def execute(inputModelFiles, **kwargs):
try:
wd = kwargs['wd']
except KeyError:
wd = os.getcwd()
transport = kwargs['transport']
outputChemkinFile = os.path.join(wd, 'chem.inp')
outputSpeciesDictionary = os.path.join(wd, 'species_dictionary.txt')
outputTransportFile = os.path.join(wd, '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),
(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))
print 'The merged model has {0:d} species and {1:d} reactions'.format(
len(finalModel.species), len(finalModel.reactions))
# Save the merged model to disk
saveChemkinFile(outputChemkinFile, finalModel.species,
finalModel.reactions)
saveSpeciesDictionary(outputSpeciesDictionary, finalModel.species)
if transport:
saveTransportFile(outputTransportFile, finalModel.species)
print 'Merged Chemkin file saved to {0}'.format(outputChemkinFile)
print 'Merged species dictionary saved to {0}'.format(
outputSpeciesDictionary)
if transport:
print 'Merged transport file saved to {0}'.format(outputTransportFile)
def combine_models(models):
"""
Takes in a list of ReactionModels and and merges them into a single ReactionModel
Reindexes species with the same label and index
"""
final_model = ReactionModel()
for i, model in enumerate(models):
print('Ignoring common species and reactions from model #{0:d}...'.
format(i + 1))
nspec0 = len(final_model.species)
nrxn0 = len(final_model.reactions)
final_model = final_model.merge(model)
nspec = len(final_model.species)
nrxn = len(final_model.reactions)
if len(model.species) > 0:
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)))
else:
print('Added {1:d} out of {2:d} unique species from model '
'#{0:d}.'.format(i + 1, nspec - nspec0, len(model.species)))
if len(model.reactions) > 0:
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)))
else:
print('Added {1:d} out of {2:d} unique reactions from model '
'#{0:d}.'.format(i + 1, nrxn - nrxn0, len(model.reactions)))
print('The merged model has {0:d} species and {1:d} reactions'
''.format(len(final_model.species), len(final_model.reactions)))
# ensure no species with same name and index
label_index_dict = {}
for s in final_model.species:
if s.label not in label_index_dict:
label_index_dict[s.label] = [s.index]
else:
if s.index in label_index_dict[s.label]:
# obtained a duplicate
s.index = max(label_index_dict[s.label]) + 1
print("Reindexed {0} due to dublicate labels and index".format(
s.label))
label_index_dict[s.label].append(s.index)
return final_model
def execute(inputModelFiles, **kwargs):
try:
wd = kwargs['wd']
except KeyError:
wd = os.getcwd()
transport = kwargs['transport']
outputChemkinFile = os.path.join(wd, 'chem.inp')
outputSpeciesDictionary = os.path.join(wd, 'species_dictionary.txt')
outputTransportFile = os.path.join(wd, '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), (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))
print 'The merged model has {0:d} species and {1:d} reactions'.format(len(finalModel.species), len(finalModel.reactions))
# Save the merged model to disk
saveChemkinFile(outputChemkinFile, finalModel.species, finalModel.reactions)
saveSpeciesDictionary(outputSpeciesDictionary, finalModel.species)
if transport:
saveTransportFile(outputTransportFile, finalModel.species)
print 'Merged Chemkin file saved to {0}'.format(outputChemkinFile)
print 'Merged species dictionary saved to {0}'.format(outputSpeciesDictionary)
if transport:
print 'Merged transport file saved to {0}'.format(outputTransportFile)
def combine_models(models):
"""
Takes in a list of ReactionModels and and merges them into a single ReactionModel
Reindexes species with the same label and index
"""
final_model = ReactionModel()
for i, model in enumerate(models):
print('Ignoring common species and reactions from model #{0:d}...'.
format(i + 1))
nspec0 = len(final_model.species)
nrxn0 = len(final_model.reactions)
final_model = final_model.merge(model)
nspec = len(final_model.species)
nrxn = len(final_model.reactions)
if len(model.species) > 0:
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)))
else:
print('Added {1:d} out of {2:d} unique species from model '
'#{0:d}.'.format(i + 1, nspec - nspec0, len(model.species)))
if len(model.reactions) > 0:
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)))
else:
print('Added {1:d} out of {2:d} unique reactions from model '
'#{0:d}.'.format(i + 1, nrxn - nrxn0, len(model.reactions)))
print('The merged model has {0:d} species and {1:d} reactions'
''.format(len(final_model.species), len(final_model.reactions)))
# reindex the unique species (to avoid name conflicts on save)
speciesIndex = 0
for spec in final_model.species:
if spec.label not in ['Ar', 'N2', 'Ne', 'He']:
spec.index = speciesIndex + 1
speciesIndex += 1
return final_model
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), (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))
print 'The merged model has {0:d} species and {1:d} reactions'.format(len(finalModel.species), len(finalModel.reactions))
# Save the merged model to disk
saveChemkinFile(outputChemkinFile, finalModel.species, finalModel.reactions)
saveSpeciesDictionary(outputSpeciesDictionary, finalModel.species)
if transport:
saveTransportFile(outputTransportFile, finalModel.species)
print 'Merged Chemkin file saved to {0}'.format(outputChemkinFile)
print 'Merged species dictionary saved to {0}'.format(outputSpeciesDictionary)
