Size atoms from a numeric property

Open Style → Atoms → Property radius mapping. This controls the drawn sphere size; it does not change coordinates, chemistry, bonds, or the cell. It can be used alongside the independent property colorscale.

  1. Open the mapping section and choose an available numeric field. The field list distinguishes coordinates, stored ASE arrays, and calculator results already present in the document. An unavailable field cannot be enabled.

  2. Choose All atoms or freeze the current selected base-atom indices. A frozen scope does not follow later selection changes. Deleting, duplicating or materializing an editable supercell remaps that scope by atom provenance. During playback, indices persist across atom-count and element changes; an absent index is ignored in that frame and resumes when it appears again.

  3. Choose identity or absolute-value transform. Fit current frame scans the displayed frame; Fit trajectory scans the loaded compatible frames without requiring a full trajectory cube in browser memory. Missing values are reported. Either fit locks its limits until you fit again. Alternatively, enter manual limits.

  4. Set minimum and maximum multipliers and the exponent, then enable the mapping. Invalid or incomplete entries stay as visible drafts without changing the last valid rendering.

For a transformed value :math:x, limits :math:x_{\min},x_{\max}, and exponent :math:p, the normalized fraction is

\[t=\operatorname{clamp}\!\left(\frac{x-x_{\min}}{x_{\max}-x_{\min}},0,1\right), \qquad f=f_{\min}+(f_{\max}-f_{\min})t^p.\]

The effective sphere radius is the existing label/per-atom radius times the global-size multiplier times :math:f. Missing or non-finite values and atoms outside the frozen scope use :math:f=1. A zero factor hides the sphere glyph but does not delete the atom or its bonds. A positive final-radius request for such an atom is rejected until its mapping is changed or disabled.

The occupancy preset uses a manual :math:[0,1] domain. Custom and charge presets fit the finite values of the selected field and scope, including signed values when the identity transform is used. Absolute-value fitting applies the transform to the actual values before finding extrema.

When an optimizer frame is displayed, coordinate fields come from those displayed positions. A per-atom property not recorded for that optimizer frame uses neutral factor 1; v_ase does not borrow values from an unrelated loaded trajectory frame.

The mapping is part of a .vase project. Frame-specific mapped sizes are also used by image/video rendering, offline HTML, and supported geometry exports. Before publishing a scientific figure, inspect its rendered image or animation rather than relying on an export-success message alone.

Atom appearance · Scalar colors · Save projects · Render images