def get_scene_and_legend(self) -> Tuple[Scene, Dict[str, str]]:
legend = Legend(self.graph.structure,
color_scheme="VESTA",
cmap_range=None)
legend.uniform_radius = 0.3
scene = get_structure_graph_scene(
self.graph,
draw_image_atoms=True,
bonded_sites_outside_unit_cell=False,
hide_incomplete_edges=True,
explicitly_calculate_polyhedra_hull=False,
group_by_symmetry=True,
draw_polyhedra=False,
legend=legend)
scene.name = "DefectStructureComponentScene"
lattice: Lattice = self.graph.structure.lattice
origin = -self.graph.structure.lattice.get_cartesian_coords(
[0.5, 0.5, 0.5])
scene_json = scene.to_json()
for idx, i in enumerate(self.interstitials, 1):
site = Site(species=DummySpecie(),
coords=lattice.get_cartesian_coords(i.frac_coords))
interstitial_scene = site.get_scene(origin=origin)
interstitial_scene.name = f"i{idx}"
interstitial_scene.contents[0].contents[0].tooltip = f"i{idx}"
scene_json["contents"].append(interstitial_scene.to_json())
return scene_json, legend.get_legend()
def get_scene_and_legend(self,
scene_additions=None
) -> Tuple[Scene, Dict[str, str]]:
legend = Legend(self.graph.structure,
color_scheme="VESTA",
radius_scheme="uniform",
cmap_range=None)
legend.uniform_radius = 0.2
scene = get_structure_graph_scene(
self.graph,
draw_image_atoms=True,
bonded_sites_outside_unit_cell=False,
hide_incomplete_edges=True,
explicitly_calculate_polyhedra_hull=False,
group_by_symmetry=False,
legend=legend)
scene.name = "DefectStructureComponentScene"
# axes = graph.structure.lattice._axes_from_lattice()
# axes.visible = True
# scene.contents.append(axes)
scene = scene.to_json()
if scene_additions:
scene["contents"].append(scene_additions)
lattice = self.graph.structure.lattice
origin = -self.graph.structure.lattice.get_cartesian_coords(
[0.5, 0.5, 0.5])
for name, frac_coords in self.vacancy_sites:
site = Site(species=DummySpecie(name),
coords=lattice.get_cartesian_coords(frac_coords))
vac_scene = site.get_scene(origin=origin)
vac_scene.name = f"{name}_{frac_coords}"
vac_scene.contents[0].contents[0].tooltip = name
scene["contents"].append(vac_scene.to_json())
return scene, legend.get_legend()