def get_lattice_scene(self, origin=None, show_axes=False, **kwargs):
o = -np.array((0, 0, 0))
a, b, c = self.matrix[0], self.matrix[1], self.matrix[2]
line_pairs = [
o,
o + a,
o,
o + b,
o,
o + c,
o + a,
o + a + b,
o + a,
o + a + c,
o + b,
o + b + a,
o + b,
o + b + c,
o + c,
o + c + a,
o + c,
o + c + b,
o + a + b,
o + a + b + c,
o + a + c,
o + a + b + c,
o + b + c,
o + a + b + c,
]
line_pairs = [line.tolist() for line in line_pairs]
name = (
f"a={self.a}, b={self.b}, c={self.c}, "
f"alpha={self.alpha}, beta={self.beta}, gamma={self.gamma}"
)
contents = [Lines(line_pairs, **kwargs)]
if show_axes:
contents.append(self._axes_from_lattice(origin=origin))
return Scene(name, contents, origin=origin)
def get_lattice_scene(self, origin=(0, 0, 0), **kwargs):
o = -np.array(origin)
a, b, c = self.matrix[0], self.matrix[1], self.matrix[2]
line_pairs = [
o,
o + a,
o,
o + b,
o,
o + c,
o + a,
o + a + b,
o + a,
o + a + c,
o + b,
o + b + a,
o + b,
o + b + c,
o + c,
o + c + a,
o + c,
o + c + b,
o + a + b,
o + a + b + c,
o + a + c,
o + a + b + c,
o + b + c,
o + a + b + c,
]
line_pairs = [line.tolist() for line in line_pairs]
name = (f"a={self.a}, b={self.b}, c={self.c}, "
f"alpha={self.alpha}, beta={self.beta}, gamma={self.gamma}")
return Scene(name, contents=[Lines(line_pairs, **kwargs)])
def plot_crystal_toolkit(
self,
spin: Optional[Spin] = None,
colors: Optional[Union[str, dict, list]] = None,
opacity: float = 1.0,
) -> "Scene":
"""
Get a crystal toolkit Scene showing the Fermi surface. The Scene can be
displayed in an interactive web app using Crystal Toolkit, can be shown
interactively in Jupyter Lab using the crystal-toolkit lab extension, or
can be converted to JSON to store for future use.
Args:
spin: Which spin channel to plot. By default plot both spin channels if
available.
colors: See the docstring for ``get_isosurfaces_and_colors()`` for the
available options.
opacity: Opacity of surface. Note that due to limitations of WebGL,
overlapping semi-transparent surfaces might result in visual artefacts.
"""
# The implementation here is very similar to the plotly implementation, except
# the crystal toolkit scene is constructed using the scene primitives from
# crystal toolkit (Spheres, Surface, Lines, etc.)
scene_contents = []
isosurfaces, colors = self.get_isosurfaces_and_colors(spin=spin,
colors=colors)
if isinstance(colors, np.ndarray):
colors = (colors * 255).astype(int)
colors = ["rgb({},{},{})".format(*c) for c in colors]
# create a mesh for each electron band which has an isosurfaces at the Fermi
# energy mesh data is generated by a marching cubes algorithm when the
# FermiSurface object is created.
surfaces = []
for c, (verts, faces) in zip(colors, isosurfaces):
positions = verts[faces].reshape(-1, 3).tolist()
surface = Surface(positions=positions, color=c, opacity=opacity)
surfaces.append(surface)
fermi_surface = Scene("fermi_surface", contents=surfaces)
scene_contents.append(fermi_surface)
# add the cell outline to the plot
lines = Lines(positions=list(self.reciprocal_space.lines.flatten()))
# alternatively,
# cylinders have finite width and are lighted, but no strong reason to choose
# one over the other
# cylinders = Cylinders(positionPairs=self.reciprocal_space.lines.tolist(),
# radius=0.01, color="rgb(0,0,0)")
scene_contents.append(lines)
spheres = []
for position, label in zip(self._symmetry_pts[0],
self._symmetry_pts[1]):
sphere = Spheres(
positions=[list(position)],
tooltip=label,
radius=0.05,
color="rgb(0, 0, 0)",
)
spheres.append(sphere)
label_scene = Scene("labels", contents=spheres)
scene_contents.append(label_scene)
return Scene("ifermi", contents=scene_contents)
def get_brillouin_zone_scene(bs: BandStructureSymmLine) -> Scene:
if not bs:
return Scene(name="brillouin_zone", contents=[])
# TODO: from BSPlotter, merge back into BSPlotter
# Brillouin zone
bz_lattice = bs.structure.lattice.reciprocal_lattice
bz = bz_lattice.get_wigner_seitz_cell()
lines = []
for iface in range(len(bz)): # pylint: disable=C0200
for line in itertools.combinations(bz[iface], 2):
for jface in range(len(bz)):
if (iface < jface
and any(np.all(line[0] == x) for x in bz[jface])
and any(np.all(line[1] == x) for x in bz[jface])):
lines += [list(line[0]), list(line[1])]
zone_lines = Lines(positions=lines)
zone_surface = Convex(positions=lines, opacity=0.05, color="#000000")
# - Strip latex math wrapping for labels
# TODO: add to string utils in pymatgen
str_replace = {
"$": "",
"\\mid": "|",
"\\Gamma": "Γ",
"\\Sigma": "Σ",
"GAMMA": "Γ",
"_1": "₁",
"_2": "₂",
"_3": "₃",
"_4": "₄",
"_{1}": "₁",
"_{2}": "₂",
"_{3}": "₃",
"_{4}": "₄",
"^{*}": "*",
}
labels = {}
for k in bs.kpoints:
if k.label:
label = k.label
for orig, new in str_replace.items():
label = label.replace(orig, new)
labels[label] = bz_lattice.get_cartesian_coords(k.frac_coords)
labels = [
Spheres(positions=[coords],
tooltip=label,
radius=0.03,
color="#5EB1BF") for label, coords in labels.items()
]
path = []
cylinder_pairs = []
for b in bs.branches:
start = bz_lattice.get_cartesian_coords(
bs.kpoints[b["start_index"]].frac_coords)
end = bz_lattice.get_cartesian_coords(
bs.kpoints[b["end_index"]].frac_coords)
path += [start, end]
cylinder_pairs += [[start, end]]
# path_lines = Lines(positions=path, color="#ff4b5c",)
path_lines = Cylinders(positionPairs=cylinder_pairs,
color="#5EB1BF",
radius=0.01)
ibz_region = Convex(positions=path, opacity=0.2, color="#5EB1BF")
contents = [zone_lines, zone_surface, path_lines, ibz_region, *labels]
cbm = bs.get_cbm()["kpoint"]
vbm = bs.get_vbm()["kpoint"]
if cbm and vbm:
if cbm.label:
cbm_label = cbm.label
for orig, new in str_replace.items():
cbm_label = cbm_label.replace(orig, new)
cbm_label = f"CBM at {cbm_label}"
else:
cbm_label = "CBM"
if cbm == vbm:
cbm_label = f"VBM and {cbm_label}"
cbm_coords = bz_lattice.get_cartesian_coords(cbm.frac_coords)
cbm = Spheres(positions=[cbm_coords],
tooltip=cbm_label,
radius=0.05,
color="#7E259B")
contents.append(cbm)
if cbm != vbm:
if vbm.label:
vbm_label = vbm.label
for orig, new in str_replace.items():
vbm_label = vbm_label.replace(orig, new)
vbm_label = f"VBM at {vbm_label}"
else:
vbm_label = "VBM"
vbm_coords = bz_lattice.get_cartesian_coords(vbm.frac_coords)
vbm = Spheres(
positions=[vbm_coords],
tooltip=vbm_label,
radius=0.05,
color="#7E259B",
)
contents.append(vbm)
return Scene(name="brillouin_zone", contents=contents)