ReactionMechanismGenerator · mjohnson541 · Sep 4, 2021 · May 12, 2021 · May 12, 2021 · May 12, 2021
diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -120,7 +120,7 @@ jobs:
     env: 
       # if running on RMG-Py but requiring changes on an un-merged branch of RMG-database, replace
       # main with the name of the branch
-      RMG_DATABASE_BRANCH: main
+      RMG_DATABASE_BRANCH: lithium
 
       # This is true only if this is a reference case for the regression testing:
       REFERENCE_JOB: ${{ github.ref == 'refs/heads/main' && github.repository == 'ReactionMechanismGenerator/RMG-Py' }}
@@ -302,7 +302,7 @@ jobs:
               export FAILED=Yes
             fi
             echo "" # blank line so next block is interpreted as markdown
-            cat "$regr_test-core.log"
+            cat "$regr_test-core.log" || (echo "Dumping the whole log failed, please download it from GitHub actions. Here are the first 100 lines:" && head -n100 "$regr_test-core.log")
             echo "</details>"
             echo "<details>"
             if python-jl scripts/checkModels.py \
@@ -319,7 +319,7 @@ jobs:
               export FAILED=Yes
             fi
             echo "" # blank line so next block is interpreted as markdown
-            cat "$regr_test-edge.log"
+            cat "$regr_test-edge.log" || (echo "Dumping the whole log failed, please download it from GitHub actions. Here are the first 100 lines:" && head -n100 "$regr_test-core.log")
             echo "</details>"
 
             # Check for Regression between Reference and Dynamic (skip superminimal)
@@ -410,4 +410,4 @@ jobs:
         uses: docker/build-push-action@v4
         with:
           push: true
-          tags: reactionmechanismgenerator/rmg:latest
+          tags: reactionmechanismgenerator/rmg:latest
diff --git a/arkane/encorr/ae.py b/arkane/encorr/ae.py
@@ -65,7 +65,9 @@
     'Methane',
     'Methyl',
     'Ammonia',
-    'Chloromethane'
+    'Chloromethane',
+    'Lithium Hydride',
+    'Lithium Fluoride'
 ]
 
 

diff --git a/arkane/encorr/bac.py b/arkane/encorr/bac.py
@@ -237,7 +237,7 @@ class BAC:
     ref_databases = {}
     atom_spins = {
         'H': 0.5, 'C': 1.0, 'N': 1.5, 'O': 1.0, 'F': 0.5,
-        'Si': 1.0, 'P': 1.5, 'S': 1.0, 'Cl': 0.5, 'Br': 0.5, 'I': 0.5
+        'Si': 1.0, 'P': 1.5, 'S': 1.0, 'Cl': 0.5, 'Br': 0.5, 'I': 0.5, 'Li': 0.5,
     }
     exp_coeff = 3.0  # Melius-type parameter (Angstrom^-1)
 

diff --git a/arkane/encorr/corrTest.py b/arkane/encorr/corrTest.py
@@ -90,7 +90,7 @@ def test_get_bac(self):
                       bac_type=bac_type,
         )
          # test value is obtained by BAC(self.freq_lot, bac_type=bac_type).get_correction(bonds=bonds, coords=CCCBDB_coords, nums=nums).value_si
-        test_value = 700
+        test_value = -466
         self.assertAlmostEqual(bac, test_value, places=None, delta=100)
 
         # test Melius BACs
@@ -100,7 +100,7 @@ def test_get_bac(self):
                       bac_type=bac_type,
         )
         # test value is obtained by BAC(self.freq_lot, bac_type=bac_type).get_correction(bonds=bonds, coords=CCCBDB_coords, nums=nums).value_si
-        test_value = 949
+        test_value = -234
         self.assertAlmostEqual(bac, test_value, places=None, delta=100)
 
     def test_assign_frequency_scale_factor(self):

diff --git a/examples/rmg/liquid_cat/input.py b/examples/rmg/liquid_cat/input.py
@@ -1,7 +1,7 @@
 # Data sources
 database(
     thermoLibraries=['surfaceThermoPt111', 'primaryThermoLibrary', 'thermo_DFT_CCSDTF12_BAC','DFT_QCI_thermo'], # 'surfaceThermoPt' is the default. Thermo data is derived using bindingEnergies for other metals
-    reactionLibraries = [],
+    reactionLibraries = [('Surface/CPOX_Pt/Deutschmann2006_adjusted', False)], # when Ni is used change the library to Surface/Deutschmann_Ni
     seedMechanisms = [],
     kineticsDepositories = ['training'],
     kineticsFamilies = ['surface','default'],

diff --git a/ipython/kinetics_library_to_training_tools.py b/ipython/kinetics_library_to_training_tools.py
@@ -185,8 +185,9 @@ def process_reactions(database, libraries, families, compare_kinetics=True, show
                     units = 'cm^3/(mol*s)'
                 elif len(lib_rxn.reactants) == 3:
                     units = 'cm^6/(mol^2*s)'
-                A = lib_rxn.kinetics.A
-                lib_rxn.kinetics.A = ScalarQuantity(value=A.value_si*A.get_conversion_factor_from_si_to_cm_mol_s(),units=units,uncertainty_type=A.uncertainty_type,uncertainty=A.uncertainty_si*A.get_conversion_factor_from_si_to_cm_mol_s())
+                if hasattr(lib_rxn.kinetics,'A'):
+                    A = lib_rxn.kinetics.A
+                    lib_rxn.kinetics.A = ScalarQuantity(value=A.value_si*A.get_conversion_factor_from_si_to_cm_mol_s(),units=units,uncertainty_type=A.uncertainty_type,uncertainty=A.uncertainty_si*A.get_conversion_factor_from_si_to_cm_mol_s())
 
                 if fam_rxn.family in reaction_dict:
                     reaction_dict[fam_rxn.family].append(lib_rxn)
@@ -436,4 +437,3 @@ def manual_selection(master_dict, multiple_dict, database):
     print('================================================================================')
     print('Manual selection of reactions completed.')
     print('================================================================================')
-
diff --git a/rmgpy/chemkin.pyx b/rmgpy/chemkin.pyx
@@ -758,7 +758,7 @@ def read_reaction_comments(reaction, comments, read=True):
                     raise ChemkinError('Unexpected species identifier {0} encountered in flux pairs '
                                        'for reaction {1}.'.format(prod_str, reaction))
                 reaction.pairs.append((reactant, product))
-            assert len(reaction.pairs) == max(len(reaction.reactants), len(reaction.products))
+            #assert len(reaction.pairs) == max(len(reaction.reactants), len(reaction.products))
 
         elif isinstance(reaction, TemplateReaction) and 'rate rule ' in line:
             bracketed_rule = tokens[-1]

diff --git a/rmgpy/constants.pxd b/rmgpy/constants.pxd
@@ -25,4 +25,4 @@
 #                                                                             #
 ###############################################################################
 
-cdef double pi, Na, kB, R, h, hbar, c, e, m_e, m_p, m_n, amu, a0, E_h
+cdef double pi, Na, kB, R, h, hbar, c, e, m_e, m_p, m_n, amu, a0, E_h, F
diff --git a/rmgpy/constants.py b/rmgpy/constants.py
@@ -110,6 +110,9 @@
 #: :math:`\pi = 3.14159 \ldots`      
 pi = float(math.pi)
 
+#: Faradays Constant F in C/mol
+F = 96485.3321233100184
+
 ################################################################################
 
 # Cython does not automatically place module-level variables into the module
@@ -130,4 +133,5 @@
     'm_n': m_n,
     'm_p': m_p,
     'pi': pi,
+    'F': F
 })
diff --git a/rmgpy/data/base.py b/rmgpy/data/base.py
@@ -42,6 +42,7 @@
 from rmgpy.data.reference import Reference, Article, Book, Thesis
 from rmgpy.exceptions import DatabaseError, InvalidAdjacencyListError
 from rmgpy.kinetics.uncertainties import RateUncertainty
+from rmgpy.kinetics.arrhenius import ArrheniusChargeTransfer, ArrheniusChargeTransferBM
 from rmgpy.molecule import Molecule, Group
 
 
@@ -228,6 +229,8 @@ def load(self, path, local_context=None, global_context=None):
         local_context['shortDesc'] = self.short_desc
         local_context['longDesc'] = self.long_desc
         local_context['RateUncertainty'] = RateUncertainty
+        local_context['ArrheniusChargeTransfer'] = ArrheniusChargeTransfer
+        local_context['ArrheniusChargeTransferBM'] = ArrheniusChargeTransferBM
         local_context['metal'] = self.metal
         local_context['site'] = self.site
         local_context['facet'] = self.facet
@@ -1350,8 +1353,8 @@ def is_molecule_forbidden(self, molecule):
                 raise NotImplementedError('Checking is only implemented for forbidden Groups, Molecule, and Species.')
 
         # Until we have more thermodynamic data of molecular ions we will forbid them
-        if molecule.get_net_charge() != 0:
-            return True
+        # if molecule.get_net_charge() != 0:
+        #     return True
 
         return False
 

diff --git a/rmgpy/data/kinetics/database.py b/rmgpy/data/kinetics/database.py
@@ -44,11 +44,12 @@
 from rmgpy.kinetics import Arrhenius, ArrheniusEP, ThirdBody, Lindemann, Troe, \
                            PDepArrhenius, MultiArrhenius, MultiPDepArrhenius, \
                            Chebyshev, KineticsData, StickingCoefficient, \
-                           StickingCoefficientBEP, SurfaceArrhenius, SurfaceArrheniusBEP, ArrheniusBM
+                           StickingCoefficientBEP, SurfaceArrhenius, SurfaceArrheniusBEP, \
+                           ArrheniusBM, SurfaceChargeTransfer, KineticsModel
 from rmgpy.molecule import Molecule, Group
 from rmgpy.reaction import Reaction, same_species_lists
 from rmgpy.species import Species
-
+from rmgpy.data.solvation import SoluteData, SoluteTSData, SoluteTSDiffData
 
 ################################################################################
 
@@ -78,8 +79,13 @@ def __init__(self):
             'StickingCoefficientBEP': StickingCoefficientBEP,
             'SurfaceArrhenius': SurfaceArrhenius,
             'SurfaceArrheniusBEP': SurfaceArrheniusBEP,
+            'SurfaceChargeTransfer': SurfaceChargeTransfer,
             'R': constants.R,
-            'ArrheniusBM': ArrheniusBM
+            'ArrheniusBM': ArrheniusBM,
+            'SoluteData': SoluteData,
+            'SoluteTSData': SoluteTSData,
+            'SoluteTSDiffData': SoluteTSDiffData,
+            'KineticsModel': KineticsModel,
         }
         self.global_context = {}
 

diff --git a/rmgpy/data/kinetics/depository.py b/rmgpy/data/kinetics/depository.py
@@ -35,6 +35,7 @@
 
 from rmgpy.data.base import Database, Entry, DatabaseError
 from rmgpy.data.kinetics.common import save_entry
+from rmgpy.kinetics import SurfaceChargeTransfer, SurfaceArrheniusBEP
 from rmgpy.reaction import Reaction
 
 
@@ -60,7 +61,8 @@
                  pairs=None,
                  depository=None,
                  family=None,
-                 entry=None
+                 entry=None,
+                 electrons=None,
                  ):
         Reaction.__init__(self,
                           index=index,
@@ -72,7 +74,8 @@
                           transition_state=transition_state,
                           duplicate=duplicate,
                           degeneracy=degeneracy,
-                          pairs=pairs
+                          pairs=pairs,
+                          electrons=electrons,
                           )
         self.depository = depository
         self.family = family
@@ -104,12 +107,34 @@
         """
         return self.depository.label
 
+    def apply_solvent_correction(self, solvent):
+        """
+        apply kinetic solvent correction
+        """
+        from rmgpy.data.rmg import get_db
+        solvation_database = get_db('solvation')
+        solvent_data = solvation_database.get_solvent_data(solvent)
+        solute_data = self.kinetics.solute
+        correction = solvation_database.get_solvation_correction(solute_data, solvent_data)
+        dHR = 0.0
+        dSR = 0.0
+        for spc in self.reactants:
+            spc_solute_data = solvation_database.get_solute_data(spc)
+            spc_correction = solvation_database.get_solvation_correction(spc_solute_data, solvent_data)
+            dHR += spc_correction.enthalpy
+            dSR += spc_correction.entropy
+
+        dH = correction.enthalpy-dHR
+        dA = np.exp((correction.entropy-dSR)/constants.R)
+        self.kinetics.Ea.value_si += dH
+        self.kinetics.A.value_si *= dA
+        self.kinetics.comment += "\nsolvation correction raised barrier by {0} kcal/mol and prefactor by factor of {1}".format(dH/4184.0,dA)
 
 ################################################################################
 
 class KineticsDepository(Database):
     """
-    A class for working with an RMG kinetics depository. Each depository 
+    A class for working with an RMG kinetics depository. Each depository
     corresponds to a reaction family (a :class:`KineticsFamily` object). Each
     entry in a kinetics depository involves a reaction defined either by a
     real reactant and product species (as in a kinetics library).
@@ -187,6 +212,9 @@
                                         ''.format(product, self.label))
                 # Same comment about molecule vs species objects as above.
                 rxn.products.append(species_dict[product])
+
+            if isinstance(entry.data, (SurfaceChargeTransfer, SurfaceArrheniusBEP)):
+                rxn.electrons = entry.data.electrons.value
 
             if not rxn.is_balanced():
                 raise DatabaseError('Reaction {0} in kinetics depository {1} was not balanced! Please reformulate.'