def load(self):
"""
Load the contents of the input file into a PressureDependenceJob object.
"""
from arkane.pdep import PressureDependenceJob
from arkane.input import load_input_file
# Seed with a PdepJob object
if self.pdep is None:
self.pdep = PressureDependenceJob(network=None)
if self.inputFileExists():
job_list = load_input_file(self.getInputFilename())[0]
assert len(job_list) == 1
job = job_list[0]
if isinstance(job, PressureDependenceJob) is False:
raise Exception('Input file given did not provide a pressure dependence network.')
self.pdep = job
self.pdep.initialize()
if self.pdep.network is not None:
self.title = self.pdep.network.label
self.save()
return self.pdep.network
def load(self):
"""
Load the contents of the input file into a PressureDependenceJob object.
"""
from arkane.pdep import PressureDependenceJob
from arkane.input import loadInputFile
# Seed with a PdepJob object
if self.pdep is None:
self.pdep = PressureDependenceJob(network=None)
if self.inputFileExists():
jobList = loadInputFile(self.getInputFilename())[0]
assert len(jobList) == 1
job = jobList[0]
if isinstance(job, PressureDependenceJob) is False:
raise Exception('Input file given did not provide a pressure dependence network.')
self.pdep = job
self.pdep.initialize()
if self.pdep.network is not None:
self.title = self.pdep.network.label
self.save()
return self.pdep.network
def pressureDependence(
method,
temperatures,
pressures,
maximumGrainSize=0.0,
minimumNumberOfGrains=0,
interpolation=None,
maximumAtoms=None,
):
from arkane.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 pressureDependence(label,
Tmin=None,
Tmax=None,
Tcount=0,
Tlist=None,
Pmin=None,
Pmax=None,
Pcount=0,
Plist=None,
maximumGrainSize=None,
minimumGrainCount=0,
method=None,
interpolationModel=None,
activeKRotor=True,
activeJRotor=True,
rmgmode=False,
sensitivity_conditions=None):
"""Generate a pressure dependent job"""
global job_list, network_dict
if isinstance(interpolationModel, str):
interpolationModel = (interpolationModel, )
nwk = None
if label in list(network_dict.keys()):
nwk = network_dict[label]
job = PressureDependenceJob(network=nwk,
Tmin=Tmin,
Tmax=Tmax,
Tcount=Tcount,
Tlist=Tlist,
Pmin=Pmin,
Pmax=Pmax,
Pcount=Pcount,
Plist=Plist,
maximumGrainSize=maximumGrainSize,
minimumGrainCount=minimumGrainCount,
method=method,
interpolationModel=interpolationModel,
activeKRotor=activeKRotor,
activeJRotor=activeJRotor,
rmgmode=rmgmode,
sensitivity_conditions=sensitivity_conditions)
job_list.append(job)
def saveForm(self, posted, form):
"""
Save form data into input.py file specified by the path.
"""
# Clean past history
self.rmg = RMG()
# Databases
#self.rmg.databaseDirectory = settings['database.directory']
self.rmg.thermoLibraries = []
if posted.thermo_libraries.all():
self.rmg.thermoLibraries = [
item.thermolib.encode()
for item in posted.thermo_libraries.all()
]
self.rmg.reactionLibraries = []
self.rmg.seedMechanisms = []
if posted.reaction_libraries.all():
for item in posted.reaction_libraries.all():
if not item.seedmech and not item.edge:
self.rmg.reactionLibraries.append(
(item.reactionlib.encode(), False))
elif not item.seedmech:
self.rmg.reactionLibraries.append(
(item.reactionlib.encode(), True))
else:
self.rmg.seedMechanisms.append(item.reactionlib.encode())
self.rmg.statmechLibraries = []
self.rmg.kineticsDepositories = 'default'
self.rmg.kineticsFamilies = 'default'
self.rmg.kineticsEstimator = 'rate rules'
# Species
self.rmg.initialSpecies = []
speciesDict = {}
initialMoleFractions = {}
self.rmg.reactionModel = CoreEdgeReactionModel()
for item in posted.reactor_species.all():
structure = Molecule().fromAdjacencyList(item.adjlist.encode())
spec, isNew = self.rmg.reactionModel.makeNewSpecies(
structure,
label=item.name.encode(),
reactive=False if item.inert else True)
self.rmg.initialSpecies.append(spec)
speciesDict[item.name.encode()] = spec
initialMoleFractions[spec] = item.molefrac
# Reactor systems
self.rmg.reactionSystems = []
for item in posted.reactor_systems.all():
T = Quantity(item.temperature, item.temperature_units.encode())
P = Quantity(item.pressure, item.pressure_units.encode())
termination = []
if item.conversion:
termination.append(
TerminationConversion(speciesDict[item.species.encode()],
item.conversion))
termination.append(
TerminationTime(
Quantity(item.terminationtime, item.time_units.encode())))
# Sensitivity Analysis
sensitiveSpecies = []
if item.sensitivity:
if isinstance(item.sensitivity.encode(), str):
sensitivity = item.sensitivity.encode().split(',')
for spec in sensitivity:
sensitiveSpecies.append(speciesDict[spec.strip()])
system = SimpleReactor(T, P, initialMoleFractions, termination,
sensitiveSpecies, item.sensitivityThreshold)
self.rmg.reactionSystems.append(system)
# Simulator tolerances
self.rmg.absoluteTolerance = form.cleaned_data['simulator_atol']
self.rmg.relativeTolerance = form.cleaned_data['simulator_rtol']
self.rmg.sensitivityAbsoluteTolerance = form.cleaned_data[
'simulator_sens_atol']
self.rmg.sensitivityRelativeTolerance = form.cleaned_data[
'simulator_sens_rtol']
self.rmg.fluxToleranceKeepInEdge = form.cleaned_data[
'toleranceKeepInEdge']
self.rmg.fluxToleranceMoveToCore = form.cleaned_data[
'toleranceMoveToCore']
self.rmg.fluxToleranceInterrupt = form.cleaned_data[
'toleranceInterruptSimulation']
self.rmg.maximumEdgeSpecies = form.cleaned_data['maximumEdgeSpecies']
self.rmg.minCoreSizeForPrune = form.cleaned_data['minCoreSizeForPrune']
self.rmg.minSpeciesExistIterationsForPrune = form.cleaned_data[
'minSpeciesExistIterationsForPrune']
self.rmg.filterReactions = form.cleaned_data['filterReactions']
# Pressure Dependence
pdep = form.cleaned_data['pdep'].encode()
if pdep != 'off':
self.rmg.pressureDependence = PressureDependenceJob(network=None)
self.rmg.pressureDependence.method = pdep
# Process interpolation model
if form.cleaned_data['interpolation'].encode() == 'chebyshev':
self.rmg.pressureDependence.interpolationModel = (
form.cleaned_data['interpolation'].encode(),
form.cleaned_data['temp_basis'],
form.cleaned_data['p_basis'])
else:
self.rmg.pressureDependence.interpolationModel = (
form.cleaned_data['interpolation'].encode(), )
# Temperature and pressure range
self.rmg.pressureDependence.Tmin = Quantity(
form.cleaned_data['temp_low'],
form.cleaned_data['temprange_units'].encode())
self.rmg.pressureDependence.Tmax = Quantity(
form.cleaned_data['temp_high'],
form.cleaned_data['temprange_units'].encode())
self.rmg.pressureDependence.Tcount = form.cleaned_data[
'temp_interp']
self.rmg.pressureDependence.generateTemperatureList()
self.rmg.pressureDependence.Pmin = Quantity(
form.cleaned_data['p_low'],
form.cleaned_data['prange_units'].encode())
self.rmg.pressureDependence.Pmax = Quantity(
form.cleaned_data['p_high'],
form.cleaned_data['prange_units'].encode())
self.rmg.pressureDependence.Pcount = form.cleaned_data['p_interp']
self.rmg.pressureDependence.generatePressureList()
# Process grain size and count
self.rmg.pressureDependence.grainSize = Quantity(
form.cleaned_data['maximumGrainSize'],
form.cleaned_data['grainsize_units'].encode())
self.rmg.pressureDependence.grainCount = form.cleaned_data[
'minimumNumberOfGrains']
self.rmg.pressureDependence.maximumAtoms = form.cleaned_data[
'maximumAtoms']
# Additional Options
self.rmg.units = 'si'
self.rmg.saveRestartPeriod = Quantity(
form.cleaned_data['saveRestartPeriod'],
form.cleaned_data['saveRestartPeriodUnits'].encode(
)) if form.cleaned_data['saveRestartPeriod'] else None
self.rmg.generateOutputHTML = form.cleaned_data['generateOutputHTML']
self.rmg.generatePlots = form.cleaned_data['generatePlots']
self.rmg.saveSimulationProfiles = form.cleaned_data[
'saveSimulationProfiles']
self.rmg.saveEdgeSpecies = form.cleaned_data['saveEdgeSpecies']
self.rmg.verboseComments = form.cleaned_data['verboseComments']
# Species Constraints
speciesConstraints = form.cleaned_data['speciesConstraints']
if speciesConstraints == 'on':
allowed = []
if form.cleaned_data['allowed_inputSpecies']:
allowed.append('input species')
if form.cleaned_data['allowed_seedMechanisms']:
allowed.append('seed mechanisms')
if form.cleaned_data['allowed_reactionLibraries']:
allowed.append('reaction libraries')
self.rmg.speciesConstraints['allowed'] = allowed
self.rmg.speciesConstraints[
'maximumCarbonAtoms'] = form.cleaned_data['maximumCarbonAtoms']
self.rmg.speciesConstraints[
'maximumOxygenAtoms'] = form.cleaned_data['maximumOxygenAtoms']
self.rmg.speciesConstraints[
'maximumNitrogenAtoms'] = form.cleaned_data[
'maximumNitrogenAtoms']
self.rmg.speciesConstraints[
'maximumSiliconAtoms'] = form.cleaned_data[
'maximumSiliconAtoms']
self.rmg.speciesConstraints[
'maximumSulfurAtoms'] = form.cleaned_data['maximumSulfurAtoms']
self.rmg.speciesConstraints[
'maximumHeavyAtoms'] = form.cleaned_data['maximumHeavyAtoms']
self.rmg.speciesConstraints[
'maximumRadicalElectrons'] = form.cleaned_data[
'maximumRadicalElectrons']
self.rmg.speciesConstraints['allowSingletO2'] = form.cleaned_data[
'allowSingletO2']
# Quantum Calculations
quantumCalc = form.cleaned_data['quantumCalc']
if quantumCalc == 'on':
from rmgpy.qm.main import QMCalculator
self.rmg.quantumMechanics = QMCalculator(
software=form.cleaned_data['software'].encode(),
method=form.cleaned_data['method'].encode(),
fileStore=form.cleaned_data['fileStore'].encode(),
scratchDirectory=form.cleaned_data['scratchDirectory'].encode(
),
onlyCyclics=form.cleaned_data['onlyCyclics'],
maxRadicalNumber=form.cleaned_data['maxRadicalNumber'],
)
# Save the input.py file
self.rmg.saveInput(self.savepath)
class Network(models.Model):
"""
A Django model of a pressure-dependent reaction network.
"""
id = models.CharField(max_length=32, primary_key=True, default=_createId)
title = models.CharField(max_length=50)
input_file = models.FileField(upload_to=uploadTo, verbose_name='Input file')
input_text = models.TextField(blank=True, verbose_name='')
user = models.ForeignKey(User, on_delete=models.CASCADE)
def __init__(self, *args, **kwargs):
super(Network, self).__init__(*args, **kwargs)
self.pdep = None
def getDirname(self):
"""
Return the absolute path of the directory that the Network object uses
to store files.
"""
return os.path.join(settings.MEDIA_ROOT, 'pdep', 'networks', str(self.pk))
def getInputFilename(self):
"""
Return the absolute path of the input file.
"""
return os.path.join(self.getDirname(), 'input.py')
def getOutputFilename(self):
"""
Return the absolute path of the output file.
"""
return os.path.join(self.getDirname(), 'output.py')
def getLogFilename(self):
"""
Return the absolute path of the log file.
"""
return os.path.join(self.getDirname(), 'arkane.log')
def getSurfaceFilenamePNG(self):
"""
Return the absolute path of the PES image file in PNG format.
"""
return os.path.join(self.getDirname(), 'network.png')
def getSurfaceFilenamePDF(self):
"""
Return the absolute path of the PES image file in PDF format.
"""
return os.path.join(self.getDirname(), 'network.pdf')
def getSurfaceFilenameSVG(self):
"""
Return the absolute path of the PES image file in SVG format.
"""
return os.path.join(self.getDirname(), 'network.svg')
def getLastModifiedDate(self):
"""
Return the date on which the network was most recently modified.
"""
if not self.inputFileExists():
return 'unknown'
mtime = os.path.getmtime(self.getInputFilename())
if self.outputFileExists():
mtime0 = os.path.getmtime(self.getOutputFilename())
if mtime < mtime0:
mtime = mtime0
if self.surfaceFilePDFExists():
mtime0 = os.path.getmtime(self.getSurfaceFilenamePDF())
if mtime < mtime0:
mtime = mtime0
if self.surfaceFilePNGExists():
mtime0 = os.path.getmtime(self.getSurfaceFilenamePNG())
if mtime < mtime0:
mtime = mtime0
if self.surfaceFileSVGExists():
mtime0 = os.path.getmtime(self.getSurfaceFilenameSVG())
if mtime < mtime0:
mtime = mtime0
gmtime = time.gmtime(mtime)
return time.strftime("%d %b %Y", gmtime)
def inputFileExists(self):
"""
Return ``True`` if the input file exists on the server or ``False`` if
not.
"""
return os.path.exists(self.getInputFilename())
def outputFileExists(self):
"""
Return ``True`` if the output file exists on the server or ``False`` if
not.
"""
return os.path.exists(self.getOutputFilename())
def logFileExists(self):
"""
Return ``True`` if the log file exists on the server or ``False`` if
not.
"""
return os.path.exists(self.getLogFilename())
def surfaceFilePNGExists(self):
"""
Return ``True`` if a potential energy surface PNG image file exists or
``False`` if not.
"""
return os.path.exists(self.getSurfaceFilenamePNG())
def surfaceFilePDFExists(self):
"""
Return ``True`` if a potential energy surface PDF image file exists or
``False`` if not.
"""
return os.path.exists(self.getSurfaceFilenamePDF())
def surfaceFileSVGExists(self):
"""
Return ``True`` if a potential energy surface SVG image file exists or
``False`` if not.
"""
return os.path.exists(self.getSurfaceFilenameSVG())
def outputFileOutOfDate(self):
"""
Return ``True`` if the output file is out of date or ``False`` if
not.
"""
return self.outputFileExists() and os.path.getmtime(self.getInputFilename()) > os.path.getmtime(self.getOutputFilename())
def surfaceFilePNGOutOfDate(self):
"""
Return ``True`` if a potential energy surface PNG image file is out of
date or ``False`` if not.
"""
return self.surfaceFilePNGExists() and os.path.getmtime(self.getInputFilename()) > os.path.getmtime(self.getSurfaceFilenamePNG())
def surfaceFilePDFOutOfDate(self):
"""
Return ``True`` if a potential energy surface PDF image file is out of
date or ``False`` if not.
"""
return self.surfaceFilePDFExists() and os.path.getmtime(self.getInputFilename()) > os.path.getmtime(self.getSurfaceFilenamePDF())
def surfaceFileSVGOutOfDate(self):
"""
Return ``True`` if a potential energy surface SVG image file is out of
date or ``False`` if not.
"""
return self.surfaceFileSVGExists() and os.path.getmtime(self.getInputFilename()) > os.path.getmtime(self.getSurfaceFilenameSVG())
def createDir(self):
"""
Create the directory (and any other needed parent directories) that
the Network uses for storing files.
"""
try:
os.makedirs(self.getDirname())
except OSError:
# Fail silently on any OS errors
pass
def deleteInputFile(self):
"""
Delete the input file for this network from the server.
"""
if self.inputFileExists():
os.remove(self.getInputFilename())
def deleteOutputFile(self):
"""
Delete the output file for this network from the server.
"""
if self.outputFileExists():
os.remove(self.getOutputFilename())
def deleteSurfaceFilePNG(self):
"""
Delete the PES image file in PNF format for this network from the
server.
"""
if os.path.exists(self.getSurfaceFilenamePNG()):
os.remove(self.getSurfaceFilenamePNG())
def deleteSurfaceFilePDF(self):
"""
Delete the PES image file in PDF format for this network from the
server.
"""
if os.path.exists(self.getSurfaceFilenamePDF()):
os.remove(self.getSurfaceFilenamePDF())
def deleteSurfaceFileSVG(self):
"""
Delete the PES image file in SVG format for this network from the
server.
"""
if os.path.exists(self.getSurfaceFilenameSVG()):
os.remove(self.getSurfaceFilenameSVG())
def loadInputText(self):
"""
Load the input file text into the inputText field.
"""
self.inputText = ''
if self.inputFileExists():
f = open(self.getInputFilename(), 'r')
for line in f:
self.inputText += line
f.close()
def saveInputText(self):
"""
Save the contents of the inputText field to the input file.
"""
f_path = self.getInputFilename()
self.createDir()
f = open(f_path, 'w')
for line in self.inputText.splitlines():
f.write(line + '\n')
f.close()
def load(self):
"""
Load the contents of the input file into a PressureDependenceJob object.
"""
from arkane.pdep import PressureDependenceJob
from arkane.input import load_input_file
# Seed with a PdepJob object
if self.pdep is None:
self.pdep = PressureDependenceJob(network=None)
if self.inputFileExists():
job_list = load_input_file(self.getInputFilename())[0]
assert len(job_list) == 1
job = job_list[0]
if isinstance(job, PressureDependenceJob) is False:
raise Exception('Input file given did not provide a pressure dependence network.')
self.pdep = job
self.pdep.initialize()
if self.pdep.network is not None:
self.title = self.pdep.network.label
self.save()
return self.pdep.network
def loadFAMEInput(path, moleculeDict=None):
"""
Load the contents of a FAME input file into the MEASURE object. FAME
is an early version of MEASURE written in Fortran and used by RMG-Java.
This script enables importing FAME input files into MEASURE so we can
use the additional functionality that MEASURE provides. Note that it
is mostly designed to load the FAME input files generated automatically
by RMG-Java, and may not load hand-crafted FAME input files. If you
specify a `moleculeDict`, then this script will use it to associate
the species with their structures.
"""
def readMeaningfulLine(f):
line = f.readline()
while line != '':
line = line.strip()
if len(line) > 0 and line[0] != '#':
return line
else:
line = f.readline()
return ''
moleculeDict = moleculeDict or {}
logging.info('Loading file "{0}"...'.format(path))
f = open(path)
job = PressureDependenceJob(network=None)
# Read method
method = readMeaningfulLine(f).lower()
if method == 'modifiedstrongcollision':
job.method = 'modified strong collision'
elif method == 'reservoirstate':
job.method = 'reservoir state'
# Read temperatures
Tcount, Tunits, Tmin, Tmax = readMeaningfulLine(f).split()
job.Tmin = Quantity(float(Tmin), Tunits)
job.Tmax = Quantity(float(Tmax), Tunits)
job.Tcount = int(Tcount)
Tlist = []
for i in range(int(Tcount)):
Tlist.append(float(readMeaningfulLine(f)))
job.Tlist = Quantity(Tlist, Tunits)
# Read pressures
Pcount, Punits, Pmin, Pmax = readMeaningfulLine(f).split()
job.Pmin = Quantity(float(Pmin), Punits)
job.Pmax = Quantity(float(Pmax), Punits)
job.Pcount = int(Pcount)
Plist = []
for i in range(int(Pcount)):
Plist.append(float(readMeaningfulLine(f)))
job.Plist = Quantity(Plist, Punits)
# Read interpolation model
model = readMeaningfulLine(f).split()
if model[0].lower() == 'chebyshev':
job.interpolationModel = ('chebyshev', int(model[1]), int(model[2]))
elif model[0].lower() == 'pdeparrhenius':
job.interpolationModel = ('pdeparrhenius', )
# Read grain size or number of grains
job.minimumGrainCount = 0
job.maximumGrainSize = None
for i in range(2):
data = readMeaningfulLine(f).split()
if data[0].lower() == 'numgrains':
job.minimumGrainCount = int(data[1])
elif data[0].lower() == 'grainsize':
job.maximumGrainSize = (float(data[2]), data[1])
# A FAME file is almost certainly created during an RMG job, so use RMG mode
job.rmgmode = True
# Create the Network
job.network = Network()
# Read collision model
data = readMeaningfulLine(f)
assert data.lower() == 'singleexpdown'
alpha0units, alpha0 = readMeaningfulLine(f).split()
T0units, T0 = readMeaningfulLine(f).split()
n = readMeaningfulLine(f)
energyTransferModel = SingleExponentialDown(
alpha0=Quantity(float(alpha0), alpha0units),
T0=Quantity(float(T0), T0units),
n=float(n),
)
speciesDict = {}
# Read bath gas parameters
bathGas = Species(label='bath_gas',
energyTransferModel=energyTransferModel)
molWtunits, molWt = readMeaningfulLine(f).split()
if molWtunits == 'u': molWtunits = 'amu'
bathGas.molecularWeight = Quantity(float(molWt), molWtunits)
sigmaLJunits, sigmaLJ = readMeaningfulLine(f).split()
epsilonLJunits, epsilonLJ = readMeaningfulLine(f).split()
assert epsilonLJunits == 'J'
bathGas.transportData = TransportData(
sigma=Quantity(float(sigmaLJ), sigmaLJunits),
epsilon=Quantity(float(epsilonLJ) / constants.kB, 'K'),
)
job.network.bathGas = {bathGas: 1.0}
# Read species data
Nspec = int(readMeaningfulLine(f))
for i in range(Nspec):
species = Species()
species.conformer = Conformer()
species.energyTransferModel = energyTransferModel
# Read species label
species.label = readMeaningfulLine(f)
speciesDict[species.label] = species
if species.label in moleculeDict:
species.molecule = [moleculeDict[species.label]]
# Read species E0
E0units, E0 = readMeaningfulLine(f).split()
species.conformer.E0 = Quantity(float(E0), E0units)
species.conformer.E0.units = 'kJ/mol'
# Read species thermo data
H298units, H298 = readMeaningfulLine(f).split()
S298units, S298 = readMeaningfulLine(f).split()
Cpcount, Cpunits = readMeaningfulLine(f).split()
Cpdata = []
for i in range(int(Cpcount)):
Cpdata.append(float(readMeaningfulLine(f)))
if S298units == 'J/mol*K': S298units = 'J/(mol*K)'
if Cpunits == 'J/mol*K': Cpunits = 'J/(mol*K)'
species.thermo = ThermoData(
H298=Quantity(float(H298), H298units),
S298=Quantity(float(S298), S298units),
Tdata=Quantity([300, 400, 500, 600, 800, 1000, 1500], "K"),
Cpdata=Quantity(Cpdata, Cpunits),
Cp0=(Cpdata[0], Cpunits),
CpInf=(Cpdata[-1], Cpunits),
)
# Read species collision parameters
molWtunits, molWt = readMeaningfulLine(f).split()
if molWtunits == 'u': molWtunits = 'amu'
species.molecularWeight = Quantity(float(molWt), molWtunits)
sigmaLJunits, sigmaLJ = readMeaningfulLine(f).split()
epsilonLJunits, epsilonLJ = readMeaningfulLine(f).split()
assert epsilonLJunits == 'J'
species.transportData = TransportData(
sigma=Quantity(float(sigmaLJ), sigmaLJunits),
epsilon=Quantity(float(epsilonLJ) / constants.kB, 'K'),
)
# Read species vibrational frequencies
freqCount, freqUnits = readMeaningfulLine(f).split()
frequencies = []
for j in range(int(freqCount)):
frequencies.append(float(readMeaningfulLine(f)))
species.conformer.modes.append(
HarmonicOscillator(frequencies=Quantity(frequencies, freqUnits), ))
# Read species external rotors
rotCount, rotUnits = readMeaningfulLine(f).split()
if int(rotCount) > 0:
raise NotImplementedError(
'Cannot handle external rotational modes in FAME input.')
# Read species internal rotors
freqCount, freqUnits = readMeaningfulLine(f).split()
frequencies = []
for j in range(int(freqCount)):
frequencies.append(float(readMeaningfulLine(f)))
barrCount, barrUnits = readMeaningfulLine(f).split()
barriers = []
for j in range(int(barrCount)):
barriers.append(float(readMeaningfulLine(f)))
if barrUnits == 'cm^-1':
barrUnits = 'J/mol'
barriers = [
barr * constants.h * constants.c * constants.Na * 100.
for barr in barriers
]
elif barrUnits in ['Hz', 's^-1']:
barrUnits = 'J/mol'
barriers = [barr * constants.h * constants.Na for barr in barriers]
elif barrUnits != 'J/mol':
raise Exception(
'Unexpected units "{0}" for hindered rotor barrier height.'.
format(barrUnits))
inertia = [
V0 / 2.0 / (nu * constants.c * 100.)**2 / constants.Na
for nu, V0 in zip(frequencies, barriers)
]
for I, V0 in zip(inertia, barriers):
species.conformer.modes.append(
HinderedRotor(
inertia=Quantity(I, "kg*m^2"),
barrier=Quantity(V0, barrUnits),
symmetry=1,
semiclassical=False,
))
# Read overall symmetry number
species.conformer.spinMultiplicity = int(readMeaningfulLine(f))
# Read isomer, reactant channel, and product channel data
Nisom = int(readMeaningfulLine(f))
Nreac = int(readMeaningfulLine(f))
Nprod = int(readMeaningfulLine(f))
for i in range(Nisom):
data = readMeaningfulLine(f).split()
assert data[0] == '1'
job.network.isomers.append(speciesDict[data[1]])
for i in range(Nreac):
data = readMeaningfulLine(f).split()
assert data[0] == '2'
job.network.reactants.append(
[speciesDict[data[1]], speciesDict[data[2]]])
for i in range(Nprod):
data = readMeaningfulLine(f).split()
if data[0] == '1':
job.network.products.append([speciesDict[data[1]]])
elif data[0] == '2':
job.network.products.append(
[speciesDict[data[1]], speciesDict[data[2]]])
# Read path reactions
Nrxn = int(readMeaningfulLine(f))
for i in range(Nrxn):
# Read and ignore reaction equation
equation = readMeaningfulLine(f)
reaction = Reaction(transitionState=TransitionState(), reversible=True)
job.network.pathReactions.append(reaction)
reaction.transitionState.conformer = Conformer()
# Read reactant and product indices
data = readMeaningfulLine(f).split()
reac = int(data[0]) - 1
prod = int(data[1]) - 1
if reac < Nisom:
reaction.reactants = [job.network.isomers[reac]]
elif reac < Nisom + Nreac:
reaction.reactants = job.network.reactants[reac - Nisom]
else:
reaction.reactants = job.network.products[reac - Nisom - Nreac]
if prod < Nisom:
reaction.products = [job.network.isomers[prod]]
elif prod < Nisom + Nreac:
reaction.products = job.network.reactants[prod - Nisom]
else:
reaction.products = job.network.products[prod - Nisom - Nreac]
# Read reaction E0
E0units, E0 = readMeaningfulLine(f).split()
reaction.transitionState.conformer.E0 = Quantity(float(E0), E0units)
reaction.transitionState.conformer.E0.units = 'kJ/mol'
# Read high-pressure limit kinetics
data = readMeaningfulLine(f)
assert data.lower() == 'arrhenius'
Aunits, A = readMeaningfulLine(f).split()
if '/' in Aunits:
index = Aunits.find('/')
Aunits = '{0}/({1})'.format(Aunits[0:index], Aunits[index + 1:])
Eaunits, Ea = readMeaningfulLine(f).split()
n = readMeaningfulLine(f)
reaction.kinetics = Arrhenius(
A=Quantity(float(A), Aunits),
Ea=Quantity(float(Ea), Eaunits),
n=Quantity(float(n)),
)
reaction.kinetics.Ea.units = 'kJ/mol'
f.close()
job.network.isomers = [
Configuration(isomer) for isomer in job.network.isomers
]
job.network.reactants = [
Configuration(*reactants) for reactants in job.network.reactants
]
job.network.products = [
Configuration(*products) for products in job.network.products
]
return job
def loadFAMEInput(path, moleculeDict=None):
"""
Load the contents of a FAME input file into the MEASURE object. FAME
is an early version of MEASURE written in Fortran and used by RMG-Java.
This script enables importing FAME input files into MEASURE so we can
use the additional functionality that MEASURE provides. Note that it
is mostly designed to load the FAME input files generated automatically
by RMG-Java, and may not load hand-crafted FAME input files. If you
specify a `moleculeDict`, then this script will use it to associate
the species with their structures.
"""
def readMeaningfulLine(f):
line = f.readline()
while line != '':
line = line.strip()
if len(line) > 0 and line[0] != '#':
return line
else:
line = f.readline()
return ''
moleculeDict = moleculeDict or {}
logging.info('Loading file "{0}"...'.format(path))
f = open(path)
job = PressureDependenceJob(network=None)
# Read method
method = readMeaningfulLine(f).lower()
if method == 'modifiedstrongcollision':
job.method = 'modified strong collision'
elif method == 'reservoirstate':
job.method = 'reservoir state'
# Read temperatures
Tcount, Tunits, Tmin, Tmax = readMeaningfulLine(f).split()
job.Tmin = Quantity(float(Tmin), Tunits)
job.Tmax = Quantity(float(Tmax), Tunits)
job.Tcount = int(Tcount)
Tlist = []
for i in range(int(Tcount)):
Tlist.append(float(readMeaningfulLine(f)))
job.Tlist = Quantity(Tlist, Tunits)
# Read pressures
Pcount, Punits, Pmin, Pmax = readMeaningfulLine(f).split()
job.Pmin = Quantity(float(Pmin), Punits)
job.Pmax = Quantity(float(Pmax), Punits)
job.Pcount = int(Pcount)
Plist = []
for i in range(int(Pcount)):
Plist.append(float(readMeaningfulLine(f)))
job.Plist = Quantity(Plist, Punits)
# Read interpolation model
model = readMeaningfulLine(f).split()
if model[0].lower() == 'chebyshev':
job.interpolationModel = ('chebyshev', int(model[1]), int(model[2]))
elif model[0].lower() == 'pdeparrhenius':
job.interpolationModel = ('pdeparrhenius',)
# Read grain size or number of grains
job.minimumGrainCount = 0
job.maximumGrainSize = None
for i in range(2):
data = readMeaningfulLine(f).split()
if data[0].lower() == 'numgrains':
job.minimumGrainCount = int(data[1])
elif data[0].lower() == 'grainsize':
job.maximumGrainSize = (float(data[2]), data[1])
# A FAME file is almost certainly created during an RMG job, so use RMG mode
job.rmgmode = True
# Create the Network
job.network = Network()
# Read collision model
data = readMeaningfulLine(f)
assert data.lower() == 'singleexpdown'
alpha0units, alpha0 = readMeaningfulLine(f).split()
T0units, T0 = readMeaningfulLine(f).split()
n = readMeaningfulLine(f)
energyTransferModel = SingleExponentialDown(
alpha0 = Quantity(float(alpha0), alpha0units),
T0 = Quantity(float(T0), T0units),
n = float(n),
)
speciesDict = {}
# Read bath gas parameters
bathGas = Species(label='bath_gas', energyTransferModel=energyTransferModel)
molWtunits, molWt = readMeaningfulLine(f).split()
if molWtunits == 'u': molWtunits = 'amu'
bathGas.molecularWeight = Quantity(float(molWt), molWtunits)
sigmaLJunits, sigmaLJ = readMeaningfulLine(f).split()
epsilonLJunits, epsilonLJ = readMeaningfulLine(f).split()
assert epsilonLJunits == 'J'
bathGas.transportData = TransportData(
sigma = Quantity(float(sigmaLJ), sigmaLJunits),
epsilon = Quantity(float(epsilonLJ) / constants.kB, 'K'),
)
job.network.bathGas = {bathGas: 1.0}
# Read species data
Nspec = int(readMeaningfulLine(f))
for i in range(Nspec):
species = Species()
species.conformer = Conformer()
species.energyTransferModel = energyTransferModel
# Read species label
species.label = readMeaningfulLine(f)
speciesDict[species.label] = species
if species.label in moleculeDict:
species.molecule = [moleculeDict[species.label]]
# Read species E0
E0units, E0 = readMeaningfulLine(f).split()
species.conformer.E0 = Quantity(float(E0), E0units)
species.conformer.E0.units = 'kJ/mol'
# Read species thermo data
H298units, H298 = readMeaningfulLine(f).split()
S298units, S298 = readMeaningfulLine(f).split()
Cpcount, Cpunits = readMeaningfulLine(f).split()
Cpdata = []
for i in range(int(Cpcount)):
Cpdata.append(float(readMeaningfulLine(f)))
if S298units == 'J/mol*K': S298units = 'J/(mol*K)'
if Cpunits == 'J/mol*K': Cpunits = 'J/(mol*K)'
species.thermo = ThermoData(
H298 = Quantity(float(H298), H298units),
S298 = Quantity(float(S298), S298units),
Tdata = Quantity([300,400,500,600,800,1000,1500], "K"),
Cpdata = Quantity(Cpdata, Cpunits),
Cp0 = (Cpdata[0], Cpunits),
CpInf = (Cpdata[-1], Cpunits),
)
# Read species collision parameters
molWtunits, molWt = readMeaningfulLine(f).split()
if molWtunits == 'u': molWtunits = 'amu'
species.molecularWeight = Quantity(float(molWt), molWtunits)
sigmaLJunits, sigmaLJ = readMeaningfulLine(f).split()
epsilonLJunits, epsilonLJ = readMeaningfulLine(f).split()
assert epsilonLJunits == 'J'
species.transportData = TransportData(
sigma = Quantity(float(sigmaLJ), sigmaLJunits),
epsilon = Quantity(float(epsilonLJ) / constants.kB, 'K'),
)
# Read species vibrational frequencies
freqCount, freqUnits = readMeaningfulLine(f).split()
frequencies = []
for j in range(int(freqCount)):
frequencies.append(float(readMeaningfulLine(f)))
species.conformer.modes.append(HarmonicOscillator(
frequencies = Quantity(frequencies, freqUnits),
))
# Read species external rotors
rotCount, rotUnits = readMeaningfulLine(f).split()
if int(rotCount) > 0:
raise NotImplementedError('Cannot handle external rotational modes in FAME input.')
# Read species internal rotors
freqCount, freqUnits = readMeaningfulLine(f).split()
frequencies = []
for j in range(int(freqCount)):
frequencies.append(float(readMeaningfulLine(f)))
barrCount, barrUnits = readMeaningfulLine(f).split()
barriers = []
for j in range(int(barrCount)):
barriers.append(float(readMeaningfulLine(f)))
if barrUnits == 'cm^-1':
barrUnits = 'J/mol'
barriers = [barr * constants.h * constants.c * constants.Na * 100. for barr in barriers]
elif barrUnits in ['Hz', 's^-1']:
barrUnits = 'J/mol'
barriers = [barr * constants.h * constants.Na for barr in barriers]
elif barrUnits != 'J/mol':
raise Exception('Unexpected units "{0}" for hindered rotor barrier height.'.format(barrUnits))
inertia = [V0 / 2.0 / (nu * constants.c * 100.)**2 / constants.Na for nu, V0 in zip(frequencies, barriers)]
for I, V0 in zip(inertia, barriers):
species.conformer.modes.append(HinderedRotor(
inertia = Quantity(I,"kg*m^2"),
barrier = Quantity(V0,barrUnits),
symmetry = 1,
semiclassical = False,
))
# Read overall symmetry number
species.conformer.spinMultiplicity = int(readMeaningfulLine(f))
# Read isomer, reactant channel, and product channel data
Nisom = int(readMeaningfulLine(f))
Nreac = int(readMeaningfulLine(f))
Nprod = int(readMeaningfulLine(f))
for i in range(Nisom):
data = readMeaningfulLine(f).split()
assert data[0] == '1'
job.network.isomers.append(speciesDict[data[1]])
for i in range(Nreac):
data = readMeaningfulLine(f).split()
assert data[0] == '2'
job.network.reactants.append([speciesDict[data[1]], speciesDict[data[2]]])
for i in range(Nprod):
data = readMeaningfulLine(f).split()
if data[0] == '1':
job.network.products.append([speciesDict[data[1]]])
elif data[0] == '2':
job.network.products.append([speciesDict[data[1]], speciesDict[data[2]]])
# Read path reactions
Nrxn = int(readMeaningfulLine(f))
for i in range(Nrxn):
# Read and ignore reaction equation
equation = readMeaningfulLine(f)
reaction = Reaction(transitionState=TransitionState(), reversible=True)
job.network.pathReactions.append(reaction)
reaction.transitionState.conformer = Conformer()
# Read reactant and product indices
data = readMeaningfulLine(f).split()
reac = int(data[0]) - 1
prod = int(data[1]) - 1
if reac < Nisom:
reaction.reactants = [job.network.isomers[reac]]
elif reac < Nisom+Nreac:
reaction.reactants = job.network.reactants[reac-Nisom]
else:
reaction.reactants = job.network.products[reac-Nisom-Nreac]
if prod < Nisom:
reaction.products = [job.network.isomers[prod]]
elif prod < Nisom+Nreac:
reaction.products = job.network.reactants[prod-Nisom]
else:
reaction.products = job.network.products[prod-Nisom-Nreac]
# Read reaction E0
E0units, E0 = readMeaningfulLine(f).split()
reaction.transitionState.conformer.E0 = Quantity(float(E0), E0units)
reaction.transitionState.conformer.E0.units = 'kJ/mol'
# Read high-pressure limit kinetics
data = readMeaningfulLine(f)
assert data.lower() == 'arrhenius'
Aunits, A = readMeaningfulLine(f).split()
if '/' in Aunits:
index = Aunits.find('/')
Aunits = '{0}/({1})'.format(Aunits[0:index], Aunits[index+1:])
Eaunits, Ea = readMeaningfulLine(f).split()
n = readMeaningfulLine(f)
reaction.kinetics = Arrhenius(
A = Quantity(float(A), Aunits),
Ea = Quantity(float(Ea), Eaunits),
n = Quantity(float(n)),
)
reaction.kinetics.Ea.units = 'kJ/mol'
f.close()
job.network.isomers = [Configuration(isomer) for isomer in job.network.isomers]
job.network.reactants = [Configuration(*reactants) for reactants in job.network.reactants]
job.network.products = [Configuration(*products) for products in job.network.products]
return job
class Network(models.Model):
"""
A Django model of a pressure-dependent reaction network.
"""
id = models.CharField(max_length=32, primary_key=True, default=_createId)
title = models.CharField(max_length=50)
inputFile = models.FileField(upload_to=uploadTo, verbose_name='Input file')
inputText = models.TextField(blank=True, verbose_name='')
user = models.ForeignKey(User)
def __init__(self, *args, **kwargs):
super(Network, self).__init__(*args, **kwargs)
self.pdep = None
def getDirname(self):
"""
Return the absolute path of the directory that the Network object uses
to store files.
"""
return os.path.join(settings.MEDIA_ROOT, 'pdep', 'networks', str(self.pk))
def getInputFilename(self):
"""
Return the absolute path of the input file.
"""
return os.path.join(self.getDirname(), 'input.py')
def getOutputFilename(self):
"""
Return the absolute path of the output file.
"""
return os.path.join(self.getDirname(), 'output.py')
def getLogFilename(self):
"""
Return the absolute path of the log file.
"""
return os.path.join(self.getDirname(), 'arkane.log')
def getSurfaceFilenamePNG(self):
"""
Return the absolute path of the PES image file in PNG format.
"""
return os.path.join(self.getDirname(), 'network.png')
def getSurfaceFilenamePDF(self):
"""
Return the absolute path of the PES image file in PDF format.
"""
return os.path.join(self.getDirname(), 'network.pdf')
def getSurfaceFilenameSVG(self):
"""
Return the absolute path of the PES image file in SVG format.
"""
return os.path.join(self.getDirname(), 'network.svg')
def getLastModifiedDate(self):
"""
Return the date on which the network was most recently modified.
"""
if not self.inputFileExists(): return 'unknown'
mtime = os.path.getmtime(self.getInputFilename())
if self.outputFileExists():
mtime0 = os.path.getmtime(self.getOutputFilename())
if mtime < mtime0: mtime = mtime0
if self.surfaceFilePDFExists():
mtime0 = os.path.getmtime(self.getSurfaceFilenamePDF())
if mtime < mtime0: mtime = mtime0
if self.surfaceFilePNGExists():
mtime0 = os.path.getmtime(self.getSurfaceFilenamePNG())
if mtime < mtime0: mtime = mtime0
if self.surfaceFileSVGExists():
mtime0 = os.path.getmtime(self.getSurfaceFilenameSVG())
if mtime < mtime0: mtime = mtime0
gmtime = time.gmtime(mtime)
return time.strftime("%d %b %Y", gmtime)
def inputFileExists(self):
"""
Return ``True`` if the input file exists on the server or ``False`` if
not.
"""
return os.path.exists(self.getInputFilename())
def outputFileExists(self):
"""
Return ``True`` if the output file exists on the server or ``False`` if
not.
"""
return os.path.exists(self.getOutputFilename())
def logFileExists(self):
"""
Return ``True`` if the log file exists on the server or ``False`` if
not.
"""
return os.path.exists(self.getLogFilename())
def surfaceFilePNGExists(self):
"""
Return ``True`` if a potential energy surface PNG image file exists or
``False`` if not.
"""
return os.path.exists(self.getSurfaceFilenamePNG())
def surfaceFilePDFExists(self):
"""
Return ``True`` if a potential energy surface PDF image file exists or
``False`` if not.
"""
return os.path.exists(self.getSurfaceFilenamePDF())
def surfaceFileSVGExists(self):
"""
Return ``True`` if a potential energy surface SVG image file exists or
``False`` if not.
"""
return os.path.exists(self.getSurfaceFilenameSVG())
def outputFileOutOfDate(self):
"""
Return ``True`` if the output file is out of date or ``False`` if
not.
"""
return self.outputFileExists() and os.path.getmtime(self.getInputFilename()) > os.path.getmtime(self.getOutputFilename())
def surfaceFilePNGOutOfDate(self):
"""
Return ``True`` if a potential energy surface PNG image file is out of
date or ``False`` if not.
"""
return self.surfaceFilePNGExists() and os.path.getmtime(self.getInputFilename()) > os.path.getmtime(self.getSurfaceFilenamePNG())
def surfaceFilePDFOutOfDate(self):
"""
Return ``True`` if a potential energy surface PDF image file is out of
date or ``False`` if not.
"""
return self.surfaceFilePDFExists() and os.path.getmtime(self.getInputFilename()) > os.path.getmtime(self.getSurfaceFilenamePDF())
def surfaceFileSVGOutOfDate(self):
"""
Return ``True`` if a potential energy surface SVG image file is out of
date or ``False`` if not.
"""
return self.surfaceFileSVGExists() and os.path.getmtime(self.getInputFilename()) > os.path.getmtime(self.getSurfaceFilenameSVG())
def createDir(self):
"""
Create the directory (and any other needed parent directories) that
the Network uses for storing files.
"""
try:
os.makedirs(self.getDirname())
except OSError:
# Fail silently on any OS errors
pass
def deleteInputFile(self):
"""
Delete the input file for this network from the server.
"""
if self.inputFileExists():
os.remove(self.getInputFilename())
def deleteOutputFile(self):
"""
Delete the output file for this network from the server.
"""
if self.outputFileExists():
os.remove(self.getOutputFilename())
def deleteSurfaceFilePNG(self):
"""
Delete the PES image file in PNF format for this network from the
server.
"""
if os.path.exists(self.getSurfaceFilenamePNG()):
os.remove(self.getSurfaceFilenamePNG())
def deleteSurfaceFilePDF(self):
"""
Delete the PES image file in PDF format for this network from the
server.
"""
if os.path.exists(self.getSurfaceFilenamePDF()):
os.remove(self.getSurfaceFilenamePDF())
def deleteSurfaceFileSVG(self):
"""
Delete the PES image file in SVG format for this network from the
server.
"""
if os.path.exists(self.getSurfaceFilenameSVG()):
os.remove(self.getSurfaceFilenameSVG())
def loadInputText(self):
"""
Load the input file text into the inputText field.
"""
self.inputText = ''
if self.inputFileExists():
f = open(self.getInputFilename(),'r')
for line in f:
self.inputText += line
f.close()
def saveInputText(self):
"""
Save the contents of the inputText field to the input file.
"""
fpath = self.getInputFilename()
self.createDir()
f = open(fpath,'w')
for line in self.inputText.splitlines():
f.write(line + '\n')
f.close()
def load(self):
"""
Load the contents of the input file into a PressureDependenceJob object.
"""
from arkane.pdep import PressureDependenceJob
from arkane.input import loadInputFile
# Seed with a PdepJob object
if self.pdep is None:
self.pdep = PressureDependenceJob(network=None)
if self.inputFileExists():
jobList = loadInputFile(self.getInputFilename())[0]
assert len(jobList) == 1
job = jobList[0]
if isinstance(job, PressureDependenceJob) is False:
raise Exception('Input file given did not provide a pressure dependence network.')
self.pdep = job
self.pdep.initialize()
if self.pdep.network is not None:
self.title = self.pdep.network.label
self.save()
return self.pdep.network