def test_atom_mapping():
"""
This is a test for the corner case where atom mapping for `LiF2 -> Li+ + F2` was
incorrect due to reordering of reactant subgraphs. It is fixed and the test should
pass now.
"""
test_file = os.path.join(
os.path.dirname(__file__),
"..",
"..",
"test_files",
"reaction_files",
"LiF2_to_Li_F2.json",
)
entries = loadfn(test_file)
bucketed_entries = bucket_mol_entries(entries)
reactions = CoordinationBondChangeReaction.generate(bucketed_entries)
assert len(reactions) == 1
rxn = reactions[0]
assert rxn.reactant_atom_mapping == [{0: 0, 1: 1, 2: 2}]
assert rxn.product_atom_mapping == [{0: 1, 1: 2}, {0: 0}]
def test_atom_mapping(self):
entries = bucket_mol_entries(
[self.LiEC_entry, self.EC_minus_entry, self.Li_entry])
reactions, families = CoordinationBondChangeReaction.generate(entries)
self.assertEqual(len(reactions), 1)
rxn = reactions[0]
self.assertEqual(rxn.reactant_ids[0], self.LiEC_entry.entry_id)
self.assertEqual(rxn.product_ids[0], self.EC_minus_entry.entry_id)
self.assertEqual(rxn.product_ids[1], self.Li_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: 2,
3: 3,
4: 4,
5: 5,
6: 7,
7: 8,
8: 9,
9: 10
}, {
0: 6
}],
)
def test_atom_mapping(self):
ents = bucket_mol_entries(
[entries["LiEC"], entries["EC_-1"], entries["Li"]])
reactions = CoordinationBondChangeReaction.generate(ents)
self.assertEqual(len(reactions), 1)
rxn = reactions[0]
self.assertEqual(rxn.reactant.entry_id, entries["LiEC"].entry_id)
self.assertEqual(rxn.product_0.entry_id, entries["EC_-1"].entry_id)
self.assertEqual(rxn.product_1.entry_id, entries["Li"].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: 2,
3: 3,
4: 4,
5: 5,
6: 7,
7: 8,
8: 9,
9: 10
}, {
0: 6
}],
)
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_atom_mapping(self):
ents = bucket_mol_entries([entries["LiEC_RO"], entries["LiEC"]])
reactions = IntramolSingleBondChangeReaction.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.entry_id, entries["LiEC"].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: 2,
1: 3,
2: 1,
3: 4,
4: 5,
5: 0,
6: 6,
7: 9,
8: 10,
9: 7,
10: 8
}],
)
def test_bucket_mol_entries():
C2H4_entry = MoleculeEntry(
Molecule.from_file(os.path.join(test_dir, "C2H4.xyz")),
energy=0.0,
enthalpy=0.0,
entropy=0.0,
)
LiEC_RO_entry = MoleculeEntry(
Molecule.from_file(os.path.join(test_dir, "LiEC_RO.xyz")),
energy=0.0,
enthalpy=0.0,
entropy=0.0,
)
C1Li1O3_entry = MoleculeEntry(
Molecule.from_file(os.path.join(test_dir, "C1Li1O3.xyz")),
energy=0.0,
enthalpy=0.0,
entropy=0.0,
)
bucket = bucket_mol_entries([C2H4_entry, LiEC_RO_entry, C1Li1O3_entry])
ref_dict = {
"C2 H4": {
5: {
0: [C2H4_entry]
}
},
"C3 H4 Li1 O3": {
11: {
0: [LiEC_RO_entry]
}
},
"C1 Li1 O3": {
5: {
0: [C1Li1O3_entry]
}
},
}
assert bucket == ref_dict
def test_atom_mapping(self):
entries = bucket_mol_entries(
[self.EC_minus_entry, self.EC_0_entry, self.EC_1_entry])
reactions, families = RedoxReaction.generate(entries)
self.assertEqual(len(reactions), 2)
for r in reactions:
self.assertEqual(
r.reactants_atom_mapping,
[{
0: 0,
1: 1,
2: 2,
3: 3,
4: 4,
5: 5,
6: 6,
7: 7,
8: 8,
9: 9
}],
)
self.assertEqual(
r.products_atom_mapping,
[{
0: 0,
1: 1,
2: 2,
3: 3,
4: 4,
5: 5,
6: 6,
7: 7,
8: 8,
9: 9
}],
)
def test_atom_mapping(self):
ents = bucket_mol_entries(
[entries["EC_-1"], entries["EC_0"], entries["EC_1"]])
reactions = RedoxReaction.generate(ents)
self.assertEqual(len(reactions), 2)
for r in reactions:
self.assertEqual(
r.reactants_atom_mapping,
[{
0: 0,
1: 1,
2: 2,
3: 3,
4: 4,
5: 5,
6: 6,
7: 7,
8: 8,
9: 9
}],
)
self.assertEqual(
r.products_atom_mapping,
[{
0: 0,
1: 1,
2: 2,
3: 3,
4: 4,
5: 5,
6: 6,
7: 7,
8: 8,
9: 9
}],
)