def test_energy(self):
reaction = IntermolecularReaction(
self.LiEC_RO_entry, [self.C1Li1O3_entry, self.C2H4_entry])
reaction.energy()
self.assertEqual(reaction.energy_A, 0.035409666514283344)
self.assertEqual(reaction.energy_B, -0.035409666514283344)
def test_free_energy(self):
reaction = IntermolecularReaction(
entries["LiEC_RO"], [entries["C1Li1O3"], entries["C2H4"]])
reaction.set_free_energy()
self.assertEqual(reaction.free_energy_A, 0.37075842588456)
self.assertEqual(reaction.free_energy_B, -0.37075842588410524)
def test_free_energy(self):
reaction = IntermolecularReaction(
self.LiEC_RO_entry, [self.C1Li1O3_entry, self.C2H4_entry])
reaction.free_energy()
self.assertEqual(reaction.free_energy_A, 0.37075842588456)
self.assertEqual(reaction.free_energy_B, -0.37075842588456)
def test_graph_representation(self):
# set up input variables
C2H4_RN_entry = entries["C2H4"]
LiEC_RO_RN_entry = entries["LiEC_RO"]
C1Li1O3_RN_entry = entries["C1Li1O3"]
C2H4_ind = C2H4_RN_entry.parameters["ind"]
LiEC_RO_ind = LiEC_RO_RN_entry.parameters["ind"]
C1Li1O3_ind = C1Li1O3_RN_entry.parameters["ind"]
# perform calc
reaction = IntermolecularReaction(LiEC_RO_RN_entry,
[C2H4_RN_entry, C1Li1O3_RN_entry])
graph = reaction.graph_representation()
# assert
self.assertCountEqual(
list(graph.nodes),
[
LiEC_RO_ind,
C2H4_ind,
C1Li1O3_ind,
str(LiEC_RO_ind) + "," + str(C1Li1O3_ind) + "+" +
str(C2H4_ind),
str(C2H4_ind) + "+PR_" + str(C1Li1O3_ind) + "," +
str(LiEC_RO_ind),
str(C1Li1O3_ind) + "+PR_" + str(C2H4_ind) + "," +
str(LiEC_RO_ind),
],
)
self.assertEqual(len(graph.edges), 7)
self.assertEqual(
graph.get_edge_data(
LiEC_RO_ind,
str(LiEC_RO_ind) + "," + str(C1Li1O3_ind) + "+" +
str(C2H4_ind),
)["softplus"],
0.5828092060367285,
)
self.assertEqual(
graph.get_edge_data(
LiEC_RO_ind,
str(C2H4_ind) + "+PR_" + str(C1Li1O3_ind) + "," +
str(LiEC_RO_ind),
),
None,
)
def test_generate(self):
reactions = IntermolecularReaction.generate(entries["RN"].entries)
self.assertEqual(len(reactions), 3029)
reaction_set = set()
for reaction in reactions:
reaction_set.add(
frozenset([
reaction.reactant.entry_id,
reaction.product_0.entry_id,
reaction.product_1.entry_id,
]))
self.assertEqual(len(reaction_set), 3029)
for r in reactions:
if r.reactant.entry_id == entries["LiEC_RO"].entry_id:
if (r.products[0].entry_id == entries["C2H4"].entry_id
or r.products[1].entry_id == entries["C2H4"].entry_id):
self.assertTrue(r.products[0].formula == "C1 Li1 O3"
or r.products[1].formula == "C1 Li1 O3")
self.assertTrue(r.products[0].get_free_energy()
== entries["C1Li1O3"].get_free_energy()
or r.products[1].get_free_energy()
== entries["C1Li1O3"].get_free_energy())
self.assertTrue(r.products[0].get_free_energy()
== entries["C1Li1O3"].get_free_energy()
or r.products[1].get_free_energy()
== entries["C1Li1O3"].get_free_energy())
def test_reaction_type(self):
reaction = IntermolecularReaction(
self.LiEC_RO_entry, [self.C1Li1O3_entry, self.C2H4_entry])
self.assertEqual(reaction.rxn_type_A,
"Molecular decomposition breaking one bond A -> B+C")
self.assertEqual(reaction.rxn_type_B,
"Molecular formation from one new bond A+B -> C")
def test_reaction_type(self):
reaction = IntermolecularReaction(
entries["LiEC_RO"], [entries["C1Li1O3"], entries["C2H4"]])
self.assertEqual(reaction.__class__.__name__, "IntermolecularReaction")
self.assertEqual(reaction.rxn_type_A,
"Molecular decomposition breaking one bond A -> B+C")
self.assertEqual(reaction.rxn_type_B,
"Molecular formation from one new bond A+B -> C")
def test_atom_mapping(self):
entries = bucket_mol_entries(
[self.LiEC_RO_entry, self.C1Li1O3_entry, self.C2H4_entry])
reactions, families = IntermolecularReaction.generate(entries)
self.assertEqual(len(reactions), 1)
rxn = reactions[0]
self.assertEqual(rxn.reactant_ids[0], self.LiEC_RO_entry.entry_id)
self.assertEqual(rxn.product_ids[0], self.C2H4_entry.entry_id)
self.assertEqual(rxn.product_ids[1], self.C1Li1O3_entry.entry_id)
self.assertEqual(
rxn.reactants_atom_mapping,
[{
0: 0,
1: 1,
2: 2,
3: 3,
4: 4,
5: 5,
6: 6,
7: 7,
8: 8,
9: 9,
10: 10
}],
)
self.assertEqual(
rxn.products_atom_mapping,
[{
0: 0,
1: 1,
2: 7,
3: 8,
4: 9,
5: 10
}, {
0: 2,
1: 3,
2: 4,
3: 5,
4: 6
}],
)
def test_atom_mapping(self):
ents = bucket_mol_entries(
[entries["LiEC_RO"], entries["C1Li1O3"], entries["C2H4"]])
reactions = IntermolecularReaction.generate(ents)
self.assertEqual(len(reactions), 1)
rxn = reactions[0]
self.assertEqual(rxn.reactant.entry_id, entries["LiEC_RO"].entry_id)
self.assertEqual(rxn.product_0.entry_id, entries["C2H4"].entry_id)
self.assertEqual(rxn.product_1.entry_id, entries["C1Li1O3"].entry_id)
self.assertEqual(
rxn.reactant_atom_mapping,
[{
0: 0,
1: 1,
2: 2,
3: 3,
4: 4,
5: 5,
6: 6,
7: 7,
8: 8,
9: 9,
10: 10
}],
)
self.assertEqual(
rxn.product_atom_mapping,
[{
0: 0,
1: 1,
2: 7,
3: 8,
4: 9,
5: 10
}, {
0: 2,
1: 3,
2: 4,
3: 5,
4: 6
}],
)
def test_generate(self):
RN = ReactionNetwork.from_input_entries(self.LiEC_reextended_entries)
reactions, families = IntermolecularReaction.generate(RN.entries)
self.assertEqual(len(reactions), 3673)
for r in reactions:
if r.reactant_ids[0] == self.LiEC_RO_entry.entry_id:
if (r.product_ids[0] == self.C2H4_entry.entry_id
or r.product_ids[1] == self.C2H4_entry.entry_id):
self.assertTrue(r.pro0_formula == "C1 Li1 O3"
or r.pro1_formula == "C1 Li1 O3")
self.assertTrue(r.pro0_charge == 0 or r.pro1_charge == 0)
self.assertTrue(r.pro0_free_energy()
== self.C1Li1O3_entry.free_energy()
or r.pro1_free_energy()
== self.C1Li1O3_entry.free_energy())
def test_generate(self):
reactions = IntermolecularReaction.generate(entries["RN"].entries)
self.assertEqual(len(reactions), 3673)
for r in reactions:
if r.reactant.entry_id == entries["LiEC_RO"].entry_id:
if (r.products[0].entry_id == entries["C2H4"].entry_id
or r.products[1].entry_id == entries["C2H4"].entry_id):
self.assertTrue(r.products[0].formula == "C1 Li1 O3"
or r.products[1].formula == "C1 Li1 O3")
self.assertTrue(r.products[0].get_free_energy()
== entries["C1Li1O3"].get_free_energy()
or r.products[1].get_free_energy()
== entries["C1Li1O3"].get_free_energy())
self.assertTrue(r.products[0].get_free_energy()
== entries["C1Li1O3"].get_free_energy()
or r.products[1].get_free_energy()
== entries["C1Li1O3"].get_free_energy())
def test_graph_representation(self):
# set up RN
RN = ReactionNetwork.from_input_entries(self.LiEC_reextended_entries)
# set up input variables
C2H4_ind = None
LiEC_RO_ind = None
C1Li1O3_ind = None
C2H4_RN_entry = None
LiEC_RO_RN_entry = None
C1Li1O3_RN_entry = None
for entry in RN.entries["C2 H4"][5][0]:
if self.C2H4_mg.isomorphic_to(entry.mol_graph):
C2H4_ind = entry.parameters["ind"]
C2H4_RN_entry = entry
break
for entry in RN.entries["C3 H4 Li1 O3"][11][0]:
if self.LiEC_RO_mg.isomorphic_to(entry.mol_graph):
LiEC_RO_ind = entry.parameters["ind"]
LiEC_RO_RN_entry = entry
break
for entry in RN.entries["C1 Li1 O3"][5][0]:
if self.C1Li1O3_mg.isomorphic_to(entry.mol_graph):
C1Li1O3_ind = entry.parameters["ind"]
C1Li1O3_RN_entry = entry
break
# perform calc
reaction = IntermolecularReaction(LiEC_RO_RN_entry,
[C2H4_RN_entry, C1Li1O3_RN_entry])
graph = reaction.graph_representation()
# assert
self.assertCountEqual(
list(graph.nodes),
[
LiEC_RO_ind,
C2H4_ind,
C1Li1O3_ind,
str(LiEC_RO_ind) + "," + str(C1Li1O3_ind) + "+" +
str(C2H4_ind),
str(C2H4_ind) + "+PR_" + str(C1Li1O3_ind) + "," +
str(LiEC_RO_ind),
str(C1Li1O3_ind) + "+PR_" + str(C2H4_ind) + "," +
str(LiEC_RO_ind),
],
)
self.assertEqual(len(graph.edges), 7)
self.assertEqual(
graph.get_edge_data(
LiEC_RO_ind,
str(LiEC_RO_ind) + "," + str(C1Li1O3_ind) + "+" +
str(C2H4_ind),
)["softplus"],
0.5828092060367285,
)
self.assertEqual(
graph.get_edge_data(
LiEC_RO_ind,
str(C2H4_ind) + "+PR_" + str(C1Li1O3_ind) + "," +
str(LiEC_RO_ind),
),
None,
)
def test_energy(self):
reaction = IntermolecularReaction(
entries["LiEC_RO"], [entries["C1Li1O3"], entries["C2H4"]])
self.assertEqual(reaction.energy_A, 0.035409666514283344)
self.assertEqual(reaction.energy_B, -0.035409666514283344)