atomode’s visualisers come in two complementary flavours:
Jupyter widgets (
plot_g3,plot_g3_compare,plot_g2,plot_g2_compare,view_structure) render directly in a notebook with live sliders, checkboxes, and species-pair dropdowns.Self-contained HTML exporters (
export_trajectory_html,export_g3_html,export_g2_html,export_g2_compare_html,export_overview_html) bake a single structure, trajectory, or group of structures into one HTML file that can be opened in any browser or embedded in Sphinx docs via<iframe>. No server, no build step. The pages load Three.js from a CDN at view time.
A static PNG / MP4 / GIF exporter (plot_structure) and the matplotlib
loss-history plot (plot_shell_relax) are also documented below.
At a glance¶
| Method | Output | Purpose |
|---|---|---|
cell.view_structure() | Jupyter widget | 3D WebGL atom viewer. Polyhedra (triangles / tetrahedra / octahedra / cuboctahedra) drawn by default for recognised materials, with live sliders for radial + angular tolerance; bonds optional; perspective / orthographic toggle. |
cell.plot_structure(output=...) | MP4 / GIF / PNG | Rotating movie or static still for publication figures. |
cell.export_trajectory_html(path) | HTML file | Play back the shell-relaxation trajectory in 3D, colour-coded by per-atom spring energy; supports single- or multi-group polyhedra overlay (e.g. sp² triangles + sp³ tetrahedra in the same carbon cell). |
atomode.export_overview_html(path, cells) | HTML file | Multiple structures rendered side-by-side with synchronised rotation; same polyhedra_groups= support as the trajectory exporter. |
cell.plot_shell_relax() | matplotlib figure | Loss-history plot from the last generate() or shell_relax() call. |
cell.plot_g2() | Jupyter widget (iframe) | Single-cell g(r) viewer with species-pair dropdown + overlay-all-pairs mode. |
cell.export_g2_html(path) | HTML file | Standalone g(r) viewer with species-pair dropdown + overlay-all-pairs. |
atomode.plot_g2_compare(cells) | Jupyter widget (iframe) | Overlaid g(r) from multiple supercells, stacked with inline per-series labels. |
atomode.export_g2_compare_html(cells, path) | HTML file | Standalone version of the compare viewer for docs embedding. |
cell.plot_g3() | Jupyter widget | Browse the measured g3 as a 2D heatmap with a radial profile. |
cell.plot_g3_compare() | Jupyter widget | Side-by-side comparison of the supercell against a target. |
cell.export_g3_html(path) | HTML file | RdBu heatmap + pair profile g(r) of the measured g3 (single triplet or all-triplets grid). |