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 __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 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_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_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_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