Dump and parse YAML files in Cantherm

rmgpy/cantherm/input.py

@@ -51,6 +51,7 @@
 from rmgpy.kinetics.chebyshev import Chebyshev
 from rmgpy.kinetics.falloff import ThirdBody, Lindemann, Troe
 from rmgpy.kinetics.kineticsdata import KineticsData, PDepKineticsData
+from rmgpy.kinetics.model import TunnelingModel
 from rmgpy.kinetics.tunneling import Wigner, Eckart
 
 from rmgpy.pdep.configuration import Configuration
@@ -65,6 +66,7 @@
 from rmgpy.cantherm.statmech import StatMechJob, assign_frequency_scale_factor
 from rmgpy.cantherm.thermo import ThermoJob
 from rmgpy.cantherm.pdep import PressureDependenceJob
+from rmgpy.cantherm.common import is_pdep
 
 ################################################################################
 
@@ -76,6 +78,7 @@
 
 ################################################################################
 
+
 def species(label, *args, **kwargs):
     global speciesDict, jobList
     if label in speciesDict:
@@ -124,15 +127,26 @@ def species(label, *args, **kwargs):
             else:
                 raise TypeError('species() got an unexpected keyword argument {0!r}.'.format(key))
 
-        if structure: spec.molecule = [structure]
+        if structure:
+            spec.molecule = [structure]
         spec.conformer = Conformer(E0=E0, modes=modes, spinMultiplicity=spinMultiplicity, opticalIsomers=opticalIsomers)
-        spec.molecularWeight = molecularWeight
+        if molecularWeight is not None:
+            spec.molecularWeight = molecularWeight
+        else:
+            if structure:
+                # If a structure was given, simply calling spec.molecularWeight will calculate the molecular weight
+                spec.molecularWeight = spec.molecularWeight
+            elif is_pdep(jobList):
+                # If one of the jobs is pdep and no molecular weight is given or calculated, raise an error
+                raise ValueError("No molecularWeight was entered for species {0}. Since a structure wasn't given"
+                                 " as well, the molecularWeight cannot be reconstructed.".format(spec.label))
         spec.transportData = collisionModel
         spec.energyTransferModel = energyTransferModel
         spec.thermo = thermo
 
     return spec
 
+
 def transitionState(label, *args, **kwargs):
     global transitionStateDict
     if label in transitionStateDict:
@@ -173,9 +187,9 @@ def transitionState(label, *args, **kwargs):
 
     return ts
 
+
 def reaction(label, reactants, products, transitionState, kinetics=None, tunneling=''):
     global reactionDict, speciesDict, transitionStateDict
-    #label = 'reaction'+transitionState
     if label in reactionDict:
         label = label+transitionState
         if label in reactionDict:
@@ -194,9 +208,9 @@ def reaction(label, reactants, products, transitionState, kinetics=None, tunneli
         raise ValueError('Unknown tunneling model {0!r}.'.format(tunneling))
     rxn = Reaction(label=label, reactants=reactants, products=products, transitionState=transitionState, kinetics=kinetics)
     reactionDict[label] = rxn
-
     return rxn
 
+
 def network(label, isomers=None, reactants=None, products=None, pathReactions=None, bathGas=None):
     global networkDict, speciesDict, reactionDict
     logging.info('Loading network {0}...'.format(label))
@@ -266,6 +280,7 @@ def network(label, isomers=None, reactants=None, products=None, pathReactions=No
     )
     networkDict[label] = network
 
+
 def kinetics(label, Tmin=None, Tmax=None, Tlist=None, Tcount=0, sensitivity_conditions=None):
     global jobList, reactionDict
     try:
@@ -276,6 +291,7 @@ def kinetics(label, Tmin=None, Tmax=None, Tlist=None, Tcount=0, sensitivity_cond
                       sensitivity_conditions=sensitivity_conditions)
     jobList.append(job)
 
+
 def statmech(label):
     global jobList, speciesDict, transitionStateDict
     if label in speciesDict or label in transitionStateDict:
@@ -287,6 +303,7 @@ def statmech(label):
     else:
         raise ValueError('Unknown species or transition state label {0!r} for statmech() job.'.format(label))
 
+
 def thermo(label, thermoClass):
     global jobList, speciesDict
     try:
@@ -296,6 +313,7 @@ def thermo(label, thermoClass):
     job = ThermoJob(species=spec, thermoClass=thermoClass)
     jobList.append(job)
 
+
 def pressureDependence(label, 
                        Tmin=None, Tmax=None, Tcount=0, Tlist=None,
                        Pmin=None, Pmax=None, Pcount=0, Plist=None,
@@ -315,17 +333,22 @@ def pressureDependence(label,
         rmgmode=rmgmode, sensitivity_conditions=sensitivity_conditions)
     jobList.append(job)
 
+
 def SMILES(smiles):
     return Molecule().fromSMILES(smiles)
 
+
 def adjacencyList(adj):
     return Molecule().fromAdjacencyList(adj)
 
+
 def InChI(inchi):
     return Molecule().fromInChI(inchi)
 
+
 ################################################################################
 
+
 def loadInputFile(path):
     """
     Load the CanTherm input file located at `path` on disk, and return a list of
@@ -388,27 +411,41 @@ def loadInputFile(path):
             logging.error('The input file {0!r} was invalid:'.format(path))
             raise
 
-    modelChemistry = local_context.get('modelChemistry', '')
+    model_chemistry = local_context.get('modelChemistry', '')
+    level_of_theory = local_context.get('levelOfTheory', '')
+    author = local_context.get('author', '')
     if 'frequencyScaleFactor' not in local_context:
         logging.debug('Assigning a frequencyScaleFactor according to the modelChemistry...')
-        frequencyScaleFactor = assign_frequency_scale_factor(modelChemistry)
+        frequency_scale_factor = assign_frequency_scale_factor(model_chemistry)
     else:
-        frequencyScaleFactor = local_context.get('frequencyScaleFactor')
-    useHinderedRotors = local_context.get('useHinderedRotors', True)
-    useAtomCorrections = local_context.get('useAtomCorrections', True)
-    useBondCorrections = local_context.get('useBondCorrections', False)
-    atomEnergies = local_context.get('atomEnergies', None)
+        frequency_scale_factor = local_context.get('frequencyScaleFactor')
+    use_hindered_rotors = local_context.get('useHinderedRotors', True)
+    use_atom_corrections = local_context.get('useAtomCorrections', True)
+    use_bond_corrections = local_context.get('useBondCorrections', False)
+    atom_energies = local_context.get('atomEnergies', None)
 
     directory = os.path.dirname(path)
 
     for job in jobList:
         if isinstance(job, StatMechJob):
             job.path = os.path.join(directory, job.path)
-            job.modelChemistry = modelChemistry.lower()
-            job.frequencyScaleFactor = frequencyScaleFactor
-            job.includeHinderedRotors = useHinderedRotors
-            job.applyAtomEnergyCorrections = useAtomCorrections
-            job.applyBondEnergyCorrections = useBondCorrections
-            job.atomEnergies = atomEnergies
+            job.modelChemistry = model_chemistry.lower()
+            job.frequencyScaleFactor = frequency_scale_factor
+            job.includeHinderedRotors = use_hindered_rotors
+            job.applyAtomEnergyCorrections = use_atom_corrections
+            job.applyBondEnergyCorrections = use_bond_corrections
+            job.atomEnergies = atom_energies
+        if isinstance(job, ThermoJob):
+            job.cantherm_species.author = author
+            job.cantherm_species.level_of_theory = level_of_theory
+            level_of_theory_energy = level_of_theory.split('//')[0]
+            if level_of_theory_energy != model_chemistry:
+                # Only log the model chemistry if it isn't identical to the first part of level_of_theory
+                job.cantherm_species.model_chemistry = model_chemistry
+            job.cantherm_species.frequency_scale_factor = frequency_scale_factor
+            job.cantherm_species.use_hindered_rotors = use_hindered_rotors
+            job.cantherm_species.use_bond_corrections = use_bond_corrections
+            if atom_energies is not None:
+                job.cantherm_species.atom_energies = atom_energies
 
     return jobList

rmgpy/cantherm/main.py

@@ -51,9 +51,11 @@
 from rmgpy.cantherm.statmech import StatMechJob
 from rmgpy.cantherm.thermo import ThermoJob
 from rmgpy.cantherm.pdep import PressureDependenceJob
+from rmgpy.cantherm.common import is_pdep
 
 ################################################################################
 
+
 class CanTherm:
     """
     The :class:`CanTherm` class represents an instance of CanTherm, a tool for
@@ -253,8 +255,10 @@ def execute(self):
 
         # run thermo jobs (printing out thermo stuff)
         for job in self.jobList:
-            if isinstance(job,ThermoJob) or isinstance(job, StatMechJob):
+            if isinstance(job, ThermoJob):
                 job.execute(outputFile=outputFile, plot=self.plot)
+            if isinstance(job, StatMechJob):
+                job.execute(outputFile=outputFile, plot=self.plot, pdep=is_pdep(self.jobList))
 
         with open(chemkinFile, 'a') as f:
             f.write('\n')

rmgpy/cantherm/statmech.py

@@ -53,6 +53,7 @@
 from rmgpy.statmech.torsion import Torsion, HinderedRotor, FreeRotor
 from rmgpy.statmech.conformer import Conformer
 from rmgpy.exceptions import InputError
+from rmgpy.cantherm.common import CanthermSpecies
 
 ################################################################################
 
@@ -66,6 +67,7 @@
 
 ################################################################################
 
+
 class ScanLog(object):
     """
     Represent a text file containing a table of angles and corresponding
@@ -180,29 +182,43 @@ def __init__(self, species, path):
         self.applyAtomEnergyCorrections = True
         self.applyBondEnergyCorrections = True
         self.atomEnergies = None
+        if isinstance(species, Species):
+            # Currently we do not dump and load transition states in YAML form
+            self.cantherm_species = CanthermSpecies(species=species)
 
-    def execute(self, outputFile=None, plot=False):
+    def execute(self, outputFile=None, plot=False, pdep=False):
         """
         Execute the statistical mechanics job, saving the results to the
         given `outputFile` on disk.
+        `pdep` passed to load()  and is used to distinguish between necessary and unnecessary
+        species attributes when loading a YAML file.
         """
-        self.load()
+        self.load(pdep)
         if outputFile is not None:
             self.save(outputFile=outputFile)
         logging.debug('Finished statmech job for species {0}.'.format(self.species))
         logging.debug(repr(self.species))
 
-    def load(self):
+    def load(self, pdep):
         """
         Load the statistical mechanics parameters for each conformer from
         the associated files on disk. Creates :class:`Conformer` objects for
         each conformer and appends them to the list of conformers on the
         species object.
         """
-        logging.info('Loading statistical mechanics parameters for {0}...'.format(self.species.label))
-
         path = self.path
         TS = isinstance(self.species, TransitionState)
+        filename, file_extension = os.path.splitext(path)
+        if file_extension in ['.yml', '.yaml']:
+            if TS:
+                raise ValueError('Loading transition states from a YAML file is still unsupported.')
+            self.cantherm_species.load_yaml(path=path, species=self.species, pdep=pdep)
+            self.species.conformer = self.cantherm_species.conformer
+            self.species.transportData = self.cantherm_species.transport_data
+            self.species.energyTransferModel = self.cantherm_species.energy_transfer_model
+            return
+
+        logging.info('Loading statistical mechanics parameters for {0}...'.format(self.species.label))
 
         global_context = {
             '__builtins__': None,
@@ -489,7 +505,6 @@ def load(self):
 
         self.species.conformer = conformer
 
-
     def save(self, outputFile):
         """
         Save the results of the statistical mechanics job to the file located
@@ -567,6 +582,7 @@ def plotHinderedRotor(self, angle, Vlist, cosineRotor, fourierRotor, rotor, roto
 
 ################################################################################
 
+
 def applyEnergyCorrections(E0, modelChemistry, atoms, bonds,
                            atomEnergies=None, applyAtomEnergyCorrections=True, applyBondEnergyCorrections=False):
     """
@@ -790,6 +806,7 @@ def applyEnergyCorrections(E0, modelChemistry, atoms, bonds,
 
     return E0
 
+
 class Log(object):
     """
     Represent a general log file.
@@ -1046,6 +1063,7 @@ def projectRotors(conformer, F, rotors, linear, TS):
 
     return numpy.sqrt(eig[-Nvib:]) / (2 * math.pi * constants.c * 100)
 
+
 def assign_frequency_scale_factor(model_chemistry):
     """
     Assign the frequency scaling factor according to the model chemistry.

rmgpy/cantherm/thermo.py

@@ -53,9 +53,11 @@
 from rmgpy.species import Species
 from rmgpy.molecule import Molecule
 from rmgpy.molecule.util import retrieveElementCount
+from rmgpy.cantherm.common import CanthermSpecies
 
 ################################################################################
 
+
 class ThermoJob(object):
     """
     A representation of a CanTherm thermodynamics job. This job is used to
@@ -65,6 +67,7 @@ class ThermoJob(object):
     def __init__(self, species, thermoClass):
         self.species = species
         self.thermoClass = thermoClass
+        self.cantherm_species = CanthermSpecies(species=species)
 
     def execute(self, outputFile=None, plot=False):
         """
@@ -73,7 +76,13 @@ def execute(self, outputFile=None, plot=False):
         """
         self.generateThermo()
         if outputFile is not None:
-            self.save(outputFile)
+            self.cantherm_species.chemkin_thermo_string = self.save(outputFile)
+            if self.species.molecule is None or len(self.species.molecule) == 0:
+                logging.debug("Not generating database file for species {0}, since its structure wasn't"
+                              " specified".format(self.species.label))
+            else:
+                self.cantherm_species.update_species_attributes(self.species)
+                self.cantherm_species.save_yaml(path=os.path.dirname(outputFile))
             if plot:
                 self.plot(os.path.dirname(outputFile))
 
@@ -88,8 +97,8 @@ def generateThermo(self):
 
         species = self.species
 
-        logging.info('Generating {0} thermo model for {1}...'.format(self.thermoClass, species))
-        
+        logging.debug('Generating {0} thermo model for {1}...'.format(self.thermoClass, species))
+
         Tlist = np.arange(10.0, 3001.0, 10.0, np.float64)
         Cplist = np.zeros_like(Tlist)
         H298 = 0.0
@@ -186,6 +195,7 @@ def save(self, outputFile):
                 f.write(species.molecule[0].toAdjacencyList(removeH=False,label=species.label))
                 f.write('\n')
         f.close()
+        return chemkin_thermo_string
 
     def plot(self, outputDirectory):
         """