Multi-Cell Overview

Render a grid of finished structures side-by-side with synchronised rotation. Useful for comparing how the same material looks across the full disorder spectrum, or for showing several materials at once.

Usage¶

import atomode as am

cells = []
for name in ["liquid", "amorphous", "SRO", "MRO",
             "LRO", "nanocrystalline"]:
    cell = am.Supercell.from_atoms(atoms, (40, 40, 40), rng_seed=42)
    cell.generate(shell_target, **am.Supercell.PRESETS[name])
    cells.append((cell, name))

am.export_overview_html("silicon_overview.html", cells)

Each entry in cells_and_labels is a (Supercell, label) pair. Labels are rendered as text badges in the top-left corner of each panel.

Features¶

One WebGL context, many scenes: each panel renders into its own viewport using setScissor / setViewport, so even six structures in one file stay responsive.
Synchronised rotation: all panels share a single camera. The structure auto-rotates at ~14°/s. Dragging any panel pauses the spin and lets the user orbit manually; the spin resumes ~0.5 s after release.
Aspect-aware framing: the camera distance is recomputed every frame to fit each cube’s bounding sphere, so cubes stay in-frame whether the iframe is tall or wide.
Cartoon style: ASE jmol colours for atoms, thin black outlines, red bonds.
Tetrahedral bond filter: only bonds that sit inside ±bond_length_tol of the first-neighbour distance and whose 4 nearest neighbours subtend angles within bond_angle_tol_deg of ideal_angle_deg are drawn. Atoms that fail either test contribute no bonds, so disordered regimes naturally show fewer bonds than crystalline ones.

Parameters¶

Parameter	Default	Description
`output_path`	required	File path for the generated HTML.
`cells_and_labels`	required	Iterable of `(Supercell, label)` pairs.
`grid_cols`	3	Number of columns in the grid. Rows are inferred.
`atom_scale`	0.18	Multiplier on each atom’s covalent radius.
`bond_radius`	0.07	Bond cylinder radius in Å.
`bond_color`	`(0.95, 0.1, 0.1)`	RGB bond colour in `[0, 1]`.
`background_color`	`"#f7f8f5"`	CSS colour for the viewport.
`title`	`""`	Unused; text should go in the surrounding page.
`subtitle`	`""`	Unused; text should go in the surrounding page.
`bond_cutoff_scale`	1.2	Bond search cutoff = `shell_target.pair_peak × bond_cutoff_scale`.
`max_bonds_per_atom`	4	Maximum bonds kept per atom before the angular filter.
`bond_length_tol`	0.10	Accept bonds within `±tol` of the ideal first-neighbour distance.
`ideal_angle_deg`	109.47	Ideal angle for the tetrahedral check (Si-like).
`bond_angle_tol_deg`	18.0	Maximum deviation of any pairwise angle from the ideal.
`tetrahedra` / `octahedra` / `cuboctahedra`	`None`	Single-group polyhedra config (one kind per scene). Dict of detector keys (`center_symbol`, `vertex_symbol`, `bond_length`, `bond_length_tol`, `ideal_angle_deg`, `angle_tol_deg`, `scale`).
`polyhedra_groups`	`None`	Multi-group polyhedra: list of dicts, each with a `kind` ∈ `{"triangles", "tetrahedra", "octahedra", "cuboctahedra"}` plus the single-group keys. Use for carbon-style sp²/sp³ blends where both triangles and tetrahedra must render in the same scene.

For a non-tetrahedral material, set ideal_angle_deg and bond_angle_tol_deg appropriately, or disable the angular filter by setting bond_angle_tol_deg to a large value (e.g. 90).

Multi-group polyhedra (carbon sp²/sp³)¶

For materials with a phase mix, pass a polyhedra_groups list so each group runs its own detector and renders with its own colour. Each group may also carry virtual_species=N to restrict detection to atoms flagged with that shell-target species index (see Supercell.generate(..., grain_sources=...)):

am.export_overview_html(
    "carbon_overview.html",
    cells,
    polyhedra_groups=[
        dict(kind="triangles",   center_symbol="C", vertex_symbol="C",
             bond_length=1.42, ideal_angle_deg=120.0, angle_tol_deg=22.0,
             virtual_species=0, scale=0.5,
             color=(0.25, 0.65, 0.35), opacity=0.85),   # sp² green
        dict(kind="tetrahedra",  center_symbol="C", vertex_symbol="C",
             bond_length=1.54, ideal_angle_deg=109.47, angle_tol_deg=22.0,
             virtual_species=1, scale=0.5,
             color=(0.20, 0.30, 0.75), opacity=0.65),   # sp³ navy
    ],
)

The triangles kind emits a 4-vertex motif [centre, j, k, l] rendered as three sub-triangles all anchored at the centre ((i, j, k), (i, k, l), (i, l, j)), so the mesh always touches the parent atom even at unequal bond lengths after relax.