def _do_interpolation(self):
log_banner("INTERPOLATION")
t0 = time.perf_counter()
interpolater = Interpolater(
self._band_structure,
num_electrons=self._num_electrons,
interpolation_factor=self.settings["interpolation_factor"],
soc=self.settings["soc"],
)
amset_data = interpolater.get_amset_data(
energy_cutoff=self.settings["energy_cutoff"],
scissor=self.settings["scissor"],
bandgap=self.settings["bandgap"],
symprec=self.settings["symprec"],
nworkers=self.settings["nworkers"],
)
if self.settings["wavefunction_coefficients"]:
overlap_calculator = WavefunctionOverlapCalculator.from_file(
self.settings["wavefunction_coefficients"])
else:
overlap_calculator = ProjectionOverlapCalculator.from_band_structure(
self._band_structure,
energy_cutoff=self.settings["energy_cutoff"],
symprec=self.settings["symprec"],
)
amset_data.set_overlap_calculator(overlap_calculator)
return amset_data, time.perf_counter() - t0
def setUp(self):
vr = Vasprun(os.path.join(gaas_files, "vasprun.xml.gz"),
parse_projected_eigen=True)
bs = vr.get_band_structure()
num_electrons = vr.parameters["NELECT"]
self.kpoints = np.array(vr.actual_kpoints)
self.interpolater = Interpolater(bs,
num_electrons,
interpolate_projections=True,
interpolation_factor=1)
def _get_interpolater(self, n_idx, t_idx):
# interpolater expects energies in eV and structure in angstrom
energies = {s: e * hartree_to_ev for s, e in self.energies.items()}
structure = get_angstrom_structure(self.structure)
bs = BandStructure(
self.ir_kpoints,
energies,
structure.lattice,
self.efermi * hartree_to_ev,
structure=structure,
)
nelect = sum([idx for idx in self.vb_idx.values()])
props = defaultdict(dict)
for spin in self.spins:
# easier to interpolate the log
props[spin]["rates"] = np.log10(
np.sum(self.scattering_rates[spin][:, n_idx, t_idx], axis=0))
return Interpolater(
bs,
nelect,
interpolation_factor=self.interpolation_factor,
soc=self.soc,
other_properties=props,
)
def __init__(
self,
bandstructure: BandStructure,
nelect: int,
soc: bool = False,
interpolation_factor=defaults["interpolation_factor"],
print_log=defaults["print_log"],
symprec=defaults["symprec"],
energy_cutoff=None,
):
if print_log:
initialize_amset_logger(filename="amset_electronic_structure_plot.log")
self.symprec = symprec
self.interpolater = Interpolater(
bandstructure, nelect, interpolation_factor=interpolation_factor, soc=soc
)
self.structure = bandstructure.structure
self.energy_cutoff = energy_cutoff
class TestBoltzTraP2Interpolater(unittest.TestCase):
"""Tests for interpolating a band structure using BoltzTraP2."""
def setUp(self):
vr = Vasprun(os.path.join(gaas_files, "vasprun.xml.gz"),
parse_projected_eigen=True)
bs = vr.get_band_structure()
num_electrons = vr.parameters["NELECT"]
self.kpoints = np.array(vr.actual_kpoints)
self.interpolater = Interpolater(bs,
num_electrons,
interpolate_projections=True,
interpolation_factor=1)
def test_initialisation(self):
"""Test coefficients and parameters are calculated correctly."""
self.interpolater.initialize()
params = self.interpolater._parameters
assert_array_equal(params[0][0], [[0, 0, 0]])
self.assertAlmostEqual(params[1][0][0], 9.14055614)
self.assertAlmostEqual(params[2][0][0].real, -2.33144546)
def test_get_energies(self):
"""Test getting the interpolated energy, velocity and effective mass."""
# test just getting energy
energies = self.interpolater.get_energies(self.kpoints,
25,
return_velocity=False,
curvature=False)
self.assertEqual(energies.shape, (138, ))
self.assertAlmostEqual(energies[0], 3.852399483908641)
# test energy + velocity
energies, velocities = self.interpolater.get_energies(
self.kpoints, 25, return_velocity=True, curvature=False)
self.assertEqual(energies.shape, (138, ))
self.assertAlmostEqual(energies[0], 3.852399483908641)
self.assertEqual(velocities.shape, (138, 3))
self.assertAlmostEqual(velocities[10][0],
5.401166156893334e6,
places=0)
# test energy + effective_mass
energies, effective_masses = self.interpolater.get_energies(
self.kpoints, 25, return_velocity=False, curvature=True)
self.assertEqual(energies.shape, (138, ))
self.assertAlmostEqual(energies[0], 3.852399483908641)
self.assertEqual(effective_masses.shape, (138, 3, 3))
self.assertAlmostEqual(effective_masses[10][0][0], 0.2242569613626494)
# test energy + velocity + effective_mass
energies, velocities, effective_masses = self.interpolater.get_energies(
self.kpoints, 25, return_velocity=True, curvature=True)
self.assertEqual(energies.shape, (138, ))
self.assertAlmostEqual(energies[0], 3.852399483908641)
self.assertEqual(velocities.shape, (138, 3))
self.assertAlmostEqual(velocities[10][0],
5.401166156893334e6,
places=0)
self.assertEqual(effective_masses.shape, (138, 3, 3))
self.assertAlmostEqual(effective_masses[10][0][0], 0.2242569613626494)
def test_get_energies_scissor(self):
"""Test scissoring of band energies."""
# test valence band
energies = self.interpolater.get_energies(self.kpoints,
25,
return_velocity=False,
curvature=False,
scissor=1.0)
self.assertEqual(energies.shape, (138, ))
self.assertAlmostEqual(energies[0], 3.852399483908641 - 0.5)
# test conduction band
energies = self.interpolater.get_energies(self.kpoints,
33,
return_velocity=False,
curvature=False,
scissor=1.0)
self.assertEqual(energies.shape, (138, ))
self.assertAlmostEqual(energies[0], 7.301700765 + 0.5)
def test_get_energies_multiple_bands(self):
"""Test getting the interpolated data for multiple bands."""
# test just getting energy
energies = self.interpolater.get_energies(self.kpoints, [25, 35],
return_velocity=False,
curvature=False)
self.assertEqual(energies.shape, (2, 138))
self.assertAlmostEqual(energies[0][0], 3.852399483908641)
self.assertAlmostEqual(energies[1][0], 9.594401616456384)
# test energy + velocity
energies, velocities = self.interpolater.get_energies(
self.kpoints, [25, 35], return_velocity=True, curvature=False)
self.assertEqual(energies.shape, (2, 138))
self.assertAlmostEqual(energies[0][0], 3.852399483908641)
self.assertAlmostEqual(energies[1][0], 9.594401616456384)
self.assertEqual(velocities.shape, (2, 138, 3))
self.assertAlmostEqual(velocities[0][10][0],
5.401166156893334e6,
places=0)
self.assertAlmostEqual(velocities[1][10][0],
1.1686720831758736e8,
places=0)
# test energy + effective_mass
energies, effective_masses = self.interpolater.get_energies(
self.kpoints, [25, 35], return_velocity=False, curvature=True)
self.assertEqual(energies.shape, (2, 138))
self.assertAlmostEqual(energies[0][0], 3.852399483908641)
self.assertAlmostEqual(energies[1][0], 9.594401616456384)
self.assertEqual(effective_masses.shape, (2, 138, 3, 3))
self.assertAlmostEqual(effective_masses[0][10][0][0],
0.224256961362649)
self.assertAlmostEqual(effective_masses[1][10][0][0],
0.009057103344700)
# test energy + velocity + effective_mass
energies, velocities, effective_masses = self.interpolater.get_energies(
self.kpoints, [25, 35], return_velocity=True, curvature=True)
self.assertEqual(energies.shape, (2, 138))
self.assertAlmostEqual(energies[0][0], 3.852399483908641)
self.assertAlmostEqual(energies[1][0], 9.594401616456384)
self.assertEqual(velocities.shape, (2, 138, 3))
self.assertAlmostEqual(velocities[0][10][0],
5.401166156893334e6,
places=0)
self.assertAlmostEqual(velocities[1][10][0],
1.1686720831758736e8,
places=0)
self.assertEqual(effective_masses.shape, (2, 138, 3, 3))
self.assertAlmostEqual(effective_masses[0][10][0][0],
0.224256961362649)
self.assertAlmostEqual(effective_masses[1][10][0][0],
0.009057103344700)
def test_get_energies_all_bands(self):
# test all bands
energies, velocities, effective_masses = self.interpolater.get_energies(
self.kpoints, None, return_velocity=True, curvature=True)
self.assertEqual(energies.shape, (96, 138))
self.assertAlmostEqual(energies[25][0], 3.852399483908641)
self.assertAlmostEqual(energies[35][0], 9.594401616456384)
self.assertEqual(velocities.shape, (96, 138, 3))
self.assertAlmostEqual(velocities[25][10][0],
5.401166156893334e6,
places=0)
self.assertAlmostEqual(velocities[35][10][0],
1.1686720831758736e8,
places=0)
self.assertEqual(effective_masses.shape, (96, 138, 3, 3))
self.assertAlmostEqual(effective_masses[25][10][0][0],
0.22425696136264)
self.assertAlmostEqual(effective_masses[35][10][0][0],
0.00905710334470)
def test_get_dos(self):
"""Test generating the interpolated DOS."""
dos = self.interpolater.get_dos([10, 10, 10],
emin=-10,
emax=10,
width=0.075)
self.assertEqual(dos.shape, (20000, 2))
self.assertEqual(dos[0][0], -10)
self.assertAlmostEqual(dos[15000][1], 3.5362612128412807)
def test_get_energies_symprec(self):
# vr = Vasprun(os.path.join(tin_dioxide_files, 'vasprun.xml.gz'),
# parse_projected_eigen=True)
vr = Vasprun(os.path.join(pbs_files, "vasprun.xml.gz"),
parse_projected_eigen=True)
bs = vr.get_band_structure()
num_electrons = vr.parameters["NELECT"]
interpolater = Interpolater(bs,
num_electrons,
interpolate_projections=True,
interpolation_factor=1)
ir_kpoints, weights, kpoints, ir_kpoints_idx, ir_to_full_idx = get_kpoints(
[13, 15, 29],
vr.final_structure,
boltztrap_ordering=True,
return_full_kpoints=True,
)
initialize_amset_logger()
(
energies,
velocities,
curvature,
projections,
sym_info,
) = interpolater.get_energies(
kpoints,
None,
return_velocity=True,
atomic_units=True,
return_curvature=True,
return_projections=True,
symprec=0.1,
return_vel_outer_prod=True,
return_kpoint_mapping=True,
)
(
energies_no_sym,
velocities_no_sym,
curvature_no_sym,
projections_no_sym,
) = interpolater.get_energies(
kpoints,
None,
return_velocity=True,
atomic_units=True,
return_curvature=True,
return_projections=True,
return_vel_outer_prod=True,
symprec=None,
)
np.testing.assert_array_equal(ir_to_full_idx,
sym_info["ir_to_full_idx"])
np.testing.assert_array_equal(ir_kpoints_idx,
sym_info["ir_kpoints_idx"])
# print(velocities[Spin.up][5, :, :, -3:])
# print(velocities_no_sym[Spin.up][5, :, :, -3:])
# print(sym_info["ir_to_full_idx"][-10:])
np.testing.assert_array_almost_equal(energies[Spin.up],
energies_no_sym[Spin.up],
decimal=12)
np.testing.assert_array_almost_equal(velocities[Spin.up],
velocities_no_sym[Spin.up],
decimal=12)
np.testing.assert_array_almost_equal(curvature[Spin.up],
curvature_no_sym[Spin.up],
decimal=12)
for l in projections[Spin.up]:
np.testing.assert_array_almost_equal(
projections[Spin.up][l], projections_no_sym[Spin.up][l])
def test_get_energies_interpolater(self):
initialize_amset_logger()
amset_data = self.interpolater.get_amset_data()
energies, velocities, projections, sym_info = self.interpolater.get_energies(
amset_data.kpoints,
None,
return_velocity=True,
atomic_units=True,
curvature=False,
return_projections=True,
symprec=0.1,
return_vel_outer_prod=True,
return_kpoint_mapping=True,
)
np.testing.assert_array_almost_equal(energies[Spin.up],
amset_data.energies[Spin.up])
np.testing.assert_array_almost_equal(
velocities[Spin.up], amset_data.velocities_product[Spin.up])
for l in projections[Spin.up]:
np.testing.assert_array_almost_equal(
projections[Spin.up][l], amset_data._projections[Spin.up][l])
np.testing.assert_array_equal(sym_info["ir_kpoints_idx"],
amset_data.ir_kpoints_idx)
np.testing.assert_array_equal(sym_info["ir_to_full_idx"],
amset_data.ir_to_full_kpoint_mapping)
def test_get_energies_symprec(self):
# vr = Vasprun(os.path.join(tin_dioxide_files, 'vasprun.xml.gz'),
# parse_projected_eigen=True)
vr = Vasprun(os.path.join(pbs_files, "vasprun.xml.gz"),
parse_projected_eigen=True)
bs = vr.get_band_structure()
num_electrons = vr.parameters["NELECT"]
interpolater = Interpolater(bs,
num_electrons,
interpolate_projections=True,
interpolation_factor=1)
ir_kpoints, weights, kpoints, ir_kpoints_idx, ir_to_full_idx = get_kpoints(
[13, 15, 29],
vr.final_structure,
boltztrap_ordering=True,
return_full_kpoints=True,
)
initialize_amset_logger()
(
energies,
velocities,
curvature,
projections,
sym_info,
) = interpolater.get_energies(
kpoints,
None,
return_velocity=True,
atomic_units=True,
return_curvature=True,
return_projections=True,
symprec=0.1,
return_vel_outer_prod=True,
return_kpoint_mapping=True,
)
(
energies_no_sym,
velocities_no_sym,
curvature_no_sym,
projections_no_sym,
) = interpolater.get_energies(
kpoints,
None,
return_velocity=True,
atomic_units=True,
return_curvature=True,
return_projections=True,
return_vel_outer_prod=True,
symprec=None,
)
np.testing.assert_array_equal(ir_to_full_idx,
sym_info["ir_to_full_idx"])
np.testing.assert_array_equal(ir_kpoints_idx,
sym_info["ir_kpoints_idx"])
# print(velocities[Spin.up][5, :, :, -3:])
# print(velocities_no_sym[Spin.up][5, :, :, -3:])
# print(sym_info["ir_to_full_idx"][-10:])
np.testing.assert_array_almost_equal(energies[Spin.up],
energies_no_sym[Spin.up],
decimal=12)
np.testing.assert_array_almost_equal(velocities[Spin.up],
velocities_no_sym[Spin.up],
decimal=12)
np.testing.assert_array_almost_equal(curvature[Spin.up],
curvature_no_sym[Spin.up],
decimal=12)
for l in projections[Spin.up]:
np.testing.assert_array_almost_equal(
projections[Spin.up][l], projections_no_sym[Spin.up][l])
class ElectronicStructurePlotter(object):
def __init__(
self,
bandstructure: BandStructure,
nelect: int,
soc: bool = False,
interpolation_factor=defaults["interpolation_factor"],
print_log=defaults["print_log"],
symprec=defaults["symprec"],
energy_cutoff=None,
):
if print_log:
initialize_amset_logger(
filename="amset_electronic_structure_plot.log")
self.symprec = symprec
self.interpolater = Interpolater(
bandstructure,
nelect,
interpolation_factor=interpolation_factor,
soc=soc)
self.structure = bandstructure.structure
self.energy_cutoff = energy_cutoff
@classmethod
def from_vasprun(cls, vasprun, **kwargs):
from pymatgen.io.vasp import Vasprun
if isinstance(vasprun, Path):
vasprun = vasprun.as_posix()
if isinstance(vasprun, str):
vasprun_gz = vasprun + ".gz"
if Path(vasprun).exists():
vasprun = Vasprun(vasprun)
elif Path(vasprun_gz).exists():
vasprun = Vasprun(vasprun_gz)
bandstructure = vasprun.get_band_structure()
nelect = vasprun.parameters["NELECT"]
soc = vasprun.parameters["LSORBIT"]
return cls(bandstructure, nelect, soc=soc, **kwargs)
def get_plot(
self,
plot_dos=True,
plot_band_structure=True,
kpath=None,
line_density=100.0,
dos_kpoints=50.0,
dos_estep=defaults["dos_estep"],
zero_to_efermi=True,
vbm_cbm_marker=False,
height=6,
width=None,
emin=None,
emax=None,
elabel="Energy (eV)",
plt=None,
dos_aspect=3,
aspect=None,
style=None,
no_base_style=False,
fonts=None,
):
if width is None and plot_band_structure:
width = 6
if self.energy_cutoff is None:
self.energy_cutoff = max([abs(emin or 6), abs(emax or 6)])
if plot_band_structure:
logger.info("Generating band structure...")
bs_plotter = self.get_bs_plotter(line_density=line_density,
kpath=kpath)
if plot_dos:
logger.info("Generating density of states...")
dos_plotter = self.get_dos_plotter(dos_density=dos_kpoints,
dos_estep=dos_estep)
logger.info("Plotting...")
common_kwargs = dict(
zero_to_efermi=zero_to_efermi,
width=width,
height=height,
plt=plt,
style=style,
no_base_style=no_base_style,
fonts=fonts,
)
if plot_band_structure:
bs_kwargs = {
"ymin": emin,
"ymax": emax,
"ylabel": elabel,
"aspect": aspect,
"vbm_cbm_marker": vbm_cbm_marker,
}
common_kwargs.update(bs_kwargs)
if plot_dos:
bs_dos_kwargs = {
# "dos_label": "DOS",
"dos_aspect": dos_aspect,
"dos_plotter": dos_plotter,
"plot_dos_legend": False,
}
common_kwargs.update(bs_dos_kwargs)
return bs_plotter.get_plot(**common_kwargs)
else:
dos_kwargs = {
"xmin": emin,
"xmax": emax,
"legend_on": False,
"xlabel": elabel,
"ylabel": "DOS",
}
common_kwargs.update(dos_kwargs)
return dos_plotter.get_plot(common_kwargs)
def get_bs_plotter(self, line_density=100, kpath=None):
lm_bs = self.interpolater.get_line_mode_band_structure(
line_density=line_density,
kpath=kpath,
symprec=self.symprec,
energy_cutoff=self.energy_cutoff,
)
return SBSPlotter(lm_bs)
def get_dos_plotter(self,
dos_density=50.0,
dos_estep=defaults["dos_estep"]):
dos = self.interpolater.get_dos(
kpoint_mesh=dos_density,
symprec=self.symprec,
estep=dos_estep,
energy_cutoff=self.energy_cutoff,
)
return SDOSPlotter(dos, {})