def _compass_from_lattice(
lattice,
origin=(0, 0, 0),
scale=0.7,
offset=0.15,
compass_style="corner",
**kwargs,
):
# TODO: add along lattice
"""
Get the display components of the compass
:param lattice: the pymatgen Lattice object that contains the primitive lattice vectors
:param origin: the reference position to place the compass
:param scale: scale all the geometric objects that makes up the compass the lattice vectors are normalized before the scaling so everything should be the same size
:param offset: shift the compass from the origin by a ratio of the diagonal of the cell relative the size
:return: list of cystal_toolkit.helper.scene objects that makes up the compass
"""
o = -np.array(origin)
o = o - offset * (lattice.matrix[0] + lattice.matrix[1] +
lattice.matrix[2])
a = lattice.matrix[0] / np.linalg.norm(lattice.matrix[0]) * scale
b = lattice.matrix[1] / np.linalg.norm(lattice.matrix[1]) * scale
c = lattice.matrix[2] / np.linalg.norm(lattice.matrix[2]) * scale
a_arrow = [[o, o + a]]
b_arrow = [[o, o + b]]
c_arrow = [[o, o + c]]
o_sphere = Spheres(positions=[o], color="black", radius=0.1 * scale)
return [
Arrows(
a_arrow,
color="red",
radius=0.7 * scale,
headLength=2.3 * scale,
headWidth=1.4 * scale,
**kwargs,
),
Arrows(
b_arrow,
color="blue",
radius=0.7 * scale,
headLength=2.3 * scale,
headWidth=1.4 * scale,
**kwargs,
),
Arrows(
c_arrow,
color="green",
radius=0.7 * scale,
headLength=2.3 * scale,
headWidth=1.4 * scale,
**kwargs,
),
o_sphere,
]
def get_site_scene(
self,
connected_sites: List[ConnectedSite] = None,
# connected_site_metadata: None,
# connected_sites_to_draw,
connected_sites_not_drawn: List[ConnectedSite] = None,
hide_incomplete_edges: bool = False,
incomplete_edge_length_scale: Optional[float] = 1.0,
connected_sites_colors: Optional[List[str]] = None,
connected_sites_not_drawn_colors: Optional[List[str]] = None,
origin: Optional[List[float]] = None,
draw_polyhedra: bool = True,
explicitly_calculate_polyhedra_hull: bool = False,
bond_radius: float = 0.1,
draw_magmoms: bool = True,
magmom_scale: float = 1.0,
legend: Optional[Legend] = None,
) -> Scene:
"""
Args:
connected_sites:
connected_sites_not_drawn:
hide_incomplete_edges:
incomplete_edge_length_scale:
connected_sites_colors:
connected_sites_not_drawn_colors:
origin:
explicitly_calculate_polyhedra_hull:
legend:
Returns:
"""
atoms = []
bonds = []
polyhedron = []
magmoms = []
legend = legend or Legend(self)
# for disordered structures
is_ordered = self.is_ordered
phiStart, phiEnd = None, None
occu_start = 0.0
position = self.coords.tolist()
radii = [legend.get_radius(sp, site=self) for sp in self.species.keys()]
max_radius = float(min(radii))
for idx, (sp, occu) in enumerate(self.species.items()):
if isinstance(sp, DummySpecie):
cube = Cubes(
positions=[position], color=legend.get_color(sp, site=self), width=0.4
)
atoms.append(cube)
else:
color = legend.get_color(sp, site=self)
radius = legend.get_radius(sp, site=self)
# TODO: make optional/default to None
# in disordered structures, we fractionally color-code spheres,
# drawing a sphere segment from phi_end to phi_start
# (think a sphere pie chart)
if not is_ordered:
phi_frac_end = occu_start + occu
phi_frac_start = occu_start
occu_start = phi_frac_end
phiStart = phi_frac_start * np.pi * 2
phiEnd = phi_frac_end * np.pi * 2
name = str(sp)
if occu != 1.0:
name += " ({}% occupancy)".format(occu)
name += f" ({position[0]:.3f}, {position[1]:.3f}, {position[2]:.3f})"
if self.properties:
for k, v in self.properties.items():
name += f" ({k} = {v})"
sphere = Spheres(
positions=[position],
color=color,
radius=radius,
phiStart=phiStart,
phiEnd=phiEnd,
clickable=True,
tooltip=name,
)
atoms.append(sphere)
# Add magmoms
if draw_magmoms:
if magmom := self.properties.get("magmom"):
# enforce type
magmom = np.array(Magmom(magmom).get_moment())
magmom = 2 * magmom_scale * max_radius * magmom
tail = np.array(position) - 0.5 * np.array(magmom)
head = np.array(position) + 0.5 * np.array(magmom)
arrow = Arrows(
positionPairs=[[tail, head]],
color="red",
radius=0.20,
headLength=0.5,
headWidth=0.4,
clickable=True,
)
magmoms.append(arrow)
def _axes_from_lattice(self, origin=None, scale=1, offset=0, **kwargs):
"""
Get the display components of the compass
:param lattice: the pymatgen Lattice object that contains the primitive
lattice vectors
:param origin: the reference position to place the compass
:param scale: scale all the geometric objects that makes up the compass
the lattice vectors are normalized before the scaling so everything should
be the same size
:param offset: shift the compass from the origin by a ratio of the diagonal
of the cell relative the size
:param **kwargs: keyword args to pass to the Arrows initializer
:return: Scene object
"""
origin = origin or [0, 0, 0]
o = np.array(origin)
# o = -self.get_cartesian_coords([0.5, 0.5, 0.5])
# o = o - offset * (self.matrix[0] + self.matrix[1] + self.matrix[2])
a = self.matrix[0] / np.linalg.norm(self.matrix[0]) * scale
b = self.matrix[1] / np.linalg.norm(self.matrix[1]) * scale
c = self.matrix[2] / np.linalg.norm(self.matrix[2]) * scale
a_arrow = [[o, o + a]]
b_arrow = [[o, o + b]]
c_arrow = [[o, o + c]]
radius_scale = 0.07
head_scale = 0.24
head_width = 0.14
o_sphere = Spheres(positions=[o],
color="white",
radius=2 * radius_scale * scale)
return Scene(
name="axes",
contents=[
Arrows(
a_arrow,
color="red",
radius=radius_scale * scale,
headLength=head_scale * scale,
headWidth=head_width * scale,
**kwargs,
),
Arrows(
b_arrow,
color="green",
radius=radius_scale * scale,
headLength=head_scale * scale,
headWidth=head_width * scale,
**kwargs,
),
Arrows(
c_arrow,
color="blue",
radius=radius_scale * scale,
headLength=head_scale * scale,
headWidth=head_width * scale,
**kwargs,
),
o_sphere,
],
origin=origin,
)