v-ase-gui 0.0.5

v_ase: a Blender-style browser GUI and editor for ASE Atoms objects.

v_ase

v_ase is built around convenience and flexibility. It keeps the low-friction workflow of ase gui: open ASE-readable structures and trajectories directly from a terminal or Python session. It adds the flexibility of a Blender-like 3D visualizer: select, move, rotate, copy, delete, wrap, and export atoms directly in an interactive browser viewport.

The goal is to put the practical convenience of ASE and the hands-on flexibility of a 3D molecular editor in the same tool.

It is intended to replace:

ase gui FILE

with:

v_ase gui FILE

For example:

v_ase gui POSCAR
v_ase gui structure.vasp
v_ase gui movie.extxyz
v_ase gui relaxation.traj

The viewer opens locally in your browser. Middle mouse tumbles the camera, left click and box drag select atoms, G moves atoms, R rotates atoms, X/Y/Z lock axes, numeric input gives exact transforms, and trajectory files show playback controls for frame-by-frame movie inspection.

Highlights

• v_ase gui FILE command-line workflow for POSCAR, VASP, extxyz, traj, and other ASE-readable files.
• Python API for notebooks and scripts: from v_ase.visualize import view.
• Blender-like viewport interaction: middle-mouse orbit, shift-middle pan, wheel zoom, click/box selection, G move, R rotate, axis locking, numeric transforms, Enter, Esc, copy/paste/undo/delete.
• ASE constraint-aware editing and visualization: FixAtoms, FixCartesian, FixedLine, FixedPlane, FixScaled, and Hookean.
• Hookean constraints are visualized as threshold-aware hook/latch springs.
• Trajectory playback with live frame slider, FPS control, image export, and video export.
• Periodic bonds, element-pair cutoff tables, manual bond pairs, supercell preview, make_supercell(P) cell transform, and wrap atoms into cell.
• Custom extxyz atom type labels such as H_type5 are preserved for GUI type settings even when ASE cannot parse them as real elements.
• Export POSCAR, pickle, PNG image, WebM video, and Blender Python scene script.

Installation

From PyPI

python -m pip install v_ase-gui

From GitHub

git clone https://github.com/lgyEthan/v_ase.git
cd v_ase
python -m pip install --upgrade pip
python -m pip install -e .

No conda and no Node.js are required. Three.js is vendored inside the package.

Quick Start

Open a structure file:

v_ase gui POSCAR
v_ase gui structure.vasp
v_ase gui trajectory.extxyz
v_ase gui relaxation.traj

The direct file form also works:

v_ase POSCAR

Use from Python:

from ase.build import molecule
from v_ase.visualize import view

atoms = molecule("H2O")
edited = view(atoms)
print(edited.positions)

Useful CLI options:

v_ase gui structure.vasp --show-bonds
v_ase gui trajectory.extxyz --index :
v_ase gui trajectory.extxyz --index -1
v_ase gui POSCAR --output edited.vasp
v_ase gui POSCAR --no-block

Case 1: Selection, FixedLine, and FixedPlane

Selected atoms get yellow Blender-style outlines. Fixed atoms are dimmed, and selected FixedLine / FixedPlane atoms show geometric guides so the allowed movement is visible before committing coordinates.

FixedLine is shown as a Li ion moving along a carbon nanotube channel. The ion can slide parallel to the tube axis, but not leave the channel direction:

FixedPlane is shown as a Li ion moving over a Cu(111) surface. The motion is restricted to the surface-parallel XY plane, so it reads as surface diffusion rather than rotation:

Example:

from ase.build import molecule
from ase.constraints import FixAtoms, FixedLine, FixedPlane
from v_ase.visualize import view

atoms = molecule("H2O")
atoms.set_constraint([
    FixAtoms(indices=[0]),
    FixedLine(1, [1, 0, 0]),
    FixedPlane(2, [0, 0, 1]),
])

view(atoms)

When Apply constraints is enabled, move and rotate previews are projected onto the allowed line or plane and the backend commit uses atoms.set_positions(..., apply_constraint=True).

Case 2: Hookean Constraints

Hookean constraints are drawn with physical meaning. The rt threshold is placed in Angstroms along the constrained direction. Below the threshold the spring is inactive and shows slack. Beyond the threshold the latch engages and the spring becomes active.

Example:

from ase.build import molecule
from ase.constraints import Hookean
from v_ase.visualize import view

atoms = molecule("H2O")
atoms.set_constraint(Hookean(1, 2, rt=1.8, k=5.0))
view(atoms)

For trajectories, the Hookean graphic updates frame by frame, so inactive, near-threshold, and active states can be inspected as a movie.

Case 3: Rotate and Move

Transforms follow Blender-style keyboard flow:

G X 1.2 Enter
R Z 30 Enter

Supported behavior:

• G: move selected atoms.
• R: rotate selected atoms.
• X, Y, Z: lock transform axis in transform mode.
• Numeric input: exact displacement or angle.
• Left click or Enter: confirm.
• Esc: cancel.
• Optional move increment in Angstrom.
• Optional rotate increment in degrees.
• Rotate pivots: selection center, global origin, or unit-cell center.
• Optional bond-strain guard for rejecting excessive periodic bond distortion.

Here a ferrocene molecule is used to show a selected cyclopentadienyl ring rotating about the X axis while the rest of the molecule remains in place:

For axis-locked rotation, the colored axis guide is drawn through the active pivot. If the pivot is the origin, the axis passes through the origin; if the pivot is the selection center of mass, it passes through that COM.

Case 4: Bonds, Periodicity, and Supercells

Bonding can be automatic, element-pair based, or manually specified.

• Auto cutoff uses covalent radii and respects periodic minimum-image distances.
• Element-pair mode exposes pair-specific rcut rows.
• Manual mode accepts pair strings such as Na-Cl: 3.2 or 0-1, 1-2.
• Supercell preview shows repeated atoms and repeated unit-cell lines.
• Set Supercell as Cell converts the preview into real editable atoms.
• Cell Transform accepts a full integer make_supercell(P) matrix.

For 2D periodic supercell/twist workflows, the cell transform applies:

H' = P H

to every trajectory frame. Non-periodic axes are protected from accidental mixing, tilting, or repetition.

Case 5: Trajectories

Multi-frame Atoms lists and ASE-readable trajectory files can be played as a movie.

v_ase gui relaxation.traj
v_ase gui movie.extxyz --index :

Controls:

• frame slider updates live while dragging
• play/pause button
• Space: play or pause
• FPS control updates immediately while playback is running
• export image and export video

Case 6: Custom Atom Types in extxyz

Some workflows store type labels such as H_type5, O_type2, or Si_type1 inside the species column. ASE itself cannot treat these strings as chemical elements, so v_ase reads them as GUI atom types while mapping them internally to valid ASE base elements.

Example extxyz line:

H_type5 82.30128 7.97802 11.47478

In v_ase:

• ASE backend uses base element H.
• GUI labels remain H_type5.
• type-specific color variants are generated.
• Appearance radius controls are grouped by H_type5, O_type2, etc.
• Bond cutoff pair tables also use the preserved type labels.

Case 7: Export

From the right panel:

• Export POSCAR
• Export Pickle
• Export Blender
• Export Image
• Export Video

Blender export downloads v_ase_blender_scene.py:

blender --python v_ase_blender_scene.py

The generated scene keeps atoms and constraint graphics as editable Blender objects where practical.

Python API

from v_ase import view_edit, view_file

edited_atoms = view_edit(
    atoms,
    notebook=False,
    block=True,
    show_cell=True,
    show_axes=True,
    show_bonds=False,
    respect_constraints=True,
    allow_relax=True,
    return_mode="atoms",
)

view_file("trajectory.extxyz")

return_mode can be:

• "atoms": edited ASE Atoms
• "positions": edited Nx3 positions array
• "none": no return value

Controls

Input	Action
Left click	Select atom or confirm transform
Shift + left click	Add/remove selection
Left drag	Box select
Middle drag	Orbit viewport
Shift + middle drag	Pan viewport
Mouse wheel	Zoom
G	Move selected atoms
R	Rotate selected atoms
X, Y, Z	Align view in select mode, lock axis in transform mode
Number keys	Numeric transform input
Enter	Confirm transform
Esc	Cancel transform
Ctrl+C / Ctrl+V	Copy / paste atoms
Ctrl+Z / Ctrl+Shift+Z	Undo / redo
Delete / Backspace	Delete selected atoms
Space	Play/pause trajectory

Notes

• The local editor server binds to 127.0.0.1.
• Relaxation uses the calculator already attached to the Atoms object.
• POSCAR export stores structural data. Pickle export can include the ASE object; calculators may not always be pickleable.
• The bundled browser UI is local-first; no Node.js build step is required.