def calc_effective_mass(args: Namespace):
vasprun, outcar = Vasprun(args.vasprun), Outcar(args.outcar)
band_edge_prop = VaspBandEdgeProperties(vasprun, outcar)
effective_mass = make_effective_mass(vasprun, args.temperature,
args.concentrations,
band_edge_prop.band_gap)
print(effective_mass)
def make_diele_func(vasprun: Vasprun,
outcar: Outcar,
use_vasp_real: bool = True,
ita: float = 0.01) -> DieleFuncData:
energies, real, imag = vasprun.dielectric_data["density"]
imag = np.array(imag)
if use_vasp_real:
real = np.array(real)
else:
# When CSHIFT = 0.0, the first component becomes 99999.0
# the following lines are copied from the vasprun.xml
# <dielectricfunction>
# <imag>
# <array>
# <dimension dim=“1”>gridpoints</dimension>
# <field>energy</field>
# <field>xx</field>
# <field>yy</field>
# <field>zz</field>
# <field>xy</field>
# <field>yz</field>
# <field>zx</field>
# <set>
# <r> 0.0000 0.0000 0.0000 -0.0000 99999.0000 99999.0000 99999.0000 </r>
imag[0] = 0.0
real = kramers_kronig_trans(imag, energies, ita)
band_gap = VaspBandEdgeProperties(vasprun, outcar).band_gap
return DieleFuncData(energies, real.tolist(), imag.tolist(), band_gap)
def test_band_edge_properties_from_vasp(test_data_files):
vasprun_file = str(test_data_files / "MnO_uniform_vasprun.xml")
vasprun = Vasprun(vasprun_file)
outcar_file = str(test_data_files / "MnO_uniform_OUTCAR")
outcar = Outcar(outcar_file)
band_edge = VaspBandEdgeProperties(vasprun, outcar)
assert pytest.approx(band_edge.band_gap) == 0.4702
def make_calc_results_from_vasp(vasprun: Vasprun,
outcar: Outcar) -> CalcResults:
structure = vasprun.final_structure
magnetization = outcar.total_mag or 0.0
symmetrizer = StructureSymmetrizer(
structure,
symprec=defaults.symmetry_length_tolerance,
angle_tolerance=defaults.symmetry_angle_tolerance,
time_reversal=abs(magnetization) > defaults.integer_criterion)
band_edge_prop = VaspBandEdgeProperties(vasprun, outcar,
defaults.integer_criterion)
return CalcResults(structure=structure,
site_symmetry=symmetrizer.point_group,
energy=outcar.final_energy,
magnetization=magnetization,
kpoint_coords=vasprun.actual_kpoints,
kpoint_weights=vasprun.actual_kpoints_weights,
potentials=[-p for p in outcar.electrostatic_potential],
vbm_info=band_edge_prop.vbm_info,
cbm_info=band_edge_prop.cbm_info,
fermi_level=vasprun.efermi,
electronic_conv=vasprun.converged_electronic,
ionic_conv=vasprun.converged_ionic)
def test_band_edge_properties_from_vasp_non_mag(test_data_files):
vasprun_file = str(test_data_files / "MgO_band_vasprun.xml")
vasprun = Vasprun(vasprun_file)
outcar_file = str(test_data_files / "MgO_band_OUTCAR")
outcar = Outcar(outcar_file)
band_edge = VaspBandEdgeProperties(vasprun, outcar)
assert pytest.approx(band_edge.band_gap) == 4.6597
def make_perfect_band_edge_state_from_vasp(
procar: Procar, vasprun: Vasprun, outcar: Outcar
) -> PerfectBandEdgeState:
band_edge_prop = VaspBandEdgeProperties(vasprun, outcar,
v_defaults.integer_criterion)
orbs, s = procar.data, vasprun.final_structure
vbm_info = get_edge_info(band_edge_prop.vbm_info, orbs, s, vasprun)
cbm_info = get_edge_info(band_edge_prop.cbm_info, orbs, s, vasprun)
return PerfectBandEdgeState(vbm_info, cbm_info)
def calc_effective_mass(args: Namespace):
vasprun, outcar = Vasprun(args.vasprun), Outcar(args.outcar)
band_edge_prop = VaspBandEdgeProperties(vasprun, outcar)
try:
vbm, cbm = band_edge_prop.vbm_cbm
except TypeError:
logger.warning("Band gap does not exist, so not suited for effective"
"mass calculation.")
return
effective_mass = make_effective_mass(vasprun, args.temperature,
args.concentrations, vbm, cbm)
print(effective_mass)
def make_unitcell_from_vasp(vasprun_band: Vasprun, outcar_band: Outcar,
outcar_dielectric_clamped,
outcar_dielectric_ionic) -> Unitcell:
outcar_dielectric_clamped.read_lepsilon()
outcar_dielectric_ionic.read_lepsilon_ionic()
band_edge_properties = VaspBandEdgeProperties(vasprun_band, outcar_band)
vbm, cbm = band_edge_properties.vbm_cbm
return Unitcell(
vbm=vbm,
cbm=cbm,
ele_dielectric_const=outcar_dielectric_clamped.dielectric_tensor,
ion_dielectric_const=outcar_dielectric_ionic.dielectric_ionic_tensor)
def make_unitcell_from_vasp(vasprun_band: Vasprun,
outcar_band: Outcar,
outcar_dielectric_clamped: Outcar,
outcar_dielectric_ionic: Outcar,
system_name: str = None) -> Unitcell:
name = (system_name
or vasprun_band.final_structure.composition.reduced_formula)
outcar_dielectric_clamped.read_lepsilon()
outcar_dielectric_ionic.read_lepsilon_ionic()
band_edge_properties = VaspBandEdgeProperties(vasprun_band, outcar_band)
vbm, cbm = band_edge_properties.vbm_cbm
return Unitcell(
system=name,
# vbm and cbm are <class 'numpy.float64'>.
vbm=float(vbm),
cbm=float(cbm),
ele_dielectric_const=outcar_dielectric_clamped.dielectric_tensor,
ion_dielectric_const=outcar_dielectric_ionic.dielectric_ionic_tensor)
def prior_info_from_calc_dir(prev_dir_path: Path,
vasprun: str = "vasprun.xml",
outcar: str = "OUTCAR",
potcar: str = "POTCAR"):
vasprun = Vasprun(str(prev_dir_path / vasprun))
outcar = Outcar(str(prev_dir_path / outcar))
potcar = Potcar.from_file(str(prev_dir_path / potcar))
charge = get_net_charge_from_vasp(vasprun.final_structure,
vasprun.parameters["NELECT"], potcar)
structure = vasprun.final_structure.copy()
energy_per_atom = outcar.final_energy / len(structure)
band_edge_property = VaspBandEdgeProperties(vasprun, outcar)
total_magnetization = outcar.total_mag
return PriorInfo(structure=structure,
charge=charge,
energy_per_atom=energy_per_atom,
band_gap=band_edge_property.band_gap,
vbm_cbm=band_edge_property.vbm_cbm,
total_magnetization=total_magnetization)
def plot_dos(args: Namespace):
vasprun = Vasprun(args.vasprun)
outcar = Outcar(args.outcar)
band_edge = VaspBandEdgeProperties(vasprun, outcar)
if band_edge.band_gap:
vertical_lines = [band_edge.vbm_info.energy, band_edge.cbm_info.energy]
else:
vertical_lines = [vasprun.efermi]
if args.base_energy is None:
base = vertical_lines[0]
else:
base = args.base_energy
dos_data_from_vasp = \
DosDataFromVasp(vasprun, vertical_lines, base, args.crop_first_value)
dos_data = dos_data_from_vasp.make_dos_data()
ylim_set = None
if args.y_max_ranges:
if dos_data.spin:
ylim_set = [[-y_max, y_max] for y_max in args.y_max_ranges]
else:
ylim_set = [[0, y_max] for y_max in args.y_max_ranges]
structure = vasprun.final_structure
grouped_atom_indices = args.type.grouped_atom_indices(
structure, args.target)
logger.info(f"Grouped atom indices: {grouped_atom_indices}")
plot_data = dos_data.dos_plot_data(grouped_atom_indices,
xlim=args.x_range,
ylim_set=ylim_set)
plot_data.to_json_file()
plotter = DosPlotter(plot_data, args.legend)
plotter.construct_plot()
plotter.plt.savefig(args.filename, format="pdf")
def band_edge_properties(args: Namespace):
vasprun = Vasprun(args.vasprun)
outcar = Outcar(args.outcar)
print(VaspBandEdgeProperties(vasprun, outcar))