def read_vasprun_pdos(filename='vasprun.xml'):
"""Read a vasprun.xml containing projected density-of-states (PDOS) data
Pymatgen must be present on the system to use this method
Args:
filename (str): Path to vasprun.xml file
Returns:
pdos_data (np.ndarray): PDOS data formatted as nestled OrderedDict of:
{element: {'energy': energies, 's': densities, 'p' ... }
"""
dos = read_vasprun(filename)
from pymatgen.electronic_structure.core import Spin, OrbitalType
pdos_data = OrderedDict()
for element in dos.structure.symbol_set:
pdos_data[element] = OrderedDict([('energy', dos.energies)])
pdos = dos.get_element_spd_dos(element)
for orb in sorted([orb.value for orb in pdos.keys()]):
# this way we can ensure the orbitals remain in the correct order
orbital = OrbitalType(orb)
# sum spin up and spin down channels
densities = pdos[orbital].densities[Spin.up]
if len(dos.densities) > 1:
densities += pdos[orbital].densities[Spin.down]
pdos_data[element][orbital.name] = densities
return pdos_data
def get_cdos():
for n in range(1, 74):
pdos = defaultdict(dict)
atom = ''
orb = ''
for a in atoms:
if os.path.exists(f'pwscf.pdos_atm#{n}({a})_wfc#{1}(s)'):
atom = Element(a)
if atom == '':
continue
for l, o in enumerate(orbital):
if os.path.exists(f'pwscf.pdos_atm#{n}({str(atom)})_wfc#{l + 1}({o})'):
orb = OrbitalType(l)
data = np.genfromtxt(f'pwscf.pdos_atm#{n}({str(atom)})_wfc#{l + 1}({orb.name})')
pdos[orb][Spin.up] = data[:, 1]
pdos[orb][Spin.down] = data[:, 2]
energies = data[:,0]
pdoss.append(pdos)
efermi = fermi_fromfile('report.scf')
total_density= six.moves.reduce(add_densities, [six.moves.reduce(add_densities, p.values()) for p in pdoss])
total_dos = Dos(efermi, energies, total_density)
s = Structure.from_file('123.cif')
return CompleteDos(s, total_dos, pdoss)
def test_get_element_spd_dos(self):
# with spin polarization
energies_spin = [
-11.25000, -7.50000, -3.75000, 0.00000, 3.75000, 7.50000
]
fermi = 0.0
PDOS_F_2s_up = [0.00000, 0.00159, 0.00000, 0.00011, 0.00000, 0.00069]
PDOS_F_2s_down = [0.00000, 0.00159, 0.00000, 0.00011, 0.00000, 0.00069]
PDOS_F_2py_up = [0.00000, 0.00160, 0.00000, 0.25801, 0.00000, 0.00029]
PDOS_F_2py_down = [
0.00000, 0.00161, 0.00000, 0.25819, 0.00000, 0.00029
]
PDOS_F_2pz_up = [0.00000, 0.00161, 0.00000, 0.25823, 0.00000, 0.00029]
PDOS_F_2pz_down = [
0.00000, 0.00160, 0.00000, 0.25795, 0.00000, 0.00029
]
PDOS_F_2px_up = [0.00000, 0.00160, 0.00000, 0.25805, 0.00000, 0.00029]
PDOS_F_2px_down = [
0.00000, 0.00161, 0.00000, 0.25814, 0.00000, 0.00029
]
self.assertListEqual(
self.LobsterCompleteDOS_spin.get_element_spd_dos(
el=Element("F"))[OrbitalType(0)].energies.tolist(),
energies_spin,
)
self.assertListEqual(
self.LobsterCompleteDOS_spin.get_element_spd_dos(
el=Element("F"))[OrbitalType(0)].densities[Spin.up].tolist(),
PDOS_F_2s_up,
)
self.assertListEqual(
self.LobsterCompleteDOS_spin.get_element_spd_dos(
el=Element("F"))[OrbitalType(0)].densities[Spin.down].tolist(),
PDOS_F_2s_down,
)
for ilistel, listel in enumerate(
self.LobsterCompleteDOS_spin.get_element_spd_dos(el=Element(
"F"))[OrbitalType(1)].densities[Spin.up].tolist()):
self.assertAlmostEqual(
listel,
(np.array(PDOS_F_2px_up) + np.array(PDOS_F_2py_up) +
np.array(PDOS_F_2pz_up)).tolist()[ilistel],
)
for ilistel, listel in enumerate(
self.LobsterCompleteDOS_spin.get_element_spd_dos(el=Element(
"F"))[OrbitalType(1)].densities[Spin.down].tolist()):
self.assertAlmostEqual(
listel,
(np.array(PDOS_F_2px_down) + np.array(PDOS_F_2py_down) +
np.array(PDOS_F_2pz_down)).tolist()[ilistel],
)
self.assertAlmostEqual(
self.LobsterCompleteDOS_spin.get_element_spd_dos(
el=Element("F"))[OrbitalType(0)].efermi,
fermi,
)
# without spin polarization
energies_nonspin = [
-11.25000, -7.50000, -3.75000, 0.00000, 3.75000, 7.50000
]
efermi = 0.0
PDOS_F_2s = [0.00000, 0.00320, 0.00000, 0.00017, 0.00000, 0.00060]
PDOS_F_2py = [0.00000, 0.00322, 0.00000, 0.51635, 0.00000, 0.00037]
PDOS_F_2pz = [0.00000, 0.00322, 0.00000, 0.51636, 0.00000, 0.00037]
PDOS_F_2px = [0.00000, 0.00322, 0.00000, 0.51634, 0.00000, 0.00037]
self.assertListEqual(
self.LobsterCompleteDOS_nonspin.get_element_spd_dos(
el=Element("F"))[OrbitalType(0)].energies.tolist(),
energies_nonspin,
)
self.assertListEqual(
self.LobsterCompleteDOS_nonspin.get_element_spd_dos(
el=Element("F"))[OrbitalType(0)].densities[Spin.up].tolist(),
PDOS_F_2s,
)
for ilistel, listel in enumerate(
self.LobsterCompleteDOS_nonspin.get_element_spd_dos(el=Element(
"F"))[OrbitalType(1)].densities[Spin.up].tolist()):
self.assertAlmostEqual(
listel,
(np.array(PDOS_F_2px) + np.array(PDOS_F_2py) +
np.array(PDOS_F_2pz)).tolist()[ilistel],
)
self.assertAlmostEqual(
self.LobsterCompleteDOS_nonspin.get_element_spd_dos(
el=Element("F"))[OrbitalType(0)].efermi,
efermi,
)
def test_get_spd_dos(self):
# with spin polarization
energies_spin = [
-11.25000, -7.50000, -3.75000, 0.00000, 3.75000, 7.50000
]
fermi = 0.0
PDOS_F_2s_up = [0.00000, 0.00159, 0.00000, 0.00011, 0.00000, 0.00069]
PDOS_F_2s_down = [0.00000, 0.00159, 0.00000, 0.00011, 0.00000, 0.00069]
PDOS_F_2py_up = [0.00000, 0.00160, 0.00000, 0.25801, 0.00000, 0.00029]
PDOS_F_2py_down = [
0.00000, 0.00161, 0.00000, 0.25819, 0.00000, 0.00029
]
PDOS_F_2pz_up = [0.00000, 0.00161, 0.00000, 0.25823, 0.00000, 0.00029]
PDOS_F_2pz_down = [
0.00000, 0.00160, 0.00000, 0.25795, 0.00000, 0.00029
]
PDOS_F_2px_up = [0.00000, 0.00160, 0.00000, 0.25805, 0.00000, 0.00029]
PDOS_F_2px_down = [
0.00000, 0.00161, 0.00000, 0.25814, 0.00000, 0.00029
]
PDOS_K_3s_up = [0.00000, 0.00000, 0.00000, 0.00008, 0.00000, 0.00007]
PDOS_K_3s_down = [0.00000, 0.00000, 0.00000, 0.00008, 0.00000, 0.00007]
PDOS_K_4s_up = [0.00000, 0.00018, 0.00000, 0.02035, 0.00000, 0.02411]
PDOS_K_4s_down = [0.00000, 0.00018, 0.00000, 0.02036, 0.00000, 0.02420]
PDOS_K_3py_up = [0.00000, 0.26447, 0.00000, 0.00172, 0.00000, 0.00000]
PDOS_K_3py_down = [
0.00000, 0.26446, 0.00000, 0.00172, 0.00000, 0.00000
]
PDOS_K_3pz_up = [0.00000, 0.26446, 0.00000, 0.00172, 0.00000, 0.00000]
PDOS_K_3pz_down = [
0.00000, 0.26447, 0.00000, 0.00172, 0.00000, 0.00000
]
PDOS_K_3px_up = [0.00000, 0.26447, 0.00000, 0.00172, 0.00000, 0.00000]
PDOS_K_3px_down = [
0.00000, 0.26446, 0.00000, 0.00172, 0.00000, 0.00000
]
PDOS_s_up = (np.array(PDOS_F_2s_up) + np.array(PDOS_K_3s_up) +
np.array(PDOS_K_4s_up)).tolist()
PDOS_s_down = (np.array(PDOS_F_2s_down) + np.array(PDOS_K_3s_down) +
np.array(PDOS_K_4s_down)).tolist()
PDOS_p_up = (np.array(PDOS_F_2py_up) + np.array(PDOS_F_2pz_up) +
np.array(PDOS_F_2px_up) + np.array(PDOS_K_3py_up) +
np.array(PDOS_K_3pz_up) +
np.array(PDOS_K_3px_up)).tolist()
PDOS_p_down = (np.array(PDOS_F_2py_down) + np.array(PDOS_F_2pz_down) +
np.array(PDOS_F_2px_down) + np.array(PDOS_K_3py_down) +
np.array(PDOS_K_3pz_down) +
np.array(PDOS_K_3px_down)).tolist()
self.assertListEqual(
self.LobsterCompleteDOS_spin.get_spd_dos()[OrbitalType(
0)].energies.tolist(),
energies_spin,
)
self.assertEqual(
self.LobsterCompleteDOS_spin.get_spd_dos()[OrbitalType(0)].efermi,
fermi)
for ilistel, listel in enumerate(
self.LobsterCompleteDOS_spin.get_spd_dos()[OrbitalType(
0)].densities[Spin.up].tolist()):
self.assertAlmostEqual(listel, PDOS_s_up[ilistel])
for ilistel, listel in enumerate(
self.LobsterCompleteDOS_spin.get_spd_dos()[OrbitalType(
0)].densities[Spin.down].tolist()):
self.assertAlmostEqual(listel, PDOS_s_down[ilistel])
for ilistel, listel in enumerate(
self.LobsterCompleteDOS_spin.get_spd_dos()[OrbitalType(
1)].densities[Spin.up].tolist()):
self.assertAlmostEqual(listel, PDOS_p_up[ilistel])
for ilistel, listel in enumerate(
self.LobsterCompleteDOS_spin.get_spd_dos()[OrbitalType(
1)].densities[Spin.down].tolist()):
self.assertAlmostEqual(listel, PDOS_p_down[ilistel])
# without spin polarization
energies_nonspin = [
-11.25000, -7.50000, -3.75000, 0.00000, 3.75000, 7.50000
]
PDOS_F_2s = [0.00000, 0.00320, 0.00000, 0.00017, 0.00000, 0.00060]
PDOS_F_2py = [0.00000, 0.00322, 0.00000, 0.51635, 0.00000, 0.00037]
PDOS_F_2pz = [0.00000, 0.00322, 0.00000, 0.51636, 0.00000, 0.00037]
PDOS_F_2px = [0.00000, 0.00322, 0.00000, 0.51634, 0.00000, 0.00037]
PDOS_K_3s = [0.00000, 0.00000, 0.00000, 0.00005, 0.00000, 0.00004]
PDOS_K_4s = [0.00000, 0.00040, 0.00000, 0.04039, 0.00000, 0.02241]
PDOS_K_3py = [0.00000, 0.52891, 0.00000, 0.00345, 0.00000, 0.00000]
PDOS_K_3pz = [0.00000, 0.52891, 0.00000, 0.00345, 0.00000, 0.00000]
PDOS_K_3px = [0.00000, 0.52891, 0.00000, 0.00345, 0.00000, 0.00000]
PDOS_s = (np.array(PDOS_F_2s) + np.array(PDOS_K_3s) +
np.array(PDOS_K_4s)).tolist()
PDOS_p = (np.array(PDOS_F_2py) + np.array(PDOS_F_2pz) +
np.array(PDOS_F_2px) + np.array(PDOS_K_3py) +
np.array(PDOS_K_3pz) + np.array(PDOS_K_3px)).tolist()
self.assertListEqual(
self.LobsterCompleteDOS_nonspin.get_spd_dos()[OrbitalType(
0)].energies.tolist(),
energies_nonspin,
)
for ilistel, listel in enumerate(
self.LobsterCompleteDOS_nonspin.get_spd_dos()[OrbitalType(
0)].densities[Spin.up].tolist()):
self.assertAlmostEqual(listel, PDOS_s[ilistel])
for ilistel, listel in enumerate(
self.LobsterCompleteDOS_nonspin.get_spd_dos()[OrbitalType(
1)].densities[Spin.up].tolist()):
self.assertAlmostEqual(listel, PDOS_p[ilistel])