def load(self):
"""
Load the contents of the input and output files into a MEASURE object.
"""
from rmgpy.measure.main import MEASURE
self.measure = MEASURE()
if self.outputFileExists():
self.measure.loadOutput(self.getOutputFilename())
elif self.inputFileExists():
self.measure.loadInput(self.getInputFilename())
if self.measure.network is not None:
self.title = self.measure.network.title
self.save()
return self.measure.network
def load(self):
"""
Load the contents of the input and output files into a MEASURE object.
"""
from rmgpy.measure.main import MEASURE
self.measure = MEASURE()
if self.outputFileExists():
self.measure.loadOutput(self.getOutputFilename())
elif self.inputFileExists():
self.measure.loadInput(self.getInputFilename())
if self.measure.network is not None:
self.title = self.measure.network.title
self.save()
return self.measure.network
class Network(models.Model):
"""
A Django model of a pressure-dependent reaction network.
"""
def upload_input_to(instance, filename):
# Always name the uploaded input file "input.py"
return 'pdep/networks/{0}/input.py'.format(instance.pk)
id = models.CharField(max_length=32, primary_key=True, default=_createId)
title = models.CharField(max_length=50)
inputFile = models.FileField(upload_to=upload_input_to, 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.measure = 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(), 'MEASURE.log')
def getSurfaceFilenamePNG(self):
"""
Return the absolute path of the PES image file in PNG format.
"""
return os.path.join(self.getDirname(), 'PES.png')
def getSurfaceFilenamePDF(self):
"""
Return the absolute path of the PES image file in PDF format.
"""
return os.path.join(self.getDirname(), 'PES.pdf')
def getSurfaceFilenameSVG(self):
"""
Return the absolute path of the PES image file in SVG format.
"""
return os.path.join(self.getDirname(), 'PES.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 and output files into a MEASURE object.
"""
from rmgpy.measure.main import MEASURE
self.measure = MEASURE()
if self.outputFileExists():
self.measure.loadOutput(self.getOutputFilename())
elif self.inputFileExists():
self.measure.loadInput(self.getInputFilename())
if self.measure.network is not None:
self.title = self.measure.network.title
self.save()
return self.measure.network
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 = ['training']
self.rmg.kineticsFamilies = ['!Intra_Disproportionation']
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())))
system = SimpleReactor(T, P, initialMoleFractions, termination)
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.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']
# Pressure Dependence
pdep = form.cleaned_data['pdep'].encode()
if pdep != 'off':
self.rmg.pressureDependence = MEASURE()
self.rmg.pressureDependence.method = pdep
# Temperature and pressure range
interpolation = (form.cleaned_data['interpolation'].encode(),
form.cleaned_data['temp_basis'],
form.cleaned_data['p_basis'])
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']
Tlist = getTemperaturesForModel(
interpolation, self.rmg.pressureDependence.Tmin.value,
self.rmg.pressureDependence.Tmax.value,
self.rmg.pressureDependence.Tcount)
self.rmg.pressureDependence.Tlist = Quantity(Tlist, "K")
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']
Plist = getPressuresForModel(
interpolation, self.rmg.pressureDependence.Pmin.value,
self.rmg.pressureDependence.Pmax.value,
self.rmg.pressureDependence.Pcount)
self.rmg.pressureDependence.Plist = Quantity(Plist, "Pa")
# 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']
# Process interpolation model
self.rmg.pressureDependence.model = interpolation
# 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.drawMolecules = form.cleaned_data['drawMolecules']
self.rmg.generatePlots = form.cleaned_data['generatePlots']
self.rmg.saveConcentrationProfiles = form.cleaned_data[
'saveConcentrationProfiles']
# Save the input.py file
self.rmg.saveInput(self.savepath)
if args.dictionary is not None:
f = open(args.dictionary[0])
adjlist = ''; label = ''
for line in f:
if len(line.strip()) == 0:
if len(adjlist.strip()) > 0:
molecule = Molecule()
molecule.fromAdjacencyList(adjlist)
moleculeDict[label] = molecule
adjlist = ''; label = ''
else:
if len(adjlist.strip()) == 0:
label = line.strip()
adjlist += line
f.close()
method = None
for fstr in args.file:
# Construct MEASURE job from FAME input
measure = MEASURE()
measure.loadFAMEInput(fstr, moleculeDict)
# Save MEASURE input file based on the above
dirname, basename = os.path.split(os.path.abspath(fstr))
basename, ext = os.path.splitext(basename)
path = os.path.join(dirname, basename + '.py')
measure.saveInput(path)
class Network(models.Model):
"""
A Django model of a pressure-dependent reaction network.
"""
def upload_input_to(instance, filename):
# Always name the uploaded input file "input.py"
return 'pdep/networks/{0}/input.py'.format(instance.pk)
id = models.CharField(max_length=32, primary_key=True, default=_createId)
title = models.CharField(max_length=50)
inputFile = models.FileField(upload_to=upload_input_to,
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.measure = 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(), 'MEASURE.log')
def getSurfaceFilenamePNG(self):
"""
Return the absolute path of the PES image file in PNG format.
"""
return os.path.join(self.getDirname(), 'PES.png')
def getSurfaceFilenamePDF(self):
"""
Return the absolute path of the PES image file in PDF format.
"""
return os.path.join(self.getDirname(), 'PES.pdf')
def getSurfaceFilenameSVG(self):
"""
Return the absolute path of the PES image file in SVG format.
"""
return os.path.join(self.getDirname(), 'PES.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 and output files into a MEASURE object.
"""
from rmgpy.measure.main import MEASURE
self.measure = MEASURE()
if self.outputFileExists():
self.measure.loadOutput(self.getOutputFilename())
elif self.inputFileExists():
self.measure.loadInput(self.getInputFilename())
if self.measure.network is not None:
self.title = self.measure.network.title
self.save()
return self.measure.network