Visualization and styling

Appearance in v_ase is layered. Element defaults establish a readable scene, label-level settings style scientific groups, atom-index overrides handle exceptions, and an optional scalar colorscale maps numeric per-atom data. Projects and supported exports preserve the resolved result.

Label and atom identity

The Appearance table separates two concepts:

  • TYPE is the ASE chemical element used for atomic defaults and scientific operations.

  • LABEL is the user-visible grouping key used for selection, appearance, bonds, and pairwise analysis.

Changing a LABEL does not change the element. Changing TYPE is a scientific identity edit and should be deliberate. Labels may contain descriptive text that is not a valid chemical symbol.

Label-level appearance

Each label row can control:

  • visibility;

  • text label;

  • color;

  • radius scale;

  • opacity; and

  • material preset.

The global atom radius multiplies the label or per-atom relative scale. This changes only drawn sphere size; it never scales coordinates or the unit cell. Materials include the current standard, metal, and rubber-like presets and are used consistently by compatible geometry exports.

Per-atom overrides

In 0.2.35, selected base-atom indices can carry persistent color, relative radius, opacity, and material overrides. Apply controls are field-scoped: an opacity edit need not replace a custom color or material already assigned to the same indices.

Index overrides are appropriate for local defects or highlighted sites. Use a new label instead when the identity should remain meaningful after atom reordering or across trajectories with changing topology. Compatible frames can retain index overrides; incompatible indices are pruned rather than silently remapped.

Selected appearance affects bonds lets connected bond segments inherit selected atoms’ material/opacity behavior. It is enabled by default.

Numeric colorscales

Per-atom colorscales can use:

  • Cartesian x, y, or z coordinates;

  • stored force magnitude or components;

  • numeric ASE per-atom arrays;

  • already stored per-atom calculator results.

The GUI’s selected scope follows the live selection. Automation can attach an explicit index list to a selected-scope colorscale when the subset must remain fixed while the researcher changes the GUI selection.

Vector and compact tensor arrays expose a norm and components. Inspecting a stored force or property never runs the attached calculator. If a value is not already present, it is unavailable rather than being calculated as a side effect.

The current-frame fit resolves one value range and holds it during ordinary playback. A deliberate full-trajectory scan streams frames to obtain global extrema without allocating one complete value cube. Manual minimum/maximum, reverse, and gamma contrast remain available.

All Matplotlib colormaps installed in the active Python environment are available. Custom maps contain 2–64 positioned hexadecimal color stops and can use continuous interpolation or discrete bands. Their definition, resolved range, and playback behavior are stored in projects and standalone HTML.

Bonds

Bond visibility and bond appearance are separate from physical constraints or calculator connectivity.

Topology modes

  • Automatic mode infers contacts from element/covalent information and the active cutoff scale.

  • Label-pair mode uses explicit enabled/cutoff records for each label pair.

  • Manual bonds preserve explicitly selected pairs.

Periodic bonds can be shown across cell boundaries. Export uses the same minimum-image topology and, for skewed cells, ASE’s exact minimum-image resolution rather than component-wise fractional rounding.

Appearance

Global or label-pair settings can control:

  • cylinder or flat shape;

  • thickness;

  • material;

  • opacity; and

  • split-by-atom or custom color.

Version 0.2.35 adds independent thickness to each label-pair row. Pair records are preserved by .vase, project/view HTML, Blender, OBJ, and 3DM output. Visual bond cutoffs and repulsive-calculator contact distances are configured separately; a drawn bond is not an energy model.

3D and flat 2D rendering

3D draws spheres, bond geometry, lighting, materials, and depth. 2D flat turns atoms, bonds, vectors, cell edges, and constraint guides into a diagram-like view with adaptive outlines. Lighting and 3D material effects are disabled in flat mode so the result is determined by colors, opacity, width, and depth ordering.

The mode changes rendering only. Coordinates, selection, analysis, and saved structure remain the same.

Camera and projection

Orthographic projection is the default for new documents and avoids perspective size distortion. Perspective is useful when spatial depth is part of the composition. Axis alignment and toolbar orbit/tilt actions operate relative to the current camera orientation, so their screen direction remains predictable after arbitrary camera motion.

Camera navigation is not added to Undo/Redo history. Exact export composition belongs to the persistent Render Area described in Projects, rendering, and export.

Cell, axes, grid, and overlays

The unit cell has independent color, thickness, and material. Displayed supercell edges are deduplicated so shared boundaries do not darken. Axes, grid, measurements, constraint guides, insertion regions, stored force vectors, and analysis overlays can be included or excluded from the viewport and export composition as supported by each output.

display.supercell and visual translation are presentation settings. They do not build a physical repeated ASE object or change atom coordinates. See Periodic cells and interfaces before exporting a structure expected to contain repeated atoms.

Lighting, quality, and theme

Viewport quality controls include antialiasing and atom smoothness. Lighting supports the current modeling/studio choices, a user-controlled Sun, and shadowed rendering where available. A scene using only standard/rubber materials does not allocate the metal reflection environment.

The System interface theme follows the browser/OS preference. Explicit Light or Dark persists in that browser. Interface theme and viewport background are distinct settings, although explicit Dark selects a matching dark viewport for a coherent starting point.

Reusing a style

  • Export Preset saves portable, structure-independent visual settings.

  • Import Preset applies compatible settings to another document.

  • Set Current as Default stores an OS-user default for new structures/tabs.

  • Restore App Defaults requires confirmation and removes that personal visual default.

Personal defaults exclude coordinates, cell contents, trajectory data, absolute camera placement, and per-atom index overrides. Use a .vase project when the exact document state must be recovered.