[Solvation] Added logging info when reading solvation inputs

Author: ssun30

rmgpy/rmg/input.py

@@ -1187,6 +1187,19 @@ def solvation(solvent, solventData=None, excludedSpecies=None, excludedLibraries
     rmg.solvation_excluded_species = excludedSpecies if excludedSpecies is not None else []
     rmg.solvation_excluded_libraries = excludedLibraries if excludedLibraries is not None else []
 
+    # Log species and libraries excluded from solvation corrections
+    if rmg.solvation_excluded_species:
+        logging.info(
+            f"Solvation corrections will be skipped for the following species: "
+            f"{', '.join(rmg.solvation_excluded_species)}"
+        )
+    if rmg.solvation_excluded_libraries:
+        logging.info(
+            f"Solvation corrections will be skipped for species from the following thermo libraries: "
+            f"{', '.join(rmg.solvation_excluded_libraries)}"
+        )
+
+
 def model(toleranceMoveToCore=None, toleranceRadMoveToCore=np.inf,
           toleranceMoveEdgeReactionToCore=np.inf, toleranceKeepInEdge=0.0,
           toleranceInterruptSimulation=1.0,
@@ -1769,7 +1782,16 @@ def save_input_file(path, rmg):
         f.write(')\n\n')
 
     if rmg.solvent:
-        f.write("solvation(\n    solvent = '{0!s}'\n)\n\n".format(rmg.solvent))
+        f.write("solvation(\n")
+        f.write("    solvent = '{0!s}',\n".format(rmg.solvent))
+
+        if rmg.solvation_excluded_species:
+            f.write("    excludedSpecies = {0},\n".format(repr(rmg.solvation_excluded_species)))
+
+        if rmg.solvation_excluded_libraries:
+            f.write("    excludedLibraries = {0},\n".format(repr(rmg.solvation_excluded_libraries)))
+
+        f.write(")\n\n")
 
     # Simulator tolerances
     f.write('simulator(\n')

rmgpy/rmg/model.py

@@ -237,6 +237,8 @@ def __init__(self, core=None, edge=None, surface=None):
         self.new_surface_spcs_loss = set()
         self.new_surface_rxns_loss = set()
         self.solvent_name = ""
+        self.solvation_excluded_species = []
+        self.solvation_excluded_libraries = []
         self.surface_site_density = None
         self.unrealgroups = [
             Group().from_adjacency_list(
@@ -557,7 +559,7 @@ def make_new_reaction(self, forward, check_existing=True, generate_thermo=True,
             elif isinstance(forward, LibraryReaction) and forward.is_surface_reaction():
                 # do fix the library reaction barrier if this is scaled from another metal
                 if any(['Binding energy corrected by LSR' in x.thermo.comment for x in forward.reactants + forward.products]):
-                    forward.fix_barrier_height(solvent=self.solvent_name)            
+                    forward.fix_barrier_height(solvent=self.solvent_name)
             elif forward.kinetics.solute:
                 forward.apply_solvent_correction(solvent=self.solvent_name)
             if self.pressure_dependence and forward.is_unimolecular():
@@ -1601,7 +1603,7 @@ def add_seed_mechanism_to_core(self, seed_mechanism, react=False, requires_rms=F
         self.new_reaction_list = []
         self.new_species_list = []
         edge_species_to_move = []
-        
+
         num_old_core_species = len(self.core.species)
         num_old_core_reactions = len(self.core.reactions)