Solvation ready to merge

examples/rmg/liquid_phase/input.py

@@ -0,0 +1,59 @@
+# Data sources
+database(
+    thermoLibraries = ['primaryThermoLibrary'],
+    reactionLibraries = [],
+    seedMechanisms = [],
+    kineticsDepositories = ['training'],
+    kineticsFamilies = ['!Intra_Disproportionation'],
+    kineticsEstimator = 'rate rules',
+)
+
+# List of species
+species(
+    label='octane',
+    reactive=True,
+    structure=SMILES("C(CCCCC)CC"),
+)
+
+species(
+    label='oxygen',
+    reactive=True,
+    structure=SMILES("[O][O]"),
+)
+
+# Reaction systems
+liquidReactor(
+    temperature=(500,'K'),
+    initialConcentrations={
+        "octane": (6.154e-3,'mol/cm^3'),
+        "oxygen": (4.953e-6,'mol/cm^3')
+    },
+    terminationConversion={
+        'octane': 0.9,
+    },
+    terminationTime=(1e6,'s'),
+)
+
+solvation(
+	solvent='octane'
+)
+
+simulator(
+    atol=1e-16,
+    rtol=1e-8,
+)
+
+model(
+    toleranceKeepInEdge=1E-9,
+    toleranceMoveToCore=0.001,
+    toleranceInterruptSimulation=0.1,
+    maximumEdgeSpecies=100000
+)
+
+options(
+    units='si',
+    saveRestartPeriod=None,
+    drawMolecules=False,
+    generatePlots=False,
+    saveConcentrationProfiles=True,
+)

examples/rmg/minimal/input.py

@@ -28,6 +28,10 @@
     terminationTime=(1e6,'s'),
 )
 
+solvation(
+	solvent='water'
+)
+
 simulator(
     atol=1e-16,
     rtol=1e-8,

rmgpy/data/kinetics/family.py

@@ -39,7 +39,7 @@
 
 from rmgpy.data.base import Database, Entry, LogicNode, LogicOr, ForbiddenStructures,\
                             ForbiddenStructureException, getAllCombinations
-from rmgpy.reaction import Reaction, ReactionError
+from rmgpy.reaction import Reaction
 from rmgpy.kinetics import Arrhenius, ArrheniusEP, ThirdBody, Lindemann, Troe, \
                            PDepArrhenius, MultiArrhenius, MultiPDepArrhenius, \
                            Chebyshev, KineticsData, PDepKineticsModel

rmgpy/data/rmg.py

@@ -39,6 +39,7 @@
 from thermo import ThermoDatabase
 from kinetics import KineticsDatabase
 from statmech import StatmechDatabase
+from solvation import SolvationDatabase
 
 # Module-level variable to store the (only) instance of RMGDatabase in use.
 database = None
@@ -55,6 +56,7 @@ def __init__(self):
         self.forbiddenStructures = None
         self.kinetics = None
         self.statmech = None
+        self.solvation = None
 
         # Store the newly created database in the module.
         global database
@@ -69,7 +71,8 @@ def load(self,
              kineticsFamilies=None,
              kineticsDepositories=None,
              statmechLibraries=None,
-             depository=True
+             depository=True,
+             solvation=True,
              ):
         """
         Load the RMG database from the given `path` on disk, where `path`
@@ -87,6 +90,9 @@ def load(self,
                           kineticsDepositories
                           )
         self.loadStatmech(os.path.join(path, 'statmech'), statmechLibraries, depository)
+
+        if solvation:
+            self.loadSolvation(os.path.join(path, 'solvation'))
 
     def loadThermo(self, path, thermoLibraries=None, depository=True):
         """
@@ -133,6 +139,14 @@ def loadKinetics(self,
                            depositories=kineticsDepositories
                            )
 
+    def loadSolvation(self, path):
+        """
+        Load the RMG solvation database from the given `path` on disk, where
+        `path` points to the top-level folder of the RMG solvation database.
+        """
+        self.solvation = SolvationDatabase()
+        self.solvation.load(path)
+
     def loadStatmech(self, path, statmechLibraries=None, depository=True):
         """
         Load the RMG statmech database from the given `path` on disk, where