Merge pull request #2929 from kirkbadger18/update_charge_Val5

Update charge for Val5, and N

Author: sevyharris

rmgpy/molecule/atomtype.py

@@ -711,7 +711,7 @@ def get_features(self):
 ATOMTYPES['R!H'].set_actions(increment_bond=['R!H'], decrement_bond=['R!H'], form_bond=['R!H'], break_bond=['R!H'], increment_radical=['R!H'], decrement_radical=['R!H'], increment_lone_pair=['R!H'], decrement_lone_pair=['R!H'], increment_charge=['R!H'], decrement_charge=['R!H'])
 ATOMTYPES['R!H!Val7'].set_actions(increment_bond=['R!H!Val7'], decrement_bond=['R!H!Val7'], form_bond=['R!H!Val7'], break_bond=['R!H!Val7'], increment_radical=['R!H!Val7'], decrement_radical=['R!H!Val7'], increment_lone_pair=['R!H!Val7'], decrement_lone_pair=['R!H!Val7'], increment_charge=[], decrement_charge=[])
 ATOMTYPES['Val4'].set_actions(increment_bond=['Val4'], decrement_bond=['Val4'], form_bond=['Val4'], break_bond=['Val4'], increment_radical=['Val4'], decrement_radical=['Val4'], increment_lone_pair=['Val4'], decrement_lone_pair=['Val4'],increment_charge=[], decrement_charge=[])
-ATOMTYPES['Val5'].set_actions(increment_bond=['Val5'], decrement_bond=['Val5'], form_bond=['Val5'], break_bond=['Val5'], increment_radical=['Val5'], decrement_radical=['Val5'], increment_lone_pair=['Val5'], decrement_lone_pair=['Val5'],increment_charge=[], decrement_charge=[])
+ATOMTYPES['Val5'].set_actions(increment_bond=['Val5'], decrement_bond=['Val5'], form_bond=['Val5'], break_bond=['Val5'], increment_radical=['Val5'], decrement_radical=['Val5'], increment_lone_pair=['Val5'], decrement_lone_pair=['Val5'],increment_charge=['Val5'], decrement_charge=['Val5'])
 ATOMTYPES['Val6'].set_actions(increment_bond=['Val6'], decrement_bond=['Val6'], form_bond=['Val6'], break_bond=['Val6'], increment_radical=['Val6'], decrement_radical=['Val6'], increment_lone_pair=['Val6'], decrement_lone_pair=['Val6'],increment_charge=[], decrement_charge=[])
 ATOMTYPES['Val7'].set_actions(increment_bond=['Val7'], decrement_bond=['Val7'], form_bond=['Val7'], break_bond=['Val7'], increment_radical=['Val7'], decrement_radical=['Val7'], increment_lone_pair=['Val7'], decrement_lone_pair=['Val7'],increment_charge=[], decrement_charge=[])
 
@@ -746,7 +746,7 @@ def get_features(self):
 ATOMTYPES['C2tc'].set_actions(increment_bond=[], decrement_bond=['C2d'], form_bond=[], break_bond=[], increment_radical=[], decrement_radical=[], increment_lone_pair=[], decrement_lone_pair=['Ct'], increment_charge=[], decrement_charge=[])
 ATOMTYPES['Cq'].set_actions(increment_bond=[], decrement_bond=['Ct'], form_bond=[], break_bond=[], increment_radical=[], decrement_radical=[], increment_lone_pair=[], decrement_lone_pair=[], increment_charge=[], decrement_charge=[])
 
-ATOMTYPES['N'].set_actions(increment_bond=['N'], decrement_bond=['N'], form_bond=['N'], break_bond=['N'], increment_radical=['N'], decrement_radical=['N'], increment_lone_pair=['N'], decrement_lone_pair=['N'],increment_charge=[], decrement_charge=[])
+ATOMTYPES['N'].set_actions(increment_bond=['N'], decrement_bond=['N'], form_bond=['N'], break_bond=['N'], increment_radical=['N'], decrement_radical=['N'], increment_lone_pair=['N'], decrement_lone_pair=['N'],increment_charge=['N'], decrement_charge=['N'])
 ATOMTYPES['N0sc'].set_actions(increment_bond=[], decrement_bond=[], form_bond=['N0sc'], break_bond=['N0sc'], increment_radical=['N0sc'], decrement_radical=['N0sc'], increment_lone_pair=[], decrement_lone_pair=['N1s', 'N1sc'],increment_charge=[], decrement_charge=[])
 ATOMTYPES['N1s'].set_actions(increment_bond=['N1dc'], decrement_bond=[], form_bond=['N1s'], break_bond=['N1s'], increment_radical=['N1s'], decrement_radical=['N1s'], increment_lone_pair=['N0sc'], decrement_lone_pair=['N3s', 'N3sc'],increment_charge=[], decrement_charge=[])
 ATOMTYPES['N1sc'].set_actions(increment_bond=[], decrement_bond=[], form_bond=['N1sc'], break_bond=['N1sc'], increment_radical=['N1sc'], decrement_radical=['N1sc'], increment_lone_pair=[], decrement_lone_pair=['N3s', 'N3sc'],increment_charge=[], decrement_charge=[])

test/rmgpy/data/kinetics/familyTest.py

@@ -72,6 +72,7 @@ def setup_class(cls):
                 "R_Addition_COm",
                 "R_Recombination",
                 'Surface_Proton_Electron_Reduction_Alpha',
+                'Surface_Dissociation_Charge_Separation',
             ],
         )
         cls.family = cls.database.families["intra_H_migration"]
@@ -291,6 +292,59 @@ def test_intra__h_migration(self):
 
         assert expected_product.is_isomorphic(products[0], mapping)
 
+    def test_surface_dissociation_charge_separation(self):
+        """
+        Test that the Surface_Dissociation_Charge_Separation family identifies
+        reatants and labels them and reacts them properly, and check that the
+        products are reacted to form the reactants again.
+        """
+        family = self.database.families["Surface_Dissociation_Charge_Separation"]
+        expected_reactants = [
+            Molecule().from_adjacency_list(
+                """
+1 X  u0  p0 c0  {2,S}
+2 N  u0  p0 c+1  {1,S} {3,D} {4,S}
+3 O  u0  p2 c0  {2,D}
+4 O  u0  p3 c-1  {2,S}
+        """
+            ),
+            Molecule().from_adjacency_list("1 X  u0 p0 c0"),
+        ]
+        expected_products = [
+            Molecule().from_adjacency_list(
+                """
+1 X  u0 p0 c0 {2,S}
+2 N  u0 p1 c0 {1,S} {3,D}
+3 O  u0 p2 c0 {2,D}
+        """
+            ),
+            Molecule().from_adjacency_list(
+                """
+1 X  u0 p0 c0 {2,D}
+2 O  u0 p2 c0 {1,D}
+        """
+            ),
+        ]
+
+        labeled_rxn = Reaction(reactants=expected_reactants, products=expected_products)
+        family.add_atom_labels_for_reaction(labeled_rxn)
+
+        fam_products = family.apply_recipe([m.molecule[0] for m in labeled_rxn.reactants])
+        assert len(fam_products) == 2
+        assert expected_products[0].is_isomorphic(fam_products[0])
+        assert expected_products[1].is_isomorphic(fam_products[1])
+
+        fam_reactants = family.apply_recipe(fam_products, forward=False)
+        assert len(fam_reactants) == 2
+        assert expected_reactants[0].is_isomorphic(fam_reactants[0])
+        assert expected_reactants[1].is_isomorphic(fam_reactants[1])
+
+        fam_product_species = [Species(molecule=[p]) for p in fam_products]
+        fam_reactant_species = [Species(molecule=[r]) for r in fam_reactants]
+
+        fam_rxn = Reaction(reactants=fam_reactant_species, products=fam_product_species)
+        assert fam_rxn.is_isomorphic(labeled_rxn)
+
     def test_h_abstraction(self):
         """
         Test that the H_Abstraction family returns a properly re-labeled product structure.

test/rmgpy/test_data/testing_database/kinetics/families/Surface_Dissociation_Charge_Separation/groups.py

@@ -0,0 +1,76 @@
+#!/usr/bin/env python
+# encoding: utf-8
+
+name = "Surface_Dissociation_Charge_Separation/groups"
+shortDesc = u""
+longDesc = u"""
+Surface bond fission of one species into two distinct adsorbates.
+Atom *1 is bonded to the surface (*3). The image below shows a single bond,
+but single and double are possible. What matters is that the bond
+between *1 and *2 must be single and have charge separation across it.
+
+   *1[+]--*2[-]          *1      *2
+    |            ---->    |      ||
+  ~*3~ + ~*4~~           ~*3~ + ~*4~~
+
+The rate, which should be in mol/m2/s,
+will be given by k * (mol/m2) * (mol/m2)
+so k should be in (m2/mol/s)
+"""
+
+template(reactants=["Combined", "VacantSite"], products=["Adsorbate1", "Adsorbate2"], ownReverse=False)
+
+reverse = "Surface_Association_Charge_Separation"
+
+reactantNum=2
+productNum=2
+
+recipe(actions=[
+    ['BREAK_BOND', '*1', 1, '*2'],
+    ['FORM_BOND', '*2', 1, '*4'],
+    ['CHANGE_BOND', '*2', 1, '*4'],
+    ['LOSE_PAIR','*2','1'],
+    ['GAIN_PAIR', '*1', '1'],
+    ['LOSE_CHARGE','*1','1'],
+    ['GAIN_CHARGE', '*2', '1'],
+])
+
+entry(
+    index = 1,
+    label = "Combined",
+    group =
+"""
+1 *1 Val5 u0 p0 c+1 {2,S} {3,[S,D]}
+2 *2 R!H u0 p[1,2,3] c-1 {1,S}
+3 *3 Xo u0 p0 c0 {1,[S,D]}
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 2,
+    label="VacantSite",
+    group =
+"""
+1 *4 Xv u0 p0 c0
+""",
+    kinetics = None,
+)
+
+tree(
+"""
+L1: Combined
+L1: VacantSite
+"""
+)
+
+forbidden(
+    label = "Surf",
+    group =
+"""
+1 *1 Val5 u0 p0 c+1 {2,S} {3,[S,D]}
+2 *2 R!H u0 p[1,2,3] c-1 {1,S} {4,[S,D,T]}
+3 *3 Xo u0 p0 c0 {1,[S,D]}
+4 Xo u0 c0 {2,[S,D,T]}
+""",
+)

test/rmgpy/test_data/testing_database/kinetics/families/Surface_Dissociation_Charge_Separation/rules.py

@@ -0,0 +1,39 @@
+#!/usr/bin/env python
+# encoding: utf-8
+
+name = "Surface_Dissociation_Charge_Separation/rules"
+shortDesc = u""
+longDesc = u"""
+"""
+entry(
+    index = 1,
+    label = "Combined;VacantSite",
+    kinetics = SurfaceArrheniusBEP(
+        A = (9.88e21, 'cm^2/(mol*s)'),
+        n = 0,
+        alpha = 0.52,
+        E0 = (126, 'kJ/mol'),
+        Tmin = (200, 'K'),
+        Tmax = (3000, 'K'),
+    ),
+    rank = 0,
+    shortDesc = u"""Default""",
+    longDesc = u"""
+This BEP is created from a mixture of data in literature taken from the following papers: 
+
+Ma and Schneider
+https://doi.org/10.1021/acscatal.8b04251
+
+Gomez-Díaz and Lopez
+https://pubs.acs.org/doi/10.1021/jp1093349
+
+Farberow et al.
+https://doi.org/10.1021/cs500668k
+
+Deng et al.
+https://pubs.rsc.org/en/content/articlelanding/2014/ra/c3ra46544f
+
+and the current manuscript in progress by Badger et al. looking at the effects
+of NO on the light out curves for hydrocarbons.
+"""
+)

test/rmgpy/test_data/testing_database/kinetics/families/Surface_Dissociation_Charge_Separation/training/dictionary.txt

@@ -0,0 +1,3 @@
+#!/usr/bin/env python
+# encoding: utf-8
+