def setUp(self):
self.loader = VasprunBSLoader(vrun)
self.bztInterp = BztInterpolator(self.loader, lpfac=2)
self.assertIsNotNone(self.bztInterp)
self.bztInterp = BztInterpolator(self.loader,
lpfac=2,
save_coeffs=True,
fname=bztinterp_fn)
self.assertIsNotNone(self.bztInterp)
self.bztInterp = BztInterpolator(self.loader,
load_bztinterp=True,
fname=bztinterp_fn)
self.assertIsNotNone(self.bztInterp)
warnings.simplefilter("ignore")
self.loader_sp = VasprunBSLoader(vrun_sp)
self.bztInterp_sp = BztInterpolator(self.loader_sp, lpfac=2)
self.assertIsNotNone(self.bztInterp_sp)
self.bztInterp_sp = BztInterpolator(self.loader_sp,
lpfac=2,
save_coeffs=True,
fname=bztinterp_fn)
self.assertIsNotNone(self.bztInterp_sp)
self.bztInterp_sp = BztInterpolator(self.loader_sp,
lpfac=2,
load_bztinterp=True,
fname=bztinterp_fn)
self.assertIsNotNone(self.bztInterp_sp)
warnings.simplefilter("ignore")
def setUp(self):
loader = VasprunBSLoader(vrun)
bztInterp = BztInterpolator(loader, lpfac=2)
self.bztTransp = BztTransportProperties(bztInterp,
temp_r=np.arange(
300, 600, 100))
self.assertIsNotNone(self.bztTransp)
warnings.simplefilter("ignore")
self.bztTransp = BztTransportProperties(bztInterp,
doping=10.0**np.arange(20, 22),
temp_r=np.arange(
300, 600, 100))
self.assertIsNotNone(self.bztTransp)
self.assertEqual(self.bztTransp.contain_props_doping, True)
warnings.simplefilter("ignore")
bztInterp = BztInterpolator(loader, lpfac=2)
self.bztTransp = BztTransportProperties(
bztInterp,
temp_r=np.arange(300, 600, 100),
save_bztTranspProps=True,
fname=bzttransp_fn,
)
self.assertIsNotNone(self.bztTransp)
warnings.simplefilter("ignore")
bztInterp = BztInterpolator(loader, lpfac=2)
self.bztTransp = BztTransportProperties(bztInterp,
load_bztTranspProps=True,
fname=bzttransp_fn)
self.assertIsNotNone(self.bztTransp)
warnings.simplefilter("ignore")
loader_sp = VasprunBSLoader(vrun_sp)
bztInterp_sp = BztInterpolator(loader_sp, lpfac=2)
self.bztTransp_sp = BztTransportProperties(bztInterp_sp,
temp_r=np.arange(
300, 600, 100))
self.assertIsNotNone(self.bztTransp_sp)
warnings.simplefilter("ignore")
bztInterp_sp = BztInterpolator(loader_sp, lpfac=2)
self.bztTransp_sp = BztTransportProperties(
bztInterp_sp,
temp_r=np.arange(300, 600, 100),
save_bztTranspProps=True,
fname=bzttransp_fn,
)
self.assertIsNotNone(self.bztTransp_sp)
warnings.simplefilter("ignore")
bztInterp_sp = BztInterpolator(loader_sp, lpfac=2)
self.bztTransp_sp = BztTransportProperties(bztInterp_sp,
load_bztTranspProps=True,
fname=bzttransp_fn)
self.assertIsNotNone(self.bztTransp_sp)
warnings.simplefilter("ignore")
def test_plot(self):
loader = VasprunBSLoader(vrun)
bztInterp = BztInterpolator(loader, lpfac=2)
bztTransp = BztTransportProperties(bztInterp, temp_r=np.arange(300, 600, 100))
self.bztPlotter = BztPlotter(bztTransp, bztInterp)
self.assertIsNotNone(self.bztPlotter)
fig = self.bztPlotter.plot_props("S", "mu", "temp", temps=[300, 500])
self.assertIsNotNone(fig)
fig = self.bztPlotter.plot_bands()
self.assertIsNotNone(fig)
fig = self.bztPlotter.plot_dos()
self.assertIsNotNone(fig)
class VasprunBSLoaderTest(unittest.TestCase):
def setUp(self):
self.loader = VasprunBSLoader(vrun)
self.assertIsNotNone(self.loader)
self.loader = VasprunBSLoader(bs, vrun.final_structure)
self.assertIsNotNone(self.loader)
self.loader = VasprunBSLoader.from_file(vrunfile)
self.assertIsNotNone(self.loader)
warnings.simplefilter("ignore")
self.loader_sp = VasprunBSLoader(vrun_sp)
self.assertIsNotNone(self.loader_sp)
self.loader_sp = VasprunBSLoader(bs_sp, vrun_sp.final_structure)
self.assertIsNotNone(self.loader_sp)
self.loader_sp = VasprunBSLoader.from_file(vrunfile_sp)
self.assertIsNotNone(self.loader_sp)
warnings.simplefilter("ignore")
def tearDown(self):
warnings.simplefilter("default")
def test_properties(self):
self.assertEqual(self.loader.is_spin_polarized, False)
self.assertAlmostEqual(self.loader.fermi, 0.185266535678, 5)
self.assertAlmostEqual(self.loader.structure.lattice.a,
4.64303565932548, 5)
self.assertEqual(self.loader.nelect_all, 20.0)
self.assertEqual(self.loader_sp.nelect_all, 10.0)
self.assertTupleEqual(self.loader.ebands_all.shape, (20, 120))
self.assertAlmostEqual(self.loader.ebands_all[10, 100], 0.2708057, 5)
self.assertEqual(len(self.loader.proj_all), 1)
self.assertTupleEqual(self.loader.proj_all[Spin.up].shape,
(120, 20, 2, 9))
self.assertEqual(self.loader_sp.is_spin_polarized, True)
self.assertTupleEqual(self.loader_sp.ebands_all.shape, (24, 198))
self.assertAlmostEqual(self.loader_sp.ebands_all[10, 100], 0.2543788,
4)
self.assertAlmostEqual(self.loader_sp.ebands_all[22, 100], 0.2494617,
4)
self.assertEqual(len(self.loader_sp.proj_all), 2)
self.assertTupleEqual(self.loader_sp.proj_all[Spin.down].shape,
(198, 12, 2, 9))
def test_get_volume(self):
self.assertAlmostEqual(self.loader.get_volume(), 477.6256714925874, 5)
def make_effective_mass(vasprun, temp, concentrations, band_gap):
try:
from pymatgen.electronic_structure.boltztrap2 import VasprunBSLoader, \
BztInterpolator, BztTransportProperties
except BoltztrapError:
raise ImportError('Calculating effective mass requires BoltzTrap2')
vl = VasprunBSLoader(vasprun)
energy_range = band_gap / 2 + 2.0
bi = BztInterpolator(vl, energy_range=energy_range)
btp = BztTransportProperties(bi, temp_r=np.array([temp]))
btp.compute_properties_doping(concentrations)
return EffectiveMass(p=btp.Effective_mass_doping["p"].tolist()[0],
n=btp.Effective_mass_doping["n"].tolist()[0],
temperature=temp,
concentrations=concentrations)
def setUp(self):
self.loader = VasprunBSLoader(vrun)
self.assertIsNotNone(self.loader)
self.loader = VasprunBSLoader(bs, vrun.final_structure)
self.assertIsNotNone(self.loader)
self.loader = VasprunBSLoader.from_file(vrunfile)
self.assertIsNotNone(self.loader)
warnings.simplefilter("ignore")
self.loader_sp = VasprunBSLoader(vrun_sp)
self.assertIsNotNone(self.loader_sp)
self.loader_sp = VasprunBSLoader(bs_sp, vrun_sp.final_structure)
self.assertIsNotNone(self.loader_sp)
self.loader_sp = VasprunBSLoader.from_file(vrunfile_sp)
self.assertIsNotNone(self.loader_sp)
warnings.simplefilter("ignore")
def bandplot_func(
filenames=None,
code='vasp',
prefix=None,
directory=None,
vbm_cbm_marker=False,
projection_selection=None,
mode='rgb',
pred=None,
interpolate_factor=4,
circle_size=150,
dos_file=None,
cart_coords=False,
scissor=None,
ylabel='Energy (eV)',
dos_label=None,
elements=None,
lm_orbitals=None,
atoms=None,
spin=None,
total_only=False,
plot_total=True,
legend_cutoff=3,
gaussian=None,
height=None,
width=None,
ymin=-6.,
ymax=6.,
colours=None,
yscale=1,
style=None,
no_base_style=False,
image_format='pdf',
dpi=400,
plt=None,
fonts=None,
boltz={
"ifinter": "T",
"lpfac": "10",
"energy_range": "50",
"curvature": "",
"load": "T",
'ismetaltolerance': '0.01'
},
nelec=0):
if not filenames:
filenames = find_vasprun_files()
elif isinstance(filenames, str):
filenames = [filenames]
# only load the orbital projects if we definitely need them
parse_projected = True if projection_selection else False
# now load all the band structure data and combine using the
# get_reconstructed_band_structure function from pymatgen
bandstructures = []
if code == 'vasp':
for vr_file in filenames:
vr = BSVasprun(vr_file, parse_projected_eigen=parse_projected)
print("BSVasprun", type(vr), vr)
print("vr.eigenvalues.keys()", type(vr.eigenvalues.keys()),
vr.eigenvalues.keys())
if pred.any():
# Fill in Model prediction
model = BSVasprun(vr_file,
parse_projected_eigen=parse_projected)
print("pred", type(pred), pred.shape)
pred = np.expand_dims(pred, axis=-1)
for key in model.eigenvalues.keys():
key_last = key
print("model.eigenvalues[key][:, :, :].shape[0]", key,
type(model.eigenvalues[key][:, :, :]),
model.eigenvalues[key][:, :, :].shape,
pred[:, :, :].shape)
bands = min(model.eigenvalues[key][:, :, :].shape[1],
pred.shape[1])
print(
"bands", bands, "attention! max: ",
max(model.eigenvalues[key][:, :, :].shape[1],
pred.shape[1]))
print(
"equel False?",
np.sum(model.eigenvalues[key][:, :bands, :] -
pred[:, :bands, :]))
model.eigenvalues[key][:, :bands, :] = pred[:, :bands, :]
print(
"equel True?",
np.sum(model.eigenvalues[key][:, :bands, :] -
pred[:, :bands, :]))
print(
"equel model vr?",
np.sum(model.eigenvalues[key][:, :bands, :] -
vr.eigenvalues[key][:, :bands, :]))
# spin = 1 # for only plotting spin up oder down 1, -1
# model.eigenvalues[key_last][:, :bands, :] = pred[:, :bands, :]
#boltztrap={'ifinter':False,'lpfac':10,'energy_range':50,'curvature':False}):
if bool(boltz['ifinter']):
b_data = VasprunBSLoader(vr)
model_data = VasprunBSLoader(model)
print("BSVasprunLoader", type(b_data), b_data)
b_inter = BztInterpolator(b_data,
lpfac=int(boltz['lpfac']),
energy_range=float(
boltz['energy_range']),
curvature=bool(boltz['curvature']),
save_bztInterp=True,
load_bztInterp=bool(boltz['load']))
model_inter = BztInterpolator(
model_data,
lpfac=int(boltz['lpfac']),
energy_range=float(boltz['energy_range']),
curvature=bool(boltz['curvature']),
save_bztInterp=True,
load_bztInterp=bool(boltz['load']))
try:
kpath = json.load(open('./kpath', 'r'))
kpaths = kpath['path']
kpoints_lbls_dict = {}
for i in range(len(kpaths)):
for j in [0, 1]:
if 'GAMMA' == kpaths[i][j]:
kpaths[i][j] = '\Gamma'
for k, v in kpath['kpoints_rel'].items():
if k == 'GAMMA':
k = '\Gamma'
kpoints_lbls_dict[k] = v
except:
kpaths = None
kpoints_lbls_dict = None
print(kpaths, kpoints_lbls_dict)
bs = b_inter.get_band_structure(
kpaths=kpaths, kpoints_lbls_dict=kpoints_lbls_dict)
model_bs = model_inter.get_band_structure(
kpaths=kpaths, kpoints_lbls_dict=kpoints_lbls_dict)
#bs_uniform = b_inter.get_band_structure()
gap = bs.get_band_gap()
nvb = int(np.ceil(nelec / (int(bs.is_spin_polarized) + 1)))
vbm = -100
print("WHC interpolated gap: %s" % gap)
for spin, v in bs.bands.items():
vbm = max(vbm, max(v[nvb - 1]))
print(
'WHC WARNNING vasp fermi %s interpolation vbm %s nelec %s nvb %s'
% (bs.efermi, vbm, nelec, nvb))
if vbm < bs.efermi:
bs.efermi = vbm
print("if vbm <")
if vbm < model_bs.efermi:
model_bs.efermi = vbm
print("if vbm <")
print(bs.bands.keys())
band_keys = list(bs.bands.keys())
print("Band shapes", bs.bands[band_keys[0]].shape,
model_bs.bands[band_keys[0]].shape)
print(
"equel bands?",
np.sum((bs.bands[band_keys[0]] - bs.efermi) -
model_bs.bands[band_keys[0]]))
bs.bands[band_keys[0]] = (
bs.bands[band_keys[0]] - bs.efermi
) # why??????????????????????????????????????????????????
# bs.bands[band_keys[1]] = (bs.bands[band_keys[1]] - bs.efermi) # why??????????????????????????????????????????????????
print(
"equel bands fermi shifted?",
np.sum((bs.bands[band_keys[0]] - bs.efermi) -
model_bs.bands[band_keys[0]]))
# bandstructures.append(bs)
# bandstructures.append(model_bs)
bs = get_reconstructed_band_structure([bs])
model_bs = get_reconstructed_band_structure([model_bs])
if bool(boltz['ifinter']):
bs.nvb = nvb
bs.ismetaltolerance = float(boltz['ismetaltolerance'])
model_bs.nvb = nvb
model_bs.ismetaltolerance = float(boltz['ismetaltolerance'])
print("dft bands", bs.bands[band_keys[0]])
print("dft ktps", len(bs.kpoints), kpts.shape)
print("dft labels", bs.labels_dict)
for key in bs.labels_dict.keys():
print(bs.labels_dict[key].label, bs.labels_dict[key].as_dict(),
bs.labels_dict[key].a, bs.labels_dict[key].b,
bs.labels_dict[key].c, bs.labels_dict[key].frac_coords)
labels = []
for i in range(len(bs.kpoints)):
# print(i, bs.kpoints[i])
for key in bs.labels_dict.keys():
if bs.labels_dict[key].label == bs.kpoints[
i].label and bs.labels_dict[
key].label != bs.kpoints[i - 1].label:
# print("Labels!!!!!", i, bs.labels_dict[key].label)
labels.append([i, bs.labels_dict[key].label])
print(labels)
print("dft efermi", bs.efermi)
print("dft lattice_rec", bs.lattice_rec)
print("dft structure", bs.structure)
print("model bands", model_bs.bands[band_keys[0]])
print("model ktps", len(model_bs.kpoints), kpts.shape)
print("model labels", model_bs.labels_dict)
print("model efermi", model_bs.efermi)
print("model lattice_rec", model_bs.lattice_rec)
print("model structure", model_bs.structure)
return bs.bands[band_keys[0]], model_bs.bands[band_keys[0]], labels
save_files = False if plt else True
dos_plotter = None
dos_opts = None
if dos_file:
dos, pdos = load_dos(dos_file, elements, lm_orbitals, atoms,
gaussian, total_only)
dos_plotter = SDOSPlotter(dos, pdos)
dos_opts = {
'plot_total': plot_total,
'legend_cutoff': legend_cutoff,
'colours': colours,
'yscale': yscale
}
model_and_dft_bs = [bs, model_bs]
plotter = SBSPlotter(model_bs)
print("spin", spin)
if len(vr.eigenvalues.keys()) == 1:
spin = None
print("spin", spin)
plt = plotter.get_plot(zero_to_efermi=True,
ymin=ymin,
ymax=ymax,
height=height,
width=width,
vbm_cbm_marker=vbm_cbm_marker,
ylabel=ylabel,
plt=plt,
dos_plotter=dos_plotter,
dos_options=dos_opts,
dos_label=dos_label,
fonts=fonts,
style=style,
no_base_style=no_base_style,
spin=spin)
# don't save if pyplot object provided
save_files = False if plt else True
if save_files:
basename = 'band.{}'.format(image_format)
filename = '{}_{}'.format(prefix, basename) if prefix else basename
if directory:
filename = os.path.join(directory, filename)
plt.savefig(filename,
format=image_format,
dpi=dpi,
bbox_inches='tight')
written = [filename]
written += save_data_files(bs, prefix=prefix, directory=directory)
return written
else:
return plt
