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input.py
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input.py
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#!/usr/bin/env python
# -*- coding: utf-8 -*-
###############################################################################
# #
# RMG - Reaction Mechanism Generator #
# #
# Copyright (c) 2002-2018 Prof. William H. Green (whgreen@mit.edu), #
# Prof. Richard H. West (r.west@neu.edu) and the RMG Team (rmg_dev@mit.edu) #
# #
# Permission is hereby granted, free of charge, to any person obtaining a #
# copy of this software and associated documentation files (the 'Software'), #
# to deal in the Software without restriction, including without limitation #
# the rights to use, copy, modify, merge, publish, distribute, sublicense, #
# and/or sell copies of the Software, and to permit persons to whom the #
# Software is furnished to do so, subject to the following conditions: #
# #
# The above copyright notice and this permission notice shall be included in #
# all copies or substantial portions of the Software. #
# #
# THE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND, EXPRESS OR #
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, #
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE #
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER #
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING #
# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER #
# DEALINGS IN THE SOFTWARE. #
# #
###############################################################################
import logging
import quantities
import os
import numpy
from rmgpy import settings
from rmgpy.molecule import Molecule
from rmgpy.quantity import Quantity
from rmgpy.solver.base import TerminationTime, TerminationConversion
from rmgpy.solver.simple import SimpleReactor
from rmgpy.solver.liquid import LiquidReactor
from rmgpy.rmg.settings import ModelSettings, SimulatorSettings
from model import CoreEdgeReactionModel
from rmgpy.scoop_framework.util import broadcast, get
from rmgpy.exceptions import InputError
################################################################################
rmg = None
speciesDict = {}
def database(
thermoLibraries = None,
transportLibraries = None,
reactionLibraries = None,
frequenciesLibraries = None,
seedMechanisms = None,
kineticsFamilies = 'default',
kineticsDepositories = 'default',
kineticsEstimator = 'rate rules',
):
# This function just stores the information about the database to be loaded
# We don't actually load the database until after we're finished reading
# the input file
if isinstance(thermoLibraries, str): thermoLibraries = [thermoLibraries]
if isinstance(transportLibraries, str): transportLibraries = [transportLibraries]
if isinstance(reactionLibraries, str): reactionLibraries = [reactionLibraries]
if isinstance(seedMechanisms, str): seedMechanisms = [seedMechanisms]
if isinstance(frequenciesLibraries, str): frequenciesLibraries = [frequenciesLibraries]
rmg.databaseDirectory = settings['database.directory']
rmg.thermoLibraries = thermoLibraries or []
rmg.transportLibraries = transportLibraries
# Modify reactionLibraries if the user didn't specify tuple input
if reactionLibraries:
index = 0
while index < len(reactionLibraries):
if isinstance(reactionLibraries[index],tuple):
pass
elif isinstance(reactionLibraries[index],str):
reactionLibraries[index] = (reactionLibraries[index], False)
else:
raise TypeError('reaction libraries must be input as tuples or strings')
index += 1
rmg.reactionLibraries = reactionLibraries or []
rmg.seedMechanisms = seedMechanisms or []
rmg.statmechLibraries = frequenciesLibraries or []
rmg.kineticsEstimator = kineticsEstimator
if kineticsDepositories == 'default':
rmg.kineticsDepositories = ['training']
elif kineticsDepositories == 'all':
rmg.kineticsDepositories = None
else:
if not isinstance(kineticsDepositories,list):
raise InputError("kineticsDepositories should be either 'default', 'all', or a list of names eg. ['training','PrIMe'].")
rmg.kineticsDepositories = kineticsDepositories
if kineticsFamilies in ('default', 'all', 'none'):
rmg.kineticsFamilies = kineticsFamilies
else:
if not isinstance(kineticsFamilies,list):
raise InputError("kineticsFamilies should be either 'default', 'all', 'none', or a list of names eg. ['H_Abstraction','R_Recombination'] or ['!Intra_Disproportionation'].")
rmg.kineticsFamilies = kineticsFamilies
def species(label, structure, reactive=True):
logging.debug('Found {0} species "{1}" ({2})'.format('reactive' if reactive else 'nonreactive', label, structure.toSMILES()))
if '+' in label:
raise InputError('species {0} label cannot include a + sign'.format(label))
spec, isNew = rmg.reactionModel.makeNewSpecies(structure, label=label, reactive=reactive)
if not isNew:
raise InputError("Species {0} is a duplicate of {1}. Species in input file must be unique".format(label,spec.label))
# Force RMG to add the species to edge first, prior to where it is added to the core, in case it is found in
# any reaction libraries along the way
rmg.reactionModel.addSpeciesToEdge(spec)
rmg.initialSpecies.append(spec)
speciesDict[label] = spec
def SMARTS(string):
return Molecule().fromSMARTS(string)
def SMILES(string):
return Molecule().fromSMILES(string)
def InChI(string):
return Molecule().fromInChI(string)
def adjacencyList(string):
return Molecule().fromAdjacencyList(string)
# Reaction systems
def simpleReactor(temperature,
pressure,
initialMoleFractions,
terminationConversion=None,
terminationTime=None,
sensitivity=None,
sensitivityThreshold=1e-3
):
logging.debug('Found SimpleReactor reaction system')
for value in initialMoleFractions.values():
if value < 0:
raise InputError('Initial mole fractions cannot be negative.')
for spec in initialMoleFractions:
initialMoleFractions[spec] = float(initialMoleFractions[spec])
totalInitialMoles = sum(initialMoleFractions.values())
if totalInitialMoles != 1:
logging.warning('Initial mole fractions do not sum to one; normalizing.')
logging.info('')
logging.info('Original composition:')
for spec, molfrac in initialMoleFractions.iteritems():
logging.info("{0} = {1}".format(spec,molfrac))
for spec in initialMoleFractions:
initialMoleFractions[spec] /= totalInitialMoles
logging.info('')
logging.info('Normalized mole fractions:')
for spec, molfrac in initialMoleFractions.iteritems():
logging.info("{0} = {1}".format(spec,molfrac))
T = Quantity(temperature)
P = Quantity(pressure)
termination = []
if terminationConversion is not None:
for spec, conv in terminationConversion.iteritems():
termination.append(TerminationConversion(speciesDict[spec], conv))
if terminationTime is not None:
termination.append(TerminationTime(Quantity(terminationTime)))
if len(termination) == 0:
raise InputError('No termination conditions specified for reaction system #{0}.'.format(len(rmg.reactionSystems)+2))
sensitiveSpecies = []
if sensitivity:
if isinstance(sensitivity, str): sensitivity = [sensitivity]
for spec in sensitivity:
sensitiveSpecies.append(speciesDict[spec])
system = SimpleReactor(T, P, initialMoleFractions, termination, sensitiveSpecies, sensitivityThreshold)
rmg.reactionSystems.append(system)
# Reaction systems
def liquidReactor(temperature,
initialConcentrations,
terminationConversion=None,
terminationTime=None,
sensitivity=None,
sensitivityThreshold=1e-3,
constantSpecies=None):
logging.debug('Found LiquidReactor reaction system')
T = Quantity(temperature)
for spec,conc in initialConcentrations.iteritems():
concentration = Quantity(conc)
# check the dimensions are ok
# convert to mol/m^3 (or something numerically nice? or must it be SI)
initialConcentrations[spec] = concentration.value_si
termination = []
if terminationConversion is not None:
for spec, conv in terminationConversion.iteritems():
termination.append(TerminationConversion(speciesDict[spec], conv))
if terminationTime is not None:
termination.append(TerminationTime(Quantity(terminationTime)))
if len(termination) == 0:
raise InputError('No termination conditions specified for reaction system #{0}.'.format(len(rmg.reactionSystems)+2))
sensitiveSpecies = []
if sensitivity:
for spec in sensitivity:
sensitiveSpecies.append(speciesDict[spec])
##chatelak: check the constant species exist
if constantSpecies is not None:
logging.debug(' Generation with constant species:')
for constantSpecie in constantSpecies:
logging.debug(" {0}".format(constantSpecie))
if not speciesDict.has_key(constantSpecie):
raise InputError('Species {0} not found in the input file'.format(constantSpecie))
system = LiquidReactor(T, initialConcentrations, termination, sensitiveSpecies, sensitivityThreshold,constantSpecies)
rmg.reactionSystems.append(system)
def simulator(atol, rtol, sens_atol=1e-6, sens_rtol=1e-4):
rmg.simulatorSettingsList.append(SimulatorSettings(atol, rtol, sens_atol, sens_rtol))
def solvation(solvent):
# If solvation module in input file, set the RMG solvent variable
if not isinstance(solvent,str):
raise InputError("solvent should be a string like 'water'")
rmg.solvent = solvent
def model(toleranceMoveToCore=None, toleranceMoveEdgeReactionToCore=numpy.inf,toleranceKeepInEdge=0.0, toleranceInterruptSimulation=1.0,
toleranceMoveEdgeReactionToSurface=numpy.inf, toleranceMoveSurfaceSpeciesToCore=numpy.inf, toleranceMoveSurfaceReactionToCore=numpy.inf,
toleranceMoveEdgeReactionToSurfaceInterrupt=None,
toleranceMoveEdgeReactionToCoreInterrupt=None, maximumEdgeSpecies=1000000, minCoreSizeForPrune=50,
minSpeciesExistIterationsForPrune=2, filterReactions=False, ignoreOverallFluxCriterion=False,
maxNumSpecies=None,maxNumObjsPerIter=1,terminateAtMaxObjects=False,toleranceThermoKeepSpeciesInEdge=numpy.inf,dynamicsTimeScale=(0.0,'sec')):
"""
How to generate the model. `toleranceMoveToCore` must be specified.
toleranceMoveReactionToCore and toleranceReactionInterruptSimulation refers to an additional criterion for forcing an edge reaction to be included in the core
by default this criterion is turned off
Other parameters are optional and control the pruning.
ignoreOverallFluxCriterion=True will cause the toleranceMoveToCore to be only applied
to the pressure dependent network expansion and not movement of species from edge to core
"""
if toleranceMoveToCore is None:
raise InputError("You must provide a toleranceMoveToCore value. It should be less than or equal to toleranceInterruptSimulation which is currently {0}".format(toleranceInterruptSimulation))
if toleranceMoveToCore > toleranceInterruptSimulation:
raise InputError("toleranceMoveToCore must be less than or equal to toleranceInterruptSimulation, which is currently {0}".format(toleranceInterruptSimulation))
rmg.modelSettingsList.append(ModelSettings(toleranceMoveToCore, toleranceMoveEdgeReactionToCore,toleranceKeepInEdge, toleranceInterruptSimulation,
toleranceMoveEdgeReactionToSurface, toleranceMoveSurfaceSpeciesToCore, toleranceMoveSurfaceReactionToCore,
toleranceMoveEdgeReactionToSurfaceInterrupt,toleranceMoveEdgeReactionToCoreInterrupt, maximumEdgeSpecies, minCoreSizeForPrune,
minSpeciesExistIterationsForPrune, filterReactions, ignoreOverallFluxCriterion, maxNumSpecies, maxNumObjsPerIter,terminateAtMaxObjects,
toleranceThermoKeepSpeciesInEdge,Quantity(dynamicsTimeScale)))
def quantumMechanics(
software,
method,
fileStore = None,
scratchDirectory = None,
onlyCyclics = False,
maxRadicalNumber = 0,
):
from rmgpy.qm.main import QMCalculator
rmg.quantumMechanics = QMCalculator(software = software,
method = method,
fileStore = fileStore,
scratchDirectory = scratchDirectory,
onlyCyclics = onlyCyclics,
maxRadicalNumber = maxRadicalNumber,
)
def pressureDependence(
method,
temperatures,
pressures,
maximumGrainSize = 0.0,
minimumNumberOfGrains = 0,
interpolation = None,
maximumAtoms=None,
):
from rmgpy.cantherm.pdep import PressureDependenceJob
# Setting the pressureDependence attribute to non-None enables pressure dependence
rmg.pressureDependence = PressureDependenceJob(network=None)
# Process method
rmg.pressureDependence.method = method
# Process interpolation model
if isinstance(interpolation, str):
interpolation = (interpolation,)
if interpolation[0].lower() not in ("chebyshev","pdeparrhenius"):
raise InputError("Interpolation model must be set to either 'Chebyshev' or 'PDepArrhenius'.")
rmg.pressureDependence.interpolationModel = interpolation
# Process temperatures
Tmin, Tmax, Tunits, Tcount = temperatures
rmg.pressureDependence.Tmin = Quantity(Tmin, Tunits)
rmg.pressureDependence.Tmax = Quantity(Tmax, Tunits)
rmg.pressureDependence.Tcount = Tcount
rmg.pressureDependence.generateTemperatureList()
# Process pressures
Pmin, Pmax, Punits, Pcount = pressures
rmg.pressureDependence.Pmin = Quantity(Pmin, Punits)
rmg.pressureDependence.Pmax = Quantity(Pmax, Punits)
rmg.pressureDependence.Pcount = Pcount
rmg.pressureDependence.generatePressureList()
# Process grain size and count
rmg.pressureDependence.maximumGrainSize = Quantity(maximumGrainSize)
rmg.pressureDependence.minimumGrainCount = minimumNumberOfGrains
# Process maximum atoms
rmg.pressureDependence.maximumAtoms = maximumAtoms
rmg.pressureDependence.activeJRotor = True
rmg.pressureDependence.activeKRotor = True
rmg.pressureDependence.rmgmode = True
def options(name='Seed', generateSeedEachIteration=False, saveSeedToDatabase=False, units='si', saveRestartPeriod=None,
generateOutputHTML=False, generatePlots=False, saveSimulationProfiles=False, verboseComments=False,
saveEdgeSpecies=False, keepIrreversible=False, wallTime='00:00:00:00'):
rmg.name = name
rmg.generateSeedEachIteration=generateSeedEachIteration
rmg.saveSeedToDatabase=saveSeedToDatabase
rmg.units = units
rmg.saveRestartPeriod = Quantity(saveRestartPeriod) if saveRestartPeriod else None
if generateOutputHTML:
logging.warning('Generate Output HTML option was turned on. Note that this will slow down model generation.')
rmg.generateOutputHTML = generateOutputHTML
rmg.generatePlots = generatePlots
rmg.saveSimulationProfiles = saveSimulationProfiles
rmg.verboseComments = verboseComments
if saveEdgeSpecies:
logging.warning('Edge species saving was turned on. This will slow down model generation for large simulations.')
rmg.saveEdgeSpecies = saveEdgeSpecies
rmg.keepIrreversible = keepIrreversible
rmg.wallTime = wallTime
def generatedSpeciesConstraints(**kwargs):
validConstraints = [
'allowed',
'maximumCarbonAtoms',
'maximumOxygenAtoms',
'maximumNitrogenAtoms',
'maximumSiliconAtoms',
'maximumSulfurAtoms',
'maximumHeavyAtoms',
'maximumRadicalElectrons',
'maximumSingletCarbenes',
'maximumCarbeneRadicals',
'allowSingletO2',
'maximumIsotopicAtoms'
]
for key, value in kwargs.items():
if key not in validConstraints:
raise InputError('Invalid generated species constraint {0!r}.'.format(key))
rmg.speciesConstraints[key] = value
def thermoCentralDatabase(host,
port,
username,
password,
application):
from rmgpy.data.thermo import ThermoCentralDatabaseInterface
rmg.thermoCentralDatabase = ThermoCentralDatabaseInterface(host,
port,
username,
password,
application)
################################################################################
def setGlobalRMG(rmg0):
"""
sets the global variable rmg to rmg0. This is used to allow for unittesting
of above methods
"""
global rmg
rmg = rmg0
def readInputFile(path, rmg0):
"""
Read an RMG input file at `path` on disk into the :class:`RMG` object
`rmg`.
"""
global rmg, speciesDict
full_path = os.path.abspath(os.path.expandvars(path))
try:
f = open(full_path)
except IOError, e:
logging.error('The input file "{0}" could not be opened.'.format(full_path))
logging.info('Check that the file exists and that you have read access.')
raise e
logging.info('Reading input file "{0}"...'.format(full_path))
logging.info(f.read())
f.seek(0)# return to beginning of file
setGlobalRMG(rmg0)
rmg.reactionModel = CoreEdgeReactionModel()
rmg.initialSpecies = []
rmg.reactionSystems = []
speciesDict = {}
global_context = { '__builtins__': None }
local_context = {
'__builtins__': None,
'True': True,
'False': False,
'database': database,
'species': species,
'SMARTS': SMARTS,
'SMILES': SMILES,
'InChI': InChI,
'adjacencyList': adjacencyList,
'simpleReactor': simpleReactor,
'liquidReactor': liquidReactor,
'simulator': simulator,
'solvation': solvation,
'model': model,
'quantumMechanics': quantumMechanics,
'pressureDependence': pressureDependence,
'options': options,
'generatedSpeciesConstraints': generatedSpeciesConstraints,
'thermoCentralDatabase': thermoCentralDatabase
}
try:
exec f in global_context, local_context
except (NameError, TypeError, SyntaxError), e:
logging.error('The input file "{0}" was invalid:'.format(full_path))
logging.exception(e)
raise
finally:
f.close()
rmg.speciesConstraints['explicitlyAllowedMolecules'] = []
broadcast(rmg.speciesConstraints, 'speciesConstraints')
# convert keys from species names into species objects.
for reactionSystem in rmg.reactionSystems:
reactionSystem.convertInitialKeysToSpeciesObjects(speciesDict)
if rmg.quantumMechanics:
rmg.quantumMechanics.setDefaultOutputDirectory(rmg.outputDirectory)
rmg.quantumMechanics.initialize()
broadcast(rmg.quantumMechanics, 'quantumMechanics')
logging.info('')
################################################################################
def readThermoInputFile(path, rmg0):
"""
Read an thermo estimation input file at `path` on disk into the :class:`RMG` object
`rmg`.
"""
global rmg, speciesDict
full_path = os.path.abspath(os.path.expandvars(path))
try:
f = open(full_path)
except IOError, e:
logging.error('The input file "{0}" could not be opened.'.format(full_path))
logging.info('Check that the file exists and that you have read access.')
raise e
logging.info('Reading input file "{0}"...'.format(full_path))
rmg = rmg0
rmg.reactionModel = CoreEdgeReactionModel()
rmg.initialSpecies = []
rmg.reactionSystems = []
speciesDict = {}
global_context = { '__builtins__': None }
local_context = {
'__builtins__': None,
'True': True,
'False': False,
'database': database,
'species': species,
'SMARTS': SMARTS,
'SMILES': SMILES,
'InChI': InChI,
'solvation': solvation,
'adjacencyList': adjacencyList,
'quantumMechanics': quantumMechanics,
}
try:
exec f in global_context, local_context
except (NameError, TypeError, SyntaxError), e:
logging.error('The input file "{0}" was invalid:'.format(full_path))
logging.exception(e)
raise
finally:
f.close()
if rmg.quantumMechanics:
rmg.quantumMechanics.setDefaultOutputDirectory(rmg.outputDirectory)
rmg.quantumMechanics.initialize()
broadcast(rmg.quantumMechanics, 'quantumMechanics')
logging.info('')
################################################################################
def saveInputFile(path, rmg):
"""
Save an RMG input file at `path` on disk from the :class:`RMG` object
`rmg`.
"""
f = open(path, 'w')
# Databases
f.write('database(\n')
#f.write(' "{0}",\n'.format(rmg.databaseDirectory))
f.write(' thermoLibraries = {0!r},\n'.format(rmg.thermoLibraries))
f.write(' reactionLibraries = {0!r},\n'.format(rmg.reactionLibraries))
f.write(' seedMechanisms = {0!r},\n'.format(rmg.seedMechanisms))
f.write(' kineticsDepositories = {0!r},\n'.format(rmg.kineticsDepositories))
f.write(' kineticsFamilies = {0!r},\n'.format(rmg.kineticsFamilies))
f.write(' kineticsEstimator = {0!r},\n'.format(rmg.kineticsEstimator))
f.write(')\n\n')
# Species
for species in rmg.initialSpecies:
f.write('species(\n')
f.write(' label = "{0}",\n'.format(species.label))
f.write(' reactive = {0},\n'.format(species.reactive))
f.write(' structure = adjacencyList(\n')
f.write('"""\n')
f.write(species.molecule[0].toAdjacencyList())
f.write('"""),\n')
f.write(')\n\n')
# Reaction systems
for system in rmg.reactionSystems:
if rmg.solvent:
f.write('liquidReactor(\n')
f.write(' temperature = ({0:g},"{1!s}"),\n'.format(system.T.getValue(),system.T.units))
f.write(' initialConcentrations={\n')
for species, conc in system.initialConcentrations.iteritems():
f.write(' "{0!s}": ({1:g},"{2!s}"),\n'.format(species.label,conc.getValue(),conc.units))
else:
f.write('simpleReactor(\n')
f.write(' temperature = ({0:g},"{1!s}"),\n'.format(system.T.getValue(),system.T.units))
# Convert the pressure from SI pascal units to bar here
# Do something more fancy later for converting to user's desired units for both T and P..
f.write(' pressure = ({0:g},"{1!s}"),\n'.format(system.P.getValue(),system.P.units))
f.write(' initialMoleFractions={\n')
for species, molfrac in system.initialMoleFractions.iteritems():
f.write(' "{0!s}": {1:g},\n'.format(species.label, molfrac))
f.write(' },\n')
# Termination criteria
conversions = ''
for term in system.termination:
if isinstance(term, TerminationTime):
f.write(' terminationTime = ({0:g},"{1!s}"),\n'.format(term.time.getValue(),term.time.units))
else:
conversions += ' "{0:s}": {1:g},\n'.format(term.species.label, term.conversion)
if conversions:
f.write(' terminationConversion = {\n')
f.write(conversions)
f.write(' },\n')
# Sensitivity analysis
if system.sensitiveSpecies:
sensitivity = []
for item in system.sensitiveSpecies:
sensitivity.append(item.label)
f.write(' sensitivity = {0},\n'.format(sensitivity))
f.write(' sensitivityThreshold = {0},\n'.format(system.sensitivityThreshold))
f.write(')\n\n')
if rmg.solvent:
f.write("solvation(\n solvent = '{0!s}'\n)\n\n".format(rmg.solvent))
# Simulator tolerances
f.write('simulator(\n')
f.write(' atol = {0:g},\n'.format(rmg.absoluteTolerance))
f.write(' rtol = {0:g},\n'.format(rmg.relativeTolerance))
f.write(' sens_atol = {0:g},\n'.format(rmg.sensitivityAbsoluteTolerance))
f.write(' sens_rtol = {0:g},\n'.format(rmg.sensitivityRelativeTolerance))
f.write(')\n\n')
# Model
f.write('model(\n')
f.write(' toleranceMoveToCore = {0:g},\n'.format(rmg.fluxToleranceMoveToCore))
f.write(' toleranceKeepInEdge = {0:g},\n'.format(rmg.fluxToleranceKeepInEdge))
f.write(' toleranceInterruptSimulation = {0:g},\n'.format(rmg.fluxToleranceInterrupt))
f.write(' maximumEdgeSpecies = {0:d},\n'.format(rmg.maximumEdgeSpecies))
f.write(' minCoreSizeForPrune = {0:d},\n'.format(rmg.minCoreSizeForPrune))
f.write(' minSpeciesExistIterationsForPrune = {0:d},\n'.format(rmg.minSpeciesExistIterationsForPrune))
f.write(' filterReactions = {0:d},\n'.format(rmg.filterReactions))
f.write(')\n\n')
# Pressure Dependence
if rmg.pressureDependence:
f.write('pressureDependence(\n')
f.write(' method = {0!r},\n'.format(rmg.pressureDependence.method))
f.write(' maximumGrainSize = ({0:g},"{1!s}"),\n'.format(rmg.pressureDependence.grainSize.getValue(),rmg.pressureDependence.grainSize.units))
f.write(' minimumNumberOfGrains = {0},\n'.format(rmg.pressureDependence.grainCount))
f.write(' temperatures = ({0:g},{1:g},"{2!s}",{3:d}),\n'.format(
rmg.pressureDependence.Tmin.getValue(),
rmg.pressureDependence.Tmax.getValue(),
rmg.pressureDependence.Tmax.units,
rmg.pressureDependence.Tcount,
))
f.write(' pressures = ({0:g},{1:g},"{2!s}",{3:d}),\n'.format(
rmg.pressureDependence.Pmin.getValue(),
rmg.pressureDependence.Pmax.getValue(),
rmg.pressureDependence.Pmax.units,
rmg.pressureDependence.Pcount,
))
f.write(' interpolation = {0},\n'.format(rmg.pressureDependence.interpolationModel))
f.write(' maximumAtoms = {0}, \n'.format(rmg.pressureDependence.maximumAtoms))
f.write(')\n\n')
# Quantum Mechanics
if rmg.quantumMechanics:
f.write('quantumMechanics(\n')
f.write(' software = {0!r},\n'.format(rmg.quantumMechanics.settings.software))
f.write(' method = {0!r},\n'.format(rmg.quantumMechanics.settings.method))
# Split paths created by QMSettings
if rmg.quantumMechanics.settings.fileStore:
f.write(' fileStore = {0!r},\n'.format(os.path.split(rmg.quantumMechanics.settings.fileStore)[0]))
else:
f.write(' fileStore = None,\n')
if rmg.quantumMechanics.settings.scratchDirectory:
f.write(' scratchDirectory = {0!r},\n'.format(os.path.split(rmg.quantumMechanics.settings.scratchDirectory)[0]))
else:
f.write(' scratchDirectory = None,\n')
f.write(' onlyCyclics = {0},\n'.format(rmg.quantumMechanics.settings.onlyCyclics))
f.write(' maxRadicalNumber = {0},\n'.format(rmg.quantumMechanics.settings.maxRadicalNumber))
f.write(')\n\n')
# Species Constraints
if rmg.speciesConstraints:
f.write('generatedSpeciesConstraints(\n')
for constraint, value in sorted(rmg.speciesConstraints.items(), key=lambda constraint: constraint[0]):
if value is not None: f.write(' {0} = {1},\n'.format(constraint,value))
f.write(')\n\n')
# Options
f.write('options(\n')
f.write(' units = "{0}",\n'.format(rmg.units))
if rmg.saveRestartPeriod:
f.write(' saveRestartPeriod = ({0},"{1}"),\n'.format(rmg.saveRestartPeriod.getValue(), rmg.saveRestartPeriod.units))
else:
f.write(' saveRestartPeriod = None,\n')
f.write(' generateOutputHTML = {0},\n'.format(rmg.generateOutputHTML))
f.write(' generatePlots = {0},\n'.format(rmg.generatePlots))
f.write(' saveSimulationProfiles = {0},\n'.format(rmg.saveSimulationProfiles))
f.write(' saveEdgeSpecies = {0},\n'.format(rmg.saveEdgeSpecies))
f.write(' keepIrreversible = {0},\n'.format(rmg.keepIrreversible))
f.write(' verboseComments = {0},\n'.format(rmg.verboseComments))
f.write(' wallTime = {0},\n'.format(rmg.wallTime))
f.write(')\n\n')
f.close()
def getInput(name):
"""
Returns the RMG input object that corresponds
to the parameter name.
First, the module level is queried. If this variable
is empty, the broadcasted variables are queried.
"""
global rmg
if rmg:
if name == 'speciesConstraints':
return rmg.speciesConstraints
elif name == 'quantumMechanics':
return rmg.quantumMechanics
elif name == 'thermoCentralDatabase':
return rmg.thermoCentralDatabase
else:
raise Exception('Unrecognized keyword: {}'.format(name))
else:
try:
obj = get(name)
if obj:
return obj
else:
raise Exception
except Exception, e:
logging.debug("Did not find a way to obtain the variable for {}.".format(name))
raise e
raise Exception('Could not get variable with name: {}'.format(name))