v_ase

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0.2.20

MODE SELECT

ENERGY -

FMAX -

CALC -

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

Repulsive placement

Temporarily fix existing atoms Allow inserted content to leave the region domain

Keep inserted atoms selected

Cutoffs Scale

Device CPU threads

Compute resources apply to this full repulsion relaxation.

Strength fmax Steps

Minimum image convention for regions and repulsion

Ready to place atoms

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.

Planar Translation

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

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 or operating-system appearance.

Projection

Background

Atom & bond display

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 0.60x

Atom color scale Map a numeric value onto atom colors

Selected atoms None

Label

Material

Type Visible Select Label Color Radius / A Material

Build with ASE

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...

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

Transform & Cell Match

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

Bonding

Connectivity

Show Bonds

Periodic image bonds

Definition

Cutoff scale

Appearance

Style

Thickness 0.25 A

Color

Relaxation

Repulsion calculator

Device

CPU threads

Cutoff definition

Cutoff scale

Strength

Repulsion starts below the ASE covalent-radius sum multiplied by the scale and is zero at or above that distance. This is not a hard minimum separation.

fmax steps

Relaxation mode

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

Export

Structure data

3D scene

Blender atoms

Include unit cell

Rendered media

Image, video, and HTML use one shared camera crop. Preview Area is the exact composition for all three.

Width Height

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 Preview 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 Save the complete working state as compact .vase, or as an HTML Project with embedded .vase recovery enabled by default.

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

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