def isCorrectlyParsed(mol, identifier):
"""Check if molecule object has been correctly parsed."""
conditions = []
if mol.atoms:
conditions.append(True)
else:
conditions.append(False)
if 'InChI' in identifier:
inchi_elementcount = util.retrieveElementCount(identifier)
mol_elementcount = util.retrieveElementCount(mol)
conditions.append(inchi_elementcount == mol_elementcount)
return all(conditions)
def isCorrectlyParsed(mol, identifier):
"""Check if molecule object has been correctly parsed."""
conditions = []
if mol.atoms:
conditions.append(True)
else:
conditions.append(False)
if 'InChI' in identifier:
inchi_elementcount = util.retrieveElementCount(identifier)
mol_elementcount = util.retrieveElementCount(mol)
conditions.append(inchi_elementcount == mol_elementcount)
return all(conditions)
def _check_output(mol, identifier):
"""Check if molecule object has been correctly parsed."""
conditions = []
# Check that the molecule has atoms
conditions.append(bool(mol.atoms))
# Check that the identifier is not blank
conditions.append(bool(identifier.strip()))
# Check that the InChI element count matches the molecule
if 'InChI=1' in identifier:
inchi_elementcount = util.retrieveElementCount(identifier)
mol_elementcount = util.retrieveElementCount(mol)
conditions.append(inchi_elementcount == mol_elementcount)
return all(conditions)
def _check_output(mol, identifier):
"""Check if molecule object has been correctly parsed."""
conditions = []
# Check that the molecule has atoms
conditions.append(bool(mol.atoms))
# Check that the identifier is not blank
conditions.append(bool(identifier.strip()))
# Check that the InChI element count matches the molecule
if 'InChI=1' in identifier:
inchi_elementcount = util.retrieveElementCount(identifier)
mol_elementcount = util.retrieveElementCount(mol)
conditions.append(inchi_elementcount == mol_elementcount)
return all(conditions)
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 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
