def test_init(self):
# test with reference file
analysis = BaderAnalysis(
chgcar_filename=os.path.join(PymatgenTest.TEST_FILES_DIR,
"CHGCAR.Fe3O4"),
potcar_filename=os.path.join(PymatgenTest.TEST_FILES_DIR,
"POTCAR.Fe3O4"),
chgref_filename=os.path.join(PymatgenTest.TEST_FILES_DIR,
"CHGCAR.Fe3O4_ref"),
)
self.assertEqual(len(analysis.data), 14)
self.assertAlmostEqual(analysis.data[0]["charge"], 6.6136782, 3)
self.assertEqual(analysis.data[0]["charge"], analysis.get_charge(0))
self.assertAlmostEqual(analysis.nelectrons, 96)
self.assertAlmostEqual(analysis.vacuum_charge, 0)
ans = [
-1.3863218,
-1.3812175,
-1.3812175,
-1.2615902,
-1.3812175,
-1.3862971,
1.021523,
1.024357,
1.021523,
1.021523,
1.021523,
1.021523,
1.021523,
1.024357,
]
for i in range(14):
self.assertAlmostEqual(ans[i], analysis.get_charge_transfer(i), 3)
self.assertEqual(analysis.get_partial_charge(0),
-analysis.get_charge_transfer(0))
s = analysis.get_oxidation_state_decorated_structure()
self.assertAlmostEqual(s[0].specie.oxi_state, 1.3863218, 3)
# make sure bader still runs without reference file
analysis = BaderAnalysis(chgcar_filename=os.path.join(
PymatgenTest.TEST_FILES_DIR, "CHGCAR.Fe3O4"))
self.assertEqual(len(analysis.data), 14)
# Test Cube file format parsing
analysis = BaderAnalysis(cube_filename=os.path.join(
PymatgenTest.TEST_FILES_DIR, "bader/elec.cube.gz"))
self.assertEqual(len(analysis.data), 9)
