Example #1
0
def runThermoEstimator(inputFile):
    """
    Estimate thermo for a list of species using RMG and the settings chosen inside a thermo input file.
    """
    
    rmg = RMG()
    rmg.loadThermoInput(inputFile)
    
    # initialize and load the database as well as any QM settings
    rmg.loadDatabase()
    if rmg.quantumMechanics:
        rmg.quantumMechanics.initialize()
    
    # Generate the thermo for all the species and write them to chemkin format as well as
    # ThermoLibrary format with values for H, S, and Cp's.
    output = open(os.path.join(rmg.outputDirectory, 'output.txt'),'wb')
    library = ThermoLibrary(name='Thermo Estimation Library')
    for species in rmg.initialSpecies:
        species.generateThermoData(rmg.database, quantumMechanics=rmg.reactionModel.quantumMechanics)

        library.loadEntry(
            index = len(library.entries) + 1,
            label = species.label,
            molecule = species.molecule[0].toAdjacencyList(),
            thermo = species.thermo.toThermoData(),
            shortDesc = species.thermo.comment,
        )
        output.write(writeThermoEntry(species))
        output.write('\n')
    
    output.close()
    library.save(os.path.join(rmg.outputDirectory,'ThermoLibrary.py'))
Example #2
0
def save_thermo_lib(species_list, path, name, lib_long_desc):
    """
    Save an RMG thermo library of all species in `species_list` in the supplied `path`
    `name` is the library's name (or project's name)
    `long_desc` is a multiline string with level of theory description
    """
    if species_list:
        lib_path = os.path.join(path, 'thermo', '{0}.py'.format(name))
        thermo_library = ThermoLibrary(name=name, longDesc=lib_long_desc)
        for i, spc in enumerate(species_list):
            if spc.thermo is not None:
                spc.long_thermo_description += '\nExternal symmetry: {0}, optical isomers: {1}\n'.format(
                    spc.external_symmetry, spc.optical_isomers)
                spc.long_thermo_description += '\nGeometry:\n{0}'.format(
                    spc.final_xyz)
                thermo_library.loadEntry(
                    index=i + 1,
                    label=spc.label,
                    molecule=spc.mol_list[0].toAdjacencyList(),
                    thermo=spc.thermo,
                    shortDesc=spc.thermo.comment,
                    longDesc=spc.long_thermo_description)
            else:
                logging.warning(
                    'Species {0} did not contain any thermo data and was omitted from the thermo'
                    ' library.'.format(str(spc)))

        thermo_library.save(lib_path)
Example #3
0
def runThermoEstimator(inputFile):
    """
    Estimate thermo for a list of species using RMG and the settings chosen inside a thermo input file.
    """

    rmg = RMG()
    rmg.loadThermoInput(inputFile)

    # initialize and load the database as well as any QM settings
    rmg.loadDatabase()
    if rmg.quantumMechanics:
        rmg.quantumMechanics.initialize()

    # Generate the thermo for all the species and write them to chemkin format as well as
    # ThermoLibrary format with values for H, S, and Cp's.
    output = open(os.path.join(rmg.outputDirectory, 'output.txt'), 'wb')
    library = ThermoLibrary(name='Thermo Estimation Library')
    for species in rmg.initialSpecies:
        species.generateThermoData(
            rmg.database, quantumMechanics=rmg.reactionModel.quantumMechanics)

        library.loadEntry(
            index=len(library.entries) + 1,
            label=species.label,
            molecule=species.molecule[0].toAdjacencyList(),
            thermo=species.thermo.toThermoData(),
            shortDesc=species.thermo.comment,
        )
        output.write(writeThermoEntry(species))
        output.write('\n')

    output.close()
    library.save(os.path.join(rmg.outputDirectory, 'ThermoLibrary.py'))
Example #4
0
def runThermoEstimator(inputFile, library_flag):
    """
    Estimate thermo for a list of species using RMG and the settings chosen inside a thermo input file.
    """

    rmg = RMG()
    rmg.loadThermoInput(inputFile)

    rmg.database = RMGDatabase()
    path = os.path.join(settings['database.directory'])

    # forbidden structure loading
    rmg.database.loadThermo(os.path.join(path, 'thermo'),
                            rmg.thermoLibraries,
                            depository=False)

    if rmg.solvent:
        rmg.database.loadSolvation(os.path.join(path, 'solvation'))
        Species.solventData = rmg.database.solvation.getSolventData(
            rmg.solvent)
        Species.solventName = rmg.solvent

    for species in rmg.initialSpecies:
        submit(species)

    if library_flag:
        library = ThermoLibrary(name='Thermo Estimation Library')
        for species in rmg.initialSpecies:
            library.loadEntry(
                index=len(library.entries) + 1,
                label=species.label,
                molecule=species.molecule[0].toAdjacencyList(),
                thermo=species.getThermoData().toThermoData(),
                shortDesc=species.getThermoData().comment,
            )
        library.save(os.path.join(rmg.outputDirectory, 'ThermoLibrary.py'))

    # Save the thermo data to chemkin format output files and dictionary, with no reactions
    saveChemkinFile(os.path.join(rmg.outputDirectory, 'chem_annotated.inp'),
                    species=rmg.initialSpecies,
                    reactions=[])
    saveSpeciesDictionary(os.path.join(rmg.outputDirectory,
                                       'species_dictionary.txt'),
                          species=rmg.initialSpecies)
Example #5
0
def runThermoEstimator(inputFile):
    """
    Estimate thermo for a list of species using RMG and the settings chosen inside a thermo input file.
    """
    
    rmg = RMG()
    rmg.loadThermoInput(inputFile)
    
    rmg.database = RMGDatabase()
    path = os.path.join(settings['database.directory'])

    # forbidden structure loading
    rmg.database.loadThermo(os.path.join(path, 'thermo'), rmg.thermoLibraries, depository=False)
   
    if rmg.solvent:
        rmg.database.loadSolvation(os.path.join(path, 'solvation'))
        Species.solventData = rmg.database.solvation.getSolventData(rmg.solvent)
        Species.solventName = rmg.solvent
        
    # Generate the thermo for all the species and write them to chemkin format as well as
    # ThermoLibrary format with values for H, S, and Cp's.
    output = open(os.path.join(rmg.outputDirectory, 'output.txt'),'wb')
    library = ThermoLibrary(name='Thermo Estimation Library')
    for species in rmg.initialSpecies:
        species.getThermoData(rmg.database)

        library.loadEntry(
            index = len(library.entries) + 1,
            label = species.label,
            molecule = species.molecule[0].toAdjacencyList(),
            thermo = species.thermo.toThermoData(),
            shortDesc = species.thermo.comment,
        )
        output.write(writeThermoEntry(species))
        output.write('\n')
    
    output.close()
    library.save(os.path.join(rmg.outputDirectory,'ThermoLibrary.py'))
 
 print removeH
 
 speciesList, reactionList = loadChemkinFile(chemkinPath, dictionaryPath)
 
 # load thermo library entries
 thermoLibrary = ThermoLibrary()
 for i in range(len(speciesList)): 
     species = speciesList[i]
     rdkitmol = species.molecule[0].toRDKitMol(removeHs=False)
     species.molecule = [Molecule().fromRDKitMol(rdkitmol)]#[0].toAdjacencyList(removeH=False)
     print species.molecule[0].toAdjacencyList(removeH = removeH)
     if species.thermo:
         thermoLibrary.loadEntry(index = i + 1,
                                 label = species.label,
                                 molecule = species.molecule[0].toAdjacencyList(removeH = removeH),
                                 thermo = species.thermo,
                                 shortDesc = species.thermo.comment
        )                
     else:
         logging.warning('Species {0} did not contain any thermo data and was omitted from the thermo library.'.format(str(species)))
                     
 # load kinetics library entries                    
 kineticsLibrary = KineticsLibrary()
 kineticsLibrary.entries = {}
 for i in range(len(reactionList)):
     reaction = reactionList[i]        
     entry = Entry(
             index = i+1,
             item = reaction,
             data = reaction.kinetics,
         )
Example #7
0
    def getLibraries(self):

        name = 'kineticsjobs'

        speciesList = self.speciesDict.values()
        reactionList = self.reactionDict.values()

        # remove duplicate species
        for rxn in reactionList:
            for i, rspc in enumerate(rxn.reactants):
                for spc in speciesList:
                    if spc.isIsomorphic(rspc):
                        rxn.reactants[i] = spc
                        break
            for i, rspc in enumerate(rxn.products):
                for spc in speciesList:
                    if spc.isIsomorphic(rspc):
                        rxn.products[i] = spc
                        break
        del_inds = []
        for i, spc1 in enumerate(speciesList):
            for j, spc2 in enumerate(speciesList):
                if j > i and spc1.isIsomorphic(spc2):
                    del_inds.append(j)

        for j in sorted(del_inds)[::-1]:
            del speciesList[j]

        thermoLibrary = ThermoLibrary(name=name)
        for i, species in enumerate(speciesList):
            if species.thermo:
                thermoLibrary.loadEntry(
                    index=i + 1,
                    label=species.label,
                    molecule=species.molecule[0].toAdjacencyList(),
                    thermo=species.thermo,
                    shortDesc=species.thermo.comment)
            else:
                logging.warning(
                    'Species {0} did not contain any thermo data and was omitted from the thermo library.'
                    .format(str(species)))

        # load kinetics library entries
        kineticsLibrary = KineticsLibrary(name=name, autoGenerated=True)
        kineticsLibrary.entries = {}
        for i, reaction in enumerate(reactionList):
            entry = Entry(
                index=i + 1,
                label=reaction.toLabeledStr(),
                item=reaction,
                data=reaction.kinetics,
            )

            if reaction.kinetics is not None:
                if hasattr(reaction, 'library') and reaction.library:
                    entry.longDesc = 'Originally from reaction library: ' +\
                                     reaction.library + "\n" + reaction.kinetics.comment
                else:
                    entry.longDesc = reaction.kinetics.comment

            kineticsLibrary.entries[i + 1] = entry

        kineticsLibrary.label = name

        return thermoLibrary, kineticsLibrary, speciesList
    def getLibraries(self):

        name = 'kineticsjobs'
                
        speciesList = self.speciesDict.values()
        reactionList = self.reactionDict.values()

        # remove duplicate species
        for rxn in reactionList:
            for i,rspc in enumerate(rxn.reactants):
                for spc in speciesList:
                    if spc.isIsomorphic(rspc):
                        rxn.reactants[i] = spc
                        break
            for i,rspc in enumerate(rxn.products):
                for spc in speciesList:
                    if spc.isIsomorphic(rspc):
                        rxn.products[i] = spc
                        break
        del_inds = []
        for i,spc1 in enumerate(speciesList):
            for j,spc2 in enumerate(speciesList):
                if j>i and spc1.isIsomorphic(spc2):
                    del_inds.append(j)
        
        for j in sorted(del_inds)[::-1]:
            del speciesList[j]
            
        thermoLibrary = ThermoLibrary(name=name)
        for i,species in enumerate(speciesList): 
            if species.thermo:
                thermoLibrary.loadEntry(index = i + 1,
                                        label = species.label,
                                        molecule = species.molecule[0].toAdjacencyList(),
                                        thermo = species.thermo,
                                        shortDesc = species.thermo.comment
               )                
            else:
                logging.warning('Species {0} did not contain any thermo data and was omitted from the thermo library.'.format(str(species)))

        # load kinetics library entries                    
        kineticsLibrary = KineticsLibrary(name=name,autoGenerated=True)
        kineticsLibrary.entries = {}
        for i,reaction in enumerate(reactionList):      
            entry = Entry(
                    index = i+1,
                    label = reaction.toLabeledStr(),
                    item = reaction,
                    data = reaction.kinetics,
                )

            if reaction.kinetics is not None:
                if hasattr(reaction,'library') and reaction.library:
                    entry.longDesc = 'Originally from reaction library: ' +\
                                     reaction.library + "\n" + reaction.kinetics.comment
                else:
                    entry.longDesc = reaction.kinetics.comment
            
            kineticsLibrary.entries[i+1] = entry
        
        kineticsLibrary.label = name
        
        return thermoLibrary,kineticsLibrary,speciesList
Example #9
0
 name = args.name[0]
     
 speciesList, reactionList = loadChemkinFile(chemkinPath, dictionaryPath)
 
 # Make full species identifier the species labels
 for species in speciesList:
     species.label = getSpeciesIdentifier(species)
     species.index = -1
 # load thermo library entries
 thermoLibrary = ThermoLibrary(name=name)
 for i in range(len(speciesList)): 
     species = speciesList[i]
     if species.thermo:
         thermoLibrary.loadEntry(index = i + 1,
                                 label = species.label,
                                 molecule = species.molecule[0].toAdjacencyList(),
                                 thermo = species.thermo,
                                 shortDesc = species.thermo.comment
        )                
     else:
         logging.warning('Species {0} did not contain any thermo data and was omitted from the thermo library.'.format(str(species)))
                     
 # load kinetics library entries                    
 kineticsLibrary = KineticsLibrary(name=name)
 kineticsLibrary.entries = {}
 for i in range(len(reactionList)):
     reaction = reactionList[i]        
     entry = Entry(
             index = i+1,
             label = str(reaction),
             item = reaction,
             data = reaction.kinetics,