def execute(self):
"""
Execute, in order, the jobs found in input file specified by the
`input_file` attribute.
"""
# Initialize the logging system (both to the console and to a file in the
# output directory)
initialize_log(self.verbose,
os.path.join(self.output_directory, 'arkane.log'))
# Print some information to the beginning of the log
log_header()
# Load the input file for the job
self.job_list = self.load_input_file(self.input_file)
logging.info('')
# Initialize (and clear!) the output files for the job
if self.output_directory is None:
self.output_directory = os.path.dirname(
os.path.abspath(self.input_file))
output_file = os.path.join(self.output_directory, 'output.py')
with open(output_file, 'w'):
pass
chemkin_file = os.path.join(self.output_directory, 'chem.inp')
# write the chemkin files and run the thermo and then kinetics jobs
with open(chemkin_file, 'w') as f:
write_elements_section(f)
f.write('SPECIES\n\n')
# write each species in species block
for job in self.job_list:
if isinstance(job, ThermoJob):
f.write(job.species.to_chemkin())
f.write('\n')
f.write('\nEND\n\n\n\n')
f.write('THERM ALL\n')
f.write(' 300.000 1000.000 5000.000\n\n')
# run thermo and statmech jobs (also writes thermo blocks to Chemkin file)
supporting_info = []
hindered_rotor_info = []
bacjob_num = 1
for job in self.job_list:
if isinstance(job, ThermoJob):
job.execute(output_directory=self.output_directory,
plot=self.plot)
if isinstance(job, StatMechJob):
job.execute(output_directory=self.output_directory,
plot=self.plot,
pdep=is_pdep(self.job_list))
if hasattr(job, 'supporting_info'):
supporting_info.append(job.supporting_info)
if hasattr(job, 'raw_hindered_rotor_data'):
for hr_info in job.raw_hindered_rotor_data:
hindered_rotor_info.append(hr_info)
if isinstance(job, BACJob):
job.execute(output_directory=self.output_directory,
plot=self.plot,
jobnum=bacjob_num)
bacjob_num += 1
with open(chemkin_file, 'a') as f:
f.write('\n')
f.write('END\n\n\n\n')
f.write('REACTIONS KCAL/MOLE MOLES\n\n')
if supporting_info:
# write supporting_info.csv for statmech jobs
supporting_info_file = os.path.join(self.output_directory,
'supporting_information.csv')
with open(supporting_info_file, 'w') as csvfile:
writer = csv.writer(csvfile,
delimiter=',',
quotechar='"',
quoting=csv.QUOTE_MINIMAL)
writer.writerow([
'Label', 'Symmetry Number', 'Number of optical isomers',
'Symmetry Group', 'Rotational constant (cm-1)',
'Calculated Frequencies (unscaled and prior to projection, cm^-1)',
'Electronic energy (J/mol)',
'E0 (electronic energy + ZPE, J/mol)',
'E0 with atom and bond corrections (J/mol)',
'Atom XYZ coordinates (angstrom)', 'T1 diagnostic',
'D1 diagnostic'
])
for row in supporting_info:
label = row[0]
rot = '-'
freq = '-'
if row[4] is not None and isinstance(
row[4].rotationalConstant.value, float):
# diatomic species have a single rotational constant
rot = '{0:.2f}'.format(row[4].rotationalConstant.value)
elif row[4] is not None:
rot = ', '.join([
'{0:.2f}'.format(s)
for s in row[4].rotationalConstant.value
])
if row[5] is not None:
freq = ''
if row[6] is not None: # there is a negative frequency
freq = '{0:.1f}'.format(abs(row[6])) + 'i, '
freq += ', '.join(
['{0:.1f}'.format(s) for s in row[5]])
atoms = ', '.join([
"{0} {1}".format(
atom, " ".join([str(c) for c in coords]))
for atom, coords in zip(row[10], row[11])
])
writer.writerow([
label, row[1], row[2], row[3], rot, freq, row[7],
row[8], row[9], atoms, row[12], row[13]
])
if hindered_rotor_info:
hr_file = os.path.join(self.output_directory,
'hindered_rotor_scan_data.csv')
# find longest length to set column number for energies
max_energy_length = max([len(hr[4]) for hr in hindered_rotor_info])
with open(hr_file, 'w') as csvfile:
writer = csv.writer(csvfile,
delimiter=',',
quotechar='"',
quoting=csv.QUOTE_MINIMAL)
writer.writerow([
'species', 'rotor_number', 'symmetry',
'resolution (degrees)', 'pivot_atoms', 'frozen_atoms'
] + [
'energy (J/mol) {}'.format(i)
for i in range(max_energy_length)
])
for row in hindered_rotor_info:
writer.writerow([
row[0], row[1], row[2], row[3][1] * 180 /
np.pi, row[5], row[6]
] + [a for a in row[4]])
# run kinetics and pdep jobs (also writes reaction blocks to Chemkin file)
for job in self.job_list:
if isinstance(job, KineticsJob):
job.execute(output_directory=self.output_directory,
plot=self.plot)
elif isinstance(job, PressureDependenceJob) and not any(
[isinstance(job, ExplorerJob) for job in self.job_list]):
# if there is an explorer job the pdep job will be run in the explorer job
if job.network is None:
raise InputError(
'No network matched the label of the pressureDependence block and there is no explorer block '
'to generate a network')
job.execute(output_file=output_file, plot=self.plot)
elif isinstance(job, ExplorerJob):
thermo_library, kinetics_library, species_list = self.get_libraries(
)
job.execute(output_file=output_file,
plot=self.plot,
species_list=species_list,
thermo_library=thermo_library,
kinetics_library=kinetics_library)
with open(chemkin_file, 'a') as f:
f.write('END\n\n')
# Print some information to the end of the log
log_footer()
if self.save_rmg_libraries:
# save RMG thermo and kinetics libraries
species, reactions = list(), list()
for job in self.job_list:
if isinstance(job, ThermoJob) and len(job.species.molecule):
species.append(job.species)
elif isinstance(job, KineticsJob) \
and all([len(species.molecule) for species in job.reaction.reactants + job.reaction.products]):
reactions.append(job.reaction)
elif isinstance(job, PressureDependenceJob):
for reaction in job.network.path_reactions:
if all([
len(species.molecule)
for species in reaction.reactants +
reaction.products
]):
reactions.append(reaction)
lib_path = os.path.join(self.output_directory, 'RMG_libraries')
model_chemistry = f' at the {self.model_chemistry} level of theory' if self.model_chemistry else ''
lib_long_desc = f'Calculated using Arkane v{__version__}{model_chemistry}.'
save_thermo_lib(species_list=species,
path=lib_path,
name='thermo',
lib_long_desc=lib_long_desc)
save_kinetics_lib(rxn_list=reactions,
path=lib_path,
name='kinetics',
lib_long_desc=lib_long_desc)
def species(label, *args, **kwargs):
"""Load a species from an input file"""
global species_dict, job_list
if label in species_dict:
raise ValueError(
'Multiple occurrences of species with label {0!r}.'.format(label))
logging.info('Loading species {0}...'.format(label))
spec = Species(label=label)
species_dict[label] = spec
path = None
if len(args) == 1:
# The argument is a path to a conformer input file
path = args[0]
job = StatMechJob(species=spec, path=path)
logging.debug('Added species {0} to a stat mech job.'.format(label))
job_list.append(job)
elif len(args) > 1:
raise InputError('species {0} can only have two non-keyword argument '
'which should be the species label and the '
'path to a quantum file.'.format(spec.label))
if len(kwargs) > 0:
# The species parameters are given explicitly
structure = None
E0 = None
modes = []
spin_multiplicity = 0
optical_isomers = 1
molecular_weight = None
collision_model = None
energy_transfer_model = None
thermo = None
reactive = True
for key, value in kwargs.items():
if key == 'structure':
structure = value
elif key == 'E0':
E0 = value
elif key == 'modes':
modes = value
elif key == 'spinMultiplicity':
spin_multiplicity = value
elif key == 'opticalIsomers':
optical_isomers = value
elif key == 'molecularWeight':
molecular_weight = value
elif key == 'collisionModel':
collision_model = value
elif key == 'energyTransferModel':
energy_transfer_model = value
elif key == 'thermo':
thermo = value
elif key == 'reactive':
reactive = value
else:
raise TypeError(
'species() got an unexpected keyword argument {0!r}.'.
format(key))
if structure:
spec.molecule = [structure]
spec.conformer = Conformer(E0=E0,
modes=modes,
spin_multiplicity=spin_multiplicity,
optical_isomers=optical_isomers)
if molecular_weight is not None:
spec.molecular_weight = molecular_weight
elif spec.molecular_weight is None and is_pdep(job_list):
# If a structure was given, simply calling spec.molecular_weight will calculate the molecular weight
# If one of the jobs is pdep and no molecular weight is given or calculated, raise an error
raise ValueError(
"No molecularWeight was entered for species {0}. Since a structure wasn't given"
" as well, the molecularWeight, which is important for pressure dependent jobs,"
" cannot be reconstructed.".format(spec.label))
spec.transport_data = collision_model
spec.energy_transfer_model = energy_transfer_model
spec.thermo = thermo
spec.reactive = reactive
if spec.reactive and path is None and spec.thermo is None and spec.conformer.E0 is None:
if not spec.molecule:
raise InputError(
'Neither thermo, E0, species file path, nor structure specified, cannot estimate'
' thermo properties of species {0}'.format(spec.label))
try:
db = get_db('thermo')
if db is None:
raise DatabaseError('Thermo database is None.')
except DatabaseError:
logging.warning(
"The database isn't loaded, cannot estimate thermo for {0}. "
"If it is a bath gas, set reactive = False to avoid generating "
"thermo.".format(spec.label))
else:
logging.info(
'No E0 or thermo found, estimating thermo and E0 of species {0} using'
' RMG-Database...'.format(spec.label))
spec.thermo = db.get_thermo_data(spec)
if spec.thermo.E0 is None:
th = spec.thermo.to_wilhoit()
spec.conformer.E0 = th.E0
spec.thermo.E0 = th.E0
else:
spec.conformer.E0 = spec.thermo.E0
if spec.reactive and spec.thermo and not spec.has_statmech(
) and structure is not None:
# generate stat mech info if it wasn't provided before
spec.generate_statmech()
if not energy_transfer_model:
# default to RMG's method of generating energy_transfer_model
spec.generate_energy_transfer_model()
return spec
def execute(self):
"""
Execute, in order, the jobs found in input file specified by the
`inputFile` attribute.
"""
# Initialize the logging system (both to the console and to a file in the
# output directory)
self.initializeLog(self.verbose,
os.path.join(self.outputDirectory, 'arkane.log'))
# Print some information to the beginning of the log
self.logHeader()
# Load the input file for the job
self.jobList = self.loadInputFile(self.inputFile)
logging.info('')
# Initialize (and clear!) the output files for the job
if self.outputDirectory is None:
self.outputDirectory = os.path.dirname(
os.path.abspath(self.inputFile))
outputFile = os.path.join(self.outputDirectory, 'output.py')
with open(outputFile, 'w') as f:
pass
chemkinFile = os.path.join(self.outputDirectory, 'chem.inp')
# write the chemkin files and run the thermo and then kinetics jobs
with open(chemkinFile, 'w') as f:
writeElementsSection(f)
f.write('SPECIES\n\n')
# write each species in species block
for job in self.jobList:
if isinstance(job, ThermoJob):
f.write(job.species.toChemkin())
f.write('\n')
f.write('\nEND\n\n\n\n')
f.write('THERM ALL\n')
f.write(' 300.000 1000.000 5000.000\n\n')
# run thermo and statmech jobs (also writes thermo blocks to Chemkin file)
supporting_info = []
for job in self.jobList:
if isinstance(job, ThermoJob):
job.execute(outputFile=outputFile, plot=self.plot)
if isinstance(job, StatMechJob):
job.execute(outputFile=outputFile,
plot=self.plot,
pdep=is_pdep(self.jobList))
supporting_info.append(job.supporting_info)
with open(chemkinFile, 'a') as f:
f.write('\n')
f.write('END\n\n\n\n')
f.write('REACTIONS KCAL/MOLE MOLES\n\n')
supporting_info_file = os.path.join(self.outputDirectory,
'supporting_information.csv')
with open(supporting_info_file, 'wb') as csvfile:
writer = csv.writer(csvfile,
delimiter=',',
quotechar='"',
quoting=csv.QUOTE_MINIMAL)
writer.writerow([
'Label', 'Rotational constant (cm-1)',
'Unscaled frequencies (cm-1)'
])
for row in supporting_info:
label = row[0]
rot = '-'
freq = '-'
if len(
row
) > 1: # monoatomic species have no frequencies nor rotational constants
if isinstance(row[1].rotationalConstant.value, float):
# diatomic species have a single rotational constant
rot = '{0:.2f}'.format(row[1].rotationalConstant.value)
else:
rot = ', '.join([
'{0:.2f}'.format(s)
for s in row[1].rotationalConstant.value
])
freq = ''
if len(row) == 4:
freq = '{0:.1f}'.format(abs(row[3])) + 'i, '
freq += ', '.join(['{0:.1f}'.format(s) for s in row[2]])
writer.writerow([label, rot, freq])
# run kinetics and pdep jobs (also writes reaction blocks to Chemkin file)
for job in self.jobList:
if isinstance(job, KineticsJob):
job.execute(outputFile=outputFile, plot=self.plot)
elif isinstance(job, PressureDependenceJob) and not any(
[isinstance(job, ExplorerJob) for job in self.jobList]):
# if there is an explorer job the pdep job will be run in the explorer job
if job.network is None:
raise InputError(
'No network matched the label of the pressureDependence block and there is no explorer block '
'to generate a network')
job.execute(outputFile=outputFile, plot=self.plot)
elif isinstance(job, ExplorerJob):
thermoLibrary, kineticsLibrary, speciesList = self.getLibraries(
)
job.execute(outputFile=outputFile,
plot=self.plot,
speciesList=speciesList,
thermoLibrary=thermoLibrary,
kineticsLibrary=kineticsLibrary)
with open(chemkinFile, 'a') as f:
f.write('END\n\n')
# Print some information to the end of the log
self.logFooter()
def execute(self):
"""
Execute, in order, the jobs found in input file specified by the
`inputFile` attribute.
"""
# Initialize the logging system (both to the console and to a file in the
# output directory)
self.initializeLog(self.verbose, os.path.join(self.outputDirectory, 'arkane.log'))
# Print some information to the beginning of the log
self.logHeader()
# Load the input file for the job
self.jobList = self.loadInputFile(self.inputFile)
logging.info('')
# Initialize (and clear!) the output files for the job
if self.outputDirectory is None:
self.outputDirectory = os.path.dirname(os.path.abspath(self.inputFile))
outputFile = os.path.join(self.outputDirectory, 'output.py')
with open(outputFile, 'w') as f:
pass
chemkinFile = os.path.join(self.outputDirectory, 'chem.inp')
# write the chemkin files and run the thermo and then kinetics jobs
with open(chemkinFile, 'w') as f:
writeElementsSection(f)
f.write('SPECIES\n\n')
# write each species in species block
for job in self.jobList:
if isinstance(job,ThermoJob):
f.write(job.species.toChemkin())
f.write('\n')
f.write('\nEND\n\n\n\n')
f.write('THERM ALL\n')
f.write(' 300.000 1000.000 5000.000\n\n')
# run thermo and statmech jobs (also writes thermo blocks to Chemkin file)
supporting_info = []
for job in self.jobList:
if isinstance(job, ThermoJob):
job.execute(outputFile=outputFile, plot=self.plot)
if isinstance(job, StatMechJob):
job.execute(outputFile=outputFile, plot=self.plot, pdep=is_pdep(self.jobList))
supporting_info.append(job.supporting_info)
with open(chemkinFile, 'a') as f:
f.write('\n')
f.write('END\n\n\n\n')
f.write('REACTIONS KCAL/MOLE MOLES\n\n')
supporting_info_file = os.path.join(self.outputDirectory, 'supporting_information.csv')
with open(supporting_info_file, 'wb') as csvfile:
writer = csv.writer(csvfile, delimiter=',', quotechar='"', quoting=csv.QUOTE_MINIMAL)
writer.writerow(['Label','Rotational constant (cm-1)','Unscaled frequencies (cm-1)'])
for row in supporting_info:
label = row[0]
rot = '-'
freq = '-'
if len(row) > 1: # monoatomic species have no frequencies nor rotational constants
if isinstance(row[1].rotationalConstant.value, float):
# diatomic species have a single rotational constant
rot = '{0:.2f}'.format(row[1].rotationalConstant.value)
else:
rot = ', '.join(['{0:.2f}'.format(s) for s in row[1].rotationalConstant.value])
freq = ''
if len(row) == 4:
freq = '{0:.1f}'.format(abs(row[3])) + 'i, '
freq += ', '.join(['{0:.1f}'.format(s) for s in row[2]])
writer.writerow([label, rot, freq])
# run kinetics and pdep jobs (also writes reaction blocks to Chemkin file)
for job in self.jobList:
if isinstance(job,KineticsJob):
job.execute(outputFile=outputFile, plot=self.plot)
elif isinstance(job, PressureDependenceJob) and not any([isinstance(job,ExplorerJob) for job in self.jobList]): #if there is an explorer job the pdep job will be run in the explorer job
if job.network is None:
raise InputError('No network matched the label of the pressureDependence block and there is no explorer block to generate a network')
job.execute(outputFile=outputFile, plot=self.plot)
elif isinstance(job, ExplorerJob):
thermoLibrary,kineticsLibrary,speciesList = self.getLibraries()
job.execute(outputFile=outputFile, plot=self.plot, speciesList=speciesList, thermoLibrary=thermoLibrary, kineticsLibrary=kineticsLibrary)
with open(chemkinFile, 'a') as f:
f.write('END\n\n')
# Print some information to the end of the log
self.logFooter()
def species(label, *args, **kwargs):
global speciesDict, jobList
if label in speciesDict:
raise ValueError('Multiple occurrences of species with label {0!r}.'.format(label))
logging.info('Loading species {0}...'.format(label))
spec = Species(label=label)
speciesDict[label] = spec
path = None
if len(args) == 1:
# The argument is a path to a conformer input file
path = args[0]
job = StatMechJob(species=spec, path=path)
logging.debug('Added species {0} to a stat mech job.'.format(label))
jobList.append(job)
elif len(args) > 1:
raise InputError('species {0} can only have two non-keyword argument '
'which should be the species label and the '
'path to a quantum file.'.format(spec.label))
if len(kwargs) > 0:
# The species parameters are given explicitly
structure = None
E0 = None
modes = []
spinMultiplicity = 0
opticalIsomers = 1
molecularWeight = None
collisionModel = None
energyTransferModel = None
thermo = None
reactive = True
for key, value in kwargs.items():
if key == 'structure':
structure = value
elif key == 'E0':
E0 = value
elif key == 'modes':
modes = value
elif key == 'spinMultiplicity':
spinMultiplicity = value
elif key == 'opticalIsomers':
opticalIsomers = value
elif key == 'molecularWeight':
molecularWeight = value
elif key == 'collisionModel':
collisionModel = value
elif key == 'energyTransferModel':
energyTransferModel = value
elif key == 'thermo':
thermo = value
elif key == 'reactive':
reactive = value
else:
raise TypeError('species() got an unexpected keyword argument {0!r}.'.format(key))
if structure:
spec.molecule = [structure]
spec.conformer = Conformer(E0=E0, modes=modes, spinMultiplicity=spinMultiplicity, opticalIsomers=opticalIsomers)
if molecularWeight is not None:
spec.molecularWeight = molecularWeight
elif spec.molecularWeight is None and is_pdep(jobList):
# If a structure was given, simply calling spec.molecularWeight will calculate the molecular weight
# If one of the jobs is pdep and no molecular weight is given or calculated, raise an error
raise ValueError("No molecularWeight was entered for species {0}. Since a structure wasn't given"
" as well, the molecularWeight, which is important for pressure dependent jobs,"
" cannot be reconstructed.".format(spec.label))
spec.transportData = collisionModel
spec.energyTransferModel = energyTransferModel
spec.thermo = thermo
spec.reactive = reactive
if spec.reactive and path is None and spec.thermo is None and spec.conformer.E0 is None:
if not spec.molecule:
raise InputError('Neither thermo, E0, species file path, nor structure specified, cannot estimate'
' thermo properties of species {0}'.format(spec.label))
try:
db = getDB('thermo')
if db is None:
raise DatabaseError('Thermo database is None.')
except DatabaseError:
logging.warn("The database isn't loaded, cannot estimate thermo for {0}. "
"If it is a bath gas, set reactive = False to avoid generating thermo.".format(spec.label))
else:
logging.info('No E0 or thermo found, estimating thermo and E0 of species {0} using'
' RMG-Database...'.format(spec.label))
spec.thermo = db.getThermoData(spec)
if spec.thermo.E0 is None:
th = spec.thermo.toWilhoit()
spec.conformer.E0 = th.E0
spec.thermo.E0 = th.E0
else:
spec.conformer.E0 = spec.thermo.E0
if spec.reactive and spec.thermo and not spec.hasStatMech() and structure is not None:
# generate stat mech info if it wasn't provided before
spec.generateStatMech()
if not energyTransferModel:
# default to RMG's method of generating energyTransferModel
spec.generateEnergyTransferModel()
return spec