v-ase-gui 0.0.44

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

v_ase

v_ase was developed for researchers who want the convenience of ASE and the flexibility of Blender in one atomistic workflow. ASE is convenient because structures and trajectories can be opened directly from Python or the terminal. Blender is flexible because objects can be selected, moved, rotated, inspected, and edited in a real 3D scene. v_ase combines those two strengths: an ase gui-style entry point for scientific files, plus direct 3D editing for atomic structures.

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. By default, v_ase gui FILE starts in a lightweight visualization mode for fast inspection, trajectory playback, bonding, supercell preview, appearance edits, wrapping, and export. Add --interactive when you want Blender-style atom editing: left click and box drag select atoms, G moves atoms, R rotates atoms, X/Y/Z lock axes, and numeric input gives exact transforms. For normal blocking CLI use, closing the browser tab or window finalizes the current session and returns control to the terminal.

Highlights

• v_ase gui FILE command-line workflow for POSCAR, VASP, extxyz, traj, and other ASE-readable files.
• Blocking CLI sessions behave like ase gui: the terminal waits while the browser tab is open, then continues after the tab/window is closed.
• Python API for notebooks and scripts: from v_ase.visualize import view.
• Lightweight OVITO-style inspection is the default CLI mode, keeping bonds, supercell, appearance, visual type labels, measurements, projection, wrapping, and export controls responsive for large structures.
• Orthographic projection is the default view, with perspective available from the View panel.
• Add --interactive for Blender-like atom editing: 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.
• Selection measurements: two selected atoms show distance, and three selected atoms show two distances plus the central angle.
• Calculator handling preserves existing ASE calculators, including SinglePointCalculator. The default lightweight visualization mode does not attach a fallback calculator; --interactive enables the soft repulsion fallback used for built-in relaxation.
• Torch is optional, not a package dependency. When torch is installed, the default repulsion calculator can use torch CPU or CUDA; otherwise it falls back to NumPy.
• ASE constraint-aware editing and visualization: FixAtoms, FixCartesian, FixedLine, FixedPlane, FixScaled, and Hookean. FixAtoms are rendered with a faceted, micro-etched material so they remain distinguishable without changing the element color. VASP selective-dynamics FixScaled masks are interpreted in fractional coordinates and displayed as cell-aware FixedPlane or FixedLine guides.
• Interactive constraint editing for selected atoms: apply or clear FixAtoms, FixedLine, and FixedPlane from the Constraints panel.
• Hookean constraints are visualized as threshold-aware hook/latch springs.
• Trajectory playback with live frame slider, FPS control, frame skip, image export, and video export.
• Interactive relaxation streams an optimization trajectory into the bottom timeline. Static single-structure sessions stay uncluttered until relaxation creates frames; loaded trajectory files keep their own movie timeline while a separate Relax row exposes the latest optimization path.
• Periodic bonds, element-pair cutoff tables, manual bond pairs, supercell preview, make_supercell(P) cell transform, and wrap atoms into cell. Auto and element-cutoff bonds are re-inferred for each trajectory frame.
• Custom extxyz atom type labels such as H_type5 are preserved for GUI type settings even when ASE cannot parse them as real elements.
• LAMMPS lammpstrj and .data integer types stay visible as labels. Valid integer type ids are also used as atomic numbers for color/radius distinction; out-of-range ids fall back to ASE-valid H while preserving the raw label.
• Appearance label edits keep row order stable. Labels with element prefixes such as O_bridge automatically update the TYPE dropdown and default radius.
• Export POSCAR, pickle, PNG image, WebM video, and Blender Python scene script. Blender export includes viewport camera, unit cell, bonds, and smooth atoms.

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.

If pip reports ERROR: Error while checking for conflicts after saying Requirement already satisfied: v_ase-gui, the package is already installed; the failure is usually caused by a different installed package with broken metadata (version=None) in that Python environment. Use:

python -m pip install --upgrade pip
python -m pip install --upgrade --force-reinstall --no-deps v_ase-gui
python -m pip check

If pip check still crashes, create a clean virtual environment or repair the package with invalid metadata before installing scientific packages into that environment.

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 ABCD --format POSCAR
v_ase gui ABCD --format XDATCAR
v_ase gui ABCD --format vasprun.xml
v_ase gui ABCD --format lammpstrj
v_ase gui ABCD --format data
v_ase gui POSCAR --interactive
v_ase gui POSCAR --output edited.vasp
v_ase gui POSCAR --no-block

--format forces the input reader when the filename is ambiguous. It accepts common aliases such as POSCAR, XDATCAR, vasprun.xml, lammpstrj, traj, xyz, extxyz, and data, plus raw ASE format names.

Example Structures

The README and demo structures can be regenerated from source:

python examples/readme_scenes.py

This writes single-structure .traj files under examples/readme_scene_assets/. Open them with normal v_ase commands:

v_ase gui examples/readme_scene_assets/fixedline.traj --show-bonds
v_ase gui examples/readme_scene_assets/fixedplane.traj --show-bonds
v_ase gui examples/readme_scene_assets/hookean.traj --show-bonds
v_ase gui examples/readme_scene_assets/ferrocene.traj --show-bonds
v_ase gui examples/readme_scene_assets/showcase.traj --show-bonds

Constraint guide design variants can be inspected without starting the app by opening docs/design/constraint_guides_preview.html in a browser. It compares five always-visible FixedLine marker candidates and five FixedPlane marker candidates on one constrained structure.

Case 1: Selection, FixedLine, and FixedPlane

Selected atoms get yellow Blender-style outlines. FixAtoms entries keep their atom color but switch to a faceted, micro-etched material, so they read as immobile without looking selected. FixedLine and FixedPlane guides stay hidden until the constrained atom is selected, then appear as a thin fading axis or a translucent CAD-style plane. When multiple FixedPlane atoms are selected, each atom keeps its own compact local plane marker so the constraint never looks anchored at the selection COM. Show Overlays can hide all of these guides for a clean structure view.

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 guide is an unbounded plane field through the selected atom, not a finite patch, so the surface-parallel XY constraint reads as diffusion over the surface 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. The example below uses a 9-atom ethanol-like adsorbate on Cu(111). The O-H group moves with oxygen while the C-O bond is pulled, so the graphic reads as a bond-retention constraint rather than an arbitrary long-range tether.

Example:

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

atoms = molecule("H2O")
atoms.set_constraint(Hookean(0, 1, rt=1.15, 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
• Skip control advances by skip + 1 frames per playback tick while preserving the selected FPS
• export image and export video

Case 6: Custom Atom Types in extxyz and LAMMPS

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.

For LAMMPS dump/data files, integer type ids are kept as GUI labels. If the type id is a valid atomic number, v_ase uses that element internally for default colors and radii:

• type=1 -> backend H, GUI label 1
• type=8 -> backend O, GUI label 8
• type=14 -> backend Si, GUI label 14

If a type id is outside the periodic table range, v_ase keeps the raw label and uses ASE-valid H internally so the structure can still be opened.

Case 7: Default Repulsion Calculator

If an input Atoms object already has a calculator, v_ase preserves and uses that calculator. This includes SinglePointCalculator results loaded from trajectory-style files and any calculator attached by the user before calling view().

In the default lightweight visualization mode, v_ase does not attach a fallback calculator and does not show calculator device controls. This keeps large-file inspection focused on rendering, bonding, supercell preview, wrapping, and export.

In --interactive, if no calculator is attached, v_ase installs a default soft repulsion calculator. The model applies harmonic pair repulsion below covalent-radius contact thresholds, so Relax can remove close contacts without requiring an external calculator. The top-right calculator controls are enabled only for this default calculator:

• DEVICE: CPU by default; CUDA is available when torch and CUDA are available in the current Python environment.
• CPU: number of CPU threads for torch CPU execution. The default is 4, capped by the machine CPU count.

Torch is intentionally not listed as a required dependency. If torch is absent, the repulsion calculator uses a NumPy implementation. Installing torch can make the default repulsion model faster, especially with CUDA hardware, but other ASE calculators remain fully user-defined and are not affected by these controls.

The repulsion calculator is also available as a normal ASE calculator from the public Python API:

from v_ase.calculators import RepulsionCalculator

atoms.calc = RepulsionCalculator(device="cpu", cpu_threads=4)

Convenience aliases are also provided for scripts that prefer shorter or compatibility-oriented imports:

from v_ase import RepulsionCalculator
from v_ase.calculator import RepulsionCalculator
from v_ase.repulsion import RepulsionCalculator

Conditioner is kept as an alias for the same calculator class, matching the reference model naming while still behaving like an ASE Calculator.

During relaxation, structure updates stream to the browser. In --interactive, if atoms are moved while relaxation is running, the current relaxation is stopped and restarted from the edited coordinates. The default visualization mode keeps atom editing and repulsion-calculator controls out of the UI.

Case 8: 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. Atom objects reuse shared sphere meshes by radius/color so large exports avoid duplicating mesh geometry for every atom.

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. If no calculator is attached, v_ase uses its default soft repulsion calculator.
• Torch is optional. It is never required by pip install v_ase-gui, but when available it can accelerate the default repulsion calculator on CPU or CUDA.
• 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.