def getThermoData(self, solventName = ''):
"""
Returns a `thermoData` object of the current Species object.
If the thermo object already exists, it is either of the (Wilhoit, ThermoData)
type, or it is a Future.
If the type of the thermo attribute is Wilhoit, or ThermoData,
then it is converted into a NASA format.
If it is a Future, then a blocking call is made to retrieve the NASA object.
If the thermo object did not exist yet, the thermo object is generated.
"""
from rmgpy.thermo.thermoengine import submit
if self.thermo:
if not isinstance(self.thermo, (NASA, Wilhoit, ThermoData)):
self.thermo = self.thermo.result()
else:
submit(self, solventName)
if not isinstance(self.thermo, (NASA, Wilhoit, ThermoData)):
self.thermo = self.thermo.result()
return self.thermo
def get_thermo_data(self, solvent_name=''):
"""
Returns a `thermoData` object of the current Species object.
If the thermo object already exists, it is either of the (Wilhoit, ThermoData)
type, or it is a Future.
If the type of the thermo attribute is Wilhoit, or ThermoData,
then it is converted into a NASA format.
If it is a Future, then a blocking call is made to retrieve the NASA object.
If the thermo object did not exist yet, the thermo object is generated.
"""
from rmgpy.thermo.thermoengine import submit
if self.thermo:
if not isinstance(self.thermo, (NASA, Wilhoit, ThermoData)):
self.thermo = self.thermo.result()
else:
submit(self, solvent_name)
if not isinstance(self.thermo, (NASA, Wilhoit, ThermoData)):
self.thermo = self.thermo.result()
return self.thermo
def funcSubmitGet():
"""
Test if we can retrieve thermo of species after submitting some of them.
"""
load()
spcs = [
Species().fromSMILES('C'),\
Species().fromSMILES('CC'), \
Species().fromSMILES('CCC')
]
for spc in spcs:
submit(spc)
absent = Species().fromSMILES('[CH3]')
data = absent.getThermoData()
if not data: return False
present = Species().fromSMILES('CC')
data = present.getThermoData()
if not data: return False
random.shuffle(spcs)
for spc in spcs:
data = spc.getThermoData()
if not data: return False
return True
def funcSubmitGet():
"""
Test if we can retrieve thermo of species after submitting some of them.
"""
load()
spcs = [
Species().fromSMILES('C'),\
Species().fromSMILES('CC'), \
Species().fromSMILES('CCC')
]
for spc in spcs:
submit(spc)
absent = Species().fromSMILES('[CH3]')
data = absent.getThermoData()
if not data: return False
present = Species().fromSMILES('CC')
data = present.getThermoData()
if not data: return False
random.shuffle(spcs)
for spc in spcs:
data = spc.getThermoData()
if not data: return False
return True
def funcSubmit():
"""
Test that we can submit a number of species.
"""
load()
spcs = [
Species().fromSMILES('C'),\
Species().fromSMILES('CC'), \
Species().fromSMILES('CCC')
]
for spc in spcs:
submit(spc)
return True
def funcSubmit():
"""
Test that we can submit a number of species.
"""
load()
spcs = [
Species().fromSMILES('C'),\
Species().fromSMILES('CC'), \
Species().fromSMILES('CCC')
]
for spc in spcs:
submit(spc)
return True
def run_thermo_estimator(input_file, library_flag):
"""
Estimate thermo for a list of species using RMG and the settings chosen inside a thermo input file.
"""
rmg = RMG()
rmg.load_thermo_input(input_file)
rmg.database = RMGDatabase()
path = os.path.join(settings['database.directory'])
# forbidden structure loading
rmg.database.load_thermo(os.path.join(path, 'thermo'),
rmg.thermo_libraries,
depository=False)
if rmg.solvent:
rmg.database.load_solvation(os.path.join(path, 'solvation'))
Species.solvent_data = rmg.database.solvation.get_solvent_data(
rmg.solvent)
Species.solvent_name = rmg.solvent
for species in rmg.initial_species:
submit(species)
if library_flag:
library = ThermoLibrary(name='Thermo Estimation Library')
for species in rmg.initial_species:
library.load_entry(
index=len(library.entries) + 1,
label=species.label,
molecule=species.molecule[0].to_adjacency_list(),
thermo=species.get_thermo_data().to_thermo_data(),
shortDesc=species.get_thermo_data().comment,
)
library.save(os.path.join(rmg.output_directory, 'ThermoLibrary.py'))
# Save the thermo data to chemkin format output files and dictionary, with no reactions
save_chemkin_file(os.path.join(rmg.output_directory, 'chem_annotated.inp'),
species=rmg.initial_species,
reactions=[])
save_species_dictionary(os.path.join(rmg.output_directory,
'species_dictionary.txt'),
species=rmg.initial_species)
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
for species in rmg.initialSpecies:
submit(species)
# library = ThermoLibrary(name='Thermo Estimation Library')
# for spc in rmg.initialSpecies:
# library.loadEntry(
# index = len(library.entries) + 1,
# label = species.label,
# molecule = species.molecule[0].toAdjacencyList(),
# thermo = species.getThermoData().toThermoData(),
# shortDesc = species.getThermoData().comment,
# )
# library.save(os.path.join(rmg.outputDirectory,'ThermoLibrary.py'))
# Save the thermo data to chemkin format output files and dictionary, with no reactions
saveChemkinFile(os.path.join(rmg.outputDirectory, 'chem_annotated.inp'),
species=rmg.initialSpecies,
reactions=[])
saveSpeciesDictionary(os.path.join(rmg.outputDirectory,
'species_dictionary.txt'),
species=rmg.initialSpecies)
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
for species in rmg.initialSpecies:
submit(species)
# library = ThermoLibrary(name='Thermo Estimation Library')
# for spc in rmg.initialSpecies:
# library.loadEntry(
# index = len(library.entries) + 1,
# label = species.label,
# molecule = species.molecule[0].toAdjacencyList(),
# thermo = species.getThermoData().toThermoData(),
# shortDesc = species.getThermoData().comment,
# )
# library.save(os.path.join(rmg.outputDirectory,'ThermoLibrary.py'))
# Save the thermo data to chemkin format output files and dictionary, with no reactions
saveChemkinFile(os.path.join(rmg.outputDirectory, 'chem_annotated.inp'), species=rmg.initialSpecies, reactions=[])
saveSpeciesDictionary(os.path.join(rmg.outputDirectory, 'species_dictionary.txt'), species=rmg.initialSpecies)