import main
main.initializeLog(logging.DEBUG)
datapath = '../data/RMG_database/'
logging.debug('General database: ' + os.path.abspath(datapath))
species.thermoDatabase = species.ThermoDatabaseSet()
species.thermoDatabase.load(datapath)
thermo.forbiddenStructures = data.Dictionary()
thermo.forbiddenStructures.load(datapath + 'forbiddenStructure.txt')
thermo.forbiddenStructures.toStructure()
#reaction.kineticsDatabase = reaction.ReactionFamilySet()
#reaction.kineticsDatabase.load(datapath)
structure = chem.Structure(); structure.fromSMILES('C')
CH4 = species.makeNewSpecies(structure)
structure = chem.Structure(); structure.fromSMILES('[H]')
H = species.makeNewSpecies(structure)
structure = chem.Structure(); structure.fromSMILES('[CH3]')
CH3 = species.makeNewSpecies(structure)
forward = reaction.Reaction([CH3, H], [CH4])
reverse = reaction.Reaction([CH4], [CH3, H])
forward.reverse = reverse
reverse.reverse = forward
kinetics = reaction.ArrheniusEPKinetics()
kinetics.fromDatabase([300, 2000, 1.93E14, 0, 0, 0.27, 0, 0, 0, 0, 3], '', 2)
forward.kinetics = [kinetics]
def loadSeedMechanism(self, path):
"""
Loads a seed mechanism from the folder indicated by `path` into the
core-edge reaction model.
"""
import os.path
import quantities as pq
import data
import species
import kinetics
import reaction
# Load the species data from the file species.txt
# This file has the format of a standard RMG dictionary
d = data.Dictionary()
d.load(os.path.join(path, 'species.txt'))
d.toStructure(addH=True)
# Load the thermo data from the file thermo.txt
# This file has the format of a standard RMG thermo library
thermoData = species.ThermoDatabase()
thermoData.load(os.path.join(path, 'species.txt'), '', os.path.join(path, 'thermo.txt'))
# Populate the main primary thermo library with this thermo data
# This will overwrite keys (but not values), so the order that the
# seed mechanisms are loaded matters!
for key, value in d.iteritems():
species.thermoDatabase.primaryDatabase.dictionary[key] = value
for key, value in thermoData.library.iteritems():
species.thermoDatabase.primaryDatabase.library[key] = value
# Create new species based on items in species.txt
speciesDict = {}; speciesList = []
for label, struct in d.iteritems():
spec = species.makeNewSpecies(struct, label, reactive=True)
speciesDict[label] = spec
speciesList.append(spec)
# Load the reactions from the file reaction.txt
reactionList = []
f = open(os.path.join(path, 'reactions.txt'), 'r')
for line in f:
line = data.removeCommentFromLine(line)
line.strip()
if len(line) > 0:
items = line.split()
if len(items) > 0:
rxn = items[0:-6]
# Extract reactants and products
if '<=>' in rxn: arrow = rxn.index('<=>')
elif '=>' in rxn: arrow = rxn.index('=>')
else: raise IOError('No arrow found in reaction equation from line %s' % line)
reactants = rxn[0:arrow:2]
products = rxn[arrow+1::2]
# Remove third body 'M' if present
thirdBody = False
if 'M' in reactants and 'M' in products:
thirdBody = True
reactants.remove('M')
products.remove('M')
# Convert strings to species objects
reactants = [speciesDict[r] for r in reactants]
products = [speciesDict[r] for r in products]
# Process Arrhenius parameters
order = len(reactants)
if (thirdBody): order += 1
Aunits = 'cm^%i/(mol^%i*s)' % (3*(order-1), order-1)
A = float(pq.Quantity(float(items[-6]), Aunits).simplified)
n = float(items[-5]) # dimensionless
Ea = float(pq.Quantity(float(items[-4]), 'cal/mol').simplified)
kin = [kinetics.ArrheniusKinetics(A=A, n=n, Ea=Ea)]
# Create reaction object and add to list
rxn = reaction.Reaction(reactants, products, 'seed', kin, thirdBody=thirdBody)
reaction.processNewReaction(rxn)
reactionList.append(rxn)
f.close()
# Add species to core
for spec in speciesList:
self.addSpeciesToCore(spec)
# Add reactions to core
for rxn in reactionList:
self.addReactionToCore(rxn)
def readInputFile(fstr):
"""
Parse an RMG input file at the location `fstr`. If successful, this
function returns a :class:`rmg.model.CoreEdgeReactionModel` object and a
list of one or more :class:`rmg.model.ReactionSystem` objects.
"""
try:
# Parse the RMG input XML file into a DOM tree
xml0 = XML(path=fstr)
# Make sure root element is a <rmginput> element
rootElement = xml0.getRootElement()
if rootElement.tagName != 'rmginput':
raise InvalidInputFileException('Incorrect root element; should be <rmginput>.')
# Process units
units = xml0.getChildElementText(rootElement, 'units', required=False, default='si')
pq.set_default_units(units)
# Read draw molecules option
drawMolecules = xml0.getChildElementText(rootElement, 'drawMolecules', required=False, default='off')
drawMolecules = drawMolecules.lower()
settings.drawMolecules = (drawMolecules == 'on' or drawMolecules == 'true' or drawMolecules == 'yes')
# Read generate plots option
generatePlots = xml0.getChildElementText(rootElement, 'generatePlots', required=False, default='off')
generatePlots = generatePlots.lower()
settings.generatePlots = (generatePlots == 'on' or generatePlots == 'true' or generatePlots == 'yes')
# Process databases
databases = []
databaseElements = xml0.getChildElements(rootElement, 'database')
for element in databaseElements:
# Get database type
databaseType = xml0.getAttribute(element, 'type', required=True)
databaseType = databaseType.lower()
if databaseType != 'general':
raise InvalidInputFileException('Invalid database type "' + databaseType + '"; valid types are "general".')
# Get database name and form path
databaseName = xml0.getElementText(element)
databasePath = os.path.dirname(__file__)
databasePath = os.path.join(databasePath, '..')
databasePath = os.path.join(databasePath, '..')
databasePath = os.path.join(databasePath, 'data')
databasePath = os.path.join(databasePath, databaseName)
if not os.path.exists(databasePath):
raise InvalidInputFileException('Database "%s" not found.' % databaseName)
databases.append([databaseName, databaseType, databasePath])
# Output info about databases
logging.info('Found %s database%s' % (len(databases), 's' if len(databases) > 1 else ''))
# Check that exactly one general database was specified
generalDatabaseCount = sum([1 for database in databases if database[1] == 'general'])
if generalDatabaseCount == 0:
raise InvalidInputFileException('No general database specified; one must be present.')
elif generalDatabaseCount > 1:
raise InvalidInputFileException('Multiple general databases specified; only one is allowed.')
# Load databases
for database in databases:
if database[1] == 'general':
logging.debug('General database: ' + database[2])
# Load thermo databases
species.thermoDatabase = species.ThermoDatabaseSet()
species.thermoDatabase.load(database[2] + os.sep)
# Load forbidden structures
thermo.forbiddenStructures = data.Dictionary()
thermo.forbiddenStructures.load(database[2] + os.sep + 'forbiddenStructure.txt')
thermo.forbiddenStructures.toStructure()
# Load kinetic databases (reaction families)
reaction.kineticsDatabase = reaction.ReactionFamilySet()
reaction.kineticsDatabase.load(database[2] + os.sep)
logging.debug('')
# Process species
coreSpecies = []; speciesDict = {}
speciesElements = xml0.getChildElements(rootElement, 'species')
logging.info('Found ' + str(len(speciesElements)) + ' species')
for element in speciesElements:
# Attributes of the species element
sid = xml0.getAttribute(element, 'id')
label = xml0.getAttribute(element, 'label')
reactive = xml0.getAttribute(element, 'reactive', required=False, default='yes')
reactive = reactive.lower()
reactive = not (reactive == 'no' or reactive == 'false' or reactive == 'n')
# Load structure
struct = structure.Structure()
cml = xml0.getChildElement(element, 'cml', required=False)
inchi = xml0.getChildElement(element, 'inchi', required=False)
smiles = xml0.getChildElement(element, 'smiles', required=False)
if cml is not None:
cmlstr = str(xml0.getChildElement(cml, 'molecule', required=True).toxml())
struct.fromCML(cmlstr)
elif inchi is not None:
inchistr = str(xml0.getElementText(inchi))
struct.fromInChI(inchistr)
elif smiles is not None:
smilesstr = str(xml0.getElementText(smiles))
struct.fromSMILES(smilesstr)
else:
raise InvalidInputFileException('Species "%s" missing structure information.' % label)
# Create a new species and append the species to the core
spec = species.makeNewSpecies(struct, label, reactive)
coreSpecies.append(spec)
# Add to local species dictionary (for matching with other parts of file)
speciesDict[sid] = spec
logging.debug('')
# Create an empty reaction model
reactionModel = model.CoreEdgeReactionModel()
# Read model flux tolerance
fluxTolerance = xml0.getChildElement(rootElement, 'fluxTolerance')
reactionModel.fluxToleranceKeepInEdge = float(xml0.getChildElementText(fluxTolerance, 'keepInEdge'))
reactionModel.fluxToleranceMoveToCore = float(xml0.getChildElementText(fluxTolerance, 'moveToCore'))
reactionModel.fluxToleranceInterrupt = float(xml0.getChildElementText(fluxTolerance, 'interruptSimulation'))
logging.debug('Model flux tolerances set to:')
logging.debug('\tKeep in edge: %s' % (reactionModel.fluxToleranceKeepInEdge) )
logging.debug('\tMove to core: %s' % (reactionModel.fluxToleranceMoveToCore) )
logging.debug('\tInterrupt simulation: %s' % (reactionModel.fluxToleranceInterrupt) )
logging.debug('')
# Read maximum model size
maxModelSize = xml0.getChildElement(rootElement, 'maximumModelSize')
if maxModelSize is None:
logging.debug('Maximum model size is not set')
else:
reactionModel.maximumEdgeSpecies = int(xml0.getChildElementText(maxModelSize, 'edgeSpecies'))
logging.debug('Maximum model size set to:')
logging.debug('\tEdge species: %s' % (reactionModel.maximumEdgeSpecies) )
logging.debug('')
# Read dynamic simulator
element = xml0.getChildElement(rootElement, 'simulator')
reactionModel.absoluteTolerance = float(xml0.getAttribute(element, 'atol'))
reactionModel.relativeTolerance = float(xml0.getAttribute(element, 'rtol'))
logging.info('Read dynamic simulator')
logging.debug('Simulator:')
logging.debug('\tAbsolute tolerance set to %s' % (reactionModel.absoluteTolerance))
logging.debug('\tRelative tolerance set to %s' % (reactionModel.relativeTolerance))
logging.debug('')
# Read termination targets
termination = xml0.getChildElement(rootElement, 'termination')
targetElements = xml0.getChildElements(termination, 'target')
for element in targetElements:
targetType = xml0.getAttribute(element, 'type')
if targetType == 'conversion':
sid = xml0.getAttribute(element, 'speciesID')
spec = speciesDict[sid]
conv = float(xml0.getElementText(element))
if conv < 0.0 or conv > 1.0:
raise InvalidInputFileException('Invalid value for termination fractional conversion.')
reactionModel.termination.append(model.TerminationConversion(spec, conv))
elif targetType == 'time':
units = str(xml0.getAttribute(element, 'units'))
time = float(xml0.getElementText(element))
time = pq.Quantity(time, units); time = float(time.simplified)
if time < 0.0:
raise InvalidInputFileException('Invalid value for termination time.')
reactionModel.termination.append(model.TerminationTime(time))
else:
raise InvalidInputFileException('Invalid termination target type "'+targetType+'".')
if len(reactionModel.termination) == 0:
raise InvalidInputFileException('No termination targets specified.')
# Output info about termination targets
if len(reactionModel.termination) == 1:
logging.info('Found ' + str(len(reactionModel.termination)) + ' termination target')
else:
logging.info('Found ' + str(len(reactionModel.termination)) + ' termination targets')
for index, target in enumerate(reactionModel.termination):
string = '\tTermination target #' + str(index+1) + ': '
if target.__class__ == model.TerminationConversion:
string += 'conversion ' + str(target.species) + ' ' + str(target.conversion)
elif target.__class__ == model.TerminationTime:
string += 'time ' + str(target.time)
logging.debug(string)
logging.debug('')
# Process reaction systems
reactionSystems = []
systemElements = xml0.getChildElements(rootElement, 'reactionSystem')
for element in systemElements:
# Create a new reaction system
rsType = xml0.getAttribute(element, 'type')
if rsType == 'batch':
reactionSystem = model.BatchReactor()
else:
raise InvalidInputFileException('Invalid reaction system type "' + rsType + '".')
# Temperature model
temperatureModel = xml0.getChildElement(element, 'temperatureModel')
tempModelType = xml0.getAttribute(temperatureModel, 'type')
if tempModelType == 'isothermal':
# Read the (constant) temperature from the file
temperature = xml0.getChildElement(temperatureModel, 'temperature')
value = float(xml0.getElementText(temperature))
units = str(xml0.getAttribute(temperature, 'units'))
T = pq.Quantity(value, units); T = float(T.simplified)
# Set the reaction system's temperature model to isothermal
reactionSystem.temperatureModel = model.TemperatureModel()
reactionSystem.temperatureModel.setIsothermal(T)
else:
raise InvalidInputFileException('Invalid temperature model type "' + tempModelType + '".')
# Pressure model
pressureModel = xml0.getChildElement(element, 'pressureModel')
pressModelType = xml0.getAttribute(pressureModel, 'type')
if pressModelType == 'isobaric':
# Read the (constant) pressure from the file
pressure = xml0.getChildElement(pressureModel, 'pressure')
value = float(xml0.getElementText(pressure))
units = str(xml0.getAttribute(pressure, 'units'))
P = pq.Quantity(value, units); P = float(P.simplified)
# Set the reaction system's pressure model to isobaric
reactionSystem.pressureModel = model.PressureModel()
reactionSystem.pressureModel.setIsobaric(P)
else:
raise InvalidInputFileException('Invalid pressure model type "' + pressModelType + '".')
# Physical property model
propModel = xml0.getChildElement(element, 'physicalPropertyModel')
propModelType = xml0.getAttribute(propModel, 'type')
if propModelType.lower() == 'idealgas':
# Set the reaction system's pressure model to isobaric
reactionSystem.equationOfState = model.IdealGas()
elif propModelType.lower() == 'incompressibleliquid':
molarVolume = xml0.getFirstChildElement(element, 'molarVolume')
value = float(xml0.getElementText(molarVolume))
units = str(xml0.getAttribute(molarVolume, 'units'))
Vmol = float(pq.Quantity(value, units).simplified);
reactionSystem.equationOfState = model.IncompressibleLiquid(
P = reactionSystem.pressureModel.getPressure(),
T = reactionSystem.temperatureModel.getTemperature(),
Vmol = Vmol
)
else:
raise InvalidInputFileException('Invalid physical property model type "' + propModelType + '".')
# Get total concentration
T = reactionSystem.temperatureModel.getTemperature(0)
P = reactionSystem.pressureModel.getPressure(0)
totalConc = 1.0 / reactionSystem.equationOfState.getVolume(T, P, [1.0])
# Initialize all initial concentrations to zero
for spec in coreSpecies:
reactionSystem.initialConcentration[spec] = 0.0
# List of initial concentrations
moleFractions = xml0.getChildElements(element, 'moleFraction')
for moleFraction in moleFractions:
# Read the concentration from the file
value = float(xml0.getElementText(moleFraction))
sid = xml0.getAttribute(moleFraction, 'speciesID')
reactionSystem.initialConcentration[speciesDict[sid]] = value * totalConc
# Append to list of reaction systems
reactionSystems.append(reactionSystem)
# Output info about reaction system
if len(reactionSystems) == 1:
logging.info('Found ' + str(len(reactionSystems)) + ' reaction system')
else:
logging.info('Found ' + str(len(reactionSystems)) + ' reaction systems')
for index, reactionSystem in enumerate(reactionSystems):
logging.debug('Reaction system #' + str(index+1) + ':')
logging.debug('\t' + str(reactionSystem.temperatureModel))
logging.debug('\t' + str(reactionSystem.pressureModel))
for spec, conc in reactionSystem.initialConcentration.iteritems():
if spec.reactive:
logging.debug('\tInitial concentration of ' + str(spec) + ': ' + str(conc))
else:
logging.debug('\tConstant concentration of ' + str(spec) + ': ' + str(conc))
logging.debug('')
# Cleanup the DOM tree when finished
xml0.cleanup()
except InvalidInputFileException, e:
logging.exception(str(e))
raise e
