def save_thermo_lib(species_list, path, name, lib_long_desc):
"""
Save an RMG thermo library of all species in `species_list` in the supplied `path`
`name` is the library's name (or project's name)
`long_desc` is a multiline string with level of theory description
"""
if species_list:
lib_path = os.path.join(path, 'thermo', '{0}.py'.format(name))
thermo_library = ThermoLibrary(name=name, longDesc=lib_long_desc)
for i, spc in enumerate(species_list):
if spc.thermo is not None:
spc.long_thermo_description += '\nExternal symmetry: {0}, optical isomers: {1}\n'.format(
spc.external_symmetry, spc.optical_isomers)
spc.long_thermo_description += '\nGeometry:\n{0}'.format(
spc.final_xyz)
thermo_library.loadEntry(
index=i + 1,
label=spc.label,
molecule=spc.mol_list[0].toAdjacencyList(),
thermo=spc.thermo,
shortDesc=spc.thermo.comment,
longDesc=spc.long_thermo_description)
else:
logging.warning(
'Species {0} did not contain any thermo data and was omitted from the thermo'
' library.'.format(str(spc)))
thermo_library.save(lib_path)
def save_thermo_lib(species_list, path, name, lib_long_desc):
"""
Save an RMG thermo library.
Args:
species_list (list): Entries are Species object instances for which thermo will be saved.
path (str): The base folder in which the thermo library will be saved.
name (str): The library name.
lib_long_desc (str): A multiline string with relevant description.
"""
if species_list:
lib_path = os.path.join(path, f'{name}.py')
thermo_library = ThermoLibrary(name=name, long_desc=lib_long_desc)
for i, spc in enumerate(species_list):
if spc.thermo is not None:
long_thermo_description = f'\nSpin multiplicity: {spc.conformer.spin_multiplicity}' \
f'\nExternal symmetry: {spc.molecule[0].symmetry_number}' \
f'\nOptical isomers: {spc.conformer.optical_isomers}\n'
xyz = get_str_xyz(spc)
if xyz is not None:
long_thermo_description += f'\nGeometry:\n{xyz}'
thermo_library.load_entry(
index=i,
label=spc.label,
molecule=spc.molecule[0].to_adjacency_list(),
thermo=spc.thermo,
shortDesc=spc.thermo.comment,
longDesc=long_thermo_description)
else:
logging.warning(
f'Species {spc.label} did not contain any thermo data and was omitted from the thermo '
f'library {name}.')
thermo_library.save(lib_path)
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 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
# 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'))
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():
entry.history.append(event)
# Save in Py format
if not os.path.exists(outputDir):
os.makedirs(os.path.join(self.path))
thermoLibrary.save(os.path.join(outputDir, 'chemkinThermoLibrary.py'), removeH=removeH)
kineticsLibrary.save(os.path.join(outputDir, 'chemkinKineticsLibrary.py'), removeH=removeH)
import argparse
import os
from rmgpy.data.thermo import ThermoLibrary
if __name__ == '__main__':
parser = argparse.ArgumentParser()
parser.add_argument('inputPath', metavar='INPUT', type=str, nargs=1,
help='the input path of the RMG-Java thermo library directory')
parser.add_argument('libraryName', metavar='OUTPUT', type=str, nargs=1,
help='the libraryName for the RMG-Py format thermo library')
args = parser.parse_args()
inputPath = args.inputPath[0]
libraryName = args.libraryName[0]
library = ThermoLibrary()
library.loadOld(
dictstr = os.path.join(inputPath, 'Dictionary.txt'),
treestr = '',
libstr = os.path.join(inputPath, 'Library.txt'),
numParameters = 12,
numLabels = 1,
pattern = False,
)
library.name = libraryName
# Save in Py format
library.save(os.path.join('input/thermo/libraries/', libraryName+'.py'))
data=reaction.kinetics,
)
try:
entry.long_desc = 'Originally from reaction library: ' + reaction.library + "\n" + reaction.kinetics.comment
except AttributeError:
entry.long_desc = reaction.kinetics.comment
kinetics_library.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 mark_duplicates = True
kinetics_library.check_for_duplicates(mark_duplicates=True)
kinetics_library.convert_duplicates_to_multi()
# Save in Py format
database_directory = settings['database.directory']
try:
os.makedirs(
os.path.join(database_directory, 'kinetics', 'libraries', name))
except:
pass
thermo_library.save(
os.path.join(database_directory, 'thermo', 'libraries', name + '.py'))
kinetics_library.save(
os.path.join(database_directory, 'kinetics', 'libraries', name,
'reactions.py'))
kinetics_library.save_dictionary(
os.path.join(database_directory, 'kinetics', 'libraries', name,
'dictionary.txt'))
)
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,
label = str(reaction),
item = reaction,
data = reaction.kinetics,
)
entry.longDesc = reaction.kinetics.comment
kineticsLibrary.entries[i+1] = entry
kineticsLibrary.checkForDuplicates()
kineticsLibrary.convertDuplicatesToMulti()
# Save in Py format
try:
os.makedirs(os.join('input/kinetics/libraries/',name))
except:
pass
thermoLibrary.save(os.path.join('input/thermo/libraries', name + '.py'))
kineticsLibrary.save(os.path.join('input/kinetics/libraries/', name, 'reactions.py'))
kineticsLibrary.saveDictionary(os.path.join('input/kinetics/libraries/', name, 'dictionary.txt'))
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
databaseDirectory = settings['database.directory']
try:
os.makedirs(os.path.join(databaseDirectory, 'kinetics', 'libraries',name))
except:
pass
thermoLibrary.save(os.path.join(databaseDirectory, 'thermo' ,'libraries', name + '.py'))
kineticsLibrary.save(os.path.join(databaseDirectory, 'kinetics', 'libraries', name, 'reactions.py'))
kineticsLibrary.saveDictionary(os.path.join(databaseDirectory, 'kinetics', 'libraries', name, 'dictionary.txt'))
import argparse
import os
from rmgpy.data.thermo import ThermoLibrary
from rmgpy import settings
if __name__ == '__main__':
parser = argparse.ArgumentParser()
parser.add_argument('inputPath', metavar='INPUT', type=str, nargs=1,
help='the input path of the RMG-Java thermo library directory')
parser.add_argument('libraryName', metavar='OUTPUT', type=str, nargs=1,
help='the libraryName for the RMG-Py format thermo library')
args = parser.parse_args()
inputPath = args.inputPath[0]
libraryName = args.libraryName[0]
library = ThermoLibrary()
library.loadOld(
dictstr = os.path.join(inputPath, 'Dictionary.txt'),
treestr = '',
libstr = os.path.join(inputPath, 'Library.txt'),
numParameters = 12,
numLabels = 1,
pattern = False,
)
library.name = libraryName
# Save in Py format
library.save(os.path.join(settings['database.directory'], 'thermo', 'libraries', libraryName+'.py'))
metavar='INPUT',
type=str,
nargs=1,
help='the input path of the RMG-Java thermo library directory')
parser.add_argument(
'libraryName',
metavar='OUTPUT',
type=str,
nargs=1,
help='the libraryName for the RMG-Py format thermo library')
args = parser.parse_args()
inputPath = args.inputPath[0]
libraryName = args.libraryName[0]
library = ThermoLibrary()
library.loadOld(
dictstr=os.path.join(inputPath, 'Dictionary.txt'),
treestr='',
libstr=os.path.join(inputPath, 'Library.txt'),
numParameters=12,
numLabels=1,
pattern=False,
)
library.name = libraryName
# Save in Py format
library.save(
os.path.join(settings['database.directory'], 'thermo', 'libraries',
libraryName + '.py'))
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():
entry.history.append(event)
# Save in Py format
if not os.path.exists(outputDir):
os.makedirs(os.path.join(self.path))
thermoLibrary.save(os.path.join(outputDir, 'chemkinThermoLibrary.py'),
removeH=removeH)
kineticsLibrary.save(os.path.join(outputDir, 'chemkinKineticsLibrary.py'),
removeH=removeH)
