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v_ase 0.4.9 — desktop visibility, placement workflow and Blender water export · Changes

An ASE-native workspace for building, editing and visualizing atomic structures, trajectories and volumetric data.

Phosphorene nanoribbon manipulation

Trajectory navigation retains double-precision coordinates and committed edits through frame switches, animation output and scientific project exports. Animation export restores the current frame and selection; an empty colorscale target maps no atoms and does not block export. GUI and agent project saves both retain the document's mode and presentation. Agent revision snapshots wait for pending change notifications to finish. Renderer scale and atom radius remain independent.

Desktop editing improvements

Selection outlines remain visible when scientific overlays are off. The Objects Constraints checkbox independently controls fixed-atom marks and direction guides in both 2D and 3D. The right panel uses one vertical scroll path, including Add Molecules at enlarged Windows display scales.

Build → Add atoms → Atoms/Molecules keeps optional Relax placement in the same panel. Place first, relax if needed, then Finish or Cancel. Clear Relaxation Trajectory → Restore Starting Structure returns to the start of that run while keeping placed atoms; Cancel placement still removes the complete addition. Placement-region guides disappear when placement finishes and stay out of image and movie exports.

Blender export now includes the water surface as an editable mesh, with color, opacity, lighting, mesh finishing, periodic copies and trajectory frames. See Blender export. Windows publisher signing is documented separately; this release does not enable it.

Water surfaces and rendering quality

Style → Water draws detected H₂O as a continuous translucent surface while keeping ions and solids atomistic. Color, opacity, smoothing and lighting are adjustable; trajectories, images, movies/GIF and offline HTML share the same surface. Stored molecule IDs distinguish water from surface hydroxyls. A cached, indexed boundary mesh replaces water sphere/bond draw instances, including visible periodic copies. This is coordinate-derived visualization, not a new MD solver. The maintained PDF manual uses exact still frames for animation examples. See Water surface and run python examples/water_surface.py for a synthetic animated example. Render → Renderer → Quality now uses numeric atom/bond segments (8–128), with independent isosurface/water subdivision (0–8) and smoothing passes (0–100). Smoothing softens mesh ripples without multiplying triangles; high subdivision is checked against a mesh budget. Style → Isosurfaces owns the isovalue and surface definition; Style → Forces styles stored force vectors. Renderer surface controls are disabled when the corresponding surface is absent or hidden. Close-ups receive the requested geometry; screen-space detail and off-screen culling keep large scenes manageable. Surface work shows progress and supports Cancel / Esc; Revert quality and Lightweight make recovery immediate. See quality and performance. Water starts from a molecular-scale 2.0 Å kernel, a 0.63 threshold, subdivision 1 and 20 smoothing passes. Existing saved settings are retained.

Installation And Launch

macOS and Windows users can install the self-contained desktop app from GitHub Releases. It runs the same GUI with native Command/Ctrl shortcuts and file dialogs; Python installation is not required. Python and Jupyter remain available independently. Drag a desktop tab out to detach it into another window. Atom magnification, render composition and Undo history survive a different destination window size. Help → About this runtime shows the installed desktop version. Dropped structures offer trajectory, new-tab and new-window destinations. Saved .vase projects open immediately in their saved Edit/View mode and presentation, using a new tab when the current document has content. Each window closes independently; Windows Alt+F4 closes the active window, while explicit Quit checks all windows. The app icon now features the full atomic-bead castle with its small Pinocchio detail and no projecting red foundation board.

Desktop download (0.4.9)	Install and launch
Mac, Apple silicon	macOS 15+: open the DMG, drag v_ase to Applications, eject the disk image, then launch the Applications copy.
Mac, Intel	Same steps; choose Intel when About This Mac shows an Intel processor.
Windows, Intel/AMD x64	Windows 10/11, 64-bit: run the EXE installer, complete installation, then launch v_ase from Start.

The Mac downloads are Developer ID signed and Apple-notarized, with stapled tickets for the app and DMG. macOS may show its normal first-open confirmation for an internet download. The Windows build is not yet publisher-signed; after verifying its source and checksum, a SmartScreen prompt may offer More info → Run anyway. Do not disable OS protection. Step-by-step installation, ZIPs, checksums and troubleshooting. Maintainer build, signing and notarization steps are in the desktop build guide.

.vase is registered as a project type. To make double-click use v_ase, choose Get Info → Open with → v_ase → Change All on Mac, or Open with → Choose another app → v_ase → Always on Windows. You can also select v_ase for .vasp, .xyz and .cif; browse to the installed application if it is not listed. Extensionless POSCAR/CONTCAR can be opened using File → Open. Complete file-association instructions.

For the Python/browser/Jupyter installation:

python -m pip install v_ase-gui
v_ase gui POSCAR

Use v_ase gui for an empty workspace or --interactive to edit a file. Installation · First session · Supported formats · Troubleshooting

Explore

Work with	Guide
Atoms and molecules	Move · Rotate · Build
Periodic interfaces	Cells, matching, registry
Trajectories and fields	Analysis · Volumetric data
Figures and projects	Appearance · Export
AI agents	MCP setup · GUI/MCP comparison
Numerical methods	Validation · Source audit

Format	Use it to
`.vase` project	Resume editing with your structures, trajectory, camera and appearance preserved.
Project HTML	Share an offline interactive view that can also reopen as an editable v_ase project.
Export HTML View	Share a lightweight offline viewing copy, without editable project data by default.

For Project HTML, enable Include interactive rendered view in File → Project save settings. Saving and sharing guide.

Work With An AI Agent

You and an external agent edit the same live document. Connect MCP · Scene workflow · CLI compatibility

ChatGPT Chat setup · personal connection.

Human and external AI agent working in one live v_ase document

python -m pip install "v_ase-gui[mcp]"
v_ase mcp

60-run comparison: MCP completed 30/30 strict targets; GUI completed 24/30. Images, token usage and success criteria

Cu₈O₄ extension: both completed 10/10; MCP used 90.9% fewer median tokens. Images and methods

A natural-language request passing through an external AI Agent into the same live revisioned v_ase GUI

Exact atom edits from a natural-language request. Agent workflow · Bundled Skill

Natural-language pyridinic N3 graphene edit in the shared GUI

Edit Structures

Select atoms, then use G to move, R to rotate and S to scale coordinates. Editing guide · Controls

Build From Scratch

Define a cell and distribute atoms; refine overlaps with repulsion. Atomic distributions · ASE crystal builder

Building an amorphous structure from an empty v_ase document

Add Atoms

Set composition, density, placement and allowed regions. Insertion workflow

Oxygen distributed through a bulk-like Cu(111) insertion region

Add Molecules

Place rigid molecules around an existing structure. Molecular insertion

Rigid water molecules placed around edge- and basal-hydroxylated graphene-oxide layers

Rotate Selected Atoms

Rotate around an active atom, center of mass or explicit pivot. Pivot controls

Ferrocene pivot rotation

Build a phosphorene twist through successive selections and rotations. Worked examples

Cumulative phosphorene manipulation

Periodic Cells And Interfaces

Commensurate Cells

Find compatible 2D cells within declared strain and search limits. Same-lattice matching

Graphene hBN commensurate rotation

Match separate host and guest lattices. Host/guest workflow

Graphene and MoS2 host/guest common-cell search with a live angle plane

Rigid Translation

Map registry or relax a selected rigid component. Registry maps · Rigid relaxation

Periodic planar translation scan with current and optimum translations

Rigid planar translation trials without a precomputed colorscale map

Analyze Structures And Fields

Ordered Geometry

Click 2, 3 or 4 atoms deliberately in order for distance, angle or torsion. Marquee, label and Select all selections show a count without incidental geometry. Measurements

Property-based atom size

The Atom appearance controls include a global-size slider with a numeric input and an independent per-atom property radius mapping. Select an available numeric field, input range, minimum/maximum size multipliers and exponent. Enabling the mapping first reveals the field picker; it does not apply a placeholder property. Custom and charge presets fit the displayed frame's finite values, including signed data and the frozen atom scope. The mapping multiplies existing label and selected-atom sizing; a zero factor hides the glyph, not its scientific atom or bonds. Current and trajectory fits lock their resulting limits until fitted again. Field, scope, fit and export details.

Ordered distance angle and torsion measurement

Trajectories And Displacement

Scrub frames and inspect displacement against a reference. Trajectory analysis

Trajectory displacement analysis

Map Per-Atom Data

Color atoms by stored properties and display force vectors. Colorscales · Forces

Trajectory-wide force-magnitude colorscale with locked limits and matching Cartesian force vectors

Volumetric Fields

Inspect charge, potential and orbital grids as isosurfaces or planar sections. Isosurfaces · Planes · Combine fields

Signed isosurface threshold moving across a fixed volumetric distribution

Interactive hkl scalar-field plane clipped to the displayed cell

Radial And Pair-distribution Functions

Plot periodic RDFs or finite pair distributions with the appropriate normalization. RDF guide

Pairwise amorphous Cu-Zr RDF curves approaching the bulk limit

Constraints And Relaxation

Constrain physical motion using ASE constraints. Constraint guide

FixedLine

Restrict motion to a line. Details

FixedLine movement

FixedPlane And FixScaled

Restrict motion in Cartesian or fractional directions. FixedPlane · FixScaled

FixedPlane movement and guide plane

Hookean

Apply spring-like restraints. Details

Hookean constraint

Hookean motion

Relaxation

Reduce overlaps or optimize with a configured calculator. Repulsion · Run relaxation

Repulsive relaxation trajectory

Coordination Polyhedra

Show coordination faces, ligand atoms and connectors in 2D/3D, with per-group color and opacity. Polyhedra guide

IrO2 coordination polyhedra with independent colors and face opacity

Style Atoms, Bonds, And Rendering

Camera controls stay beside the viewport, with matching camera visibility in the Renderer panel. Render area and camera lock.

Control colors, radii and visibility by label or atom index. Appearance

View-mode label and appearance editing on Cu5O4

Choose Standard, Metal, Rubber or flat 2D rendering. Materials and rendering

Standard Metal and Rubber atom materials

Set bond topology and appearance by pair or exact atom indices. Bond controls

Pairwise Cu O bonds in a Cu2O(111) film on Cu(111)

Export And Save

Images and video · Render Area · Blender / OBJ / Rhino · Projects and presets

Python And Remote Systems

from ase.build import molecule
from v_ase import view

view(molecule("H2O"))

Python API · Jupyter · SSH / remote files

License And Citation

AGPL-3.0-or-later · Three.js MIT license · Cite v_ase

Metadata

Release files for v-ase-gui 0.4.9

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for v-ase-gui 0.4.9
File	Size	Uploaded
v_ase_gui-0.4.9.tar.gz	34.0 MB	Sep 28, 2026	Details

Built distribution (wheel)

Table of built distributions (wheels) for v-ase-gui 0.4.9
File	Interpreter	ABI	Platform	Reset
v_ase_gui-0.4.9-py3-none-any.whl 6.6 MB Sep 28, 2026	Python 3	none	any	Details

Total release size: 40.6 MB

Release files / v_ase_gui-0.4.9.tar.gz

Download URL	v_ase_gui-0.4.9.tar.gz
Size	34.0 MB
Tags	Source
SHA-256 checksum How to use checksums	`cb02e86c88b251a77028f0acc63e6745d2281b70f1202840b1fc28de75c0a24d`
BLAKE2b-256 checksum How to use checksums	`94ac61c06a2ffc445ed714b3372b4752e9d37cdcb128fcbe315aa983b9fbd97e`
Upload date	Sep 28, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/6.2.0 CPython/3.13.5`

Release files / v_ase_gui-0.4.9-py3-none-any.whl

Download URL	v_ase_gui-0.4.9-py3-none-any.whl
Size	6.6 MB
Tags	Python 3
SHA-256 checksum How to use checksums	`a7582e0acbb0611e5a5d15418dd20f98a0a6323f376dde198a6c831d25ba576a`
BLAKE2b-256 checksum How to use checksums	`9a164913df990ef065aa0d320bca0f64005cc713064352d8aec75944d92eef1b`
Upload date	Sep 28, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/6.2.0 CPython/3.13.5`