Ejemplo n.º 1
0
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)
Ejemplo n.º 2
0
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
Ejemplo n.º 3
0
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)
Ejemplo n.º 4
0
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
Ejemplo n.º 5
0
    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)