v_ase

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0.4.2

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MODE SELECT

ENERGY -

FMAX -

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Find a command or section

Scene

Build

Analyze

Render

Add Atoms

Type Label Position / Å

Insert

Atoms

Initial distribution

Random samples every accessible volume element with equal probability.

Insertion domain

Base domainPeriodic unit cell

The complete unit cell is available. Add regions to include or exclude specific volumes.

Accessible volume —

Allow regions are combined; Reject regions are subtracted.

Placement seed

Placement relaxation

Temporarily fix existing atoms Enforce Allow and Reject regions during relaxation

Atoms remain inside the Allow union and outside every Reject region. Rigid molecules use their ASE template origin.

Keep inserted atoms selected

Minimum image convention for regions and repulsion

Shared Relaxation settings Calculator, cutoff, device, fmax, and steps are controlled in Structure > Relaxation.

Ready to place atoms

Bulk crystal ase.build.bulk

ASE

Generate a periodic crystal from ASE reference data or an explicit prototype. Building replaces the active structure and trajectory; Undo restores them.

Formula Crystal structure Cell shape

Choose a compatible ASE reference element or type a custom formula.

a / Å

Loading ASE catalog Checking compatible materials and cell shapes...

Inspect

Structure Info

Atoms- Selected0 PBC-

Selection

Indices - Elements - Center (unwrapped)- Measure-

Displacement

Show vectors

Reference

Minimum image

Vector style

Vector scale 1.00x

Thickness 0.08 A

Color

No displacement data Load a trajectory with at least two frames.

Forces

Show vectors

Vector style

Length scale 1.00 A per eV/A

Thickness 0.08 A

Color

Force vectors hidden Enable Show vectors when per-atom forces are available.

Volumetric Data

CHGCAR, LOCPOT, PARCHG, ELFCAR, Cube, and XSF scalar fields.

Import precision

Applied while reading the next scalar field. FP64 uses twice the grid memory.

No scalar field loaded.

Dataset

Isosurface Thresholded 3D field

Show isosurface

Surface

Isovalue

0 voxel distribution 1

Mesh detail

Field smearing σ (voxels)

Mesh smoothing passes

Smearing filters only the displayed field. Mesh smoothing refines the extracted surface. Set either value to 0 to preserve that stage exactly.

Surface colors

Isosurface opacity 0.72

Planar Sections Cell-clipped field maps

In View and Edit modes, set the reciprocal-space normal and signed distance from the grid origin here. Edit mode also supports viewport G and R transforms.

Panel controls are available in both modes.

Plane 1 1 selected

Visible

Dataset

(h k l)

Distance from grid origin / Å

Settled resolution

Colormap

Reverse colormap

Color range

Minimum Maximum

Plane opacity 0.88

No planar section Add one or more planes without transferring the full grid.

Ready Grid values remain on the local v_ase server.

Radial / Pair Distribution

Cutoff / Å

Bins

Pair curves

Ready Bulk g(r) for 3D periodic cells; finite pair probability for non-periodic structures.

Rigid Translation

Move the selected atoms as one rigid component in a periodic (hkl) plane. The cell, host atoms, and selected internal coordinates remain fixed.

Degrees of freedom

Plane (h k l)

Rigid translation mode

Activate first, then use G or optimize the shared two-coordinate translation.

fmax / eV Å⁻¹ Steps

Mode inactive Select the movable atoms and activate the plane.

Optional translation map

The plane is shown immediately. Calculate only when a sampled geometry score is needed.

Metric

Grid

Map not calculated Activate translation mode to inspect the physical plane and cell boundary.

Viewport

Interface theme

System follows the browser chrome and keeps the structure canvas white. Dark switches both interface and canvas.

Projection

Background

Viewport rendering

Anti-aliasing

Atom smoothness

Atomic scale

px/Å

Viewport span: -- Å × -- Å

Unit Cell

Color Thickness / Å Material

Axes

Grid

Show Overlays

Appearance

Atom radius

All atoms · size 0.60x

Property radius mapping Multiply manual sizes by a stored per-atom value

Color

Atom color scale Map a numeric value onto atom colors

Atom types

Surface

Apply surface to

Material Opacity

Changes apply to the chosen types.

Selected atom properties

Selected atoms None

Label Material Color Opacity

Radius scale 1.00x

Match bond material & opacity

Cell & Replication

Unit cell matrix / Å

PBC x y z

Sets Cartesian cell vectors without moving existing atoms.

Replicate cell

Translate atoms

Offsets displayed atoms after cell replication. ASE coordinates and the unit cell remain unchanged.

Cell Transform

Switch to Edit to apply a physical cell transformation.

Scene fields

Select a dataset or plane to edit its surface, visibility, or map properties.

Vector layers

Displacements Show layer

Stored forces Show layer

Transform selection / Match periodic cells

Rotate pivot

Move increment / A

Rotate increment / deg

Exact selection rotation

Axis Angle / deg

Commensurate atoms Periodic in-plane matching about global Z

Constraints

Select atoms to edit constraints.

Apply constraints

FixAtoms

Directional

Vector

Coordination Polyhedra

Build faces around specified centers and surrounding atoms. Cutoffs are independent of displayed bonds.

Show polyhedra

Atoms with polyhedra

Complete periodic ligand atoms

Center–ligand connectors

Respect hidden centers

Rule

Choose centers and a ligand cutoff, then apply a rule.

Bonding

Connectivity

Show Bonds

Periodic image bonds

Definition

Cutoff scale

On Label pair r_cut / Å

Appearance

Style

Material

Thickness 0.25 A

Color

Opacity 100%

Label-pair appearance

Label pair

Override global appearance

Style

Material

Thickness 0.25 A

Color

Opacity 100%

Relaxation

Repulsion calculator

Device

CPU threads

Cutoff definition

Reference radii

Contact-distance multiplier

Set all pairs / Å

Pairwise cutoff Independent from displayed bonds

OnLabel pairDistance / Å

Strength

Each enabled label pair repels below its own distance, even when that pair is not drawn as a bond. Pair force is zero at and beyond the cutoff.

fmax steps

Relaxation mode

Optimization frames use a separate movie timeline until this mode is closed.

Renderer

Lighting

Mode

Sun brightness

Sun source XYZ

Sun target XYZ

Quality

Atom smoothness

Anti-aliasing

Output frame & scale

Width Height

Framing

Output scale px/Å

Overlays, background & render area

Include grid Include axes Include cell

Background

Follow viewport

Image

Format

Uses the Renderer frame, lighting, quality, and overlay settings above. Export opens a detached preview before writing.

Video

Container

Frames per second

Interpolation

Minimum image convention

Uses the Renderer frame, lighting, and overlays. Video backgrounds are opaque white.

Interactive HTML

Embed editable project

The standalone view works offline. An embedded project permits restoration in v_ase but increases file size. Export previews the exact poster and crop before writing.

Export

Structure data

3D scene

Blender atoms

Include unit cell

Rendered media

Image, video, and HTML use this persistent Render Area camera and crop.

v_ase Project

Save the complete editable structure, trajectory, constraints, labels, camera, and visual setup.

Visual Settings

Appearance, bonds, lighting, viewport, display replication, visual translation, and render quality only. Atom coordinates and cell contents are not included.

Personal default Using v_ase defaults

Portable preset

Rhino 3DM Editable instanced atoms and bonds, optional cell layers, and saved camera views in Angstrom units. Requires the optional rhino3dm package.

OBJ Bundle Dependency-free static geometry. The ZIP keeps OBJ mesh, MTL colors, and a camera/metadata JSON sidecar together.

HTML View A self-contained offline 3D viewer using the exact Render Area crop. Lightweight view-only is the default; complete .vase recovery is optional.

ASE Pickle Current ASE structure, labels, cell, constraints, arrays, and valid single-point results. No visualization settings.

v_ase Project One Save Project dialog creates compact .vase by default. Include the interactive rendered view to switch the output visibly to a complete HTML project.

Visual Settings A reusable appearance preset for other structures; coordinates are never included.