3D Structure Viewer

Interactive WebGL viewer in Jupyter, built on Three.js via anywidget.

cell.view_structure()

Default behaviour¶

For recognised materials (Si / C, Cu, SiO₂, SrTiO₃, …) the viewer picks a coordination polyhedron and renders it as a translucent mesh around every atom whose first shell passes the detector, with no bond cylinders by default:

Species	Polyhedron	Centre-vertex bond	Scale
Si / C (diamond)	tetrahedron	2.35 / 1.54 Å (self)	0.5 (vertices at bond midpoints)
C (graphite, sp²)	triangle (3-sub-triangle fan, 120°)	1.42 Å (self)	0.5
Cu	cuboctahedron (FCC 12-coord)	2.56 Å (self)	0.5
SiO₂	SiO₄ tetrahedron	1.61 Å (Si → O)	1.0
SrTiO₃	TiO₆ octahedron	1.96 Å (Ti → O)	1.0

For blended materials (sp²/sp³ carbon; SiO₂/Si₃N₄ mixes, …) pass polyhedra_groups=[...] to export_overview_html or export_trajectory_html. Each entry carries its own kind (triangles, tetrahedra, octahedra, cuboctahedra), colour, opacity, and an optional virtual_species filter that restricts detection to atoms flagged with that shell-target species index. See Carbon for a worked example where green sp²-C triangle fans and navy sp³-C tetrahedra render in the same scene.

Override with the polyhedra= kwarg:

# Explicit kind + tolerances
cell.view_structure(polyhedra={
    'kind': 'octahedra',
    'center_symbol': 'Ti', 'vertex_symbol': 'O',
    'bond_length': 1.96, 'bond_length_tol': 0.15,
    'angle_tol_deg': 18.0, 'scale': 1.0,
})

# Disable polyhedra, show bonds instead
cell.view_structure(polyhedra=False, show_bonds=True)

Live controls¶

All sliders recompute on release, pushing the result back through the anywidget traitlet bridge so the 3D scene updates without a full rebuild:

Drag to rotate, scroll to zoom, right-click drag to pan.
Atom size – sphere radius scale factor (default 0.2).
Bond radius / bond cutoff – when bonds are shown.
Bond type checkboxes – per species-pair visibility.
Polyhedra controls – a group of four sliders (shown when the polyhedra kind has been auto-detected or explicitly set):
- bond length (Å) – radial centre of the first-shell window; dragging this moves the polyhedra in and out as more / fewer atoms pass the distance test.
- radial tolerance (fraction) – 2 % – 40 %; widens the accepted band around bond_length.
- angle tolerance (°) – 1° – 45°; controls how much the local shell can deviate from the ideal polyhedral angles (109.47° for tets, 90° for octahedra, FCC spectrum for cuboctahedra).
- polyhedra scale – 0.2 – 1.0; shrinks the rendered polyhedron toward its centre. scale=0.5 places vertices at bond midpoints (natural for single-species cases where the “vertices” are just neighbouring atoms); scale=1.0 sits vertices on the neighbour atoms themselves (natural for cation-anion motifs like SiO₄).
- polyhedra opacity – 0.05 – 0.95 (default 0.2).
Slab x / y / z dual-range sliders – clip the view to a fractional coordinate range.
Show cell / Show bonds / Show polyhedra checkboxes – toggle each overlay independently; combinations are fine (e.g. polyhedra and bonds for debugging the first-shell detector).
Orthographic checkbox – swaps between PerspectiveCamera(fov=45°) and an OrthographicCamera whose frustum is computed from the cube’s bounding sphere. Parallel lattice planes read as parallel in ortho mode, which makes cubic crystalline panels easier to interpret.

Parameters¶

Parameter	Default	Description
`polyhedra`	`True` (auto-pick)	Config dict; `True` / `None` auto-picks from species, `False` disables. See table above for auto-pick rules.
`atom_scale`	0.2	Sphere radius scale factor (`covalent_radius × scale`).
`bond_cutoff`	from `shell_target.max_pair_outer`	Maximum bond length (Å).
`bond_radius`	0.08	Cylinder radius for bonds (Å).
`show_bonds`	False	Render bonds. Auto-default flipped to False once polyhedra became the primary overlay.
`show_cell`	True	Render cell outline.
`orthographic`	False	Start in orthographic mode.
`slab_x`, `slab_y`, `slab_z`	`(0, 1)`	Fractional range to display.

Colours come from ASE’s jmol colour scheme; the polyhedra colour defaults to a material-specific hint (blue for Si-tets, orange for Ti-octa, copper-orange for Cu-cubocta, …).

Example: silicon MRO¶

Here is the live widget as rendered from am.Supercell.PRESETS["MRO"] on Si at 40 × 40 × 40 Å. The blue tetrahedra mark Si atoms whose four nearest neighbours pass the 109.5° / 2.35 Å first-shell filter, with the tets shrunk to half-size so their corners meet at Si-Si bond midpoints:

(The embedded viewer above is the exported trajectory version; the notebook view_structure() widget uses the same Three.js scene + controls on a single final frame.)