RMG-generated network__.py doesn't run in measure.py

examples/rmg/methylformate/input.py

@@ -0,0 +1,144 @@
+# Data sources
+database(
+    '../RMG-database/input',
+    thermoLibraries = ['primaryThermoLibrary','DFT_QCI_thermo','GRI-Mech3.0'],
+    reactionLibraries = ['Methylformate','Glarborg/highP'],
+    seedMechanisms = ['GRI-Mech3.0'],
+)
+
+# List of species
+species(
+    label='Mfmt',
+    reactive=True,
+    structure=SMILES("COC=O"),
+)
+species(
+    label='O2',
+    reactive=True,
+    structure=SMILES("[O][O]"),
+)
+species(
+    label='C2H',
+    reactive=True,
+    structure=SMILES("C#[C]"),
+)
+species(
+    label='C2H',
+    reactive=True,
+    structure=SMILES("C#[C]"),
+)
+species(
+    label='CH',
+    reactive=True,
+    structure=adjacencyList(
+        """
+        1     C     3 {2,S}
+        2     H     0 {1,S}
+        """),
+)
+species(
+    label='H2O',
+    reactive=True,
+    structure=SMILES("O"),
+)
+species(
+    label='H2',
+    reactive=True,
+    structure=SMILES("[H][H]"),
+)
+species(
+    label='CO',
+    reactive=True,
+    structure=SMILES("[C]=O"),
+)
+species(
+    label='CO2',
+    reactive=True,
+    structure=SMILES("C(=O)=O"),
+)
+species(
+    label='CH4',
+    reactive=True,
+    structure=SMILES("C"),
+)
+species(
+    label='CH3',
+    reactive=True,
+    structure=SMILES("[CH3]"),
+)
+species(
+    label='CH3OH',
+    reactive=True,
+    structure=SMILES("CO"),
+)
+species(
+    label='C2H4',
+    reactive=True,
+    structure=SMILES("C=C"),
+)
+species(
+    label='C2H2',
+    reactive=True,
+    structure=SMILES("C#C"),
+)
+species(
+    label='CH2O',
+    reactive=True,
+    structure=SMILES("C=O"),
+)
+species(
+    label='CH3CHO',
+    reactive=True,
+    structure=SMILES("CC=O"),
+)
+
+
+# Bath gas
+species(
+    label='Ar',
+    reactive=False,
+    structure=InChI("InChI=1S/Ar"),
+)
+
+# Reaction systems
+simpleReactor(
+    temperature=(1350,'K'),
+    pressure=(1.0,'bar'),
+    initialMoleFractions={
+        "Mfmt": 0.01,
+        "O2": 0.02,
+        "Ar": 0.97,
+    },
+)
+
+termination(
+    time=(0.5,'s'),
+)
+
+simulator(
+    atol=1e-22,
+    rtol=1e-8,
+)
+
+model(
+    toleranceKeepInEdge=0.0,
+    toleranceMoveToCore=0.005,
+    toleranceInterruptSimulation=1.0,
+    maximumEdgeSpecies=100000
+)
+
+pressureDependence(
+    method='modified strong collision', # 'reservoir state'
+    minimumGrainSize=(2.0,'kcal/mol'),
+    minimumNumberOfGrains=200,
+    temperatures=(290,'K',3500,'K',8),
+    pressures=(0.02,'bar',100,'bar',5),
+    interpolation=('Chebyshev', 6, 4),
+)
+
+options(
+    units='si',
+    saveRestart=False,
+    drawMolecules=False,
+    generatePlots=True,
+)

rmg.py

@@ -251,6 +251,10 @@ def execute(args):
     # Read input file
     reactionModel, coreSpecies, reactionSystems, database, seedMechanisms = readInputFile(inputFile)
 
+    # Delete previous HTML file
+    from rmgpy.rmg.output import saveOutputHTML
+    saveOutputHTML(os.path.join(settings.outputDirectory, 'output.html'), reactionModel)
+
     # Initialize reaction model
     if args.restart:
         reactionModel = loadRestartFile(os.path.join(settings.outputDirectory,'restart.pkl.gz'))
@@ -335,12 +339,16 @@ def execute(args):
 
         # Save the current state of the model core to a pretty HTML file
         logging.info('Saving latest model core to HTML file...')
-        from rmgpy.rmg.output import saveOutputHTML
         saveOutputHTML(os.path.join(settings.outputDirectory, 'output.html'), reactionModel)
 
         # Save a Chemkin file containing the current model core
         logging.info('Saving latest model core to Chemkin file...')
-        reactionModel.saveChemkinFile(os.path.join(settings.outputDirectory, 'chemkin', 'chem%04i.inp' % len(reactionModel.core.species)))
+        this_chemkin_path = os.path.join(settings.outputDirectory, 'chemkin', 'chem%04i.inp' % len(reactionModel.core.species))
+        latest_chemkin_path = os.path.join(settings.outputDirectory, 'chemkin','chem.inp')
+        reactionModel.saveChemkinFile(this_chemkin_path)
+        if os.path.exists(latest_chemkin_path):
+            os.unlink(latest_chemkin_path)
+        os.link(this_chemkin_path,latest_chemkin_path)
 
         # Save the restart file if desired
         if settings.saveRestart:

rmgpy/data/thermo.py

@@ -582,7 +582,7 @@ def getThermoDataFromGroups(self, molecule):
 
         thermoData = None
 
-        if sum([atom.radicalElectrons for atom in molecule.atoms]) > 0:
+        if sum([atom.radicalElectrons for atom in molecule.atoms]) > 0: # radical species
 
             # Make a copy of the structure so we don't change the original
             saturatedStruct = molecule.copy(deep=True)
@@ -646,7 +646,7 @@ def getThermoDataFromGroups(self, molecule):
 
             # Correct the entropy for the symmetry number
 
-        else:
+        else: # non-radical species
             # Generate estimate of thermodynamics
             for atom in molecule.atoms:
                 # Iterate over heavy (non-hydrogen) atoms

rmgpy/measure/output.py

@@ -118,10 +118,10 @@ def writeNetworkConfigurations(f, network):
     """
     # Write isomer configurations
     for isomer in network.isomers:
-        f.write('isomer("{0}")\n\n'.format(isomer.label))
+        f.write('isomer("{0}")\n\n'.format(isomer))
     # Write reactant configurations
     for reactants in network.reactants:
-        f.write('reactants("{0}", "{1}")\n\n'.format(reactants[0].label, reactants[1].label))
+        f.write('reactants("{0}", "{1}")\n\n'.format(reactants[0], reactants[1]))
     # No need to write product configurations, as these are assumed
 
 ################################################################################

rmgpy/rmg/model.py

@@ -488,8 +488,8 @@ def update(self, reactionModel, database):
         self.collisionModel = SingleExponentialDownModel(alpha0=4.86 * 4184)
 
         # Save input file
-        rmgpy.measure.output.writeInput(os.path.join(settings.outputDirectory, 'pdep', 'network{0:d}_{1:d}.py'.format(self.index, len(self.isomers))),
-            self, Tlist, Plist, (grainSize, numGrains), method, model)
+        rmgpy.measure.output.writeFile(os.path.join(settings.outputDirectory, 'pdep', 'network{0:d}_{1:d}.py'.format(self.index, len(self.isomers))),
+            self, Tlist, Plist, (grainSize, numGrains), method, model, Tmin, Tmax, Pmin, Pmax)
 
         self.printSummary(level=logging.INFO)
 

unittest/moleculeTest.py

@@ -856,7 +856,22 @@ def testPickle(self):
         self.assertEqual(molecule0.getFormula(), molecule.getFormula())
         self.assertTrue(molecule0.isIsomorphic(molecule))
         self.assertTrue(molecule.isIsomorphic(molecule0))
-
+
+    def testRadicalCH(self):
+        """
+        Test that the species [CH] has three radical electrons and a spin multiplicity of 4.
+        """
+        molecule = Molecule().fromSMILES('[CH]')
+        self.assertEqual(molecule.atoms[0].radicalElectrons, 3)
+        self.assertEqual(molecule.atoms[0].spinMultiplicity, 4)
+
+    def testRadicalCH2(self):
+        """
+        Test that the species [CH2] has two radical electrons and a spin multiplicity of 3.
+        """
+        molecule = Molecule().fromSMILES('[CH2]')
+        self.assertEqual(molecule.atoms[0].radicalElectrons, 2)
+        self.assertEqual(molecule.atoms[0].spinMultiplicity, 3)
 ################################################################################
 
 class TestMoleculeSymmetry(unittest.TestCase):