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)
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,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)
def execute(chemkin1, speciesDict1, thermo1, chemkin2, speciesDict2, thermo2, **kwargs):
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)
try:
diffOnly = kwargs['diffOnly']
except KeyError:
diffOnly = False
try:
commonDiffOnly = kwargs['commonDiffOnly']
except KeyError:
commonDiffOnly = False
if diffOnly or commonDiffOnly:
commonSpecies = filter(lambda x: not identicalThermo(x), commonSpecies)
commonReactions = filter(lambda x: not identicalKinetics(x), commonReactions)
if commonDiffOnly:
uniqueSpecies1 = []
uniqueSpecies2 = []
uniqueReactions1 = []
uniqueReactions2 = []
try:
web = kwargs['web']
except KeyError:
web = False
if not web:
logging.info('{0:d} species were found in both models:'.format(len(commonSpecies)))
for spec1, spec2 in commonSpecies:
logging.info(' {0!s}'.format(spec1))
if spec1.thermo and spec2.thermo:
spec1.molecule[0].getSymmetryNumber()
logging.info(' {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,
spec1.thermo.getHeatCapacity(300) / 4.184,
spec1.thermo.getHeatCapacity(400) / 4.184,
spec1.thermo.getHeatCapacity(500) / 4.184,
spec1.thermo.getHeatCapacity(600) / 4.184,
spec1.thermo.getHeatCapacity(800) / 4.184,
spec1.thermo.getHeatCapacity(1000) / 4.184,
spec1.thermo.getHeatCapacity(1500) / 4.184,
))
logging.info(' {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(
spec2.thermo.getEnthalpy(300) / 4184.,
spec2.thermo.getEntropy(300) / 4.184,
spec2.thermo.getHeatCapacity(300) / 4.184,
spec2.thermo.getHeatCapacity(400) / 4.184,
spec2.thermo.getHeatCapacity(500) / 4.184,
spec2.thermo.getHeatCapacity(600) / 4.184,
spec2.thermo.getHeatCapacity(800) / 4.184,
spec2.thermo.getHeatCapacity(1000) / 4.184,
spec2.thermo.getHeatCapacity(1500) / 4.184,
))
logging.info('{0:d} species were only found in the first model:'.format(len(uniqueSpecies1)))
for spec in uniqueSpecies1:
logging.info(' {0!s}'.format(spec))
logging.info('{0:d} species were only found in the second model:'.format(len(uniqueSpecies2)))
for spec in uniqueSpecies2:
logging.info(' {0!s}'.format(spec))
logging.info('{0:d} reactions were found in both models:'.format(len(commonReactions)))
for rxn1, rxn2 in commonReactions:
logging.info(' {0!s}'.format(rxn1))
if rxn1.kinetics and rxn2.kinetics:
logging.info(' {0:7.2f} {1:7.2f} {2:7.2f} {3:7.2f} {4:7.2f} {5:7.2f} {6:7.2f} {7:7.2f}'.format(
math.log10(rxn1.kinetics.getRateCoefficient(300, 1e5)),
math.log10(rxn1.kinetics.getRateCoefficient(400, 1e5)),
math.log10(rxn1.kinetics.getRateCoefficient(500, 1e5)),
math.log10(rxn1.kinetics.getRateCoefficient(600, 1e5)),
math.log10(rxn1.kinetics.getRateCoefficient(800, 1e5)),
math.log10(rxn1.kinetics.getRateCoefficient(1000, 1e5)),
math.log10(rxn1.kinetics.getRateCoefficient(1500, 1e5)),
math.log10(rxn1.kinetics.getRateCoefficient(2000, 1e5)),
))
logging.info(' {0:7.2f} {1:7.2f} {2:7.2f} {3:7.2f} {4:7.2f} {5:7.2f} {6:7.2f} {7:7.2f}'.format(
math.log10(rxn2.kinetics.getRateCoefficient(300, 1e5)),
math.log10(rxn2.kinetics.getRateCoefficient(400, 1e5)),
math.log10(rxn2.kinetics.getRateCoefficient(500, 1e5)),
math.log10(rxn2.kinetics.getRateCoefficient(600, 1e5)),
math.log10(rxn2.kinetics.getRateCoefficient(800, 1e5)),
math.log10(rxn2.kinetics.getRateCoefficient(1000, 1e5)),
math.log10(rxn2.kinetics.getRateCoefficient(1500, 1e5)),
math.log10(rxn2.kinetics.getRateCoefficient(2000, 1e5)),
))
logging.info('{0:d} reactions were only found in the first model:'.format(len(uniqueReactions1)))
for rxn in uniqueReactions1:
logging.info(' {0!s}'.format(rxn))
logging.info('{0:d} reactions were only found in the second model:'.format(len(uniqueReactions2)))
for rxn in uniqueReactions2:
logging.info(' {0!s}'.format(rxn))
logging.info("Saving output in diff.html")
try:
wd = kwargs['wd']
except KeyError:
wd = os.getcwd()
outputPath = os.path.join(wd, 'diff.html')
saveDiffHTML(outputPath, commonSpecies, uniqueSpecies1, uniqueSpecies2, commonReactions, uniqueReactions1, uniqueReactions2)
logging.info("Finished!")
return commonSpecies, uniqueSpecies1, uniqueSpecies2, commonReactions, uniqueReactions1, uniqueReactions2
math.log10(rxn1.kinetics.getRateCoefficient(1500, 1e5)),
math.log10(rxn1.kinetics.getRateCoefficient(2000, 1e5)),
)
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}'.format(
math.log10(rxn2.kinetics.getRateCoefficient(300, 1e5)),
math.log10(rxn2.kinetics.getRateCoefficient(400, 1e5)),
math.log10(rxn2.kinetics.getRateCoefficient(500, 1e5)),
math.log10(rxn2.kinetics.getRateCoefficient(600, 1e5)),
math.log10(rxn2.kinetics.getRateCoefficient(800, 1e5)),
math.log10(rxn2.kinetics.getRateCoefficient(1000, 1e5)),
math.log10(rxn2.kinetics.getRateCoefficient(1500, 1e5)),
math.log10(rxn2.kinetics.getRateCoefficient(2000, 1e5)),
)
print '{0:d} reactions were only found in the first model:'.format(
len(uniqueReactions1))
for rxn in uniqueReactions1:
print ' {0!s}'.format(rxn)
print '{0:d} reactions were only found in the second model:'.format(
len(uniqueReactions2))
for rxn in uniqueReactions2:
print ' {0!s}'.format(rxn)
#commonSpecies.sort(key = enthalpyDiff)
#commonReactions.sort(key = kineticsDiff)
print "Saving output in diff.html"
outputPath = 'diff.html'
saveDiffHTML(outputPath, commonSpecies, uniqueSpecies1, uniqueSpecies2,
commonReactions, uniqueReactions1, uniqueReactions2)
print "Finished!"
def execute(chemkin1, speciesDict1, thermo1, chemkin2, speciesDict2, thermo2,
**kwargs):
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)
try:
diffOnly = kwargs['diffOnly']
except KeyError:
diffOnly = False
try:
commonDiffOnly = kwargs['commonDiffOnly']
except KeyError:
commonDiffOnly = False
if diffOnly or commonDiffOnly:
commonSpecies = filter(lambda x: not identicalThermo(x), commonSpecies)
commonReactions = filter(lambda x: not identicalKinetics(x),
commonReactions)
if commonDiffOnly:
uniqueSpecies1 = []
uniqueSpecies2 = []
uniqueReactions1 = []
uniqueReactions2 = []
try:
web = kwargs['web']
except KeyError:
web = False
if not web:
logging.info('{0:d} species were found in both models:'.format(
len(commonSpecies)))
for spec1, spec2 in commonSpecies:
logging.info(' {0!s}'.format(spec1))
if spec1.thermo and spec2.thermo:
spec1.molecule[0].getSymmetryNumber()
logging.info(
' {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,
spec1.thermo.getHeatCapacity(300) / 4.184,
spec1.thermo.getHeatCapacity(400) / 4.184,
spec1.thermo.getHeatCapacity(500) / 4.184,
spec1.thermo.getHeatCapacity(600) / 4.184,
spec1.thermo.getHeatCapacity(800) / 4.184,
spec1.thermo.getHeatCapacity(1000) / 4.184,
spec1.thermo.getHeatCapacity(1500) / 4.184,
))
logging.info(
' {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(
spec2.thermo.getEnthalpy(300) / 4184.,
spec2.thermo.getEntropy(300) / 4.184,
spec2.thermo.getHeatCapacity(300) / 4.184,
spec2.thermo.getHeatCapacity(400) / 4.184,
spec2.thermo.getHeatCapacity(500) / 4.184,
spec2.thermo.getHeatCapacity(600) / 4.184,
spec2.thermo.getHeatCapacity(800) / 4.184,
spec2.thermo.getHeatCapacity(1000) / 4.184,
spec2.thermo.getHeatCapacity(1500) / 4.184,
))
logging.info(
'{0:d} species were only found in the first model:'.format(
len(uniqueSpecies1)))
for spec in uniqueSpecies1:
logging.info(' {0!s}'.format(spec))
logging.info(
'{0:d} species were only found in the second model:'.format(
len(uniqueSpecies2)))
for spec in uniqueSpecies2:
logging.info(' {0!s}'.format(spec))
logging.info('{0:d} reactions were found in both models:'.format(
len(commonReactions)))
for rxn1, rxn2 in commonReactions:
logging.info(' {0!s}'.format(rxn1))
if rxn1.kinetics and rxn2.kinetics:
logging.info(
' {0:7.2f} {1:7.2f} {2:7.2f} {3:7.2f} {4:7.2f} {5:7.2f} {6:7.2f} {7:7.2f}'
.format(
math.log10(rxn1.kinetics.getRateCoefficient(300, 1e5)),
math.log10(rxn1.kinetics.getRateCoefficient(400, 1e5)),
math.log10(rxn1.kinetics.getRateCoefficient(500, 1e5)),
math.log10(rxn1.kinetics.getRateCoefficient(600, 1e5)),
math.log10(rxn1.kinetics.getRateCoefficient(800, 1e5)),
math.log10(rxn1.kinetics.getRateCoefficient(1000,
1e5)),
math.log10(rxn1.kinetics.getRateCoefficient(1500,
1e5)),
math.log10(rxn1.kinetics.getRateCoefficient(2000,
1e5)),
))
logging.info(
' {0:7.2f} {1:7.2f} {2:7.2f} {3:7.2f} {4:7.2f} {5:7.2f} {6:7.2f} {7:7.2f}'
.format(
math.log10(rxn2.kinetics.getRateCoefficient(300, 1e5)),
math.log10(rxn2.kinetics.getRateCoefficient(400, 1e5)),
math.log10(rxn2.kinetics.getRateCoefficient(500, 1e5)),
math.log10(rxn2.kinetics.getRateCoefficient(600, 1e5)),
math.log10(rxn2.kinetics.getRateCoefficient(800, 1e5)),
math.log10(rxn2.kinetics.getRateCoefficient(1000,
1e5)),
math.log10(rxn2.kinetics.getRateCoefficient(1500,
1e5)),
math.log10(rxn2.kinetics.getRateCoefficient(2000,
1e5)),
))
logging.info(
'{0:d} reactions were only found in the first model:'.format(
len(uniqueReactions1)))
for rxn in uniqueReactions1:
logging.info(' {0!s}'.format(rxn))
logging.info(
'{0:d} reactions were only found in the second model:'.format(
len(uniqueReactions2)))
for rxn in uniqueReactions2:
logging.info(' {0!s}'.format(rxn))
logging.info("Saving output in diff.html")
try:
wd = kwargs['wd']
except KeyError:
wd = os.getcwd()
outputPath = os.path.join(wd, 'diff.html')
saveDiffHTML(outputPath, commonSpecies, uniqueSpecies1, uniqueSpecies2,
commonReactions, uniqueReactions1, uniqueReactions2)
logging.info("Finished!")
return commonSpecies, uniqueSpecies1, uniqueSpecies2, commonReactions, uniqueReactions1, uniqueReactions2
math.log10(rxn1.kinetics.getRateCoefficient(600, 1e5)),
math.log10(rxn1.kinetics.getRateCoefficient(800, 1e5)),
math.log10(rxn1.kinetics.getRateCoefficient(1000, 1e5)),
math.log10(rxn1.kinetics.getRateCoefficient(1500, 1e5)),
math.log10(rxn1.kinetics.getRateCoefficient(2000, 1e5)),
)
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}'.format(
math.log10(rxn2.kinetics.getRateCoefficient(300, 1e5)),
math.log10(rxn2.kinetics.getRateCoefficient(400, 1e5)),
math.log10(rxn2.kinetics.getRateCoefficient(500, 1e5)),
math.log10(rxn2.kinetics.getRateCoefficient(600, 1e5)),
math.log10(rxn2.kinetics.getRateCoefficient(800, 1e5)),
math.log10(rxn2.kinetics.getRateCoefficient(1000, 1e5)),
math.log10(rxn2.kinetics.getRateCoefficient(1500, 1e5)),
math.log10(rxn2.kinetics.getRateCoefficient(2000, 1e5)),
)
print '{0:d} reactions were only found in the first model:'.format(len(uniqueReactions1))
for rxn in uniqueReactions1:
print ' {0!s}'.format(rxn)
print '{0:d} reactions were only found in the second model:'.format(len(uniqueReactions2))
for rxn in uniqueReactions2:
print ' {0!s}'.format(rxn)
#commonSpecies.sort(key = enthalpyDiff)
#commonReactions.sort(key = kineticsDiff)
print "Saving output in diff.html"
outputPath = 'diff.html'
saveDiffHTML(outputPath, commonSpecies, uniqueSpecies1, uniqueSpecies2, commonReactions, uniqueReactions1, uniqueReactions2)
print "Finished!"
