Pmin.value_si / 101325., kinetics.Pmax.value_si / 101325.)
string += 'CHEB/ {0:d} {1:d}/\n'.format(kinetics.degreeT, kinetics.degreeP)
if kinetics.degreeP < 6:
for i in range(kinetics.degreeT):
string += 'CHEB/'
for j in range(kinetics.degreeP):
string += ' {0:<12.3e}'.format(coeffs[i,j])
string += '/\n'
else:
coeffs_list = []
for i in range(kinetics.degreeT):
for j in range(kinetics.degreeP):
coeffs_list.append(coeffs[i,j])
coeffs_list[0] += 6 * (numReactants - 1)
for i in range(len(coeffs_list)):
if i % 5 == 0: string += ' CHEB/'
string += ' {0:<12.3e}'.format(coeffs_list[i])
if i % 5 == 4: string += '/\n'
f.write('{0}\n'.format(string))
f.close()
def save(self, outputFile):
"""
Save the results of the thermodynamics job to the file located
at `path` on disk.
"""
species = self.species
logging.info('Saving thermo for {0}...'.format(species.label))
f = open(outputFile, 'a')
f.write('# Thermodynamics for {0}:\n'.format(species.label))
H298 = species.thermo.getEnthalpy(298) / 4184.
S298 = species.thermo.getEntropy(298) / 4.184
f.write(
'# Enthalpy of formation (298 K) = {0:9.3f} kcal/mol\n'.format(
H298))
f.write('# Entropy of formation (298 K) = {0:9.3f} cal/(mol*K)\n'.
format(S298))
f.write(
'# =========== =========== =========== =========== ===========\n'
)
f.write(
'# Temperature Heat cap. Enthalpy Entropy Free energy\n'
)
f.write(
'# (K) (cal/mol*K) (kcal/mol) (cal/mol*K) (kcal/mol)\n'
)
f.write(
'# =========== =========== =========== =========== ===========\n'
)
for T in [300, 400, 500, 600, 800, 1000, 1500, 2000, 2400]:
Cp = species.thermo.getHeatCapacity(T) / 4.184
H = species.thermo.getEnthalpy(T) / 4184.
S = species.thermo.getEntropy(T) / 4.184
G = species.thermo.getFreeEnergy(T) / 4184.
f.write('# {0:11g} {1:11.3f} {2:11.3f} {3:11.3f} {4:11.3f}\n'.
format(T, Cp, H, S, G))
f.write(
'# =========== =========== =========== =========== ===========\n'
)
string = 'thermo(label={0!r}, thermo={1!r})'.format(
species.label, species.thermo)
f.write('{0}\n\n'.format(prettify(string)))
f.close()
f = open(os.path.join(os.path.dirname(outputFile), 'chem.inp'), 'a')
thermo = species.thermo
if isinstance(thermo, NASA):
poly_low = thermo.polynomials[0]
poly_high = thermo.polynomials[1]
# Determine the number of each type of element in the molecule
elements = ['C', 'H', 'N', 'O']
elementCounts = [0, 0, 0, 0]
# Remove elements with zero count
index = 2
while index < len(elementCounts):
if elementCounts[index] == 0:
del elements[index]
del elementCounts[index]
else:
index += 1
# Line 1
string = '{0:<16} '.format(species.label)
if len(elements) <= 4:
# Use the original Chemkin syntax for the element counts
for symbol, count in zip(elements, elementCounts):
string += '{0!s:<2}{1:<3d}'.format(symbol, count)
string += ' ' * (4 - len(elements))
else:
string += ' ' * 4
string += 'G{0:<10.3f}{1:<10.3f}{2:<8.2f} 1'.format(
poly_low.Tmin.value_si, poly_high.Tmax.value_si,
poly_low.Tmax.value_si)
if len(elements) > 4:
string += '&\n'
# Use the new-style Chemkin syntax for the element counts
# This will only be recognized by Chemkin 4 or later
for symbol, count in zip(elements, elementCounts):
string += '{0!s:<2}{1:<3d}'.format(symbol, count)
string += '\n'
# Line 2
string += '{0:< 15.8E}{1:< 15.8E}{2:< 15.8E}{3:< 15.8E}{4:< 15.8E} 2\n'.format(
poly_high.c0, poly_high.c1, poly_high.c2, poly_high.c3,
poly_high.c4)
# Line 3
string += '{0:< 15.8E}{1:< 15.8E}{2:< 15.8E}{3:< 15.8E}{4:< 15.8E} 3\n'.format(
poly_high.c5, poly_high.c6, poly_low.c0, poly_low.c1,
poly_low.c2)
# Line 4
string += '{0:< 15.8E}{1:< 15.8E}{2:< 15.8E}{3:< 15.8E} 4\n'.format(
poly_low.c3, poly_low.c4, poly_low.c5, poly_low.c6)
f.write(string)
f.close()
def save(self, outputFile):
logging.info(
'Saving pressure dependence results for {0} network...'.format(
self.network.label))
f = open(outputFile, 'a')
Nreac = self.network.Nisom + self.network.Nreac
Nprod = Nreac + self.network.Nprod
Tlist = self.Tlist.value_si
Plist = self.Plist.value_si
Tcount = Tlist.shape[0]
Pcount = Plist.shape[0]
count = 0
for prod in range(Nprod):
for reac in range(Nreac):
if reac == prod: continue
reaction = self.network.netReactions[count]
count += 1
kdata = self.K[:, :, prod, reac].copy()
order = len(reaction.reactants)
kdata *= 1e6**(order - 1)
kunits = {
1: 's^-1',
2: 'cm^3/(mol*s)',
3: 'cm^6/(mol^2*s)'
}[order]
f.write('# =========== ')
f.write('=========== ' * Pcount)
f.write('\n')
f.write('# T \ P ')
f.write(' '.join(['{0:11.3e}'.format(P * 1e-5)
for P in Plist]))
f.write('\n')
f.write('# =========== ')
f.write('=========== ' * Pcount)
f.write('\n')
for t in range(Tcount):
f.write('# {0:11g}'.format(Tlist[t]))
for p in range(Pcount):
f.write(' {0:11.3e}'.format(kdata[t, p]))
f.write('\n')
f.write('# =========== ')
f.write('=========== ' * Pcount)
f.write('\n')
string = 'pdepreaction(reactants={0!r}, products={1!r}, kinetics={2!r})'.format(
[reactant.label for reactant in reaction.reactants],
[product.label for product in reaction.products],
reaction.kinetics,
)
f.write('{0}\n\n'.format(prettify(string)))
f.close()
f = open(os.path.join(os.path.dirname(outputFile), 'chem.inp'), 'a')
count = 0
for prod in range(Nprod):
for reac in range(Nreac):
if reac == prod: continue
reaction = self.network.netReactions[count]
count += 1
string = writeKineticsEntry(reaction,
speciesList=None,
verbose=False)
f.write('{0}\n'.format(string))
f.close()
def save(self, outputFile):
"""
Save the results of the kinetics job to the file located
at `path` on disk.
"""
reaction = self.reaction
ks = []
k0s = []
k0revs = []
krevs = []
logging.info('Saving kinetics for {0}...'.format(reaction))
order = len(self.reaction.reactants)
factor = 1e6 ** (order-1)
f = open(outputFile, 'a')
f.write('# ======= =========== =========== =========== ===============\n')
f.write('# Temp. k (TST) Tunneling k (TST+T) Units\n')
f.write('# ======= =========== =========== =========== ===============\n')
if self.Tlist is None:
Tlist = [300,400,500,600,800,1000,1500,2000]
else:
Tlist =self.Tlist.value_si
for T in Tlist:
tunneling = reaction.transitionState.tunneling
reaction.transitionState.tunneling = None
k0 = reaction.calculateTSTRateCoefficient(T) * factor
reaction.transitionState.tunneling = tunneling
k = reaction.calculateTSTRateCoefficient(T) * factor
tunneling = reaction.transitionState.tunneling
kappa = k / k0
ks.append(k)
k0s.append(k0)
f.write('# {0:4g} K {1:11.3e} {2:11g} {3:11.3e} {4}\n'.format(T, k0, kappa, k, self.kunits))
f.write('# ======= =========== =========== =========== ===============\n')
f.write('\n\n')
f.write('# ======= ============ =========== ============ ============= =========\n')
f.write('# Temp. Kc (eq) Units krev (TST) krev (TST+T) Units\n')
f.write('# ======= ============ =========== ============ ============= =========\n')
for n,T in enumerate(Tlist):
k = ks[n]
k0 = k0s[n]
Keq = reaction.getEquilibriumConstant(T)
k0rev = k0/Keq
krev = k/Keq
k0revs.append(k0rev)
krevs.append(krev)
f.write('# {0:4g} K {1:11.3e} {2} {3:11.3e} {4:11.3e} {5}\n'.format(T, Keq, self.Kequnits, k0rev, krev, self.krunits))
f.write('# ======= ============ =========== ============ ============= =========\n')
f.write('\n\n')
kinetics0rev = Arrhenius().fitToData(Tlist, numpy.array(k0revs), kunits=self.krunits)
kineticsrev = Arrhenius().fitToData(Tlist, numpy.array(krevs), kunits=self.krunits)
f.write('# krev (TST) = {0} \n'.format(kinetics0rev))
f.write('# krev (TST+T) = {0} \n\n'.format(kineticsrev))
# Reaction path degeneracy is INCLUDED in the kinetics itself!
string = 'kinetics(label={0!r}, kinetics={1!r})'.format(reaction.label, reaction.kinetics)
f.write('{0}\n\n'.format(prettify(string)))
f.close()
# Also save the result to chem.inp
f = open(os.path.join(os.path.dirname(outputFile), 'chem.inp'), 'a')
reaction = self.reaction
kinetics = reaction.kinetics
string = '{0!s:51} {1:9.3e} {2:9.3f} {3:9.3f}\n'.format(
reaction,
kinetics.A.value_si * factor,
kinetics.n.value_si,
kinetics.Ea.value_si / 4184.,
)
f.write('{0}\n'.format(string))
f.close()
def save(self, outputFile):
"""
Save the results of the thermodynamics job to the file located
at `path` on disk.
"""
species = self.species
logging.info('Saving thermo for {0}...'.format(species.label))
f = open(outputFile, 'a')
f.write('# Thermodynamics for {0}:\n'.format(species.label))
H298 = species.getThermoData().getEnthalpy(298) / 4184.
S298 = species.getThermoData().getEntropy(298) / 4.184
f.write(
'# Enthalpy of formation (298 K) = {0:9.3f} kcal/mol\n'.format(
H298))
f.write('# Entropy of formation (298 K) = {0:9.3f} cal/(mol*K)\n'.
format(S298))
f.write(
'# =========== =========== =========== =========== ===========\n'
)
f.write(
'# Temperature Heat cap. Enthalpy Entropy Free energy\n'
)
f.write(
'# (K) (cal/mol*K) (kcal/mol) (cal/mol*K) (kcal/mol)\n'
)
f.write(
'# =========== =========== =========== =========== ===========\n'
)
for T in [300, 400, 500, 600, 800, 1000, 1500, 2000, 2400]:
Cp = species.getThermoData().getHeatCapacity(T) / 4.184
H = species.getThermoData().getEnthalpy(T) / 4184.
S = species.getThermoData().getEntropy(T) / 4.184
G = species.getThermoData().getFreeEnergy(T) / 4184.
f.write('# {0:11g} {1:11.3f} {2:11.3f} {3:11.3f} {4:11.3f}\n'.
format(T, Cp, H, S, G))
f.write(
'# =========== =========== =========== =========== ===========\n'
)
string = 'thermo(label={0!r}, thermo={1!r})'.format(
species.label, species.getThermoData())
f.write('{0}\n\n'.format(prettify(string)))
f.close()
# write chemkin file
f = open(os.path.join(os.path.dirname(outputFile), 'chem.inp'), 'a')
if isinstance(species, Species):
if species.molecule and isinstance(species.molecule[0], Molecule):
elementCounts = retrieveElementCount(species.molecule[0])
else:
try:
elementCounts = species.props['elementCounts']
except KeyError:
elementCounts = {'C': 0, 'H': 0}
else:
elementCounts = {'C': 0, 'H': 0}
string = writeThermoEntry(species,
elementCounts=elementCounts,
verbose=False)
f.write('{0}\n'.format(string))
f.close()
# write species dictionary
f = open(
os.path.join(os.path.dirname(outputFile),
'species_dictionary.txt'), 'a')
if isinstance(species, Species):
if species.molecule and isinstance(species.molecule[0], Molecule):
f.write(species.molecule[0].toAdjacencyList(
removeH=False, label=species.label))
f.write('\n')
f.close()
def saveEntry(f, entry):
"""
Save an `entry` in the kinetics database by writing a string to
the given file object `f`.
"""
from rmgpy.cantherm.output import prettify
def sortEfficiencies(efficiencies0):
efficiencies = {}
for mol, eff in efficiencies0.iteritems():
smiles = mol.toSMILES()
efficiencies[smiles] = eff
keys = efficiencies.keys()
keys.sort()
return [(key, efficiencies[key]) for key in keys]
f.write('entry(\n')
f.write(' index = {0:d},\n'.format(entry.index))
if entry.label != '':
f.write(' label = "{0}",\n'.format(entry.label))
if isinstance(entry.item, Reaction):
for i, reactant in enumerate(entry.item.reactants):
if isinstance(reactant, Molecule):
f.write(' reactant{0:d} = \n'.format(i+1))
f.write('"""\n')
f.write(reactant.toAdjacencyList(removeH=True))
f.write('""",\n')
elif isinstance(reactant, Species):
f.write(' reactant{0:d} = \n'.format(i+1))
f.write('"""\n')
f.write(reactant.molecule[0].toAdjacencyList(label=reactant.label, removeH=True))
f.write('""",\n')
elif isinstance(reactant, Group):
f.write(' group{0:d} = \n'.format(i+1))
f.write('"""\n')
f.write(reactant.toAdjacencyList())
f.write('""",\n')
elif isinstance(reactant, LogicNode):
f.write(' group{0:d} = "{1}",\n'.format(i+1, reactant))
for i, product in enumerate(entry.item.products):
if isinstance(product, Molecule):
f.write(' product{0:d} = \n'.format(i+1))
f.write('"""\n')
f.write(product.toAdjacencyList(removeH=True))
f.write('""",\n')
elif isinstance(reactant, Species):
f.write(' product{0:d} = \n'.format(i+1))
f.write('"""\n')
f.write(product.molecule[0].toAdjacencyList(label=product.label, removeH=True))
f.write('""",\n')
if not isinstance(entry.item.reactants[0], Group) and not isinstance(entry.item.reactants[0], LogicNode):
f.write(' degeneracy = {0:d},\n'.format(entry.item.degeneracy))
if entry.item.duplicate:
f.write(' duplicate = {0!r},\n'.format(entry.item.duplicate))
if not entry.item.reversible:
f.write(' reversible = {0!r},\n'.format(entry.item.reversible))
elif isinstance(entry.item, Group):
f.write(' group = \n')
f.write('"""\n')
f.write(entry.item.toAdjacencyList())
f.write('""",\n')
elif isinstance(entry.item, LogicNode):
f.write(' group = "{0}",\n'.format(entry.item))
else:
raise DatabaseError("Encountered unexpected item of type {0} while saving database.".format(entry.item.__class__))
# Write kinetics
if isinstance(entry.data, str):
f.write(' kinetics = "{0}",\n'.format(entry.data))
elif entry.data is not None:
efficiencies = None
if hasattr(entry.data, 'efficiencies'):
efficiencies = entry.data.efficiencies
entry.data.efficiencies = dict(sortEfficiencies(entry.data.efficiencies))
kinetics = prettify(repr(entry.data))
kinetics = ' kinetics = {0},\n'.format(kinetics.replace('\n', '\n '))
f.write(kinetics)
if hasattr(entry.data, 'efficiencies'):
entry.data.efficiencies = efficiencies
else:
f.write(' kinetics = None,\n')
# Write reference
if entry.reference is not None:
reference = entry.reference.toPrettyRepr()
lines = reference.splitlines()
f.write(' reference = {0}\n'.format(lines[0]))
for line in lines[1:-1]:
f.write(' {0}\n'.format(line))
f.write(' ),\n'.format(lines[0]))
else:
f.write(' reference = None,\n')
f.write(' referenceType = "{0}",\n'.format(entry.referenceType))
if entry.rank is not None:
f.write(' rank = {0},\n'.format(entry.rank))
f.write(' shortDesc = u"""')
f.write(entry.shortDesc)
f.write('""",\n')
f.write(' longDesc = \n')
f.write('u"""\n')
f.write(entry.longDesc.strip() + "\n")
f.write('""",\n')
f.write(' history = [\n')
for time, user, action, description in entry.history:
f.write(' ("{0}","{1}","{2}","""{3}"""),\n'.format(time, user, action, description))
f.write(' ],\n')
f.write(')\n\n')
def saveEntry(f, entry):
"""
Save an `entry` in the kinetics database by writing a string to
the given file object `f`.
"""
from rmgpy.cantherm.output import prettify
def sortEfficiencies(efficiencies0):
efficiencies = {}
for mol, eff in efficiencies0.iteritems():
if isinstance(mol, str):
# already in SMILES string format
smiles = mol
else:
smiles = mol.toSMILES()
efficiencies[smiles] = eff
keys = efficiencies.keys()
keys.sort()
return [(key, efficiencies[key]) for key in keys]
f.write('entry(\n')
f.write(' index = {0:d},\n'.format(entry.index))
if entry.label != '':
f.write(' label = "{0}",\n'.format(entry.label))
#Entries for kinetic rules, libraries, training reactions
#and depositories will have an Reaction object for its item
if isinstance(entry.item, Reaction):
#Write out additional data if depository or library
#kinetic rules would have a Group object for its reactants instead of Species
if isinstance(entry.item.reactants[0], Species):
# Add degeneracy if the reaction is coming from a depository or kinetics library
f.write(' degeneracy = {0:.1f},\n'.format(entry.item.degeneracy))
if entry.item.duplicate:
f.write(' duplicate = {0!r},\n'.format(entry.item.duplicate))
if not entry.item.reversible:
f.write(' reversible = {0!r},\n'.format(entry.item.reversible))
#Entries for groups with have a group or logicNode for its item
elif isinstance(entry.item, Group):
f.write(' group = \n')
f.write('"""\n')
f.write(entry.item.toAdjacencyList())
f.write('""",\n')
elif isinstance(entry.item, LogicNode):
f.write(' group = "{0}",\n'.format(entry.item))
else:
raise DatabaseError("Encountered unexpected item of type {0} while saving database.".format(entry.item.__class__))
# Write kinetics
if isinstance(entry.data, str):
f.write(' kinetics = "{0}",\n'.format(entry.data))
elif entry.data is not None:
efficiencies = None
if hasattr(entry.data, 'efficiencies'):
efficiencies = entry.data.efficiencies
entry.data.efficiencies = dict(sortEfficiencies(entry.data.efficiencies))
kinetics = prettify(repr(entry.data))
kinetics = ' kinetics = {0},\n'.format(kinetics.replace('\n', '\n '))
f.write(kinetics)
if hasattr(entry.data, 'efficiencies'):
entry.data.efficiencies = efficiencies
else:
f.write(' kinetics = None,\n')
# Write reference
if entry.reference is not None:
reference = entry.reference.toPrettyRepr()
lines = reference.splitlines()
f.write(' reference = {0}\n'.format(lines[0]))
for line in lines[1:-1]:
f.write(' {0}\n'.format(line))
f.write(' ),\n'.format(lines[0]))
if entry.referenceType != "":
f.write(' referenceType = "{0}",\n'.format(entry.referenceType))
if entry.rank is not None:
f.write(' rank = {0},\n'.format(entry.rank))
if entry.shortDesc.strip() !='':
f.write(' shortDesc = u"""')
try:
f.write(entry.shortDesc.encode('utf-8'))
except:
f.write(entry.shortDesc.strip().encode('ascii', 'ignore')+ "\n")
f.write('""",\n')
if entry.longDesc.strip() !='':
f.write(' longDesc = \n')
f.write('u"""\n')
try:
f.write(entry.longDesc.strip().encode('utf-8') + "\n")
except:
f.write(entry.longDesc.strip().encode('ascii', 'ignore')+ "\n")
f.write('""",\n')
f.write(')\n\n')
def save(self, outputFile):
logging.info('Saving pressure dependence results for {0} network...'.format(self.network.label))
f = open(outputFile, 'a')
Nreac = self.network.Nisom + self.network.Nreac
Nprod = Nreac + self.network.Nprod
Tlist = self.Tlist.value_si
Plist = self.Plist.value_si
Tcount = Tlist.shape[0]
Pcount = Plist.shape[0]
count = 0
for prod in range(Nprod):
for reac in range(Nreac):
if reac == prod: continue
reaction = self.network.netReactions[count]
count += 1
kdata = self.K[:,:,prod,reac].copy()
order = len(reaction.reactants)
kdata *= 1e6 ** (order-1)
kunits = {1: 's^-1', 2: 'cm^3/(mol*s)', 3: 'cm^6/(mol^2*s)'}[order]
f.write('# =========== ')
f.write('=========== ' * Pcount)
f.write('\n')
f.write('# T \ P ')
f.write(' '.join(['{0:11.3e}'.format(P*1e-5) for P in Plist]))
f.write('\n')
f.write('# =========== ')
f.write('=========== ' * Pcount)
f.write('\n')
for t in range(Tcount):
f.write('# {0:11g}'.format(Tlist[t]))
for p in range(Pcount):
f.write(' {0:11.3e}'.format(kdata[t,p]))
f.write('\n')
f.write('# =========== ')
f.write('=========== ' * Pcount)
f.write('\n')
string = 'pdepreaction(reactants={0!r}, products={1!r}, kinetics={2!r})'.format(
[reactant.label for reactant in reaction.reactants],
[product.label for product in reaction.products],
reaction.kinetics,
)
f.write('{0}\n\n'.format(prettify(string)))
f.close()
f = open(os.path.join(os.path.dirname(outputFile), 'chem.inp'), 'a')
count = 0
for prod in range(Nprod):
for reac in range(Nreac):
if reac == prod: continue
reaction = self.network.netReactions[count]
kinetics = reaction.kinetics
count += 1
string = '{0!s:51} 1.0 0.0 0.0\n'.format(reaction)
if isinstance(kinetics, PDepArrhenius):
for P, arrhenius in zip(kinetics.pressures.value_si, kinetics.arrhenius):
string += 'PLOG/ {0:<9.3f} {1:<11.3e} {2:<8.2f} {3:<8.2f}/\n'.format(P / 101325.,
arrhenius.A.value_si / (arrhenius.T0.value_si ** arrhenius.n.value_si) * 1e6 ** (len(reaction.reactants) - 1),
arrhenius.n.value_si,
arrhenius.Ea.value_si / 4184.
)
elif isinstance(kinetics, Chebyshev):
coeffs = kinetics.coeffs.value_si.copy()
coeffs[0,0] += 6 * (len(reaction.reactants) - 1)
string += 'TCHEB/ {0:<9.3f} {1:<9.3f}/\n'.format(kinetics.Tmin.value_si, kinetics.Tmax.value_si)
string += 'PCHEB/ {0:<9.3f} {1:<9.3f}/\n'.format(kinetics.Pmin.value_si / 101325., kinetics.Pmax.value_si / 101325.)
string += 'CHEB/ {0:d} {1:d}/\n'.format(kinetics.degreeT, kinetics.degreeP)
if kinetics.degreeP < 6:
for i in range(kinetics.degreeT):
string += 'CHEB/'
for j in range(kinetics.degreeP):
string += ' {0:<12.3e}'.format(coeffs[i,j])
string += '/\n'
else:
coeffs_list = []
for i in range(kinetics.degreeT):
for j in range(kinetics.degreeP):
coeffs_list.append(coeffs[i,j])
coeffs_list[0] += 6 * (numReactants - 1)
for i in range(len(coeffs_list)):
if i % 5 == 0: string += ' CHEB/'
string += ' {0:<12.3e}'.format(coeffs_list[i])
if i % 5 == 4: string += '/\n'
f.write('{0}\n'.format(string))
f.close()
def save(self, outputFile):
logging.info('Saving pressure dependence results for {0} network...'.format(self.network.label))
f = open(outputFile, 'a')
f_chemkin = open(os.path.join(os.path.dirname(outputFile), 'chem.inp'), 'a')
Nreac = self.network.Nisom + self.network.Nreac
Nprod = Nreac + self.network.Nprod
Tlist = self.Tlist.value_si
Plist = self.Plist.value_si
Tcount = Tlist.shape[0]
Pcount = Plist.shape[0]
count = 0
printed_reactions = [] # list of rxns already printed
for prod in range(Nprod):
for reac in range(Nreac):
if reac == prod: continue
reaction = self.network.netReactions[count]
count += 1
# make sure we aren't double counting any reactions
if not any([reaction.isIsomorphic(other_rxn,checkOnlyLabel=True) \
for other_rxn in printed_reactions]):
duplicate = False
# add reaction to printed reaction
printed_reactions.append(reaction)
else:
# comment out the extra reverse reaction
duplicate = True
# write chemkin output.
string = writeKineticsEntry(reaction, speciesList=None, verbose=False, commented = duplicate)
f_chemkin.write('{0}\n'.format(string))
# write to 'output.py'
kdata = self.K[:,:,prod,reac].copy()
order = len(reaction.reactants)
kdata *= 1e6 ** (order-1)
kunits = {1: 's^-1', 2: 'cm^3/(mol*s)', 3: 'cm^6/(mol^2*s)'}[order]
f.write('# =========== ')
f.write('=========== ' * Pcount)
f.write('\n')
f.write('# T \ P ')
f.write(' '.join(['{0:11.3e}'.format(P*1e-5) for P in Plist]))
f.write('\n')
f.write('# =========== ')
f.write('=========== ' * Pcount)
f.write('\n')
for t in range(Tcount):
f.write('# {0:11g}'.format(Tlist[t]))
for p in range(Pcount):
f.write(' {0:11.3e}'.format(kdata[t,p]))
f.write('\n')
f.write('# =========== ')
f.write('=========== ' * Pcount)
f.write('\n')
string = 'pdepreaction(reactants={0!r}, products={1!r}, kinetics={2!r})'.format(
[reactant.label for reactant in reaction.reactants],
[product.label for product in reaction.products],
reaction.kinetics,
)
pdep_function = '{0}\n\n'.format(prettify(string))
if duplicate:
# add comments to the start of the string
pdep_function = '# ' + pdep_function.replace('\n','\n# ')
f.write(pdep_function)
f.close()
f_chemkin.close()
def save(self, outputFile):
"""
Save the results of the kinetics job to the file located
at `path` on disk.
"""
reaction = self.reaction
ks = []
k0s = []
k0revs = []
krevs = []
logging.info('Saving kinetics for {0}...'.format(reaction))
order = len(self.reaction.reactants)
factor = 1e6 ** (order-1)
f = open(outputFile, 'a')
f.write('# ======= =========== =========== =========== ===============\n')
f.write('# Temp. k (TST) Tunneling k (TST+T) Units\n')
f.write('# ======= =========== =========== =========== ===============\n')
if self.Tlist is None:
Tlist = numpy.array([300,400,500,600,800,1000,1500,2000])
else:
Tlist =self.Tlist.value_si
for T in Tlist:
tunneling = reaction.transitionState.tunneling
reaction.transitionState.tunneling = None
k0 = reaction.calculateTSTRateCoefficient(T) * factor
reaction.transitionState.tunneling = tunneling
k = reaction.calculateTSTRateCoefficient(T) * factor
tunneling = reaction.transitionState.tunneling
kappa = k / k0
ks.append(k)
k0s.append(k0)
f.write('# {0:4g} K {1:11.3e} {2:11g} {3:11.3e} {4}\n'.format(T, k0, kappa, k, self.kunits))
f.write('# ======= =========== =========== =========== ===============\n')
f.write('\n\n')
f.write('# ======= ============ =========== ============ ============= =========\n')
f.write('# Temp. Kc (eq) Units krev (TST) krev (TST+T) Units\n')
f.write('# ======= ============ =========== ============ ============= =========\n')
for n,T in enumerate(Tlist):
k = ks[n]
k0 = k0s[n]
Keq = reaction.getEquilibriumConstant(T)
k0rev = k0/Keq
krev = k/Keq
k0revs.append(k0rev)
krevs.append(krev)
f.write('# {0:4g} K {1:11.3e} {2} {3:11.3e} {4:11.3e} {5}\n'.format(T, Keq, self.Kequnits, k0rev, krev, self.krunits))
f.write('# ======= ============ =========== ============ ============= =========\n')
f.write('\n\n')
kinetics0rev = Arrhenius().fitToData(Tlist, numpy.array(k0revs), kunits=self.krunits)
kineticsrev = Arrhenius().fitToData(Tlist, numpy.array(krevs), kunits=self.krunits)
f.write('# krev (TST) = {0} \n'.format(kinetics0rev))
f.write('# krev (TST+T) = {0} \n\n'.format(kineticsrev))
# Reaction path degeneracy is INCLUDED in the kinetics itself!
string = 'kinetics(label={0!r}, kinetics={1!r})'.format(reaction.label, reaction.kinetics)
f.write('{0}\n\n'.format(prettify(string)))
f.close()
# Also save the result to chem.inp
f = open(os.path.join(os.path.dirname(outputFile), 'chem.inp'), 'a')
reaction = self.reaction
kinetics = reaction.kinetics
string = '{0!s:51} {1:9.3e} {2:9.3f} {3:9.3f}\n'.format(
reaction,
kinetics.A.value_si * factor,
kinetics.n.value_si,
kinetics.Ea.value_si / 4184.,
)
f.write('{0}\n'.format(string))
f.close()
def saveEntry(f, entry):
"""
Save an `entry` in the kinetics database by writing a string to
the given file object `f`.
"""
from rmgpy.cantherm.output import prettify
def sortEfficiencies(efficiencies0):
efficiencies = {}
for mol, eff in efficiencies0.iteritems():
if isinstance(mol, str):
# already in SMILES string format
smiles = mol
else:
smiles = mol.toSMILES()
efficiencies[smiles] = eff
keys = efficiencies.keys()
keys.sort()
return [(key, efficiencies[key]) for key in keys]
f.write('entry(\n')
f.write(' index = {0:d},\n'.format(entry.index))
if entry.label != '':
f.write(' label = "{0}",\n'.format(entry.label))
if isinstance(entry.item, Reaction):
if entry.label != str(entry.item):
raise KineticsError("Reactions are now defined solely by their labels, "
"but reaction {0!s} has label {1!r}".format(
entry.item, entry.label))
# for i, reactant in enumerate(entry.item.reactants):
# if isinstance(reactant, Molecule):
# f.write(' reactant{0:d} = \n'.format(i+1))
# f.write('"""\n')
# f.write(reactant.toAdjacencyList(removeH=False))
# f.write('""",\n')
# elif isinstance(reactant, Species):
# f.write(' reactant{0:d} = \n'.format(i+1))
# f.write('"""\n')
# f.write(reactant.molecule[0].toAdjacencyList(label=reactant.label, removeH=False))
# f.write('""",\n')
# for i, product in enumerate(entry.item.products):
# if isinstance(product, Molecule):
# f.write(' product{0:d} = \n'.format(i+1))
# f.write('"""\n')
# f.write(product.toAdjacencyList(removeH=False))
# f.write('""",\n')
# elif isinstance(reactant, Species):
# f.write(' product{0:d} = \n'.format(i+1))
# f.write('"""\n')
# f.write(product.molecule[0].toAdjacencyList(label=product.label, removeH=False))
# f.write('""",\n')
if isinstance(entry.item.reactants[0], Species):
# Add degeneracy if the reaction is coming from a depository or kinetics library
f.write(' degeneracy = {0:d},\n'.format(entry.item.degeneracy))
if entry.item.duplicate:
f.write(' duplicate = {0!r},\n'.format(entry.item.duplicate))
if not entry.item.reversible:
f.write(' reversible = {0!r},\n'.format(entry.item.reversible))
elif isinstance(entry.item, Group):
f.write(' group = \n')
f.write('"""\n')
f.write(entry.item.toAdjacencyList())
f.write('""",\n')
elif isinstance(entry.item, LogicNode):
f.write(' group = "{0}",\n'.format(entry.item))
else:
raise DatabaseError("Encountered unexpected item of type {0} while saving database.".format(entry.item.__class__))
# Write kinetics
if isinstance(entry.data, str):
f.write(' kinetics = "{0}",\n'.format(entry.data))
elif entry.data is not None:
efficiencies = None
if hasattr(entry.data, 'efficiencies'):
efficiencies = entry.data.efficiencies
entry.data.efficiencies = dict(sortEfficiencies(entry.data.efficiencies))
kinetics = prettify(repr(entry.data))
kinetics = ' kinetics = {0},\n'.format(kinetics.replace('\n', '\n '))
f.write(kinetics)
if hasattr(entry.data, 'efficiencies'):
entry.data.efficiencies = efficiencies
else:
f.write(' kinetics = None,\n')
# Write reference
if entry.reference is not None:
reference = entry.reference.toPrettyRepr()
lines = reference.splitlines()
f.write(' reference = {0}\n'.format(lines[0]))
for line in lines[1:-1]:
f.write(' {0}\n'.format(line))
f.write(' ),\n'.format(lines[0]))
if entry.referenceType != "":
f.write(' referenceType = "{0}",\n'.format(entry.referenceType))
if entry.rank is not None:
f.write(' rank = {0},\n'.format(entry.rank))
if entry.shortDesc.strip() !='':
f.write(' shortDesc = u"""')
try:
f.write(entry.shortDesc.encode('utf-8'))
except:
f.write(entry.shortDesc.strip().encode('ascii', 'ignore')+ "\n")
f.write('""",\n')
if entry.longDesc.strip() !='':
f.write(' longDesc = \n')
f.write('u"""\n')
try:
f.write(entry.longDesc.strip().encode('utf-8') + "\n")
except:
f.write(entry.longDesc.strip().encode('ascii', 'ignore')+ "\n")
f.write('""",\n')
f.write(')\n\n')
def saveEntry(f, entry):
"""
Save an `entry` in the kinetics database by writing a string to
the given file object `f`.
"""
from rmgpy.cantherm.output import prettify
def sortEfficiencies(efficiencies0):
efficiencies = {}
for mol, eff in efficiencies0.iteritems():
if isinstance(mol, str):
# already in SMILES string format
smiles = mol
else:
smiles = mol.toSMILES()
efficiencies[smiles] = eff
keys = efficiencies.keys()
keys.sort()
return [(key, efficiencies[key]) for key in keys]
f.write('entry(\n')
f.write(' index = {0:d},\n'.format(entry.index))
if entry.label != '':
f.write(' label = "{0}",\n'.format(entry.label))
if isinstance(entry.item, Reaction):
if entry.label != str(entry.item):
raise KineticsError("Reactions are now defined solely by their labels, "
"but reaction {0!s} has label {1!r}".format(
entry.item, entry.label))
# for i, reactant in enumerate(entry.item.reactants):
# if isinstance(reactant, Molecule):
# f.write(' reactant{0:d} = \n'.format(i+1))
# f.write('"""\n')
# f.write(reactant.toAdjacencyList(removeH=False))
# f.write('""",\n')
# elif isinstance(reactant, Species):
# f.write(' reactant{0:d} = \n'.format(i+1))
# f.write('"""\n')
# f.write(reactant.molecule[0].toAdjacencyList(label=reactant.label, removeH=False))
# f.write('""",\n')
# for i, product in enumerate(entry.item.products):
# if isinstance(product, Molecule):
# f.write(' product{0:d} = \n'.format(i+1))
# f.write('"""\n')
# f.write(product.toAdjacencyList(removeH=False))
# f.write('""",\n')
# elif isinstance(reactant, Species):
# f.write(' product{0:d} = \n'.format(i+1))
# f.write('"""\n')
# f.write(product.molecule[0].toAdjacencyList(label=product.label, removeH=False))
# f.write('""",\n')
if isinstance(entry.item.reactants[0], Species):
# Add degeneracy if the reaction is coming from a depository or kinetics library
f.write(' degeneracy = {0:d},\n'.format(entry.item.degeneracy))
if entry.item.duplicate:
f.write(' duplicate = {0!r},\n'.format(entry.item.duplicate))
if not entry.item.reversible:
f.write(' reversible = {0!r},\n'.format(entry.item.reversible))
elif isinstance(entry.item, Group):
f.write(' group = \n')
f.write('"""\n')
f.write(entry.item.toAdjacencyList())
f.write('""",\n')
elif isinstance(entry.item, LogicNode):
f.write(' group = "{0}",\n'.format(entry.item))
else:
raise DatabaseError("Encountered unexpected item of type {0} while saving database.".format(entry.item.__class__))
# Write kinetics
if isinstance(entry.data, str):
f.write(' kinetics = "{0}",\n'.format(entry.data))
elif entry.data is not None:
efficiencies = None
if hasattr(entry.data, 'efficiencies'):
efficiencies = entry.data.efficiencies
entry.data.efficiencies = dict(sortEfficiencies(entry.data.efficiencies))
kinetics = prettify(repr(entry.data))
kinetics = ' kinetics = {0},\n'.format(kinetics.replace('\n', '\n '))
f.write(kinetics)
if hasattr(entry.data, 'efficiencies'):
entry.data.efficiencies = efficiencies
else:
f.write(' kinetics = None,\n')
# Write reference
if entry.reference is not None:
reference = entry.reference.toPrettyRepr()
lines = reference.splitlines()
f.write(' reference = {0}\n'.format(lines[0]))
for line in lines[1:-1]:
f.write(' {0}\n'.format(line))
f.write(' ),\n'.format(lines[0]))
if entry.referenceType != "":
f.write(' referenceType = "{0}",\n'.format(entry.referenceType))
if entry.rank is not None:
f.write(' rank = {0},\n'.format(entry.rank))
if entry.shortDesc.strip() !='':
f.write(' shortDesc = u"""')
try:
f.write(entry.shortDesc.encode('utf-8'))
except:
f.write(entry.shortDesc.strip().encode('ascii', 'ignore')+ "\n")
f.write('""",\n')
if entry.longDesc.strip() !='':
f.write(' longDesc = \n')
f.write('u"""\n')
try:
f.write(entry.longDesc.strip().encode('utf-8') + "\n")
except:
f.write(entry.longDesc.strip().encode('ascii', 'ignore')+ "\n")
f.write('""",\n')
f.write(')\n\n')
def save(self, outputFile):
logging.info('Saving pressure dependence results for {0} network...'.format(self.network.label))
f = open(outputFile, 'a')
Nreac = self.network.Nisom + self.network.Nreac
Nprod = Nreac + self.network.Nprod
Tlist = self.Tlist.value_si
Plist = self.Plist.value_si
Tcount = Tlist.shape[0]
Pcount = Plist.shape[0]
count = 0
for prod in range(Nprod):
for reac in range(Nreac):
if reac == prod: continue
reaction = self.network.netReactions[count]
count += 1
kdata = self.K[:,:,prod,reac].copy()
order = len(reaction.reactants)
kdata *= 1e6 ** (order-1)
kunits = {1: 's^-1', 2: 'cm^3/(mol*s)', 3: 'cm^6/(mol^2*s)'}[order]
f.write('# =========== ')
f.write('=========== ' * Pcount)
f.write('\n')
f.write('# T \ P ')
f.write(' '.join(['{0:11.3e}'.format(P*1e-5) for P in Plist]))
f.write('\n')
f.write('# =========== ')
f.write('=========== ' * Pcount)
f.write('\n')
for t in range(Tcount):
f.write('# {0:11g}'.format(Tlist[t]))
for p in range(Pcount):
f.write(' {0:11.3e}'.format(kdata[t,p]))
f.write('\n')
f.write('# =========== ')
f.write('=========== ' * Pcount)
f.write('\n')
string = 'pdepreaction(reactants={0!r}, products={1!r}, kinetics={2!r})'.format(
[reactant.label for reactant in reaction.reactants],
[product.label for product in reaction.products],
reaction.kinetics,
)
f.write('{0}\n\n'.format(prettify(string)))
f.close()
f = open(os.path.join(os.path.dirname(outputFile), 'chem.inp'), 'a')
count = 0
for prod in range(Nprod):
for reac in range(Nreac):
if reac == prod: continue
reaction = self.network.netReactions[count]
count += 1
string = writeKineticsEntry(reaction, speciesList=None, verbose=False)
f.write('{0}\n'.format(string))
f.close()
