Fix broken examples

examples/rmg/MR_test/input.py

@@ -275,8 +275,8 @@
  	minimumNumberOfGrains=250,
  	#the conditions for the rate to be output over
  	#parameter order is: low_value, high_value, units, internal points
- 	temperatures=(300,2200,'K',2),
- 	pressures=(0.01,100.01,'bar',3),
+ 	temperatures=(300,2200,'K',10),
+ 	pressures=(0.01,100.01,'bar',10),
  	#The two options for interpolation are 'PDepArrhenius' (no extra arguments) and 
  	#'Chebyshev' which is followed by the number of basis sets in 
  	#Temperature and Pressure. These values must be less than the number of 

examples/rmg/TEOS/input.py

@@ -4,7 +4,7 @@
 	reactionLibraries = [],
 	seedMechanisms = [],
 	kineticsDepositories = ['training'],
-	kineticsFamilies = ['!Intra_Disproportionation','!Substitution_O'],
+	kineticsFamilies = ['!Intra_Disproportionation','!Substitution_O', '!surface'],
 	kineticsEstimator = 'rate rules',
 )
 

examples/rmg/catalysis/methane_steam/input.py

@@ -1,7 +1,7 @@
 # Data sources
 database(
     thermoLibraries=['surfaceThermoNi111', 'surfaceThermoPt111', 'primaryThermoLibrary', 'thermo_DFT_CCSDTF12_BAC'], 
-    reactionLibraries = [('Surface/Deutschmann_Ni', True)], # when Pt is used change the library to Surface/CPOX_Pt/Deutschmann2006
+    reactionLibraries = [('Surface/Methane/Deutschmann_Ni', True)], # when Pt is used change the library to Surface/CPOX_Pt/Deutschmann2006
     seedMechanisms = [],
     kineticsDepositories = ['training'],
     kineticsFamilies = ['surface','default'],

examples/rmg/commented/input.py

@@ -250,8 +250,8 @@
     minimumNumberOfGrains=250,
     # the conditions for the rate to be output over
     # parameter order is: low_value, high_value, units, internal points
-    temperatures=(300, 2200, 'K', 2),
-    pressures=(0.01, 100, 'bar', 3),
+    temperatures=(300, 2200, 'K', 10),
+    pressures=(0.01, 100, 'bar', 10),
     # The two options for interpolation are 'PDepArrhenius' (no extra arguments) and
     # 'Chebyshev' which is followed by the number of basis sets in
     # Temperature and Pressure. These values must be less than the number of

examples/rmg/e85/input.py

@@ -4,7 +4,7 @@
     reactionLibraries = [],
     seedMechanisms = ['GRI-Mech3.0'],
     kineticsDepositories = ['training'],
-    kineticsFamilies = ['!Intra_Disproportionation','!Substitution_O'],
+    kineticsFamilies = ['!Intra_Disproportionation','!Substitution_O', '!surface'],
     kineticsEstimator = 'rate rules',
 )
 

examples/rmg/gri_mech_rxn_lib/input.py

@@ -40,6 +40,10 @@
     maximumEdgeSpecies=100000
 )
 
+generatedSpeciesConstraints(
+    maximumCarbeneRadicals=2,
+)
+
 options(
     units='si',
     generateOutputHTML=False,

examples/rmg/methylformate/input.py

@@ -4,7 +4,7 @@
     reactionLibraries = [('Methylformate',False),('Glarborg/highP',False)],
     seedMechanisms = ['Glarborg/C2'],
     kineticsDepositories = ['training'],
-    kineticsFamilies = ['!Intra_Disproportionation','!Substitution_O'],
+    kineticsFamilies = ['!Intra_Disproportionation','!Substitution_O', '!surface'],
     kineticsEstimator = 'rate rules',
 )
 

examples/rmg/minimal_sensitivity/input.py

@@ -4,7 +4,7 @@
     reactionLibraries = [],
     seedMechanisms = [],
     kineticsDepositories = ['training'],
-    kineticsFamilies = ['!Intra_Disproportionation','!Substitution_O'],
+    kineticsFamilies = ['!Intra_Disproportionation','!Substitution_O', '!surface'],
     kineticsEstimator = 'rate rules',
 )
 

examples/rmg/nox_transitory_edge/input.py

@@ -12,10 +12,12 @@
     reactive=True,	
     structure=SMILES("CC"),
 )
+
 species(
     label='O2',
     structure=SMILES("[O][O]"),
 )
+
 species(
     label='N2',
     reactive=False,
@@ -76,6 +78,7 @@
 
 generatedSpeciesConstraints(
     allowed=['input species','seed mechanisms','reaction libraries'],
+    allowSingletO2=True,
     #maximumCarbonAtoms=5,
     #maximumOxygenAtoms=8,
     #maximumNitrogenAtoms=0,

rmgpy/constraints.py

@@ -61,7 +61,8 @@ def pass_cutting_threshold(species):
 def fails_species_constraints(species):
     """
     Pass in either a `Species` or `Molecule` object and checks whether it passes 
-    the speciesConstraints set by the user.  If not, returns `True` for failing speciesConstraints.
+    the speciesConstraints set by the user.  If the species fails constraints, returns 
+    a string `reason` describing which constraint failed. If all constraints pass, returns `False`.
     """
 
     from rmgpy.rmg.input import get_input
@@ -86,57 +87,58 @@ def fails_species_constraints(species):
     max_carbon_atoms = species_constraints.get('maximumCarbonAtoms', -1)
     if max_carbon_atoms != -1:
         if struct.get_num_atoms('C') > max_carbon_atoms:
-            return True
+            return f"Exceeded maximumCarbonAtoms: {struct.get_num_atoms('C')} > {max_carbon_atoms}"
 
     max_oxygen_atoms = species_constraints.get('maximumOxygenAtoms', -1)
     if max_oxygen_atoms != -1:
         if struct.get_num_atoms('O') > max_oxygen_atoms:
-            return True
+            return f"Exceeded maximumOxygenAtoms: {struct.get_num_atoms('O')} > {max_oxygen_atoms}"
 
     max_nitrogen_atoms = species_constraints.get('maximumNitrogenAtoms', -1)
     if max_nitrogen_atoms != -1:
         if struct.get_num_atoms('N') > max_nitrogen_atoms:
-            return True
+            return f"Exceeded maximumNitrogenAtoms: {struct.get_num_atoms('N')} > {max_nitrogen_atoms}"
 
     max_silicon_atoms = species_constraints.get('maximumSiliconAtoms', -1)
     if max_silicon_atoms != -1:
         if struct.get_num_atoms('Si') > max_silicon_atoms:
-            return True
+            return f"Exceeded maximumSiliconAtoms: {struct.get_num_atoms('Si')} > {max_silicon_atoms}"
 
     max_sulfur_atoms = species_constraints.get('maximumSulfurAtoms', -1)
     if max_sulfur_atoms != -1:
         if struct.get_num_atoms('S') > max_sulfur_atoms:
-            return True
+            return f"Exceeded maximumSulfurAtoms: {struct.get_num_atoms('S')} > {max_sulfur_atoms}"
 
     max_heavy_atoms = species_constraints.get('maximumHeavyAtoms', -1)
     if max_heavy_atoms != -1:
-        if struct.get_num_atoms() - struct.get_num_atoms('H') > max_heavy_atoms:
-            return True
+        heavy_atoms = struct.get_num_atoms() - struct.get_num_atoms('H')
+        if heavy_atoms > max_heavy_atoms:
+            return f"Exceeded maximumHeavyAtoms: {heavy_atoms} > {max_heavy_atoms}"
 
     max_surface_sites = species_constraints.get('maximumSurfaceSites', -1)
     if max_surface_sites != -1:
         if struct.get_num_atoms('X') > max_surface_sites:
-            return True
+            return f"Exceeded maximumSurfaceSites: {struct.get_num_atoms('X')} > {max_surface_sites}"
 
     max_surface_bond_order = species_constraints.get('maximumSurfaceBondOrder', -1)
     if max_surface_bond_order != -1:
         for site in struct.get_surface_sites():
             if site.get_total_bond_order() > max_surface_bond_order:
-                return True
+                return f"Exceeded maximumSurfaceBondOrder at site: {site.get_total_bond_order()} > {max_surface_bond_order}"
 
     max_radicals = species_constraints.get('maximumRadicalElectrons', -1)
     if max_radicals != -1:
         if struct.get_radical_count() > max_radicals:
-            return True
+            return f"Exceeded maximumRadicalElectrons: {struct.get_radical_count()} > {max_radicals}"
 
     max_carbenes = species_constraints.get('maximumSingletCarbenes', 1)
-    if max_radicals != -1:
+    if max_carbenes != -1:
         if struct.get_singlet_carbene_count() > max_carbenes:
-            return True
+            return f"Exceeded maximumSingletCarbenes: {struct.get_singlet_carbene_count()} > {max_carbenes}"
 
     max_carbene_radicals = species_constraints.get('maximumCarbeneRadicals', 0)
     if max_carbene_radicals != -1:
         if struct.get_singlet_carbene_count() > 0 and struct.get_radical_count() > max_carbene_radicals:
-            return True
+            return f"Exceeded maximumCarbeneRadicals: {struct.get_radical_count()} > {max_carbene_radicals}"
 
     return False

rmgpy/data/kinetics/family.py

@@ -1655,7 +1655,12 @@ def _generate_product_structures(self, reactant_structures, maps, forward, relab
             if self.is_molecule_forbidden(struct):
                 raise ForbiddenStructureException()
             if fails_species_constraints(struct):
-                raise ForbiddenStructureException()
+                reason = fails_species_constraints(struct)
+                raise ForbiddenStructureException(
+                    "Species constraints forbids product species {0}. Please "
+                    "reformulate constraints, or explicitly "
+                    "allow it. Reason: {1}".format(struct, reason)
+                )
 
         return product_structures
 

rmgpy/kinetics/chebyshev.pyx

@@ -193,7 +193,7 @@ cdef class Chebyshev(PDepKineticsModel):
             raise KineticsError("The master equation data needs more temperature and pressure data "
                                 "points than are placed into Chebyshev polynomial. Currently, the "
                                 "data has {0} temperatures and the polynomial is set to have {1}. "
-                                "The data has {2} pressures and the polynomial is set ot have {3}"
+                                "The data has {2} pressures and the polynomial is set to have {3}"
                                 "".format(nT, degreeT, nP, degreeP))
         elif nT < 1.25 * degreeT or nP < 1.25 * degreeP:
             logging.warning('This Chebyshev fitting has few degrees of freedom and may not be '

rmgpy/rmg/main.py

@@ -587,9 +587,9 @@ def initialize(self, **kwargs):
             shutil.copyfile(self.species_map_path, os.path.join(filters_restart, "species_map.yml"))
 
             # Load the seed mechanism to get the core and edge species
-            self.database.kinetics.load_libraries(restart_dir, libraries=["restart", "restart_edge"])
+            self.database.kinetics.load_libraries(restart_dir)#, libraries=["restart", "restart_edge"])
             self.seed_mechanisms.append("restart")
-            self.reaction_libraries.append(("restart_edge", False))
+#            self.reaction_libraries.append(("restart_edge", False))
 
         # Set trimolecular reactant flags of reaction systems
         if self.trimolecular:
@@ -693,10 +693,11 @@ def initialize(self, **kwargs):
                 if "allowed" in self.species_constraints and "input species" in self.species_constraints["allowed"]:
                     self.species_constraints["explicitlyAllowedMolecules"].append(spec.molecule[0])
                 else:
+                    reason = fails_species_constraints(spec)
                     raise ForbiddenStructureException(
                         "Species constraints forbids input species {0}. Please "
                         "reformulate constraints, remove the species, or explicitly "
-                        "allow it.".format(spec.label)
+                        "allow it. Reason: {1}".format(spec.label, reason)
                     )
 
         # For liquidReactor, checks whether the solvent is listed as one of the initial species.

rmgpy/rmg/model.py

@@ -1677,10 +1677,11 @@ def add_seed_mechanism_to_core(self, seed_mechanism, react=False, requires_rms=F
                 if "allowed" in rmg.species_constraints and "seed mechanisms" in rmg.species_constraints["allowed"]:
                     rmg.species_constraints["explicitlyAllowedMolecules"].extend(spec.molecule)
                 else:
+                    reason = fails_species_constraints(spec)
                     raise ForbiddenStructureException(
                         "Species constraints forbids species {0} from seed mechanism {1}."
                         " Please reformulate constraints, remove the species, or"
-                        " explicitly allow it.".format(spec.label, seed_mechanism.label)
+                        " explicitly allow it. Reason: {2}".format(spec.label, seed_mechanism.label, reason)
                     )
 
         for spec in edge_species_to_move+self.new_species_list:
@@ -1804,10 +1805,11 @@ def add_reaction_library_to_edge(self, reaction_library, requires_rms=False):
                 if "allowed" in rmg.species_constraints and "reaction libraries" in rmg.species_constraints["allowed"]:
                     rmg.species_constraints["explicitlyAllowedMolecules"].extend(spec.molecule)
                 else:
+                    reason = fails_species_constraints(spec)
                     raise ForbiddenStructureException(
                         "Species constraints forbids species {0} from reaction library "
                         "{1}. Please reformulate constraints, remove the species, or "
-                        "explicitly allow it.".format(spec.label, reaction_library.label)
+                        "explicitly allow it. Reason: {2}".format(spec.label, reaction_library.label, reason)
                     )
 
         for spec in self.new_species_list:

test/rmgpy/constraintsTest.py

@@ -83,7 +83,6 @@ def test_constraints_not_loaded(self, mock_logging):
         rmgpy.rmg.input.rmg = None
 
         mol = Molecule(smiles="C")
-
         assert not fails_species_constraints(mol)
 
         mock_logging.debug.assert_called_with("Species constraints could not be found.")
@@ -210,9 +209,11 @@ def test_surface_site_constraint(self):
         self.rmg.species_constraints["maximumHeavyAtoms"] = 6
 
         assert not fails_species_constraints(mol_1site)
+
         assert not fails_species_constraints(mol_2site)
 
         assert fails_species_constraints(mol_3site_vdW)
+
         assert fails_species_constraints(mol_3site)
 
         self.rmg.species_constraints["maximumCarbonAtoms"] = max_carbon