1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
|
from __future__ import annotations
import numpy as np
from numpy.testing import assert_allclose
from pymatgen.core import Structure
from pymatgen.io.optimade import OptimadeStructureAdapter
from pymatgen.util.testing import TEST_FILES_DIR, VASP_IN_DIR
STRUCTURE = Structure.from_file(f"{VASP_IN_DIR}/POSCAR")
XYZ_STRUCTURE = f"{TEST_FILES_DIR}/io/xyz/acetylene.xyz"
def test_get_optimade_structure_roundtrip():
optimade_structure = OptimadeStructureAdapter.get_optimade_structure(STRUCTURE)
assert optimade_structure["attributes"]["nsites"] == len(STRUCTURE)
assert optimade_structure["attributes"]["elements"] == ["Fe", "O", "P"]
assert optimade_structure["attributes"]["nelements"] == 3
assert optimade_structure["attributes"]["chemical_formula_reduced"] == "FeO4P"
assert optimade_structure["attributes"]["species_at_sites"] == 4 * ["Fe"] + 4 * ["P"] + 16 * ["O"]
assert_allclose(
np.abs(optimade_structure["attributes"]["lattice_vectors"]),
np.abs(STRUCTURE.lattice.matrix),
)
# Set an OPTIMADE ID and some custom properties and ensure they are preserved in the properties
test_id = "test_id"
optimade_structure["id"] = test_id
custom_properties = {"_custom_field": "test_custom_field", "_custom_band_gap": 2.2}
optimade_structure["attributes"].update(custom_properties)
roundtrip_structure = OptimadeStructureAdapter.get_structure(optimade_structure)
assert roundtrip_structure.properties["optimade_id"] == test_id
assert roundtrip_structure.properties["optimade_attributes"] == custom_properties
# Delete the properties before the check for equality
roundtrip_structure.properties = {}
assert roundtrip_structure == STRUCTURE
|
