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_from_path(self):
test_dir = os.path.join(PymatgenTest.TEST_FILES_DIR, "bader")
analysis = BaderAnalysis.from_path(test_dir)
chgcar = os.path.join(test_dir, "CHGCAR.gz")
chgref = os.path.join(test_dir, "_CHGCAR_sum.gz")
analysis0 = BaderAnalysis(chgcar_filename=chgcar,
chgref_filename=chgref)
charge = np.array(analysis.summary["charge"])
charge0 = np.array(analysis0.summary["charge"])
self.assertTrue(np.allclose(charge, charge0))
if os.path.exists("CHGREF"):
os.remove("CHGREF")
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))
def test_atom_parsing(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"),
parse_atomic_densities=True,
)
self.assertEqual(len(analysis.atomic_densities),
len(analysis.chgcar.structure))
self.assertAlmostEqual(
np.sum(analysis.chgcar.data["total"]),
np.sum([np.sum(d["data"]) for d in analysis.atomic_densities]),
)
def from_files(cls, density_path, pseudopotential_paths, with_core=True, workdir=None, **kwargs):
"""
Uses the abinit density files and the bader_ executable from Henkelmann et al. to calculate
the bader charges of the system. If pseudopotentials are given, the atomic charges will be
extracted as well. See also :cite:`Henkelman2006`.
The extraction of the core charges may be a time consuming calculation, depending on the
size of the system. A tuning of the parameters may be required (see Density.ae_core_density_on_mesh).
Args:
density_path: Path to the abinit density file. Can be a fortran _DEN or a netCDF DEN.nc file.
In case of fortran file, requires cut3d (version >= 8.6.1) for the convertion.
pseudopotential_paths: Dictionary {element: pseudopotential path} for all the elements present
in the system.
with_core: Core charges will be extracted from the pseudopotentials with the
Density.ae_core_density_on_mesh method. Requires pseudopotential_paths.
workdir: Working directory. If None, a temporary directory is created.
kwargs: arguments passed to the method ``Density.ae_core_density_on_mesh``
Returns:
An instance of :class:`BaderCharges`
"""
# read the valence density
# if density is not a netcdf file, convert with cut3d
if not density_path.endswith('.nc'):
dff = DensityFortranFile.from_file(density_path)
density = dff.get_density()
else:
density = Density.from_file(density_path)
structure = density.structure
atomic_charges = None
if with_core:
if not pseudopotential_paths:
raise ValueError("pseudopotentials should be provided to extract the core densities")
try:
from pseudo_dojo.ppcodes.oncvpsp import psp8_get_densities
except ImportError as exc:
print("PseudoDojo package required to extract core densities. "
"Please install it with `pip install pseudo_dojo`")
raise exc
# extract core charge from pseudopotentials on a radial grid in the correct units
rhoc = {}
for specie, ppath in pseudopotential_paths.items():
r = psp8_get_densities(ppath)
rhoc[specie] = [r.rmesh * bohr_to_angstrom, r.aecore / (4.0 * np.pi) / (bohr_to_angstrom ** 3)]
workdir = tempfile.mkdtemp() if workdir is None else workdir
# extrapolate the core density on the density grid
core_density = Density.ae_core_density_on_mesh(density, structure, rhoc, **kwargs)
density += core_density
atomic_charges = [s.specie.Z for s in structure]
elif pseudopotential_paths:
pseudos = {k: Pseudo.from_file(p) for k, p in pseudopotential_paths.items()}
atomic_charges = [pseudos[s.specie.name].Z_val for s in structure]
chgcar_path = os.path.join(workdir, 'CHGCAR')
density.to_chgcar(chgcar_path)
ba = BaderAnalysis(chgcar_path)
charges = [ba.get_charge(i) for i in range(len(structure))]
return cls(charges, structure, atomic_charges)
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)
def from_files(cls, density_path, pseudopotential_paths, with_core=True, workdir=None, **kwargs):
"""
Uses the abinit density files and the bader_ executable from Henkelmann et al. to calculate
the bader charges of the system. If pseudopotentials are given, the atomic charges will be
extracted as well. See also :cite:`Henkelman2006`.
The extraction of the core charges may be a time consuming calculation, depending on the
size of the system. A tuning of the parameters may be required (see Density.ae_core_density_on_mesh).
Args:
density_path: Path to the abinit density file. Can be a fortran _DEN or a netCDF DEN.nc file.
In case of fortran file, requires cut3d (version >= 8.6.1) for the convertion.
pseudopotential_paths: Dictionary {element: pseudopotential path} for all the elements present
in the system.
with_core: Core charges will be extracted from the pseudopotentials with the
Density.ae_core_density_on_mesh method. Requires pseudopotential_paths.
workdir: Working directory. If None, a temporary directory is created.
kwargs: arguments passed to the method ``Density.ae_core_density_on_mesh``
Returns:
An instance of :class:`BaderCharges`
"""
# read the valence density
# if density is not a netcdf file, convert with cut3d
if not density_path.endswith('.nc'):
dff = DensityFortranFile.from_file(density_path)
density = dff.get_density()
else:
density = Density.from_file(density_path)
structure = density.structure
atomic_charges = None
if with_core:
if not pseudopotential_paths:
raise ValueError("pseudopotentials should be provided to extract the core densities")
try:
from pseudo_dojo.ppcodes.oncvpsp import psp8_get_densities
except ImportError as exc:
print("PseudoDojo package required to extract core densities. "
"Please install it with `pip install pseudo_dojo`")
raise exc
# extract core charge from pseudopotentials on a radial grid in the correct units
rhoc = {}
for specie, ppath in pseudopotential_paths.items():
r = psp8_get_densities(ppath)
rhoc[specie] = [r.rmesh * bohr_to_angstrom, r.aecore / (4.0 * np.pi) / (bohr_to_angstrom ** 3)]
workdir = tempfile.mkdtemp() if workdir is None else workdir
# extrapolate the core density on the density grid
core_density = Density.ae_core_density_on_mesh(density, structure, rhoc, **kwargs)
density += core_density
atomic_charges = [s.specie.Z for s in structure]
elif pseudopotential_paths:
pseudos = {k: Pseudo.from_file(p) for k, p in pseudopotential_paths.items()}
atomic_charges = [pseudos[s.specie.name].Z_val for s in structure]
chgcar_path = os.path.join(workdir, 'CHGCAR')
density.to_chgcar(chgcar_path)
ba = BaderAnalysis(chgcar_path)
charges = [ba.get_charge(i) for i in range(len(structure))]
return cls(charges, structure, atomic_charges)
These two charge density files can be summed using the chgsum.pl script:
chgsum.pl AECCAR0 AECCAR2
The total charge will be written to CHGCAR_sum.
The bader analysis can then be done on this total charge density file:
bader CHGCAR -ref CHGCAR_sum
One finally note is that you need a fine fft grid to accurately reproduce the correct total core charge.
It is essential to do a few calculations, increasing NG(X,Y,Z)F until the total charge is correct.
"""
ba = BaderAnalysis(
'CHGCAR',
'POTCAR') # this is a good example for running code and capturing stdout
# print(ba.get_charge(1))
from ocelot.routines.pbc import PBCparser
from pymatgen.core.structure import Structure
struct = Structure.from_file('CONTCAR')
mols, unwrap_str_sorted, unwrap_pblock_list = PBCparser.unwrap(struct)
def parse_acf(acfdata_fn='./ACF.dat'):
acfdata = []
with open(acfdata_fn, 'r') as f:
ls = f.readlines()
for l in ls[2:-4]:
