def get_interpolated_ebands_plotter(self,
vertices_names=None,
knames=None,
line_density=20,
ngkpt=None,
shiftk=(0, 0, 0),
kpoints=None,
**kwargs):
"""
Args:
vertices_names: Used to specify the k-path for the interpolated QP band structure
It's a 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.
knames: List of strings with the k-point labels defining the k-path. It has precedence over `vertices_names`.
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.
Return: |ElectronBandsPlotter| object.
"""
diff_str = self.has_different_structures()
if diff_str: cprint(diff_str, "yellow")
# Need KpointList object (assume same structures in Robot)
nc0 = self.abifiles[0]
if kpoints is None:
if ngkpt is not None:
# IBZ sampling
kpoints = IrredZone.from_ngkpt(nc0.structure,
ngkpt,
shiftk,
kptopt=1,
verbose=0)
else:
# K-Path
if knames is not None:
kpoints = Kpath.from_names(nc0.structure,
knames,
line_density=line_density)
else:
if vertices_names is None:
vertices_names = [(k.frac_coords, k.name)
for k in nc0.structure.hsym_kpoints]
kpoints = Kpath.from_vertices_and_names(
nc0.structure,
vertices_names,
line_density=line_density)
plotter = ElectronBandsPlotter()
for label, abiwan in self.items():
plotter.add_ebands(label,
abiwan.interpolate_ebands(kpoints=kpoints))
return plotter
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 get_interpolated_ebands_plotter(self, vertices_names=None, knames=None, line_density=20,
ngkpt=None, shiftk=(0, 0, 0), kpoints=None, **kwargs):
"""
Args:
vertices_names: Used to specify the k-path for the interpolated QP band structure
It's a 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.
knames: List of strings with the k-point labels defining the k-path. It has precedence over `vertices_names`.
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.
Return: |ElectronBandsPlotter| object.
"""
diff_str = self.has_different_structures()
if diff_str: cprint(diff_str, "yellow")
# Need KpointList object (assume same structures in Robot)
nc0 = self.abifiles[0]
if kpoints is None:
if ngkpt is not None:
# IBZ sampling
kpoints = IrredZone.from_ngkpt(nc0.structure, ngkpt, shiftk, kptopt=1, verbose=0)
else:
# K-Path
if knames is not None:
kpoints = Kpath.from_names(nc0.structure, knames, line_density=line_density)
else:
if vertices_names is None:
vertices_names = [(k.frac_coords, k.name) for k in nc0.structure.hsym_kpoints]
kpoints = Kpath.from_vertices_and_names(nc0.structure, vertices_names, line_density=line_density)
plotter = ElectronBandsPlotter()
for label, abiwan in self.items():
plotter.add_ebands(label, abiwan.interpolate_ebands(kpoints=kpoints))
return plotter
def OnCompareEbands(self, event):
"""Plot multiple electron bands"""
plotter = ElectronBandsPlotter()
for path, ebands in zip(self.ebands_filepaths, self.ebands_list):
label = os.path.relpath(path)
plotter.add_ebands(label, ebands)
try:
print(plotter.bands_statdiff())
except:
pass
plotter.plot()
def OnCompareEbands(self, event):
"""Plot multiple electron bands"""
plotter = ElectronBandsPlotter()
for path, ebands in zip(self.ebands_filepaths, self.ebands_list):
label = os.path.relpath(path)
plotter.add_ebands(label, ebands)
try:
print(plotter.bands_statdiff())
except:
pass
plotter.plot()
def test_ebands_plotter(self):
"""Testing ElelectronBandsPlotter."""
plotter = ElectronBandsPlotter(key_ebands=[("Si1", abidata.ref_file("si_scf_GSR.nc"))])
plotter.add_ebands("Si2", abidata.ref_file("si_scf_GSR.nc"))
repr(plotter); str(plotter)
assert len(plotter.ebands_list) == 2
assert len(plotter.edoses_list) == 0
with self.assertRaises(ValueError):
plotter.add_ebands("Si2", abidata.ref_file("si_scf_GSR.nc"))
# __add__ should merge plotters
p2 = plotter.add_plotter(plotter)
assert len(p2.ebands_list) == 2
assert len(p2.edoses_list) == 0
assert hasattr(p2, "combiplot")
print(plotter.bands_statdiff())
df = plotter.get_ebands_frame()
assert df is not None
if self.has_matplotlib():
assert plotter.combiplot(title="Silicon band structure", show=False)
# Alias for combiplot
assert plotter.plot(e0=2, width_ratios=(3, 1), fontsize=12, show=False)
if self.has_seaborn():
plotter.combiboxplot(title="Silicon band structure", swarm=True, show=False)
assert plotter.gridplot(title="Silicon band structure", with_gaps=True, show=False)
assert plotter.boxplot(title="Silicon band structure", swarm=True, show=False)
assert plotter.animate(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))
pickle_path = self.get_tmpname(text=True)
plotter.pickle_dump(pickle_path)
same = ElectronBandsPlotter.pickle_load(pickle_path)
assert len(same.ebands_dict) == len(plotter.ebands_dict)
assert list(same.ebands_dict.keys()) == list(plotter.ebands_dict.keys())
def test_ebands_plotter(self):
"""Testing ElelectronBandsPlotter."""
plotter = ElectronBandsPlotter(
key_ebands=[("Si1", abidata.ref_file("si_scf_GSR.nc"))])
plotter.add_ebands("Si2", abidata.ref_file("si_scf_GSR.nc"))
repr(plotter)
str(plotter)
assert len(plotter.ebands_list) == 2
assert len(plotter.edoses_list) == 0
with self.assertRaises(ValueError):
plotter.add_ebands("Si2", abidata.ref_file("si_scf_GSR.nc"))
# __add__ should merge plotters
p2 = plotter.add_plotter(plotter)
assert len(p2.ebands_list) == 2
assert len(p2.edoses_list) == 0
assert hasattr(p2, "combiplot")
print(plotter.bands_statdiff())
df = plotter.get_ebands_frame()
assert df is not None
if self.has_matplotlib():
assert plotter.combiplot(title="Silicon band structure",
show=False)
# Alias for combiplot
assert plotter.plot(e0=2,
width_ratios=(3, 1),
fontsize=12,
show=False)
if self.has_seaborn():
plotter.combiboxplot(title="Silicon band structure",
swarm=True,
show=False)
assert plotter.gridplot(title="Silicon band structure", show=False)
assert plotter.boxplot(title="Silicon band structure",
swarm=True,
show=False)
assert plotter.animate(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))
pickle_path = self.get_tmpname(text=True)
plotter.pickle_dump(pickle_path)
same = ElectronBandsPlotter.pickle_load(pickle_path)
assert len(same.ebands_dict) == len(plotter.ebands_dict)
assert list(same.ebands_dict.keys()) == list(
plotter.ebands_dict.keys())
def test_api(self):
"""Test ElelectronBandsPlotter API."""
plotter = ElectronBandsPlotter(
key_ebands=[("Si1", abidata.ref_file("si_scf_GSR.nc"))])
plotter.add_ebands("Si2", abidata.ref_file("si_scf_GSR.nc"))
print(repr(plotter))
assert len(plotter.ebands_list) == 2
assert len(plotter.edoses_list) == 0
with self.assertRaises(ValueError):
plotter.add_ebands("Si2", abidata.ref_file("si_scf_GSR.nc"))
print(plotter.bands_statdiff())
df = plotter.get_ebands_frame()
assert df is not None
if self.has_matplotlib():
plotter.combiplot(title="Silicon band structure", show=False)
if self.has_seaborn():
plotter.combiboxplot(title="Silicon band structure",
show=False)
plotter.gridplot(title="Silicon band structure", show=False)
plotter.boxplot(title="Silicon band structure",
swarm=True,
show=False)
plotter.animate(show=False)
if self.has_nbformat():
plotter.write_notebook(nbpath=self.get_tmpname(text=True))