def test_read_ebands_from_WFK(self):
"""Read ElectronBands from WFK files."""
for filename in data.WFK_NCFILES:
ebands = ElectronBands.from_file(filename)
ebands.to_pymatgen()
ebands.to_pdframe()
assert ElectronBands.as_ebands(ebands) is ebands
def test_read_ebands_from_WFK(self):
"""Read ElectronBands from WFK files."""
for filename in data.WFK_NCFILES:
ebands = ElectronBands.from_file(filename)
ebands.to_pymatgen()
ebands.to_pdframe()
assert ElectronBands.as_ebands(ebands) is ebands
def test_jdos(self):
"""Test JDOS methods."""
bands = ElectronBands.from_file(data.ref_file("si_scf_GSR.nc"))
spin = 0
conduction = [4,]
for v in range(1,5):
valence = range(0,v)
jdos = bands.get_ejdos(spin, valence, conduction)
intg = jdos.integral()[-1][-1]
self.assert_almost_equal(intg, len(conduction) * len(valence))
self.serialize_with_pickle(jdos, protocols=[-1])
nscf_bands = ElectronBands.from_file(data.ref_file("si_nscf_GSR.nc"))
# Test the detection of denerate states.
degs = nscf_bands.degeneracies(spin=0, kpoint=[0,0,0], bands_range=range(8))
ref_degbands = [[0], [1,2,3], [4,5,6], [7]]
for i, (e, deg_bands) in enumerate(degs):
self.assertEqual(deg_bands, ref_degbands[i])
# JDOS a homogeneous sampling.
with self.assertRaises(ValueError):
nscf_bands.get_ejdos(spin, 0, 4)
def test_jdos(self):
"""Test JDOS methods."""
bands = ElectronBands.from_file(data.ref_file("si_scf_GSR.nc"))
spin = 0
conduction = [
4,
]
for v in range(1, 5):
valence = range(0, v)
jdos = bands.get_ejdos(spin, valence, conduction)
intg = jdos.integral()[-1][-1]
self.assert_almost_equal(intg, len(conduction) * len(valence))
self.serialize_with_pickle(jdos, protocols=[-1])
nscf_bands = ElectronBands.from_file(data.ref_file("si_nscf_GSR.nc"))
# Test the detection of denerate states.
degs = nscf_bands.degeneracies(spin=0,
kpoint=[0, 0, 0],
bands_range=range(8))
ref_degbands = [[0], [1, 2, 3], [4, 5, 6], [7]]
for i, (e, deg_bands) in enumerate(degs):
self.assertEqual(deg_bands, ref_degbands[i])
# JDOS a homogeneous sampling.
with self.assertRaises(ValueError):
nscf_bands.get_ejdos(spin, 0, 4)
def test_read_ebands_from_GSR(self):
"""Read ElectronBands from GSR files."""
for filename in abidata.GSR_NCFILES:
ebands = ElectronBands.from_file(filename)
ebands.to_pymatgen()
ebands.to_pdframe()
self.serialize_with_pickle(ebands, test_eq=False)
ElectronBands.from_dict(ebands.as_dict())
self.assertMSONable(ebands, test_if_subclass=False)
def test_read_ebands_from_WFK(self):
"""Read ElectronBands from WFK files."""
for ii, filename in enumerate(abidata.WFK_NCFILES):
ebands = ElectronBands.from_file(filename)
ebands.to_pymatgen()
ebands.to_pdframe()
assert ElectronBands.as_ebands(ebands) is ebands
self.serialize_with_pickle(ebands, test_eq=False)
ElectronBands.from_dict(ebands.as_dict())
self.assertMSONable(ebands, test_if_subclass=False)
if ii == 0:
if self.has_matplotlib(): ebands.plot(show=False)
ebands.to_xmgrace(self.get_tmpname(text=True))
def test_ebands_skw_interpolation(self):
"""Testing SKW interpolation."""
si_ebands_kmesh = ElectronBands.from_file(abidata.ref_file("si_scf_GSR.nc"))
# Test interpolation.
vertices_names = [((0.0, 0.0, 0.0), "G"), ((0.5, 0.5, 0.0), "M")]
r = si_ebands_kmesh.interpolate(lpratio=10, vertices_names=vertices_names,
kmesh=[8, 8, 8], verbose=1)
assert r.ebands_kpath is not None
assert r.ebands_kpath.kpoints.is_path
assert not r.ebands_kpath.kpoints.is_ibz
mpdivs, shifts = r.ebands_kpath.kpoints.mpdivs_shifts
assert mpdivs is None and shifts is None
assert r.ebands_kmesh is not None
assert r.ebands_kmesh.kpoints.is_ibz
assert not r.ebands_kmesh.kpoints.is_path
assert r.ebands_kmesh.kpoints.ksampling is not None
assert r.ebands_kmesh.kpoints.is_mpmesh
mpdivs, shifts = r.ebands_kmesh.kpoints.mpdivs_shifts
self.assert_equal(mpdivs, [8, 8, 8])
self.assert_equal(shifts.flatten(), [0, 0, 0])
# Export it in BXSF format.
r.ebands_kmesh.to_bxsf(self.get_tmpname(text=True))
def test_ebands_skw_interpolation(self):
if sys.version[0:3] >= '3.4':
raise unittest.SkipTest(
"SKW interpolation is not tested if Python version >= 3.4 (linalg.solve portability issue)"
)
bands = ElectronBands.from_file(abidata.ref_file("si_scf_GSR.nc"))
# Test interpolate.
vertices_names = [((0.0, 0.0, 0.0), "G"), ((0.5, 0.5, 0.0), "M")]
r = bands.interpolate(lpratio=10,
vertices_names=vertices_names,
kmesh=[8, 8, 8],
verbose=1)
assert r.ebands_kpath is not None
assert r.ebands_kpath.kpoints.is_path
assert not r.ebands_kpath.kpoints.is_ibz
mpdivs, shifts = r.ebands_kpath.kpoints.mpdivs_shifts
assert mpdivs is None and shifts is None
assert r.ebands_kmesh is not None
assert r.ebands_kmesh.kpoints.is_ibz
assert not r.ebands_kmesh.kpoints.is_path
assert r.ebands_kmesh.kpoints.ksampling is not None
assert r.ebands_kmesh.kpoints.is_mpmesh
mpdivs, shifts = r.ebands_kmesh.kpoints.mpdivs_shifts
self.assert_equal(mpdivs, [8, 8, 8])
self.assert_equal(shifts.flatten(), [0, 0, 0])
# Export it in BXSF format.
r.ebands_kmesh.to_bxsf(self.get_tmpname(text=True))
def test_ebands_skw_interpolation(self):
"""Testing SKW interpolation."""
si_ebands_kmesh = ElectronBands.from_file(
abidata.ref_file("si_scf_GSR.nc"))
# Test interpolation.
vertices_names = [((0.0, 0.0, 0.0), "G"), ((0.5, 0.5, 0.0), "M")]
r = si_ebands_kmesh.interpolate(lpratio=10,
vertices_names=vertices_names,
kmesh=[8, 8, 8],
verbose=1)
assert r.ebands_kpath is not None
assert r.ebands_kpath.kpoints.is_path
assert not r.ebands_kpath.kpoints.is_ibz
mpdivs, shifts = r.ebands_kpath.kpoints.mpdivs_shifts
assert mpdivs is None and shifts is None
assert r.ebands_kmesh is not None
assert r.ebands_kmesh.kpoints.is_ibz
assert not r.ebands_kmesh.kpoints.is_path
assert r.ebands_kmesh.kpoints.ksampling is not None
assert r.ebands_kmesh.kpoints.is_mpmesh
mpdivs, shifts = r.ebands_kmesh.kpoints.mpdivs_shifts
self.assert_equal(mpdivs, [8, 8, 8])
self.assert_equal(shifts.flatten(), [0, 0, 0])
# Export it in BXSF format.
r.ebands_kmesh.to_bxsf(self.get_tmpname(text=True))
def test_derivatives(self):
"""Testing computation of effective masses."""
ebands = ElectronBands.from_file(abidata.ref_file("si_nscf_GSR.nc"))
# Hack eigens to simulate free-electron bands.
# This should produce all(effective masses == 1)
new_eigens = np.empty(ebands.shape)
branch = 0.5 * units.Ha_to_eV * np.array(
[(k.norm * units.bohr_to_ang)**2 for k in ebands.kpoints])
for spin in ebands.spins:
for band in range(ebands.mband):
new_eigens[spin, :, band] = branch
ebands._eigens = new_eigens
effm_lines = ebands.effective_masses(spin=0, band=0, acc=2)
# Flatten structure (.flatten does not work in this case)
values = []
for arr in effm_lines:
values.extend(arr)
self.assert_almost_equal(np.array(values), 1.0)
em = ebands.effmass_line(spin=0, kpoint=(0, 0, 0), band=0)
repr(em)
str(em)
def test_api(self):
"""Testing ElelectronDosPlotter API."""
gsr_path = abidata.ref_file("si_scf_GSR.nc")
gs_bands = ElectronBands.from_file(gsr_path)
si_edos = gs_bands.get_edos()
plotter = ElectronDosPlotter()
plotter.add_edos("edos1", si_edos)
with self.assertRaises(ValueError):
plotter.add_edos("edos1", si_edos)
plotter.add_edos("edos2",
gsr_path,
edos_kwargs=dict(method="gaussian",
step=0.2,
width=0.4))
assert len(plotter.edos_list) == 2
assert not plotter._can_use_basenames_as_labels()
if self.has_matplotlib():
assert plotter.combiplot(show=False)
assert plotter.gridplot(show=False)
if self.has_ipywidgets():
assert plotter.ipw_select_plot() is not None
if self.has_nbformat():
assert plotter.write_notebook(nbpath=self.get_tmpname(text=True))
def __init__(self,
ebands_kpath,
phbst_file,
phdos_file,
ebands_kmesh=None):
self.eb_kpath = ElectronBands.as_ebands(ebands_kpath)
self.eb_kmesh = ElectronBands.as_ebands(
ebands_kmesh) if ebands_kmesh is not None else None
self.phbst_file = phbst_file
if duck.is_string(self.phbst_file):
self.phbst_file = PhbstFile(self.phbst_file)
self.phb_qpath = self.phbst_file.phbands
self.phdos_file = phdos_file
if duck.is_string(self.phdos_file):
self.phdos_file = PhdosFile(phdos_file)
def interpolate_ebands(self, vertices_names=None, line_density=20, ngkpt=None, shiftk=(0, 0, 0), kpoints=None):
"""
Build new |ElectronBands| object by interpolating the KS Hamiltonian with Wannier functions.
Supports k-path via (vertices_names, line_density), IBZ mesh defined by ngkpt and shiftk
or input list of kpoints.
Args:
vertices_names: Used to specify the k-path for the interpolated QP band structure
List of tuple, each tuple is of the form (kfrac_coords, kname) where
kfrac_coords are the reduced coordinates of the k-point and kname is a string with the name of
the k-point. Each point represents a vertex of the k-path. ``line_density`` defines
the density of the sampling. If None, the k-path is automatically generated according
to the point group of the system.
line_density: Number of points in the smallest segment of the k-path. Used with ``vertices_names``.
ngkpt: Mesh divisions. Used if bands should be interpolated in the IBZ.
shiftk: Shifts for k-meshs. Used with ngkpt.
kpoints: |KpointList| object taken e.g from a previous ElectronBands.
Has precedence over vertices_names and line_density.
Returns: |ElectronBands| object with Wannier-interpolated energies.
"""
# Need KpointList object.
if kpoints is None:
if ngkpt is not None:
# IBZ sampling
kpoints = IrredZone.from_ngkpt(self.structure, ngkpt, shiftk, kptopt=1, verbose=0)
else:
# K-Path
if vertices_names is None:
vertices_names = [(k.frac_coords, k.name) for k in self.structure.hsym_kpoints]
kpoints = Kpath.from_vertices_and_names(self.structure, vertices_names, line_density=line_density)
nk = len(kpoints)
eigens = np.zeros((self.nsppol, nk, self.mwan))
# Interpolate Hamiltonian for each kpoint and spin.
start = time.time()
write_warning = True
for spin in range(self.nsppol):
num_wan = self.nwan_spin[spin]
for ik, kpt in enumerate(kpoints):
oeigs = self.hwan.eval_sk(spin, kpt.frac_coords)
eigens[spin, ik, :num_wan] = oeigs
if num_wan < self.mwan:
# May have different number of wannier functions if nsppol == 2.
# Here I use the last value to fill eigens matrix (not very clean but oh well).
eigens[spin, ik, num_wan:self.mwan] = oeigs[-1]
if write_warning:
cprint("Different number of wannier functions for spin. Filling last bands with oeigs[-1]",
"yellow")
write_warning = False
print("Interpolation completed in %.3f [s]" % (time.time() - start))
occfacts = np.zeros_like(eigens)
return ElectronBands(self.structure, kpoints, eigens, self.ebands.fermie,
occfacts, self.ebands.nelect, self.nspinor, self.nspden,
smearing=self.ebands.smearing)
def test_dos(self):
"""Test DOS methods."""
gs_bands = ElectronBands.from_file(data.ref_file("si_scf_GSR.nc"))
dos = gs_bands.get_edos()
mu = dos.find_mu(8, atol=1.e-4)
imu = dos.tot_idos.find_mesh_index(mu)
self.assert_almost_equal(dos.tot_idos[imu][1], 8, decimal=2)
self.serialize_with_pickle(dos, protocols=[-1], test_eq=False)
def ebands(self):
"""
|ElectronBands| object with the single-particle energies used to compute the screening.
"""
ebands = ElectronBands.from_file(self.filepath)
# FIXME
cprint("Setting Fermi energy to zero since `fermie_energy` is not initialized in Abinit v8.2", "yellow")
ebands.fermie = 0
return ebands
def ebands(self):
"""
|ElectronBands| object with the single-particle energies used to compute the screening.
"""
ebands = ElectronBands.from_file(self.filepath)
# FIXME
cprint("Setting Fermi energy to zero since `fermie_energy` is not initialized in Abinit v8.2", "yellow")
ebands.fermie = 0
return ebands
def test_dos(self):
"""Test DOS methods."""
gs_bands = ElectronBands.from_file(data.ref_file("si_scf_GSR.nc"))
dos = gs_bands.get_edos()
mu = dos.find_mu(8, atol=1.e-4)
imu = dos.tot_idos.find_mesh_index(mu)
self.assert_almost_equal(dos.tot_idos[imu][1], 8, decimal=2)
self.serialize_with_pickle(dos, protocols=[-1], test_eq=False)
def test_jdos(self):
"""Test JDOS methods."""
bands = ElectronBands.from_file(abidata.ref_file("si_scf_GSR.nc"))
spin = 0
conduction = [
4,
]
for v in range(1, 5):
valence = range(0, v)
jdos = bands.get_ejdos(spin, valence, conduction)
intg = jdos.integral()[-1][-1]
self.assert_almost_equal(intg, len(conduction) * len(valence))
self.serialize_with_pickle(jdos, protocols=[-1])
nscf_bands = ElectronBands.from_file(
abidata.ref_file("si_nscf_GSR.nc"))
diffs = nscf_bands.statdiff(nscf_bands)
print(diffs)
# Test the detection of denerate states.
degs = nscf_bands.degeneracies(spin=0,
kpoint=[0, 0, 0],
bands_range=range(8))
ref_degbands = [[0], [1, 2, 3], [4, 5, 6], [7]]
for i, (e, deg_bands) in enumerate(degs):
self.assertEqual(deg_bands, ref_degbands[i])
# Test Electron
e1 = nscf_bands._electron_state(spin=0, kpoint=[0, 0, 0], band=0)
str(e1)
e1_copy = e1.copy()
assert isinstance(e1.as_dict(), dict)
assert isinstance(e1.to_strdict(), dict)
assert e1.spin == 0
assert e1.skb[0] == 0
str(e1.tips)
# JDOS requires a homogeneous sampling.
with self.assertRaises(ValueError):
nscf_bands.get_ejdos(spin, 0, 4)
def get_plotter_from_ebands(self, ebands):
"""
Interpolate energies using the k-points given in input |ElectronBands| ebands.
Return: |ElectronBandsPlotter| object.
"""
ebands = ElectronBands.as_ebands(ebands)
wan_ebands = self.interpolate_ebands(kpoints=ebands.kpoints)
return ElectronBandsPlotter(key_ebands=[("Ab-initio", ebands), ("Interpolated", wan_ebands)])
def test_frame_from_ebands(self):
"""Testing dataframe_from_ebands."""
gsr_kmesh = abidata.ref_file("si_scf_GSR.nc")
si_ebands_kmesh = ElectronBands.as_ebands(gsr_kmesh)
gsr_nscf_path = abidata.ref_file("si_nscf_GSR.nc")
index = ["foo", "bar", "hello"]
df = dataframe_from_ebands([gsr_kmesh, si_ebands_kmesh, gsr_nscf_path], index=index, with_spglib=True)
#str(df)
assert all(f == "Si2" for f in df["formula"])
assert all(num == 227 for num in df["abispg_num"])
assert all(df["spglib_num"] == df["abispg_num"])
def test_frame_from_ebands(self):
"""Testing dataframe_from_ebands."""
gsr_kmesh = abidata.ref_file("si_scf_GSR.nc")
si_ebands_kmesh = ElectronBands.as_ebands(gsr_kmesh)
gsr_nscf_path = abidata.ref_file("si_nscf_GSR.nc")
index = ["foo", "bar", "hello"]
df = dataframe_from_ebands([gsr_kmesh, si_ebands_kmesh, gsr_nscf_path], index=index, with_spglib=True)
#str(df)
assert all(f == "Si2" for f in df["formula"])
assert all(num == 227 for num in df["abispg_num"])
assert all(df["spglib_num"] == df["abispg_num"])
def test_dos(self):
"""Test DOS methods."""
gs_bands = ElectronBands.from_file(data.ref_file("si_scf_GSR.nc"))
dos = gs_bands.get_edos()
print(dos)
assert ElectronDos.as_edos(dos, {}) is dos
edos_samevals = ElectronDos.as_edos(gs_bands, {})
assert ElectronDos.as_edos(gs_bands, {}) == dos
assert ElectronDos.as_edos(data.ref_file("si_scf_GSR.nc"), {}) == dos
mu = dos.find_mu(8)
imu = dos.tot_idos.find_mesh_index(mu)
self.assert_almost_equal(dos.tot_idos[imu][1], 8, decimal=2)
self.serialize_with_pickle(dos, protocols=[-1], test_eq=False)
def test_dos(self):
"""Test DOS methods."""
gs_bands = ElectronBands.from_file(data.ref_file("si_scf_GSR.nc"))
dos = gs_bands.get_edos()
print(dos)
assert ElectronDos.as_edos(dos, {}) is dos
edos_samevals = ElectronDos.as_edos(gs_bands, {})
assert ElectronDos.as_edos(gs_bands, {}) == dos
assert ElectronDos.as_edos(data.ref_file("si_scf_GSR.nc"), {}) == dos
mu = dos.find_mu(8)
imu = dos.tot_idos.find_mesh_index(mu)
self.assert_almost_equal(dos.tot_idos[imu][1], 8, decimal=2)
self.serialize_with_pickle(dos, protocols=[-1], test_eq=False)
def test_derivatives(self):
"""Testing computation of effective masses."""
ebands = ElectronBands.from_file(data.ref_file("si_nscf_GSR.nc"))
# Hack eigens to simulate free-electron bands. This will produce all(effective masses == 1)
new_eigens = np.empty(ebands.shape)
branch = 0.5 * units.Ha_to_eV * np.array([(k.norm * units.bohr_to_ang)**2 for k in ebands.kpoints])
for spin in ebands.spins:
for band in range(ebands.mband):
new_eigens[spin, :, band] = branch
ebands._eigens = new_eigens
effm_lines = ebands.effective_masses(spin=0, band=0, acc=2)
# Flatten structure (.flatten does not work in this case)
values = []
for arr in effm_lines:
values.extend(arr)
self.assertArrayAlmostEqual(np.array(values), 1.0)
def test_api(self):
"""Test ElelectronDosPlotter API."""
gsr_path = abidata.ref_file("si_scf_GSR.nc")
gs_bands = ElectronBands.from_file(gsr_path)
edos = gs_bands.get_edos()
plotter = ElectronDosPlotter()
plotter.add_edos("edos1", edos)
plotter.add_edos("edos2",
gsr_path,
edos_kwargs=dict(method="gaussian",
step=0.2,
width=0.4))
assert len(plotter.edos_list) == 2
if self.has_matplotlib():
plotter.combiplot(show=False)
plotter.gridplot(show=False)
if self.has_nbformat():
plotter.write_notebook(nbpath=self.get_tmpname(text=True))
def test_api(self):
"""Testing ElelectronDosPlotter API."""
gsr_path = abidata.ref_file("si_scf_GSR.nc")
gs_bands = ElectronBands.from_file(gsr_path)
si_edos = gs_bands.get_edos()
plotter = ElectronDosPlotter()
plotter.add_edos("edos1", si_edos)
with self.assertRaises(ValueError):
plotter.add_edos("edos1", si_edos)
plotter.add_edos("edos2", gsr_path, edos_kwargs=dict(method="gaussian", step=0.2, width=0.4))
assert len(plotter.edos_list) == 2
assert not plotter._can_use_basenames_as_labels()
if self.has_matplotlib():
assert plotter.combiplot(show=False)
assert plotter.gridplot(show=False)
if self.has_ipywidgets():
assert plotter.ipw_select_plot() is not None
if self.has_nbformat():
assert plotter.write_notebook(nbpath=self.get_tmpname(text=True))
def test_dos(self):
"""Test DOS methods."""
gs_bands = ElectronBands.from_file(abidata.ref_file("si_scf_GSR.nc"))
assert not gs_bands.has_metallic_scheme
# Test get_e0
assert gs_bands.get_e0("fermie") == gs_bands.fermie
assert gs_bands.get_e0(None) == 0.0
assert gs_bands.get_e0("None") == 0.0
assert gs_bands.get_e0(1.0) == 1.0
edos = gs_bands.get_edos()
print(edos)
assert ElectronDos.as_edos(edos, {}) is edos
edos_samevals = ElectronDos.as_edos(gs_bands, {})
assert ElectronDos.as_edos(gs_bands, {}) == edos
assert ElectronDos.as_edos(abidata.ref_file("si_scf_GSR.nc"),
{}) == edos
mu = edos.find_mu(8)
imu = edos.tot_idos.find_mesh_index(mu)
self.assert_almost_equal(edos.tot_idos[imu][1], 8, decimal=2)
d, i = edos.dos_idos(spin=0)
tot_d, tot_i = edos.dos_idos()
self.assert_almost_equal(2 * d.values, tot_d.values)
self.assert_almost_equal(2 * i.values, tot_i.values)
self.serialize_with_pickle(edos, protocols=[-1], test_eq=False)
# Test plot methods
if self.has_matplotlib():
edos.plot(show=False)
edos.plot_dos_idos(show=False)
edos.plot_up_minus_down(show=False)
gs_bands.plot_with_edos(dos=edos, show=False)
if self.has_seaborn(): gs_bands.boxplot(show=False)
def test_nickel_ebands_spin(self):
"""Testing Nickel electron bands with nsppol == 2"""
ref_nelect = 18
ni_ebands_kmesh = ElectronBands.from_file(
abidata.ref_file("ni_666k_GSR.nc"))
assert ElectronBands.as_ebands(ni_ebands_kmesh) is ni_ebands_kmesh
with self.assertRaises(TypeError):
ElectronBands.as_ebands(1)
repr(ni_ebands_kmesh)
str(ni_ebands_kmesh)
assert ni_ebands_kmesh.nsppol == 2 and ni_ebands_kmesh.nspinor == 1 and ni_ebands_kmesh.nspden == 2
assert ni_ebands_kmesh.nelect == ref_nelect
assert ni_ebands_kmesh.kpoints.is_ibz and ni_ebands_kmesh.has_bzmesh and not ni_ebands_kmesh.has_bzpath
assert ni_ebands_kmesh.has_timrev
assert ni_ebands_kmesh.has_metallic_scheme
smearing = ni_ebands_kmesh.smearing
assert smearing.has_metallic_scheme
assert smearing.occopt == 7
self.assert_almost_equal(smearing.tsmear_ev.to("Ha"), 0.0075)
assert smearing.scheme == "gaussian"
ni_ebands_kmesh.copy()
ni_ebands_kmesh.deepcopy()
ni_edos = ni_ebands_kmesh.get_edos()
repr(ni_edos)
str(ni_edos)
assert ni_edos.to_string(verbose=2)
# Get ElectronDosPlotter with nsppol == 2 and test matplotlib methods.
edos_plotter = ni_ebands_kmesh.compare_gauss_edos(widths=[0.2, 0.4],
step=0.2)
assert len(edos_plotter) == 2
if self.has_matplotlib():
# Combiplot.
assert edos_plotter.combiplot(title="default values", show=False)
assert edos_plotter.combiplot(what_list=("dos", "idos"),
spin_mode="resolved",
show=False)
assert edos_plotter.combiplot(e0=0,
what_list="dos",
spin_mode="resolved",
fontsize=12,
show=False)
# Gridplot
assert edos_plotter.gridplot(title="default values", show=False)
assert edos_plotter.gridplot(what="idos",
spin_mode="resolved",
xlims=(-10, 10),
show=False)
assert edos_plotter.gridplot(e0=0,
what="dos",
spin_mode="resolved",
fontsize=12,
show=False)
ni_ebands_kpath = ElectronBands.from_file(
abidata.ref_file("ni_kpath_GSR.nc"))
assert not ni_ebands_kpath.has_linewidths
ni_ebands_kpath.linewidths = np.ones(ni_ebands_kpath.shape)
assert ni_ebands_kpath.has_linewidths
repr(ni_ebands_kpath)
str(ni_ebands_kpath)
assert ni_ebands_kpath.nsppol == 2 and ni_ebands_kpath.nspinor == 1 and ni_ebands_kpath.nspden == 2
assert ni_ebands_kpath.nelect == ref_nelect
assert ni_ebands_kpath.kpoints.is_path and not ni_ebands_kpath.has_bzmesh and ni_ebands_kpath.has_bzpath
assert ni_ebands_kpath.has_timrev
assert ni_ebands_kpath.fermie == ni_ebands_kmesh.fermie
# Serialization
self.serialize_with_pickle(ni_ebands_kpath, test_eq=False)
self.assertMSONable(ni_ebands_kpath, test_if_subclass=False)
assert len(ni_ebands_kpath.to_json())
od = ni_ebands_kmesh.get_dict4pandas(with_spglib=False)
assert od["nsppol"] == 2 and od["nspinor"] == 1 and od["nspden"] == 2
df = ni_ebands_kpath.get_dataframe()
ni_ebands_kpath.to_xmgrace(self.get_tmpname(text=True))
ni_ebands_kpath.to_xmgrace(sys.stdout)
# BXSF cannot be produced because.
#ngkpt 6 6 6
#nshiftk 4
#shiftk 1/2 1/2 1/2 1/2 0.0 0.0 0.0 1/2 0.0 0.0 0.0 1/2
with self.assertRaises(ValueError):
ni_ebands_kmesh.to_bxsf(self.get_tmpname(text=True))
# Interpolation
r = ni_ebands_kmesh.interpolate(lpratio=10, kmesh=[8, 8, 8], verbose=1)
assert r.ebands_kpath is not None
assert r.ebands_kpath.kpoints.is_path
assert not r.ebands_kpath.kpoints.is_ibz
mpdivs, shifts = r.ebands_kpath.kpoints.mpdivs_shifts
assert mpdivs is None and shifts is None
assert r.ebands_kmesh is not None
assert r.ebands_kmesh.kpoints.is_ibz
assert not r.ebands_kmesh.kpoints.is_path
assert r.ebands_kmesh.kpoints.ksampling is not None
assert r.ebands_kmesh.kpoints.is_mpmesh
mpdivs, shifts = r.ebands_kmesh.kpoints.mpdivs_shifts
self.assert_equal(mpdivs, [8, 8, 8])
self.assert_equal(shifts.flatten(), [0, 0, 0])
# Test __add__ and __radd__ (should return ElectronBandsPlotter)
p = ni_ebands_kmesh + r.ebands_kmesh + r.ebands_kpath
assert hasattr(p, "combiplot")
# Test plot methods
if self.has_matplotlib():
elims = [-10, 2]
assert ni_ebands_kmesh.plot(show=False)
assert ni_ebands_kmesh.plot_bz(show=False)
assert ni_ebands_kpath.plot(ylims=elims, show=False)
assert ni_ebands_kpath.plot_with_edos(ni_edos,
ylims=elims,
show=False)
assert ni_ebands_kpath.plot_bz(show=False)
assert ni_ebands_kpath.plot_transitions(4.4,
qpt=(0, 0, 0),
atol_ev=0.1,
atol_kdiff=1e-4,
show=False)
assert ni_ebands_kpath.plot_transitions(4.4,
qpt=(0.03, 0, 0),
atol_ev=0.5,
atol_kdiff=0.2,
show=False)
assert ni_ebands_kpath.plot_scatter3d(spin=0, band=8, show=False)
assert ni_edos.plot(xlims=elims, show=False)
assert ni_edos.plot_dos_idos(xlims=elims, show=False)
assert ni_edos.plot_up_minus_down(xlims=elims, show=False)
# Test linewidths
assert ni_ebands_kmesh.plot_lws_vs_e0(show=False) is None
assert ni_ebands_kpath.plot_lws_vs_e0(show=False)
# TODO Generaliza jdos to metals.
#vrange, crange = range(0, 4), range(4, 5)
#assert ni_ebands_kmesh.plot_ejdosvc(vrange, crange, cumulative=False, show=False)
#assert ni_ebands_kmesh.plot_ejdosvc(vrange, crange, cumulative=True, show=False)
if self.has_seaborn():
assert ni_ebands_kmesh.boxplot(
brange=[5, 10],
show=False,
title="Boxplot for up and down spin and 10 > band >= 5")
# Test Abipy --> Pymatgen converter.
pmg_bands_kpath = ni_ebands_kpath.to_pymatgen()
assert hasattr(pmg_bands_kpath,
"get_branch") # Should be BandStructureSymmLine
assert pmg_bands_kpath.efermi == ni_ebands_kpath.fermie
assert pmg_bands_kpath.is_spin_polarized
assert pmg_bands_kpath.is_metal()
# Test Pymatgen --> Abipy converter.
same_ekpath = ElectronBands.from_pymatgen(pmg_bands_kpath,
ni_ebands_kpath.nelect)
repr(same_ekpath)
str(same_ekpath)
self.assert_equal(same_ekpath.eigens, ni_ebands_kpath.eigens)
assert same_ekpath.fermie == ni_ebands_kpath.fermie
pmg_bands_kmesh = ni_ebands_kmesh.to_pymatgen()
#assert hasattr(pmg_bands_kmesh, "get_branch") # Should be BandStructure
assert pmg_bands_kmesh.efermi == ni_ebands_kmesh.fermie
assert pmg_bands_kmesh.is_spin_polarized
assert pmg_bands_kmesh.is_metal()
# Test Pymatgen --> Abipy converter.
same_ekmesh = ElectronBands.from_pymatgen(pmg_bands_kmesh,
ni_ebands_kmesh.nelect)
self.assert_equal(same_ekmesh.eigens, ni_ebands_kmesh.eigens)
assert same_ekmesh.fermie == ni_ebands_kmesh.fermie
def test_read_ebands_from_WFK(self):
"""Read ElectronBands from WFK files."""
for filename in data.WFK_NCFILES:
ebands = ElectronBands.from_file(filename)
def test_silicon_ebands(self):
"""Testing electron bands with nsppol == 1"""
si_ebands_kmesh = ElectronBands.from_file(abidata.ref_file("si_scf_GSR.nc"))
assert not si_ebands_kmesh.has_metallic_scheme
repr(si_ebands_kmesh); str(si_ebands_kmesh)
assert si_ebands_kmesh.to_string(title="Title",
with_structure=False, with_kpoints=True, verbose=1)
for spin, ik, band in si_ebands_kmesh.skb_iter():
assert spin == 0
assert si_ebands_kmesh.nkpt >= ik >= 0
assert si_ebands_kmesh.nband_sk[spin, ik] >= band >= 0
# Test ElectronBands get_e0
assert si_ebands_kmesh.get_e0("fermie") == si_ebands_kmesh.fermie
assert si_ebands_kmesh.get_e0(None) == 0.0
assert si_ebands_kmesh.get_e0("None") == 0.0
assert si_ebands_kmesh.get_e0(1.0) == 1.0
with self.assertRaises(ValueError):
si_ebands_kmesh.get_e0("foo")
r = si_ebands_kmesh.with_points_along_path(knames=["G", "X", "L", "G"])
assert r.ebands.kpoints.is_path
assert r.ebands.kpoints[0].is_gamma
assert r.ebands.kpoints[0] == r.ebands.kpoints[-1]
assert si_ebands_kmesh.kpoints[r.ik_new2prev[0]].is_gamma
# Serialization
self.serialize_with_pickle(si_ebands_kmesh, test_eq=False)
self.assertMSONable(si_ebands_kmesh, test_if_subclass=False)
assert len(si_ebands_kmesh.to_json())
dless_states = si_ebands_kmesh.dispersionless_states()
assert not dless_states
estats = si_ebands_kmesh.spacing()
self.assert_almost_equal(estats.mean, 2.3100587301616917)
self.assert_almost_equal(estats.stdev, 2.164400652355628)
self.assert_almost_equal(estats.min, 0)
self.assert_almost_equal(estats.max, 11.855874158768694)
repr(estats); str(estats)
with self.assertRaises(NotImplementedError):
si_ebands_kmesh.get_edos(method="tetrahedron")
si_edos = si_ebands_kmesh.get_edos()
repr(si_edos); str(si_edos)
assert ElectronDos.as_edos(si_edos, {}) is si_edos
assert si_edos == si_edos and not (si_edos != si_edos)
edos_samevals = ElectronDos.as_edos(si_ebands_kmesh, {})
assert ElectronDos.as_edos(si_ebands_kmesh, {}) == si_edos
assert ElectronDos.as_edos(abidata.ref_file("si_scf_GSR.nc"), {}) == si_edos
with self.assertRaises(TypeError):
ElectronDos.as_edos({}, {})
mu = si_edos.find_mu(8)
imu = si_edos.tot_idos.find_mesh_index(mu)
self.assert_almost_equal(si_edos.tot_idos[imu][1], 8, decimal=2)
d, i = si_edos.dos_idos(spin=0)
tot_d, tot_i = si_edos.dos_idos()
self.assert_almost_equal(2 * d.values, tot_d.values)
self.assert_almost_equal(2 * i.values, tot_i.values)
self.assert_equal(si_edos.up_minus_down.mesh, si_edos.tot_dos.mesh)
self.assert_equal(si_edos.up_minus_down.values, 0)
# Test ElectronDos get_e0
assert si_edos.get_e0("fermie") == si_edos.fermie
assert si_edos.get_e0(None) == 0.0
assert si_edos.get_e0("None") == 0.0
assert si_edos.get_e0(1.0) == 1.0
with self.assertRaises(TypeError):
si_edos.get_e0("foo")
self.serialize_with_pickle(si_edos, protocols=[-1], test_eq=False)
# Test plot methods
if self.has_matplotlib():
klabels = {
(0,0,0): "$\Gamma$",
(0.375, 0.375, 0.7500): "K",
(0.5, 0.5, 1.0): "X",
(0.5, 0.5, 0.5): "L",
(0.5, 0.0, 0.5): "X",
(0.5, 0.25, 0.75): "W",
}
assert si_edos.plot(show=False)
assert si_edos.plot_dos_idos(show=False)
assert si_edos.plot_up_minus_down(show=False)
assert si_ebands_kmesh.plot_with_edos(edos=si_edos, klabels=klabels, with_gaps=True, show=False)
assert si_ebands_kmesh.kpoints.plot(show=False)
vrange, crange = range(0, 4), range(4, 5)
assert si_ebands_kmesh.plot_ejdosvc(vrange, crange, cumulative=False, show=False)
assert si_ebands_kmesh.plot_ejdosvc(vrange, crange, cumulative=True, show=False)
assert si_ebands_kmesh.kpoints.plot(show=False)
if self.has_seaborn():
assert si_ebands_kmesh.boxplot(swarm=True, show=False)
if self.has_ipywidgets():
assert si_ebands_kmesh.ipw_edos_widget()
# Test Abipy --> Pymatgen converter.
pmg_bands_kmesh = si_ebands_kmesh.to_pymatgen()
assert pmg_bands_kmesh.efermi == si_ebands_kmesh.fermie
assert not pmg_bands_kmesh.is_spin_polarized
#assert not pmg_bands_kmesh.is_metal()
# Test Pymatgen --> Abipy converter.
same_ekmesh = ElectronBands.from_pymatgen(pmg_bands_kmesh, si_ebands_kmesh.nelect)
repr(same_ekmesh); str(same_ekmesh)
self.assert_equal(same_ekmesh.eigens, si_ebands_kmesh.eigens)
assert same_ekmesh.fermie == si_ebands_kmesh.fermie
assert len(same_ekmesh.kpoints) == len(pmg_bands_kmesh.kpoints)
# Test JDOS methods.
spin = 0
conduction = [4,]
for v in range(1, 5):
valence = range(0, v)
jdos = si_ebands_kmesh.get_ejdos(spin, valence, conduction)
intg = jdos.integral()[-1][-1]
self.assert_almost_equal(intg, len(conduction) * len(valence))
self.serialize_with_pickle(jdos, protocols=[-1])
si_ebands_kpath = ElectronBands.from_file(abidata.ref_file("si_nscf_GSR.nc"))
diffs = si_ebands_kpath.statdiff(si_ebands_kpath)
assert diffs is not None
repr(diffs); str(diffs)
h**o = si_ebands_kpath.homos[0]
repr(h**o); str(h**o)
assert h**o.spin == 0 and h**o.occ == 2.0 and h**o.band == 3
assert h**o.kpoint == [0, 0, 0]
assert h**o == h**o
assert si_ebands_kpath.kpoints[h**o.kidx] == h**o.kpoint
self.assert_almost_equal(h**o.eig, 5.5983129712050665)
assert "eig" in h**o.__class__.get_fields()
lumo = si_ebands_kpath.lumos[0]
assert h**o != lumo
assert lumo.spin == 0 and lumo.occ == 0.0 and lumo.band == 4
self.assert_almost_equal(lumo.kpoint.frac_coords, [0., 0.4285714, 0.4285714])
assert si_ebands_kpath.kpoints[lumo.kidx] == lumo.kpoint
self.assert_almost_equal(lumo.eig, 6.1226526474610843)
dir_gap = si_ebands_kpath.direct_gaps[0]
fun_gap = si_ebands_kpath.fundamental_gaps[0]
assert fun_gap.energy <= dir_gap.energy
assert dir_gap.qpoint == [0, 0, 0]
assert dir_gap.is_direct
assert dir_gap == dir_gap
assert dir_gap != fun_gap
assert si_ebands_kpath.get_gaps_string()
#print("repr_fun_gap", repr(fun_gap), id(fun_gap), id(fun_gap.qpoint))
#print("repr_dir_gap", repr(dir_gap), id(dir_gap), id(dir_gap.qpoint))
self.assert_almost_equal(dir_gap.energy, 2.5318279814319133)
self.assert_almost_equal(fun_gap.qpoint.frac_coords, [0., 0.4285714, 0.4285714])
self.assert_almost_equal(fun_gap.energy, 0.52433967625601774)
assert not fun_gap.is_direct
e1 = si_ebands_kpath.lomo_sk(spin=0, kpoint=0)
e2 = si_ebands_kpath.lomo_sk(spin=0, kpoint=si_ebands_kpath.kpoints[0])
assert e1.eig == e2.eig
# Test abipy-->pymatgen converter
pmg_bands_kpath = si_ebands_kpath.to_pymatgen()
assert hasattr(pmg_bands_kpath, "get_branch") # Should be BandStructureSymmLine
assert pmg_bands_kpath.efermi == si_ebands_kpath.fermie
assert not pmg_bands_kpath.is_spin_polarized
assert not pmg_bands_kpath.is_metal()
# Test the detection of denerate states.
degs = si_ebands_kpath.degeneracies(spin=0, kpoint=[0, 0, 0], bands_range=range(8))
ref_degbands = [[0], [1, 2, 3], [4, 5, 6], [7]]
for i, (e, deg_bands) in enumerate(degs):
self.assertEqual(deg_bands, ref_degbands[i])
# Test Electron
e1 = si_ebands_kpath._electron_state(spin=0, kpoint=[0, 0, 0], band=0)
repr(e1); str(e1)
e1_copy = e1.copy()
assert isinstance(e1.as_dict(), dict)
assert isinstance(e1.to_strdict(), dict)
assert e1.spin == 0
assert e1.skb[0] == 0
str(e1.tips)
# JDOS requires a homogeneous sampling.
with self.assertRaises(ValueError):
si_ebands_kpath.get_ejdos(spin, 0, 4)
if self.has_matplotlib():
assert si_ebands_kpath.plot(spin=0, e0=0, with_gaps=True, max_phfreq=0.1, show=False)
def test_silicon_ebands(self):
"""Testing electron bands with nsppol == 1"""
si_ebands_kmesh = ElectronBands.from_file(
abidata.ref_file("si_scf_GSR.nc"))
assert not si_ebands_kmesh.has_metallic_scheme
repr(si_ebands_kmesh)
str(si_ebands_kmesh)
assert si_ebands_kmesh.to_string(title="Title",
with_structure=False,
with_kpoints=True,
verbose=1)
for spin, ik, band in si_ebands_kmesh.skb_iter():
assert spin == 0
assert si_ebands_kmesh.nkpt >= ik >= 0
assert si_ebands_kmesh.nband_sk[spin, ik] >= band >= 0
# Test ElectronBands get_e0
assert si_ebands_kmesh.get_e0("fermie") == si_ebands_kmesh.fermie
assert si_ebands_kmesh.get_e0(None) == 0.0
assert si_ebands_kmesh.get_e0("None") == 0.0
assert si_ebands_kmesh.get_e0(1.0) == 1.0
with self.assertRaises(ValueError):
si_ebands_kmesh.get_e0("foo")
# Serialization
self.serialize_with_pickle(si_ebands_kmesh, test_eq=False)
self.assertMSONable(si_ebands_kmesh, test_if_subclass=False)
assert len(si_ebands_kmesh.to_json())
dless_states = si_ebands_kmesh.dispersionless_states()
assert not dless_states
estats = si_ebands_kmesh.spacing()
self.assert_almost_equal(estats.mean, 2.3100587301616917)
self.assert_almost_equal(estats.stdev, 2.164400652355628)
self.assert_almost_equal(estats.min, 0)
self.assert_almost_equal(estats.max, 11.855874158768694)
repr(estats)
str(estats)
with self.assertRaises(NotImplementedError):
si_ebands_kmesh.get_edos(method="tetrahedron")
si_edos = si_ebands_kmesh.get_edos()
repr(si_edos)
str(si_edos)
assert ElectronDos.as_edos(si_edos, {}) is si_edos
assert si_edos == si_edos and not (si_edos != si_edos)
edos_samevals = ElectronDos.as_edos(si_ebands_kmesh, {})
assert ElectronDos.as_edos(si_ebands_kmesh, {}) == si_edos
assert ElectronDos.as_edos(abidata.ref_file("si_scf_GSR.nc"),
{}) == si_edos
with self.assertRaises(TypeError):
ElectronDos.as_edos({}, {})
mu = si_edos.find_mu(8)
imu = si_edos.tot_idos.find_mesh_index(mu)
self.assert_almost_equal(si_edos.tot_idos[imu][1], 8, decimal=2)
d, i = si_edos.dos_idos(spin=0)
tot_d, tot_i = si_edos.dos_idos()
self.assert_almost_equal(2 * d.values, tot_d.values)
self.assert_almost_equal(2 * i.values, tot_i.values)
self.assert_equal(si_edos.up_minus_down.mesh, si_edos.tot_dos.mesh)
self.assert_equal(si_edos.up_minus_down.values, 0)
# Test ElectronDos get_e0
assert si_edos.get_e0("fermie") == si_edos.fermie
assert si_edos.get_e0(None) == 0.0
assert si_edos.get_e0("None") == 0.0
assert si_edos.get_e0(1.0) == 1.0
with self.assertRaises(TypeError):
si_edos.get_e0("foo")
self.serialize_with_pickle(si_edos, protocols=[-1], test_eq=False)
# Test plot methods
if self.has_matplotlib():
klabels = {
(0, 0, 0): "$\Gamma$",
(0.375, 0.375, 0.7500): "K",
(0.5, 0.5, 1.0): "X",
(0.5, 0.5, 0.5): "L",
(0.5, 0.0, 0.5): "X",
(0.5, 0.25, 0.75): "W",
}
assert si_edos.plot(show=False)
assert si_edos.plot_dos_idos(show=False)
assert si_edos.plot_up_minus_down(show=False)
assert si_ebands_kmesh.plot_with_edos(edos=si_edos,
klabels=klabels,
show=False)
assert si_ebands_kmesh.kpoints.plot(show=False)
vrange, crange = range(0, 4), range(4, 5)
assert si_ebands_kmesh.plot_ejdosvc(vrange,
crange,
cumulative=False,
show=False)
assert si_ebands_kmesh.plot_ejdosvc(vrange,
crange,
cumulative=True,
show=False)
assert si_ebands_kmesh.kpoints.plot(show=False)
if self.has_seaborn():
assert si_ebands_kmesh.boxplot(swarm=True, show=False)
if self.has_ipywidgets():
assert si_ebands_kmesh.ipw_edos_widget()
# Test Abipy --> Pymatgen converter.
pmg_bands_kmesh = si_ebands_kmesh.to_pymatgen()
assert pmg_bands_kmesh.efermi == si_ebands_kmesh.fermie
assert not pmg_bands_kmesh.is_spin_polarized
#assert not pmg_bands_kmesh.is_metal()
# Test Pymatgen --> Abipy converter.
same_ekmesh = ElectronBands.from_pymatgen(pmg_bands_kmesh,
si_ebands_kmesh.nelect)
repr(same_ekmesh)
str(same_ekmesh)
self.assert_equal(same_ekmesh.eigens, si_ebands_kmesh.eigens)
assert same_ekmesh.fermie == si_ebands_kmesh.fermie
assert len(same_ekmesh.kpoints) == len(pmg_bands_kmesh.kpoints)
# Test JDOS methods.
spin = 0
conduction = [
4,
]
for v in range(1, 5):
valence = range(0, v)
jdos = si_ebands_kmesh.get_ejdos(spin, valence, conduction)
intg = jdos.integral()[-1][-1]
self.assert_almost_equal(intg, len(conduction) * len(valence))
self.serialize_with_pickle(jdos, protocols=[-1])
si_ebands_kpath = ElectronBands.from_file(
abidata.ref_file("si_nscf_GSR.nc"))
diffs = si_ebands_kpath.statdiff(si_ebands_kpath)
assert diffs is not None
repr(diffs)
str(diffs)
h**o = si_ebands_kpath.homos[0]
repr(h**o)
str(h**o)
assert h**o.spin == 0 and h**o.occ == 2.0 and h**o.band == 3
assert h**o.kpoint == [0, 0, 0]
assert si_ebands_kpath.kpoints[h**o.kidx] == h**o.kpoint
self.assert_almost_equal(h**o.eig, 5.5983129712050665)
assert "eig" in h**o.__class__.get_fields()
lumo = si_ebands_kpath.lumos[0]
assert lumo.spin == 0 and lumo.occ == 0.0 and lumo.band == 4
self.assert_almost_equal(lumo.kpoint.frac_coords,
[0., 0.4285714, 0.4285714])
assert si_ebands_kpath.kpoints[lumo.kidx] == lumo.kpoint
self.assert_almost_equal(lumo.eig, 6.1226526474610843)
dir_gap = si_ebands_kpath.direct_gaps[0]
fun_gap = si_ebands_kpath.fundamental_gaps[0]
assert fun_gap.energy <= dir_gap.energy
assert dir_gap.qpoint == [0, 0, 0]
assert dir_gap.is_direct
#print("repr_fun_gap", repr(fun_gap), id(fun_gap), id(fun_gap.qpoint))
#print("repr_dir_gap", repr(dir_gap), id(dir_gap), id(dir_gap.qpoint))
self.assert_almost_equal(dir_gap.energy, 2.5318279814319133)
self.assert_almost_equal(fun_gap.qpoint.frac_coords,
[0., 0.4285714, 0.4285714])
self.assert_almost_equal(fun_gap.energy, 0.52433967625601774)
assert not fun_gap.is_direct
e1 = si_ebands_kpath.lomo_sk(spin=0, kpoint=0)
e2 = si_ebands_kpath.lomo_sk(spin=0, kpoint=si_ebands_kpath.kpoints[0])
assert e1.eig == e2.eig
# Test abipy-->pymatgen converter
pmg_bands_kpath = si_ebands_kpath.to_pymatgen()
assert hasattr(pmg_bands_kpath,
"get_branch") # Should be BandStructureSymmLine
assert pmg_bands_kpath.efermi == si_ebands_kpath.fermie
assert not pmg_bands_kpath.is_spin_polarized
assert not pmg_bands_kpath.is_metal()
# Test the detection of denerate states.
degs = si_ebands_kpath.degeneracies(spin=0,
kpoint=[0, 0, 0],
bands_range=range(8))
ref_degbands = [[0], [1, 2, 3], [4, 5, 6], [7]]
for i, (e, deg_bands) in enumerate(degs):
self.assertEqual(deg_bands, ref_degbands[i])
# Test Electron
e1 = si_ebands_kpath._electron_state(spin=0, kpoint=[0, 0, 0], band=0)
repr(e1)
str(e1)
e1_copy = e1.copy()
assert isinstance(e1.as_dict(), dict)
assert isinstance(e1.to_strdict(), dict)
assert e1.spin == 0
assert e1.skb[0] == 0
str(e1.tips)
# JDOS requires a homogeneous sampling.
with self.assertRaises(ValueError):
si_ebands_kpath.get_ejdos(spin, 0, 4)
def test_pymatgen_converter(self):
"""Test abipy-->pymatgen converter"""
nscf_bands = ElectronBands.from_file(data.ref_file("si_nscf_GSR.nc"))
pmg_bands = nscf_bands.to_pymatgen()
def __init__(self, path):
self.ks_bands = ElectronBands.from_file(path)
self.nsppol = self.ks_bands.nsppol
super(SigresReader, self).__init__(path)
try:
self.nomega_r = self.read_dimvalue("nomega_r")
except self.Error:
self.nomega_r = 0
#self.nomega_i = self.read_dim("nomega_i")
# Save important quantities needed to simplify the API.
self.structure = self.read_structure()
self.gwcalctyp = self.read_value("gwcalctyp")
self.usepawu = self.read_value("usepawu")
# 1) The K-points of the homogeneous mesh.
self.ibz = self.ks_bands.kpoints
# 2) The K-points where QPState corrections have been calculated.
gwred_coords = self.read_redc_gwkpoints()
self.gwkpoints = KpointList(self.structure.reciprocal_lattice, gwred_coords)
# minbnd[nkptgw,nsppol] gives the minimum band index computed
# Note conversion between Fortran and python convention.
self.gwbstart_sk = self.read_value("minbnd") - 1
self.gwbstop_sk = self.read_value("maxbnd")
# min and Max band index for GW corrections.
self.min_gwbstart = np.min(self.gwbstart_sk)
self.max_gwbstart = np.max(self.gwbstart_sk)
self.min_gwbstop = np.min(self.gwbstop_sk)
self.max_gwbstop = np.max(self.gwbstop_sk)
self._egw = self.read_value("egw", cmode="c")
# Read and save important matrix elements.
# All these arrays are dimensioned
# vxcme(b1gw:b2gw,nkibz,nsppol*nsig_ab))
self._vxcme = self.read_value("vxcme")
self._sigxme = self.read_value("sigxme")
self._hhartree = self.read_value("hhartree", cmode="c")
self._vUme = self.read_value("vUme")
#if self.usepawu == 0: self._vUme.fill(0.0)
# Complex arrays
self._sigcmee0 = self.read_value("sigcmee0", cmode="c")
self._ze0 = self.read_value("ze0", cmode="c")
# Frequencies for the spectral function.
if self.has_spfunc:
self._omega_r = self.read_value("omega_r")
self._sigcme = self.read_value("sigcme", cmode="c")
self._sigxcme = self.read_value("sigxcme", cmode="c")
# Self-consistent case
self._en_qp_diago = self.read_value("en_qp_diago")
# <KS|QPState>
self._eigvec_qp = self.read_value("eigvec_qp", cmode="c")
def test_read_ebands_from_GSR(self):
"""Read ElectronBands from GSR files."""
for filename in data.GSR_NCFILES:
ebands = ElectronBands.from_file(filename)
ebands.to_pymatgen()
def test_read_ebands_from_WFK(self):
"""Read ElectronBands from WFK files."""
for filename in data.WFK_NCFILES:
ebands = ElectronBands.from_file(filename)
def test_read_ebands_from_GSR(self):
"""Read ElectronBands from GSR files."""
for filename in data.GSR_NCFILES:
ebands = ElectronBands.from_file(filename)
def __init__(self, path):
self.ks_bands = ElectronBands.from_file(path)
self.nsppol = self.ks_bands.nsppol
super(SIGRES_Reader, self).__init__(path)
try:
self.nomega_r = self.read_dimvalue("nomega_r")
except self.Error:
self.nomega_r = 0
#self.nomega_i = self.read_dim("nomega_i")
# Save important quantities needed to simplify the API.
self.structure = self.read_structure()
self.gwcalctyp = self.read_value("gwcalctyp")
self.usepawu = self.read_value("usepawu")
# 1) The K-points of the homogeneous mesh.
self.kpoints = kpoints_factory(self)
# 2) The K-points where QPState corrections have been calculated.
gwred_coords = self.read_redc_gwkpoints()
self.gwkpoints = askpoints(gwred_coords, self.structure.reciprocal_lattice)
# minbnd[nkptgw,nsppol] gives the minimum band index computed
# Note conversion between Fortran and python convention.
self.gwbstart_sk = self.read_value("minbnd") - 1
self.gwbstop_sk = self.read_value("maxbnd")
# min and Max band index for GW corrections.
self.min_gwbstart = np.min(self.gwbstart_sk)
self.max_gwbstop = np.max(self.gwbstop_sk)
self._egw = self.read_value("egw", cmode="c")
# Read and save important matrix elements.
# All these arrays are dimensioned
# vxcme(b1gw:b2gw,nkibz,nsppol*nsig_ab))
self._vxcme = self.read_value("vxcme")
self._sigxme = self.read_value("sigxme")
self._hhartree = self.read_value("hhartree", cmode="c")
self._vUme = self.read_value("vUme")
#if self.usepawu == 0: self._vUme.fill(0.0)
# Complex arrays
self._sigcmee0 = self.read_value("sigcmee0", cmode="c")
self._ze0 = self.read_value("ze0", cmode="c")
# Frequencies for the spectral function.
if self.has_spfunc:
self._omega_r = self.read_value("omega_r")
self._sigcme = self.read_value("sigcme", cmode="c")
self._sigxcme = self.read_value("sigxcme", cmode="c")
# Self-consistent case
self._en_qp_diago = self.read_value("en_qp_diago")
# <KS|QPState>
self._eigvec_qp = self.read_value("eigvec_qp", cmode="c")
def test_nickel_ebands_spin(self):
"""Testing Nickel electron bands with nsppol == 2"""
ref_nelect = 18
ni_ebands_kmesh = ElectronBands.from_file(abidata.ref_file("ni_666k_GSR.nc"))
assert ElectronBands.as_ebands(ni_ebands_kmesh) is ni_ebands_kmesh
with self.assertRaises(TypeError):
ElectronBands.as_ebands(1)
repr(ni_ebands_kmesh); str(ni_ebands_kmesh)
assert ni_ebands_kmesh.nsppol == 2 and ni_ebands_kmesh.nspinor == 1 and ni_ebands_kmesh.nspden == 2
assert ni_ebands_kmesh.nelect == ref_nelect
assert ni_ebands_kmesh.kpoints.is_ibz and ni_ebands_kmesh.has_bzmesh and not ni_ebands_kmesh.has_bzpath
assert ni_ebands_kmesh.has_timrev
assert ni_ebands_kmesh.has_metallic_scheme
smearing = ni_ebands_kmesh.smearing
assert smearing.has_metallic_scheme
assert smearing.occopt == 7
self.assert_almost_equal(smearing.tsmear_ev.to("Ha"), 0.0075)
assert smearing.scheme == "gaussian"
assert not ni_ebands_kmesh.get_gaps_string()
#ni_ebands_kmesh.copy()
#ni_ebands_kmesh.deepcopy()
ni_edos = ni_ebands_kmesh.get_edos()
repr(ni_edos); str(ni_edos)
assert ni_edos.to_string(verbose=2)
# Get ElectronDosPlotter with nsppol == 2 and test matplotlib methods.
edos_plotter = ni_ebands_kmesh.compare_gauss_edos(widths=[0.2, 0.4], step=0.2)
assert len(edos_plotter) == 2
if self.has_matplotlib():
# Combiplot.
assert edos_plotter.combiplot(title="default values", show=False)
assert edos_plotter.combiplot(what_list=("dos", "idos"), spin_mode="resolved", show=False)
assert edos_plotter.combiplot(e0=0, what_list="dos", spin_mode="automatic", fontsize=12, show=False)
# Gridplot
assert edos_plotter.gridplot(title="default values", show=False)
assert edos_plotter.gridplot(what="idos", spin_mode="resolved", xlims=(-10, 10), show=False)
assert edos_plotter.gridplot(e0=0, what="dos", spin_mode="resolved", fontsize=12, show=False)
ni_ebands_kpath = ElectronBands.from_file(abidata.ref_file("ni_kpath_GSR.nc"))
assert not ni_ebands_kpath.has_linewidths
ni_ebands_kpath.linewidths = np.ones(ni_ebands_kpath.shape)
assert ni_ebands_kpath.has_linewidths
repr(ni_ebands_kpath); str(ni_ebands_kpath)
assert ni_ebands_kpath.nsppol == 2 and ni_ebands_kpath.nspinor == 1 and ni_ebands_kpath.nspden == 2
assert ni_ebands_kpath.nelect == ref_nelect
assert ni_ebands_kpath.kpoints.is_path and not ni_ebands_kpath.has_bzmesh and ni_ebands_kpath.has_bzpath
assert ni_ebands_kpath.has_timrev
assert ni_ebands_kpath.fermie == ni_ebands_kmesh.fermie
# Serialization
self.serialize_with_pickle(ni_ebands_kpath, test_eq=False)
self.assertMSONable(ni_ebands_kpath, test_if_subclass=False)
assert len(ni_ebands_kpath.to_json())
od = ni_ebands_kmesh.get_dict4pandas(with_spglib=False)
assert od["nsppol"] == 2 and od["nspinor"] == 1 and od["nspden"] == 2
df = ni_ebands_kpath.get_dataframe()
ni_ebands_kpath.to_xmgrace(self.get_tmpname(text=True))
ni_ebands_kpath.to_xmgrace(sys.stdout)
# BXSF cannot be produced because.
#ngkpt 6 6 6
#nshiftk 4
#shiftk 1/2 1/2 1/2 1/2 0.0 0.0 0.0 1/2 0.0 0.0 0.0 1/2
with self.assertRaises(ValueError):
ni_ebands_kmesh.to_bxsf(self.get_tmpname(text=True))
# Interpolation
r = ni_ebands_kmesh.interpolate(lpratio=10, kmesh=[8, 8, 8], verbose=1)
assert r.ebands_kpath is not None
assert r.ebands_kpath.kpoints.is_path
assert not r.ebands_kpath.kpoints.is_ibz
mpdivs, shifts = r.ebands_kpath.kpoints.mpdivs_shifts
assert mpdivs is None and shifts is None
assert r.ebands_kmesh is not None
assert r.ebands_kmesh.kpoints.is_ibz
assert not r.ebands_kmesh.kpoints.is_path
assert r.ebands_kmesh.kpoints.ksampling is not None
assert r.ebands_kmesh.kpoints.is_mpmesh
mpdivs, shifts = r.ebands_kmesh.kpoints.mpdivs_shifts
self.assert_equal(mpdivs, [8, 8, 8])
self.assert_equal(shifts.flatten(), [0, 0, 0])
# Test __add__ and __radd__ (should return ElectronBandsPlotter)
p = ni_ebands_kmesh + r.ebands_kmesh + r.ebands_kpath
assert hasattr(p, "combiplot")
# Test plot methods
if self.has_matplotlib():
elims = [-10, 2]
assert ni_ebands_kmesh.plot(show=False)
assert ni_ebands_kmesh.plot_bz(show=False)
assert ni_ebands_kpath.plot(ylims=elims, with_gaps=True, show=False)
assert ni_ebands_kpath.plot_with_edos(ni_edos, ylims=elims, show=False)
assert ni_ebands_kpath.plot_bz(show=False)
assert ni_ebands_kpath.plot_transitions(4.4, qpt=(0, 0, 0), atol_ev=0.1, atol_kdiff=1e-4, show=False)
assert ni_ebands_kpath.plot_transitions(4.4, qpt=(0.03, 0, 0), atol_ev=0.5, atol_kdiff=0.2, show=False)
assert ni_ebands_kpath.plot_scatter3d(spin=0, band=8, show=False)
assert ni_edos.plot(xlims=elims, show=False)
assert ni_edos.plot_dos_idos(xlims=elims, show=False)
assert ni_edos.plot_up_minus_down(xlims=elims, show=False)
# Test linewidths
assert ni_ebands_kmesh.plot_lws_vs_e0(show=False) is None
assert ni_ebands_kpath.plot_lws_vs_e0(show=False)
# TODO Generaliza jdos to metals.
#vrange, crange = range(0, 4), range(4, 5)
#assert ni_ebands_kmesh.plot_ejdosvc(vrange, crange, cumulative=False, show=False)
#assert ni_ebands_kmesh.plot_ejdosvc(vrange, crange, cumulative=True, show=False)
if self.has_seaborn():
assert ni_ebands_kmesh.boxplot(brange=[5, 10], show=False,
title="Boxplot for up and down spin and 10 > band >= 5")
# Test Abipy --> Pymatgen converter.
pmg_bands_kpath = ni_ebands_kpath.to_pymatgen()
assert hasattr(pmg_bands_kpath, "get_branch") # Should be BandStructureSymmLine
assert pmg_bands_kpath.efermi == ni_ebands_kpath.fermie
assert pmg_bands_kpath.is_spin_polarized
assert pmg_bands_kpath.is_metal()
# Test Pymatgen --> Abipy converter.
same_ekpath = ElectronBands.from_pymatgen(pmg_bands_kpath, ni_ebands_kpath.nelect)
repr(same_ekpath); str(same_ekpath)
self.assert_equal(same_ekpath.eigens, ni_ebands_kpath.eigens)
assert same_ekpath.fermie == ni_ebands_kpath.fermie
pmg_bands_kmesh = ni_ebands_kmesh.to_pymatgen()
#assert hasattr(pmg_bands_kmesh, "get_branch") # Should be BandStructure
assert pmg_bands_kmesh.efermi == ni_ebands_kmesh.fermie
assert pmg_bands_kmesh.is_spin_polarized
assert pmg_bands_kmesh.is_metal()
# Test Pymatgen --> Abipy converter.
same_ekmesh = ElectronBands.from_pymatgen(pmg_bands_kmesh, ni_ebands_kmesh.nelect)
self.assert_equal(same_ekmesh.eigens, ni_ebands_kmesh.eigens)
assert same_ekmesh.fermie == ni_ebands_kmesh.fermie
def test_pymatgen_converter(self):
"""Test abipy-->pymatgen converter"""
nscf_bands = ElectronBands.from_file(data.ref_file("si_nscf_GSR.nc"))
pmg_bands = nscf_bands.to_pymatgen()
