def test_init(self):
test_dir = os.path.join(os.path.dirname(__file__), "..", "..", "..", "test_files")
analysis = BaderAnalysis(os.path.join(test_dir, "CHGCAR.Fe3O4"), os.path.join(test_dir, "POTCAR.Fe3O4"))
self.assertEqual(len(analysis.data), 14)
self.assertAlmostEqual(analysis.data[0]["charge"], 6.1485)
self.assertAlmostEqual(analysis.nelectrons, 96)
self.assertAlmostEqual(analysis.vacuum_charge, 0)
ans = [
-1.8515,
-1.8132,
-1.8132,
-1.5562,
-1.8132,
-1.8515,
1.3369,
1.3378,
1.3373,
1.3374,
1.3374,
1.3369,
1.3373,
1.3378,
]
for i in range(14):
self.assertAlmostEqual(ans[i], analysis.get_charge_transfer(i))
s = analysis.get_oxidation_state_decorated_structure()
self.assertAlmostEqual(s[0].specie.oxi_state, -1.8515)
def test_init(self):
test_dir = os.path.join(os.path.dirname(__file__), "..", "..", "..",
'test_files')
analysis = BaderAnalysis(os.path.join(test_dir, "CHGCAR.Fe3O4"),
os.path.join(test_dir, "POTCAR.Fe3O4"))
self.assertEqual(len(analysis.data), 14)
self.assertAlmostEqual(analysis.data[0]["charge"], 6.1485)
self.assertAlmostEqual(analysis.nelectrons, 96)
self.assertAlmostEqual(analysis.vacuum_charge, 0)
ans = [-1.8515, -1.8132, -1.8132, -1.5562, -1.8132, -1.8515, 1.3369,
1.3378, 1.3373, 1.3374, 1.3374, 1.3369, 1.3373, 1.3378]
for i in range(14):
self.assertAlmostEqual(ans[i], analysis.get_charge_transfer(i))
s = analysis.get_oxidation_state_decorated_structure()
self.assertAlmostEqual(s[0].specie.oxi_state, -1.8515)
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)
