def saveCompareHTML(outputDir,chemkinPath1,speciesDictPath1,chemkinPath2,speciesDictPath2):
"""
Saves a model comparison HTML file based on two sets of chemkin and species dictionary
files.
"""
model1 = ReactionModel()
model1.species, model1.reactions = loadChemkinFile(chemkinPath1, speciesDictPath1)
model2 = ReactionModel()
model2.species, model2.reactions = loadChemkinFile(chemkinPath2, speciesDictPath2)
commonReactions, uniqueReactions1, uniqueReactions2 = compareModelReactions(model1, model2)
outputPath = outputDir + 'diff.html'
speciesList1 = []
speciesList1 = model1.species
commonSpeciesList = []
speciesList2 = []
for spec2 in model2.species:
for spec1 in speciesList1:
if spec2.isIsomorphic(spec1):
spec2.label = spec1.label
speciesList1.remove(spec1)
commonSpeciesList.append(spec2)
break
else:
speciesList2.append(spec2)
saveDiffHTML(outputPath, commonSpeciesList,speciesList1,speciesList2,commonReactions,uniqueReactions1,uniqueReactions2)
def saveCompareHTML(outputDir,chemkinPath1,speciesDictPath1,chemkinPath2,speciesDictPath2):
"""
Saves a model comparison HTML file based on two sets of chemkin and species dictionary
files.
"""
model1 = ReactionModel()
model1.species, model1.reactions = loadChemkinFile(chemkinPath1, speciesDictPath1)
model2 = ReactionModel()
model2.species, model2.reactions = loadChemkinFile(chemkinPath2, speciesDictPath2)
commonReactions, uniqueReactions1, uniqueReactions2 = compareModelReactions(model1, model2)
commonSpecies, uniqueSpecies1, uniqueSpecies2 = compareModelSpecies(model1, model2)
outputPath = outputDir + 'diff.html'
saveDiffHTML(outputPath, commonSpecies, uniqueSpecies1, uniqueSpecies2, commonReactions, uniqueReactions1, uniqueReactions2)
def saveCompareHTML(outputDir,
chemkinPath1,
speciesDictPath1,
chemkinPath2,
speciesDictPath2,
readComments1=True,
readComments2=True):
"""
Saves a model comparison HTML file based on two sets of chemkin and species dictionary
files.
"""
model1 = ReactionModel()
model1.species, model1.reactions = loadChemkinFile(
chemkinPath1, speciesDictPath1, readComments=readComments1)
model2 = ReactionModel()
model2.species, model2.reactions = loadChemkinFile(
chemkinPath2, speciesDictPath2, readComments=readComments2)
commonReactions, uniqueReactions1, uniqueReactions2 = compareModelReactions(
model1, model2)
commonSpecies, uniqueSpecies1, uniqueSpecies2 = compareModelSpecies(
model1, model2)
outputPath = outputDir + 'diff.html'
saveDiffHTML(outputPath, commonSpecies, uniqueSpecies1, uniqueSpecies2,
commonReactions, uniqueReactions1, uniqueReactions2)
parser = argparse.ArgumentParser()
parser.add_argument('files', metavar='FILE', type=str, nargs='+',
help='the Chemkin files and species dictionaries of each model to merge')
args = parser.parse_args()
outputChemkinFile = 'chem.inp'
outputSpeciesDictionary = 'species_dictionary.txt'
assert len(args.files) % 2 == 0
# Load the models to merge
models = []
for chemkin, speciesDict in zip(args.files[0::2], args.files[1::2]):
print 'Loading model #{0:d}...'.format(len(models)+1)
model = ReactionModel()
model.species, model.reactions = loadChemkinFile(chemkin, speciesDict)
models.append(model)
finalModel = ReactionModel()
for i, model in enumerate(models):
print 'Ignoring common species and reactions from model #{0:d}...'.format(i+1)
Nspec0 = len(finalModel.species)
Nrxn0 = len(finalModel.reactions)
finalModel = finalModel.merge(model)
Nspec = len(finalModel.species)
Nrxn = len(finalModel.reactions)
print 'Added {1:d} out of {2:d} ({3:.1f}%) unique species from model #{0:d}.'.format(i+1, Nspec - Nspec0, len(model.species), (Nspec - Nspec0) * 100. / len(model.species))
print 'Added {1:d} out of {2:d} ({3:.1f}%) unique reactions from model #{0:d}.'.format(i+1, Nrxn - Nrxn0, len(model.reactions), (Nrxn - Nrxn0) * 100. / len(model.reactions))
help='the species dictionary file of the second model')
parser.add_argument('thermo2',
metavar='THERMO2',
type=str,
nargs=1,
help='the thermo file of the second model')
args = parser.parse_args()
chemkin1 = args.chemkin1[0]
speciesDict1 = args.speciesDict1[0]
thermo1 = args.thermo1[0]
chemkin2 = args.chemkin2[0]
speciesDict2 = args.speciesDict2[0]
thermo2 = args.thermo2[0]
model1 = ReactionModel()
model1.species, model1.reactions = loadChemkinFile(chemkin1,
speciesDict1,
thermoPath=thermo1)
model2 = ReactionModel()
model2.species, model2.reactions = loadChemkinFile(chemkin2,
speciesDict2,
thermoPath=thermo2)
commonSpecies, uniqueSpecies1, uniqueSpecies2 = compareModelSpecies(
model1, model2)
commonReactions, uniqueReactions1, uniqueReactions2 = compareModelReactions(
model1, model2)
print '{0:d} species were found in both models:'.format(len(commonSpecies))
for spec1, spec2 in commonSpecies:
parser.add_argument('chemkin1', metavar='CHEMKIN1', type=str, nargs=1,
help='the Chemkin file of the first model')
parser.add_argument('speciesDict1', metavar='SPECIESDICT1', type=str, nargs=1,
help='the species dictionary file of the first model')
parser.add_argument('chemkin2', metavar='CHEMKIN2', type=str, nargs=1,
help='the Chemkin file of the second model')
parser.add_argument('speciesDict2', metavar='SPECIESDICT2', type=str, nargs=1,
help='the species dictionary file of the second model')
args = parser.parse_args()
chemkin1 = args.chemkin1[0]
speciesDict1 = args.speciesDict1[0]
chemkin2 = args.chemkin2[0]
speciesDict2 = args.speciesDict2[0]
model1 = ReactionModel()
model1.species, model1.reactions = loadChemkinFile(chemkin1, speciesDict1)
model2 = ReactionModel()
model2.species, model2.reactions = loadChemkinFile(chemkin2, speciesDict2)
commonSpecies, uniqueSpecies1, uniqueSpecies2 = compareModelSpecies(model1, model2)
commonReactions, uniqueReactions1, uniqueReactions2 = compareModelReactions(model1, model2)
print '{0:d} species were found in both models:'.format(len(commonSpecies))
for spec1, spec2 in commonSpecies:
print ' {0!s}'.format(spec1)
if spec1.thermo and spec2.thermo:
spec1.molecule[0].calculateSymmetryNumber()
print ' {0:7.2f} {1:7.2f} {2:7.2f} {3:7.2f} {4:7.2f} {5:7.2f} {6:7.2f} {7:7.2f} {8:7.2f}'.format(
spec1.thermo.getEnthalpy(298) / 4184.,
spec1.thermo.getEntropy(298) / 4.184,
inputModelFiles.append((model[0], model[1], None))
elif len(model) == 3:
transport = True
inputModelFiles.append((model[0], model[1], model[2]))
else:
raise Exception
outputChemkinFile = 'chem.inp'
outputSpeciesDictionary = 'species_dictionary.txt'
outputTransportFile = 'tran.dat' if transport else None
# Load the models to merge
models = []
for chemkin, speciesPath, transportPath in inputModelFiles:
print 'Loading model #{0:d}...'.format(len(models) + 1)
model = ReactionModel()
model.species, model.reactions = loadChemkinFile(
chemkin, speciesPath, transportPath=transportPath)
models.append(model)
finalModel = ReactionModel()
for i, model in enumerate(models):
print 'Ignoring common species and reactions from model #{0:d}...'.format(
i + 1)
Nspec0 = len(finalModel.species)
Nrxn0 = len(finalModel.reactions)
finalModel = finalModel.merge(model)
Nspec = len(finalModel.species)
Nrxn = len(finalModel.reactions)
print 'Added {1:d} out of {2:d} ({3:.1f}%) unique species from model #{0:d}.'.format(
i + 1, Nspec - Nspec0, len(model.species),
parser.add_argument('chemkin2', metavar='CHEMKIN2', type=str, nargs=1,
help='the Chemkin file of the second model')
parser.add_argument('speciesDict2', metavar='SPECIESDICT2', type=str, nargs=1,
help='the species dictionary file of the second model')
parser.add_argument('thermo2', metavar = 'THERMO2', type=str, nargs = 1,
help = 'the thermo file of the second model')
args = parser.parse_args()
chemkin1 = args.chemkin1[0]
speciesDict1 = args.speciesDict1[0]
thermo1 = args.thermo1[0]
chemkin2 = args.chemkin2[0]
speciesDict2 = args.speciesDict2[0]
thermo2 = args.thermo2[0]
model1 = ReactionModel()
model1.species, model1.reactions = loadChemkinFile(chemkin1, speciesDict1, thermoPath = thermo1)
model2 = ReactionModel()
model2.species, model2.reactions = loadChemkinFile(chemkin2, speciesDict2, thermoPath = thermo2)
commonSpecies, uniqueSpecies1, uniqueSpecies2 = compareModelSpecies(model1, model2)
commonReactions, uniqueReactions1, uniqueReactions2 = compareModelReactions(model1, model2)
print '{0:d} species were found in both models:'.format(len(commonSpecies))
for spec1, spec2 in commonSpecies:
print ' {0!s}'.format(spec1)
if spec1.thermo and spec2.thermo:
spec1.molecule[0].calculateSymmetryNumber()
print ' {0:7.2f} {1:7.2f} {2:7.2f} {3:7.2f} {4:7.2f} {5:7.2f} {6:7.2f} {7:7.2f} {8:7.2f}'.format(
spec1.thermo.getEnthalpy(300) / 4184.,
spec1.thermo.getEntropy(300) / 4.184,
