nargs=1,
help='The path of the RMG dictionary file')
parser.add_argument('outputPath',
metavar='OUTPUT',
type=str,
nargs=1,
help='The path where the output will be saved')
args = parser.parse_args()
inputPath = args.inputPath[0]
dictionaryPath = args.dictionaryPath[0]
outputPath = args.outputPath[0]
# Read RMG input file
rmg = RMG()
readInputFile(inputPath, rmg)
# Read species dictionary
speciesDict = loadSpeciesDictionary(dictionaryPath)
addedMoleFractions = {}
for key, spec in speciesDict.items():
for existing in rmg.initialSpecies:
if spec.isIsomorphic(existing):
break
else:
rmg.initialSpecies.append(spec)
addedMoleFractions[spec] = 0
for system in rmg.reactionSystems:
system.initialMoleFractions.update(addedMoleFractions)
def loadForm(self, path):
"""
Load input.py file onto form initial data.
"""
readInputFile(path, self.rmg)
# Databases
initial_thermo_libraries = []
if self.rmg.thermoLibraries:
for item in self.rmg.thermoLibraries:
initial_thermo_libraries.append({'thermolib': item})
initial_reaction_libraries = []
if self.rmg.seedMechanisms:
for item in self.rmg.seedMechanisms:
initial_reaction_libraries.append({
'reactionlib': item,
'seedmech': True,
'edge': False
})
if self.rmg.reactionLibraries:
for item, edge in self.rmg.reactionLibraries:
initial_reaction_libraries.append({
'reactionlib': item,
'seedmech': False,
'edge': edge
})
# Reactor systems
initial_reactor_systems = []
for system in self.rmg.reactionSystems:
temperature = system.T.getValue()
temperature_units = system.T.units
pressure = system.P.getValue()
pressure_units = system.P.units
initialMoleFractions = system.initialMoleFractions
for item in system.termination:
if isinstance(item, TerminationTime):
terminationtime = item.time.getValue()
time_units = item.time.units
else:
species = item.species.label
conversion = item.conversion
# Sensitivity
if system.sensitiveSpecies:
sensitivity = []
for item in system.sensitiveSpecies:
sensitivity.append(item.label)
sensitivity = ','.join(sensitivity)
sensitivityThreshold = system.sensitivityThreshold
else:
sensitivity = ''
sensitivityThreshold = 0.001
initial_reactor_systems.append({
'temperature':
temperature,
'temperature_units':
temperature_units,
'pressure':
pressure,
'pressure_units':
pressure_units,
'terminationtime':
terminationtime,
'time_units':
time_units,
'species':
species,
'conversion':
conversion,
'sensitivity':
sensitivity,
'sensitivityThreshold':
sensitivityThreshold
})
# Species
initial_species = []
for item in self.rmg.initialSpecies:
name = item.label
adjlist = item.molecule[0].toAdjacencyList()
inert = False if item.reactive else True
spec, isNew = self.rmg.reactionModel.makeNewSpecies(
item.molecule[0], label=item.label, reactive=item.reactive)
molefrac = initialMoleFractions[spec]
initial_species.append({
'name': name,
'adjlist': adjlist,
'inert': inert,
'molefrac': molefrac
})
# Tolerances
initial = {}
initial['simulator_atol'] = self.rmg.absoluteTolerance
initial['simulator_rtol'] = self.rmg.relativeTolerance
initial['simulator_sens_atol'] = self.rmg.sensitivityAbsoluteTolerance
initial['simulator_sens_rtol'] = self.rmg.sensitivityRelativeTolerance
initial['toleranceKeepInEdge'] = self.rmg.fluxToleranceKeepInEdge
initial['toleranceMoveToCore'] = self.rmg.fluxToleranceMoveToCore
initial[
'toleranceInterruptSimulation'] = self.rmg.fluxToleranceInterrupt
initial['maximumEdgeSpecies'] = self.rmg.maximumEdgeSpecies
initial['minCoreSizeForPrune'] = self.rmg.minCoreSizeForPrune
initial[
'minSpeciesExistIterationsForPrune'] = self.rmg.minSpeciesExistIterationsForPrune
initial['filterReactions'] = self.rmg.filterReactions
# Pressure Dependence
if self.rmg.pressureDependence:
# Pressure dependence method
initial['pdep'] = self.rmg.pressureDependence.method.lower()
# Process interpolation model
initial[
'interpolation'] = self.rmg.pressureDependence.interpolationModel[
0].lower()
if initial['interpolation'] == 'chebyshev':
initial[
'temp_basis'] = self.rmg.pressureDependence.interpolationModel[
1]
initial[
'p_basis'] = self.rmg.pressureDependence.interpolationModel[
2]
# Temperature and pressure ranges
initial['temp_low'] = self.rmg.pressureDependence.Tmin.getValue()
initial['temp_high'] = self.rmg.pressureDependence.Tmax.getValue()
initial['temprange_units'] = self.rmg.pressureDependence.Tmax.units
initial['temp_interp'] = self.rmg.pressureDependence.Tcount
initial['p_low'] = self.rmg.pressureDependence.Pmin.getValue()
initial['p_high'] = self.rmg.pressureDependence.Pmax.getValue()
initial['prange_units'] = self.rmg.pressureDependence.Pmax.units
initial['p_interp'] = self.rmg.pressureDependence.Pcount
# Process grain size and count
initial[
'maximumGrainSize'] = self.rmg.pressureDependence.maximumGrainSize.getValue(
)
initial[
'grainsize_units'] = self.rmg.pressureDependence.maximumGrainSize.units
initial[
'minimumNumberOfGrains'] = self.rmg.pressureDependence.minimumGrainCount
initial['maximumAtoms'] = self.rmg.pressureDependence.maximumAtoms
else:
initial['pdep'] = 'off'
# Species Constraints
if self.rmg.speciesConstraints:
initial['speciesConstraints'] = 'on'
for key, value in self.rmg.speciesConstraints.items():
if key == 'allowed':
allowed_dict = {
'input species': 'allowed_inputSpecies',
'reaction libraries': 'allowed_reactionLibraries',
'seed mechanisms': 'allowed_seedMechanisms'
}
if isinstance(value, list):
for allowed_name in value:
field = allowed_dict[allowed_name.lower()]
initial[field] = True
else:
raise Exception(
"Input File generatedSpeciesConstraints(allowed='[..]'), allowed block must be a list containing either 'reaction libraries', 'seed mechanisms', or 'input species'."
)
else:
initial[key] = value
else:
initial['speciesConstraints'] = 'off'
# Quantum Calculations
if self.rmg.quantumMechanics:
initial['quantumCalc'] = 'on'
initial['software'] = self.rmg.quantumMechanics.settings.software
initial['method'] = self.rmg.quantumMechanics.settings.method
if self.rmg.quantumMechanics.settings.fileStore:
initial['fileStore'] = os.path.split(
self.rmg.quantumMechanics.settings.fileStore)[0]
else:
initial['fileStore'] = ''
if self.rmg.quantumMechanics.settings.scratchDirectory:
initial['scratchDirectory'] = os.path.split(
self.rmg.quantumMechanics.settings.scratchDirectory)[0]
else:
initial['scratchDirectory'] = ''
initial[
'onlyCyclics'] = self.rmg.quantumMechanics.settings.onlyCyclics
initial[
'maxRadicalNumber'] = self.rmg.quantumMechanics.settings.maxRadicalNumber
else:
initial['quantumCalc'] = 'off'
# Additional Options
if self.rmg.saveRestartPeriod:
initial['saveRestartPeriod'] = self.rmg.saveRestartPeriod.getValue(
)
initial[
'saveRestartPeriodUnits'] = self.rmg.saveRestartPeriod.units
if self.rmg.generateOutputHTML:
initial['generateOutputHTML'] = True
if self.rmg.generatePlots:
initial['generatePlots'] = True
if self.rmg.saveSimulationProfiles:
initial['saveSimulationProfiles'] = True
if self.rmg.saveEdgeSpecies:
initial['saveEdgeSpecies'] = True
if self.rmg.verboseComments:
initial['verboseComments'] = True
return initial_thermo_libraries, initial_reaction_libraries, initial_reactor_systems, initial_species, initial
def loadForm(self, path):
"""
Load input.py file onto form initial data.
"""
readInputFile(path, self.rmg)
# Databases
initial_thermo_libraries = []
if self.rmg.thermoLibraries:
for item in self.rmg.thermoLibraries:
initial_thermo_libraries.append({'thermolib': item})
initial_reaction_libraries = []
if self.rmg.seedMechanisms:
for item in self.rmg.seedMechanism:
initial_reaction_libraries.append({'reactionlib': item, 'seedmech': True, 'edge': False})
if self.rmg.reactionLibraries:
for item, edge in self.rmg.reactionLibraries:
initial_reaction_libraries.append({'reactionlib': item, 'seedmech': False, 'edge': edge})
# Reactor systems
initial_reactor_systems = []
for system in self.rmg.reactionSystems:
temperature = system.T.getValue()
temperature_units = system.T.units
pressure = system.P.getValue()
pressure_units = system.P.units
initialMoleFractions = system.initialMoleFractions
for item in system.termination:
if isinstance(item, TerminationTime):
terminationtime = item.time.getValue()
time_units = item.time.units
else:
species = item.species.label
conversion = item.conversion
initial_reactor_systems.append({'temperature': temperature, 'temperature_units': temperature_units,
'pressure': pressure, 'pressure_units': pressure_units,
'terminationtime': terminationtime, 'time_units': time_units,
'species': species, 'conversion': conversion})
# Species
initial_species = []
for item in self.rmg.initialSpecies:
name = item.label
adjlist = item.molecule[0].toAdjacencyList()
inert = False if item.reactive else True
spec, isNew = self.rmg.reactionModel.makeNewSpecies(item.molecule[0], label = item.label, reactive = item.reactive)
molefrac = initialMoleFractions[spec]
initial_species.append({'name': name, 'adjlist': adjlist,
'inert': inert, 'molefrac': molefrac})
# Tolerances
initial = {}
initial['simulator_atol'] = self.rmg.absoluteTolerance
initial['simulator_rtol'] = self.rmg.relativeTolerance
initial['toleranceKeepInEdge'] = self.rmg.fluxToleranceKeepInEdge
initial['toleranceMoveToCore']= self.rmg.fluxToleranceMoveToCore
initial['toleranceInterruptSimulation'] = self.rmg.fluxToleranceInterrupt
initial['maximumEdgeSpecies'] = self.rmg.maximumEdgeSpecies
# Pressure Dependence
if self.rmg.pressureDependence:
initial['interpolation'] = self.rmg.pressureDependence.model[0]
initial['temp_basis'] = self.rmg.pressureDependence.model[1]
initial['p_basis'] = self.rmg.pressureDependence.model[2]
initial['temp_low'] = self.rmg.pressureDependence.Tmin.getValue()
initial['temp_high'] = self.rmg.pressureDependence.Tmax.getValue()
initial['temprange_units'] = self.rmg.pressureDependence.Tmax.units
initial['temp_interp'] = self.rmg.pressureDependence.Tcount
initial['p_low'] = self.rmg.pressureDependence.Pmin.getValue()
initial['p_high'] = self.rmg.pressureDependence.Pmax.getValue()
initial['prange_units'] = self.rmg.pressureDependence.Pmax.units
initial['p_interp'] = self.rmg.pressureDepence.Pcount
initial['maximumGrainSize'] = self.rmg.pressureDependence.grainSize.getValue()
initial['grainsize_units'] = self.rmg.pressureDependence.grainSize.units
initial['minimumNumberOfGrains'] = self.rmg.pressureDependence.grainCount
else:
initial['pdep'] = 'off'
# Additional Options
if self.rmg.saveRestartPeriod:
initial['saveRestartPeriod'] = self.rmg.saveRestartPeriod.getValue()
initial['saveRestartPeriodUnits'] = self.rmg.saveRestartPeriod.units
if self.rmg.drawMolecules:
initial['drawMolecules'] = True
if self.rmg.generatePlots:
initial['generatePlots'] = True
if self.rmg.saveSimulationProfiles:
initial['saveSimulationProfiles'] = True
return initial_thermo_libraries, initial_reaction_libraries, initial_reactor_systems, initial_species, initial
def loadForm(self, path):
"""
Load input.py file onto form initial data.
"""
readInputFile(path, self.rmg)
# Databases
initial_thermo_libraries = []
if self.rmg.thermoLibraries:
for item in self.rmg.thermoLibraries:
initial_thermo_libraries.append({'thermolib': item})
initial_reaction_libraries = []
if self.rmg.seedMechanisms:
for item in self.rmg.seedMechanism:
initial_reaction_libraries.append({
'reactionlib': item,
'seedmech': True,
'edge': False
})
if self.rmg.reactionLibraries:
for item, edge in self.rmg.reactionLibraries:
initial_reaction_libraries.append({
'reactionlib': item,
'seedmech': False,
'edge': edge
})
# Reactor systems
initial_reactor_systems = []
for system in self.rmg.reactionSystems:
temperature = system.T.getValueInGivenUnits()
temperature_units = system.T.units
pressure = system.P.getValueInGivenUnits()
pressure_units = system.P.units
initialMoleFractions = system.initialMoleFractions
for item in system.termination:
if isinstance(item, TerminationTime):
terminationtime = item.time.getValueInGivenUnits()
time_units = item.time.units
else:
species = item.species.label
conversion = item.conversion
initial_reactor_systems.append({
'temperature': temperature,
'temperature_units': temperature_units,
'pressure': pressure,
'pressure_units': pressure_units,
'terminationtime': terminationtime,
'time_units': time_units,
'species': species,
'conversion': conversion
})
# Species
initial_species = []
for item in self.rmg.initialSpecies:
name = item.label
adjlist = item.molecule[0].toAdjacencyList()
inert = False if item.reactive else True
spec, isNew = self.rmg.reactionModel.makeNewSpecies(
item.molecule[0], label=item.label, reactive=item.reactive)
molefrac = initialMoleFractions[spec]
initial_species.append({
'name': name,
'adjlist': adjlist,
'inert': inert,
'molefrac': molefrac
})
# Tolerances
initial = {}
initial['simulator_atol'] = self.rmg.absoluteTolerance
initial['simulator_rtol'] = self.rmg.relativeTolerance
initial['toleranceKeepInEdge'] = self.rmg.fluxToleranceKeepInEdge
initial['toleranceMoveToCore'] = self.rmg.fluxToleranceMoveToCore
initial[
'toleranceInterruptSimulation'] = self.rmg.fluxToleranceInterrupt
initial['maximumEdgeSpecies'] = self.rmg.maximumEdgeSpecies
# Pressure Dependence
if self.rmg.pressureDependence:
initial['interpolation'] = self.rmg.pressureDependence.model[0]
initial['temp_basis'] = self.rmg.pressureDependence.model[1]
initial['p_basis'] = self.rmg.pressureDependence.model[2]
initial[
'temp_low'] = self.rmg.pressureDependence.Tmin.getValueInGivenUnits(
)
initial[
'temp_high'] = self.rmg.pressureDependence.Tmax.getValueInGivenUnits(
)
initial['temprange_units'] = self.rmg.pressureDependence.Tmax.units
initial['temp_interp'] = self.rmg.pressureDependence.Tcount
initial[
'p_low'] = self.rmg.pressureDependence.Pmin.getValueInGivenUnits(
)
initial[
'p_high'] = self.rmg.pressureDependence.Pmax.getValueInGivenUnits(
)
initial['prange_units'] = self.rmg.pressureDependence.Pmax.units
initial['p_interp'] = self.rmg.pressureDepence.Pcount
initial[
'maximumGrainSize'] = self.rmg.pressureDependence.grainSize.getValueInGivenUnits(
)
initial[
'grainsize_units'] = self.rmg.pressureDependence.grainSize.units
initial[
'minimumNumberOfGrains'] = self.rmg.pressureDependence.grainCount
else:
initial['pdep'] = 'off'
# Additional Options
if self.rmg.saveRestartPeriod:
initial[
'saveRestartPeriod'] = self.rmg.saveRestartPeriod.getValueInGivenUnits(
)
initial[
'saveRestartPeriodUnits'] = self.rmg.saveConcentrationProfiles.units
if self.rmg.drawMolecules:
initial['drawMolecules'] = True
if self.rmg.generatePlots:
initial['generatePlots'] = True
if self.rmg.saveConcentrationProfiles:
initial['saveConcentrationProfiles'] = True
return initial_thermo_libraries, initial_reaction_libraries, initial_reactor_systems, initial_species, initial
def loadForm(self, path):
"""
Load input.py file onto form initial data.
"""
readInputFile(path, self.rmg)
# Databases
initial_thermo_libraries = []
if self.rmg.thermoLibraries:
for item in self.rmg.thermoLibraries:
initial_thermo_libraries.append({"thermolib": item})
initial_reaction_libraries = []
if self.rmg.seedMechanisms:
for item in self.rmg.seedMechanisms:
initial_reaction_libraries.append({"reactionlib": item, "seedmech": True, "edge": False})
if self.rmg.reactionLibraries:
for item, edge in self.rmg.reactionLibraries:
initial_reaction_libraries.append({"reactionlib": item, "seedmech": False, "edge": edge})
# Reactor systems
initial_reactor_systems = []
for system in self.rmg.reactionSystems:
temperature = system.T.getValue()
temperature_units = system.T.units
pressure = system.P.getValue()
pressure_units = system.P.units
initialMoleFractions = system.initialMoleFractions
for item in system.termination:
if isinstance(item, TerminationTime):
terminationtime = item.time.getValue()
time_units = item.time.units
else:
species = item.species.label
conversion = item.conversion
# Sensitivity
if system.sensitiveSpecies:
sensitivity = []
for item in system.sensitiveSpecies:
sensitivity.append(item.label)
sensitivity = ",".join(sensitivity)
sensitivityThreshold = system.sensitivityThreshold
else:
sensitivity = ""
sensitivityThreshold = 0.001
initial_reactor_systems.append(
{
"temperature": temperature,
"temperature_units": temperature_units,
"pressure": pressure,
"pressure_units": pressure_units,
"terminationtime": terminationtime,
"time_units": time_units,
"species": species,
"conversion": conversion,
"sensitivity": sensitivity,
"sensitivityThreshold": sensitivityThreshold,
}
)
# Species
initial_species = []
for item in self.rmg.initialSpecies:
name = item.label
adjlist = item.molecule[0].toAdjacencyList()
inert = False if item.reactive else True
spec, isNew = self.rmg.reactionModel.makeNewSpecies(
item.molecule[0], label=item.label, reactive=item.reactive
)
molefrac = initialMoleFractions[spec]
initial_species.append({"name": name, "adjlist": adjlist, "inert": inert, "molefrac": molefrac})
# Tolerances
initial = {}
initial["simulator_atol"] = self.rmg.absoluteTolerance
initial["simulator_rtol"] = self.rmg.relativeTolerance
initial["simulator_sens_atol"] = self.rmg.sensitivityAbsoluteTolerance
initial["simulator_sens_rtol"] = self.rmg.sensitivityRelativeTolerance
initial["toleranceKeepInEdge"] = self.rmg.fluxToleranceKeepInEdge
initial["toleranceMoveToCore"] = self.rmg.fluxToleranceMoveToCore
initial["toleranceInterruptSimulation"] = self.rmg.fluxToleranceInterrupt
initial["maximumEdgeSpecies"] = self.rmg.maximumEdgeSpecies
# Pressure Dependence
if self.rmg.pressureDependence:
# Pressure dependence method
initial["pdep"] = self.rmg.pressureDependence.method.lower()
# Process interpolation model
initial["interpolation"] = self.rmg.pressureDependence.interpolationModel[0].lower()
if initial["interpolation"] == "chebyshev":
initial["temp_basis"] = self.rmg.pressureDependence.interpolationModel[1]
initial["p_basis"] = self.rmg.pressureDependence.interpolationModel[2]
# Temperature and pressure ranges
initial["temp_low"] = self.rmg.pressureDependence.Tmin.getValue()
initial["temp_high"] = self.rmg.pressureDependence.Tmax.getValue()
initial["temprange_units"] = self.rmg.pressureDependence.Tmax.units
initial["temp_interp"] = self.rmg.pressureDependence.Tcount
initial["p_low"] = self.rmg.pressureDependence.Pmin.getValue()
initial["p_high"] = self.rmg.pressureDependence.Pmax.getValue()
initial["prange_units"] = self.rmg.pressureDependence.Pmax.units
initial["p_interp"] = self.rmg.pressureDependence.Pcount
# Process grain size and count
initial["maximumGrainSize"] = self.rmg.pressureDependence.maximumGrainSize.getValue()
initial["grainsize_units"] = self.rmg.pressureDependence.maximumGrainSize.units
initial["minimumNumberOfGrains"] = self.rmg.pressureDependence.minimumGrainCount
initial["maximumAtoms"] = self.rmg.pressureDependence.maximumAtoms
else:
initial["pdep"] = "off"
# Species Constraints
if self.rmg.speciesConstraints:
initial["speciesConstraints"] = "on"
for key, value in self.rmg.speciesConstraints.items():
if key == "allowed":
allowed_dict = {
"input species": "allowed_inputSpecies",
"reaction libraries": "allowed_reactionLibraries",
"seed mechanisms": "allowed_seedMechanisms",
}
if isinstance(value, list):
for allowed_name in value:
field = allowed_dict[allowed_name.lower()]
initial[field] = True
else:
raise Exception(
"Input File generatedSpeciesConstraints(allowed='[..]'), allowed block must be a list containing either 'reaction libraries', 'seed mechanisms', or 'input species'."
)
else:
initial[key] = value
else:
initial["speciesConstraints"] = "off"
# Quantum Calculations
if self.rmg.quantumMechanics:
initial["quantumCalc"] = "on"
initial["software"] = self.rmg.quantumMechanics.settings.software
initial["method"] = self.rmg.quantumMechanics.settings.method
if self.rmg.quantumMechanics.settings.fileStore:
initial["fileStore"] = os.path.split(self.rmg.quantumMechanics.settings.fileStore)[0]
else:
initial["fileStore"] = ""
if self.rmg.quantumMechanics.settings.scratchDirectory:
initial["scratchDirectory"] = os.path.split(self.rmg.quantumMechanics.settings.scratchDirectory)[0]
else:
initial["scratchDirectory"] = ""
initial["onlyCyclics"] = self.rmg.quantumMechanics.settings.onlyCyclics
initial["maxRadicalNumber"] = self.rmg.quantumMechanics.settings.maxRadicalNumber
else:
initial["quantumCalc"] = "off"
# Additional Options
if self.rmg.saveRestartPeriod:
initial["saveRestartPeriod"] = self.rmg.saveRestartPeriod.getValue()
initial["saveRestartPeriodUnits"] = self.rmg.saveRestartPeriod.units
if self.rmg.generateOutputHTML:
initial["generateOutputHTML"] = True
if self.rmg.generatePlots:
initial["generatePlots"] = True
if self.rmg.saveSimulationProfiles:
initial["saveSimulationProfiles"] = True
if self.rmg.saveEdgeSpecies:
initial["saveEdgeSpecies"] = True
if self.rmg.verboseComments:
initial["verboseComments"] = True
return initial_thermo_libraries, initial_reaction_libraries, initial_reactor_systems, initial_species, initial
def loadForm(self, path):
"""
Load input.py file onto form initial data.
"""
readInputFile(path, self.rmg)
# Databases
initial_thermo_libraries = []
if self.rmg.thermoLibraries:
for item in self.rmg.thermoLibraries:
initial_thermo_libraries.append({'thermolib': item})
initial_reaction_libraries = []
if self.rmg.seedMechanisms:
for item in self.rmg.seedMechanisms:
initial_reaction_libraries.append({'reactionlib': item, 'seedmech': True, 'edge': False})
if self.rmg.reactionLibraries:
for item, edge in self.rmg.reactionLibraries:
initial_reaction_libraries.append({'reactionlib': item, 'seedmech': False, 'edge': edge})
# Reactor systems
initial_reactor_systems = []
for system in self.rmg.reactionSystems:
temperature = system.T.getValue()
temperature_units = system.T.units
pressure = system.P.getValue()
pressure_units = system.P.units
initialMoleFractions = system.initialMoleFractions
for item in system.termination:
if isinstance(item, TerminationTime):
terminationtime = item.time.getValue()
time_units = item.time.units
else:
species = item.species.label
conversion = item.conversion
# Sensitivity
if system.sensitiveSpecies:
sensitivity = []
for item in system.sensitiveSpecies:
sensitivity.append(item.label)
sensitivity = ','.join(sensitivity)
sensitivityThreshold = system.sensitivityThreshold
else:
sensitivity = ''
sensitivityThreshold = 0.001
initial_reactor_systems.append({'temperature': temperature, 'temperature_units': temperature_units,
'pressure': pressure, 'pressure_units': pressure_units,
'terminationtime': terminationtime, 'time_units': time_units,
'species': species, 'conversion': conversion,
'sensitivity': sensitivity, 'sensitivityThreshold': sensitivityThreshold})
# Species
initial_species = []
for item in self.rmg.initialSpecies:
name = item.label
adjlist = item.molecule[0].toAdjacencyList()
inert = False if item.reactive else True
spec, isNew = self.rmg.reactionModel.makeNewSpecies(item.molecule[0], label = item.label, reactive = item.reactive)
molefrac = initialMoleFractions[spec]
initial_species.append({'name': name, 'adjlist': adjlist,
'inert': inert, 'molefrac': molefrac})
# Tolerances
initial = {}
initial['simulator_atol'] = self.rmg.absoluteTolerance
initial['simulator_rtol'] = self.rmg.relativeTolerance
initial['simulator_sens_atol'] = self.rmg.sensitivityAbsoluteTolerance
initial['simulator_sens_rtol'] = self.rmg.sensitivityRelativeTolerance
initial['toleranceKeepInEdge'] = self.rmg.fluxToleranceKeepInEdge
initial['toleranceMoveToCore']= self.rmg.fluxToleranceMoveToCore
initial['toleranceInterruptSimulation'] = self.rmg.fluxToleranceInterrupt
initial['maximumEdgeSpecies'] = self.rmg.maximumEdgeSpecies
initial['minCoreSizeForPrune'] = self.rmg.minCoreSizeForPrune
initial['minSpeciesExistIterationsForPrune'] = self.rmg.minSpeciesExistIterationsForPrune
# Pressure Dependence
if self.rmg.pressureDependence:
# Pressure dependence method
initial['pdep'] = self.rmg.pressureDependence.method.lower()
# Process interpolation model
initial['interpolation'] = self.rmg.pressureDependence.interpolationModel[0].lower()
if initial['interpolation'] == 'chebyshev':
initial['temp_basis'] = self.rmg.pressureDependence.interpolationModel[1]
initial['p_basis'] = self.rmg.pressureDependence.interpolationModel[2]
# Temperature and pressure ranges
initial['temp_low'] = self.rmg.pressureDependence.Tmin.getValue()
initial['temp_high'] = self.rmg.pressureDependence.Tmax.getValue()
initial['temprange_units'] = self.rmg.pressureDependence.Tmax.units
initial['temp_interp'] = self.rmg.pressureDependence.Tcount
initial['p_low'] = self.rmg.pressureDependence.Pmin.getValue()
initial['p_high'] = self.rmg.pressureDependence.Pmax.getValue()
initial['prange_units'] = self.rmg.pressureDependence.Pmax.units
initial['p_interp'] = self.rmg.pressureDependence.Pcount
# Process grain size and count
initial['maximumGrainSize'] = self.rmg.pressureDependence.maximumGrainSize.getValue()
initial['grainsize_units'] = self.rmg.pressureDependence.maximumGrainSize.units
initial['minimumNumberOfGrains'] = self.rmg.pressureDependence.minimumGrainCount
initial['maximumAtoms'] = self.rmg.pressureDependence.maximumAtoms
else:
initial['pdep'] = 'off'
# Species Constraints
if self.rmg.speciesConstraints:
initial['speciesConstraints'] = 'on'
for key, value in self.rmg.speciesConstraints.items():
if key == 'allowed':
allowed_dict = {'input species':'allowed_inputSpecies', 'reaction libraries':'allowed_reactionLibraries', 'seed mechanisms':'allowed_seedMechanisms'}
if isinstance(value,list):
for allowed_name in value:
field = allowed_dict[allowed_name.lower()]
initial[field] = True
else:
raise Exception("Input File generatedSpeciesConstraints(allowed='[..]'), allowed block must be a list containing either 'reaction libraries', 'seed mechanisms', or 'input species'." )
else:
initial[key] = value
else:
initial['speciesConstraints'] = 'off'
# Quantum Calculations
if self.rmg.quantumMechanics:
initial['quantumCalc'] = 'on'
initial['software'] = self.rmg.quantumMechanics.settings.software
initial['method'] = self.rmg.quantumMechanics.settings.method
if self.rmg.quantumMechanics.settings.fileStore:
initial['fileStore'] = os.path.split(self.rmg.quantumMechanics.settings.fileStore)[0]
else:
initial['fileStore'] = ''
if self.rmg.quantumMechanics.settings.scratchDirectory:
initial['scratchDirectory'] = os.path.split(self.rmg.quantumMechanics.settings.scratchDirectory)[0]
else:
initial['scratchDirectory'] = ''
initial['onlyCyclics'] = self.rmg.quantumMechanics.settings.onlyCyclics
initial['maxRadicalNumber'] = self.rmg.quantumMechanics.settings.maxRadicalNumber
else:
initial['quantumCalc'] = 'off'
# Additional Options
if self.rmg.saveRestartPeriod:
initial['saveRestartPeriod'] = self.rmg.saveRestartPeriod.getValue()
initial['saveRestartPeriodUnits'] = self.rmg.saveRestartPeriod.units
if self.rmg.generateOutputHTML:
initial['generateOutputHTML'] = True
if self.rmg.generatePlots:
initial['generatePlots'] = True
if self.rmg.saveSimulationProfiles:
initial['saveSimulationProfiles'] = True
if self.rmg.saveEdgeSpecies:
initial['saveEdgeSpecies'] = True
if self.rmg.verboseComments:
initial['verboseComments'] = True
return initial_thermo_libraries, initial_reaction_libraries, initial_reactor_systems, initial_species, initial
def loadForm(self, path):
"""
Load input.py file onto form initial data.
"""
readInputFile(path, self.rmg)
# Databases
initial_thermo_libraries = []
if self.rmg.thermoLibraries:
for item in self.rmg.thermoLibraries:
initial_thermo_libraries.append({"thermolib": item})
initial_reaction_libraries = []
if self.rmg.seedMechanisms:
for item in self.rmg.seedMechanism:
initial_reaction_libraries.append({"reactionlib": item, "seedmech": True, "edge": False})
if self.rmg.reactionLibraries:
for item, edge in self.rmg.reactionLibraries:
initial_reaction_libraries.append({"reactionlib": item, "seedmech": False, "edge": edge})
# Reactor systems
initial_reactor_systems = []
for system in self.rmg.reactionSystems:
temperature = system.T.getValueInGivenUnits()
temperature_units = system.T.units
pressure = system.P.getValueInGivenUnits()
pressure_units = system.P.units
initialMoleFractions = system.initialMoleFractions
for item in system.termination:
if isinstance(item, TerminationTime):
terminationtime = item.time.getValueInGivenUnits()
time_units = item.time.units
else:
species = item.species.label
conversion = item.conversion
initial_reactor_systems.append(
{
"temperature": temperature,
"temperature_units": temperature_units,
"pressure": pressure,
"pressure_units": pressure_units,
"terminationtime": terminationtime,
"time_units": time_units,
"species": species,
"conversion": conversion,
}
)
# Species
initial_species = []
for item in self.rmg.initialSpecies:
name = item.label
adjlist = item.molecule[0].toAdjacencyList()
inert = False if item.reactive else True
spec, isNew = self.rmg.reactionModel.makeNewSpecies(
item.molecule[0], label=item.label, reactive=item.reactive
)
molefrac = initialMoleFractions[spec]
initial_species.append({"name": name, "adjlist": adjlist, "inert": inert, "molefrac": molefrac})
# Tolerances
initial = {}
initial["simulator_atol"] = self.rmg.absoluteTolerance
initial["simulator_rtol"] = self.rmg.relativeTolerance
initial["toleranceKeepInEdge"] = self.rmg.fluxToleranceKeepInEdge
initial["toleranceMoveToCore"] = self.rmg.fluxToleranceMoveToCore
initial["toleranceInterruptSimulation"] = self.rmg.fluxToleranceInterrupt
initial["maximumEdgeSpecies"] = self.rmg.maximumEdgeSpecies
# Pressure Dependence
if self.rmg.pressureDependence:
initial["interpolation"] = self.rmg.pressureDependence.model[0]
initial["temp_basis"] = self.rmg.pressureDependence.model[1]
initial["p_basis"] = self.rmg.pressureDependence.model[2]
initial["temp_low"] = self.rmg.pressureDependence.Tmin.getValueInGivenUnits()
initial["temp_high"] = self.rmg.pressureDependence.Tmax.getValueInGivenUnits()
initial["temprange_units"] = self.rmg.pressureDependence.Tmax.units
initial["temp_interp"] = self.rmg.pressureDependence.Tcount
initial["p_low"] = self.rmg.pressureDependence.Pmin.getValueInGivenUnits()
initial["p_high"] = self.rmg.pressureDependence.Pmax.getValueInGivenUnits()
initial["prange_units"] = self.rmg.pressureDependence.Pmax.units
initial["p_interp"] = self.rmg.pressureDepence.Pcount
initial["maximumGrainSize"] = self.rmg.pressureDependence.grainSize.getValueInGivenUnits()
initial["grainsize_units"] = self.rmg.pressureDependence.grainSize.units
initial["minimumNumberOfGrains"] = self.rmg.pressureDependence.grainCount
else:
initial["pdep"] = "off"
# Additional Options
if self.rmg.saveRestartPeriod:
initial["saveRestartPeriod"] = self.rmg.saveRestartPeriod.getValueInGivenUnits()
initial["saveRestartPeriodUnits"] = self.rmg.saveConcentrationProfiles.units
if self.rmg.drawMolecules:
initial["drawMolecules"] = True
if self.rmg.generatePlots:
initial["generatePlots"] = True
if self.rmg.saveConcentrationProfiles:
initial["saveConcentrationProfiles"] = True
return initial_thermo_libraries, initial_reaction_libraries, initial_reactor_systems, initial_species, initial