def test_make_new_reaction(self):
"""
Test that CoreEdgeReactionModel.make_new_reaction method correctly works.
"""
procnum = 2
spcA = Species().from_smiles('[OH]')
spcs = [Species().from_smiles('CC'), Species().from_smiles('[CH3]')]
spc_tuples = [((spcA, spc), ['H_Abstraction']) for spc in spcs]
rxns = list(itertools.chain.from_iterable(react(spc_tuples, procnum)))
cerm = CoreEdgeReactionModel()
for rxn in rxns:
cerm.make_new_reaction(rxn)
"""
3 expected H-abstraction reactions:
OH + CC = H2O + C[CH2]
OH + [CH3] = H2O + [CH2]
OH + [CH3] = [O] + C
"""
# count no. of entries in reactionDict:
counter = 0
for fam, v1 in cerm.reaction_dict.items():
for key2, v2 in v1.items():
for key3, rxnList in v2.items():
counter += len(rxnList)
self.assertEquals(counter, 3)
def test_add_new_surface_objects(self):
"""
basic test that surface movement object management works properly
"""
# create object with ReactionSystem behavior
class rsys:
pass
class item:
pass
T = item()
P = item()
T.value_si = 1000.0
P.value_si = 101000.0
rsys.T = T
rsys.P = P
procnum = 2
cerm = CoreEdgeReactionModel()
spcA = Species().from_smiles('[OH]')
spcs = [Species().from_smiles('CC'), Species().from_smiles('[CH3]')]
spc_tuples = [((spcA, spc), ['H_Abstraction']) for spc in spcs]
rxns = list(itertools.chain.from_iterable(react(spc_tuples, procnum)))
rxns += list(
itertools.chain.from_iterable(
react([((spcs[0], spcs[1]), ['H_Abstraction'])], procnum)))
for rxn in rxns:
cerm.make_new_reaction(rxn)
cerm.core.species = [spcA] + spcs
corerxns = []
edgerxns = []
edgespcs = set()
for rxn in rxns:
if set(rxn.reactants + rxn.products) <= set(cerm.core.species):
corerxns.append(rxn)
else:
edgespcs |= set(
cerm.core.species) - set(rxn.reactants + rxn.products)
edgerxns.append(rxn)
cerm.edge.species += list(edgespcs)
cerm.core.reactions = corerxns
cerm.edge.reactions = edgerxns
cerm.surface.species = []
cerm.surface.reactions = []
new_surface_reactions = [cerm.edge.reactions[0]]
new_surface_species = []
obj = new_surface_reactions
cerm.add_new_surface_objects(obj, new_surface_species,
new_surface_reactions, rsys)
empty = set()
self.assertEqual(cerm.new_surface_spcs_add, empty)
self.assertEqual(cerm.new_surface_spcs_loss, empty)
self.assertEqual(cerm.new_surface_rxns_loss, empty)
self.assertEqual(cerm.new_surface_rxns_add,
set([cerm.edge.reactions[0]]))