RENDER AREA 1920 x 1080

# Open a structure

Structures, trajectories, and .vase projects
Preparing workspace
Loading structure...
0% Estimating time remaining...
z coordinate A
0 1
Selected atoms
Add Atoms ACTIVE
Type
Label Position / Å
Insert
Atoms
Type Label Count
ASE molecules
Target g/cm³
Actual —
Molecule Label Count
Randomize molecular orientation Preserve molecular geometry during placement
Initial distribution
Spacing basis
Account for periodic boundaries Grid spacing Å

Random samples every accessible volume element with equal probability.

Insertion domain
Base domain Periodic unit cell
The complete unit cell is available. Add regions to include or exclude specific volumes.
x min x max y min y max z min z max
Region rule

Click or Shift-click region edges. Press G to move or S to scale the selection; rotation is disabled.

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 b / Å c / Å c/a α / degree Internal u
Fractional basis
N × 3 JSON coordinates
Loading ASE catalog Checking compatible materials and cell shapes...
Structure Info
Atoms- Selected 0 PBC-
Selection
Indices -
Elements -
Center (unwrapped)- Measure-
Displacement
Show vectors
Reference
Frame
Minimum image
Vector style
Vector scale 1.00x
Thickness 0.08 A
Color
No displacement data Load a trajectory with at least two frames.
Frames- Mapped- Mean / RMS- Maximum-
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

Mixed values are blank. Entering a value applies it to every selected plane.

No planar section Add one or more planes without transferring the full grid.
Field Arithmetic Linear combinations

Select compatible grids and assign coefficients such as +1, -1, -1.

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)
Max shift / axis / Å
Rigid translation mode ACTIVE

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 0.60x
Atom color scale Map a numeric value onto atom colors
Property
Colormap
Apply to
Reverse
Range CURRENT FRAME
vmin vmax
Contrast (gamma) 1.00

Values load only while this option is enabled.

Selected atoms None
Label
Material
Type Visible Select Label Color Radius Opacity Material
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
HOST Current structure
GUEST Select a layer or load a structure
Guest rotation / deg
Interlayer gap / Å

Guest minimum z minus host maximum z.

Apply residual strain to
Maximum strain / %
Maximum area ratio
Search & display
Maximum lattice index
Show preview atoms
Magnetic angle snap
Snap range / deg
Enable the workspace to search periodic in-plane matches.
SUGGESTED COMMON CELL -

Host, guest, and suggested common-cell vectors remain distinct while the guest rotates. Preview atoms and their boundary bonds are optional.

Constraints
Select atoms to edit constraints.
Apply constraints
FixAtoms
Directional
Vector
Bonding
Connectivity
Show Bonds
Periodic image bonds
Definition
Cutoff scale
On Label pair
Max / A

Enter zero-based atom index pairs. Valid rows update immediately.

Appearance
Style
Material
Thickness 0.25 A
Color
Bond color
Opacity 100%
Label-pair appearance
Label pair
Override global appearance
Style
Material
Color
Bond 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
On Label pair Distance / 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 ACTIVE

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 this persistent Render Area camera and crop.

Width Height
Follow viewport
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 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.
ANALYSIS Structural Distribution

## Shortcuts

Left click Select / confirm transform Shift + click Add or remove selection Left drag Box select Middle drag Orbit viewport Shift + middle drag Pan viewport Space Play or pause the selected timeline ← / →Previous or next frame in the selected timeline Tab / Esc Open the control panel while it is collapsed G Move selected atoms or Sun handle R Rotate selected atoms or Sun direction S Scale selected atom spacing or insertion regions about the pivot Sun source + G Move source and target together Sun target + G Move target only Sun handle + R Rotate target around source X / Y / Z Restore canonical +axis view; repeat from that exact pose for -axis X / Y / Z Lock the global Cartesian axis in G/R/S mode Enter Confirm transform Esc Cancel a transform, close a modal, or close the open control panel and return focus to the viewport Ctrl+C / V / Z Copy, paste, undo an edit or visual setting Delete Delete selected atoms

### Opening Files

Replace this tab Replace the current structure or trajectory. A .vase project also restores its saved visual setup. Add to trajectory Append every selected frame to the current movie while keeping this tab's visual setup. A .vase file contributes structures only. Open in new tab Create an independent structure tab. A .vase project restores its complete state in that new tab.

### Saving

ASE Pickle (.pkl) Current ASE Atoms data for Python: coordinates, labels, cell, PBC, constraints, arrays, and valid SinglePointCalculator results. Visual settings are excluded. Visual Settings (.json) Reusable display preset: bonds, appearance, camera, lighting, quality, and supercell preview. Atomic coordinates are not included. Personal default Automatic starting style for new structures and tabs on this OS account. It excludes coordinates, trajectory data, absolute camera placement, and per-atom overrides. v_ase Project (.vase) Complete working state: structures or trajectory, current frame, coordinates, cell, constraints, labels, cached results, and visual setup. HTML View / HTML Project Both use the image/video Render Area crop. HTML View is lightweight by default; HTML Project embeds complete .vase recovery by default.

### License

AGPL-3.0-or-later Copyright (C) 2026 v_ase contributors. This software is provided without warranty. View license · Get source