def runThermoEstimator(inputFile):
"""
Estimate thermo for a list of species using RMG and the settings chosen inside a thermo input file.
"""
rmg = RMG()
rmg.loadThermoInput(inputFile)
# initialize and load the database as well as any QM settings
rmg.loadDatabase()
if rmg.quantumMechanics:
rmg.quantumMechanics.initialize()
# Generate the thermo for all the species and write them to chemkin format as well as
# ThermoLibrary format with values for H, S, and Cp's.
output = open(os.path.join(rmg.outputDirectory, 'output.txt'),'wb')
library = ThermoLibrary(name='Thermo Estimation Library')
for species in rmg.initialSpecies:
species.generateThermoData(rmg.database, quantumMechanics=rmg.reactionModel.quantumMechanics)
library.loadEntry(
index = len(library.entries) + 1,
label = species.label,
molecule = species.molecule[0].toAdjacencyList(),
thermo = species.thermo.toThermoData(),
shortDesc = species.thermo.comment,
)
output.write(writeThermoEntry(species))
output.write('\n')
output.close()
library.save(os.path.join(rmg.outputDirectory,'ThermoLibrary.py'))
def runThermoEstimator(inputFile):
"""
Estimate thermo for a list of species using RMG and the settings chosen inside a thermo input file.
"""
rmg = RMG()
rmg.loadThermoInput(inputFile)
# initialize and load the database as well as any QM settings
rmg.loadDatabase()
if rmg.quantumMechanics:
rmg.quantumMechanics.initialize()
# Generate the thermo for all the species and write them to chemkin format as well as
# ThermoLibrary format with values for H, S, and Cp's.
output = open(os.path.join(rmg.outputDirectory, 'output.txt'), 'wb')
library = ThermoLibrary(name='Thermo Estimation Library')
for species in rmg.initialSpecies:
species.generateThermoData(
rmg.database, quantumMechanics=rmg.reactionModel.quantumMechanics)
library.loadEntry(
index=len(library.entries) + 1,
label=species.label,
molecule=species.molecule[0].toAdjacencyList(),
thermo=species.thermo.toThermoData(),
shortDesc=species.thermo.comment,
)
output.write(writeThermoEntry(species))
output.write('\n')
output.close()
library.save(os.path.join(rmg.outputDirectory, 'ThermoLibrary.py'))
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]:
try:
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))
except ValueError:
logging.debug("Valid thermo for {0} is outside range for temperature {1}".format(species,T))
f.write('# =========== =========== =========== =========== ===========\n')
thermo_string = 'thermo(label={0!r}, thermo={1!r})'.format(species.label, species.getThermoData())
f.write('{0}\n\n'.format(prettify(thermo_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}
chemkin_thermo_string = writeThermoEntry(species, elementCounts=elementCounts, verbose=True)
f.write('{0}\n'.format(chemkin_thermo_string))
f.close()
# write species dictionary
if isinstance(species, Species):
if species.molecule and isinstance(species.molecule[0], Molecule):
with open(os.path.join(os.path.dirname(outputFile), 'species_dictionary.txt'), 'a') as f:
f.write(species.molecule[0].toAdjacencyList(removeH=False, label=species.label))
f.write('\n')
return chemkin_thermo_string
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 runThermoEstimator(inputFile):
"""
Estimate thermo for a list of species using RMG and the settings chosen inside a thermo input file.
"""
rmg = RMG()
rmg.loadThermoInput(inputFile)
rmg.database = RMGDatabase()
path = os.path.join(settings['database.directory'])
# forbidden structure loading
rmg.database.loadThermo(os.path.join(path, 'thermo'), rmg.thermoLibraries, depository=False)
if rmg.solvent:
rmg.database.loadSolvation(os.path.join(path, 'solvation'))
Species.solventData = rmg.database.solvation.getSolventData(rmg.solvent)
Species.solventName = rmg.solvent
# Generate the thermo for all the species and write them to chemkin format as well as
# ThermoLibrary format with values for H, S, and Cp's.
output = open(os.path.join(rmg.outputDirectory, 'output.txt'),'wb')
library = ThermoLibrary(name='Thermo Estimation Library')
for species in rmg.initialSpecies:
species.getThermoData(rmg.database)
library.loadEntry(
index = len(library.entries) + 1,
label = species.label,
molecule = species.molecule[0].toAdjacencyList(),
thermo = species.thermo.toThermoData(),
shortDesc = species.thermo.comment,
)
output.write(writeThermoEntry(species))
output.write('\n')
output.close()
library.save(os.path.join(rmg.outputDirectory,'ThermoLibrary.py'))
def write_chemkin(self, output_directory):
"""
Appends the thermo block to `chem.inp` and species name to
`species_dictionary.txt` within the `outut_directory` specified
"""
species = self.species
with open(os.path.join(output_directory, 'chem.inp'), 'a') as f:
if isinstance(species, Species):
if species.molecule and isinstance(species.molecule[0], Molecule):
element_counts = retrieveElementCount(species.molecule[0])
else:
try:
element_counts = species.props['element_counts']
except KeyError:
element_counts = self.element_count_from_conformer()
else:
element_counts = {'C': 0, 'H': 0}
chemkin_thermo_string = writeThermoEntry(species, elementCounts=element_counts, verbose=True)
f.write('{0}\n'.format(chemkin_thermo_string))
# write species dictionary
if isinstance(species, Species):
if species.molecule and isinstance(species.molecule[0], Molecule):
spec_dict_path = os.path.join(output_directory, 'species_dictionary.txt')
is_species_in_dict = False
if os.path.isfile(spec_dict_path):
with open(spec_dict_path, 'r') as f:
# check whether the species dictionary contains this species, in which case do not re-append
for line in f.readlines():
if species.label == line.strip():
is_species_in_dict = True
break
if not is_species_in_dict:
with open(spec_dict_path, 'a') as f:
f.write(species.molecule[0].toAdjacencyList(removeH=False, label=species.label))
f.write('\n')
return chemkin_thermo_string
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()