Metadata-Version: 2.4
Name: v_ase-gui
Version: 0.1.9
Summary: A local 3D viewer, editor, and analysis workspace for atomistic structures, trajectories, and DFT fields.
Author: v_ase contributors
License-Expression: MIT
Project-URL: Homepage, https://github.com/lgyEthan/v_ase
Project-URL: Repository, https://github.com/lgyEthan/v_ase
Project-URL: Issues, https://github.com/lgyEthan/v_ase/issues
Keywords: ase,atomistic-simulation,materials-science,molecular-visualization,trajectory-analysis,density-functional-theory,scientific-visualization
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Topic :: Scientific/Engineering :: Chemistry
Classifier: Topic :: Scientific/Engineering :: Physics
Requires-Python: >=3.10
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: ase>=3.23
Requires-Dist: fastapi>=0.110
Requires-Dist: uvicorn[standard]>=0.29
Requires-Dist: numpy>=1.24
Requires-Dist: scipy>=1.10
Requires-Dist: scikit-image>=0.23
Requires-Dist: plotly>=5.24
Requires-Dist: imageio-ffmpeg>=0.5
Requires-Dist: Pillow>=10
Requires-Dist: requests>=2.31
Provides-Extra: dev
Requires-Dist: pytest>=8; extra == "dev"
Requires-Dist: playwright>=1.40; extra == "dev"
Requires-Dist: build>=1.2; extra == "dev"
Requires-Dist: twine>=5; extra == "dev"
Provides-Extra: rhino
Requires-Dist: rhino3dm>=8.0; extra == "rhino"
Dynamic: license-file

<p align="center">
  <img src="https://raw.githubusercontent.com/lgyEthan/v_ase/main/docs/assets/v_ase-logo.png" width="720" alt="v_ase logo">
</p>

# v_ase

[![PyPI version](https://img.shields.io/pypi/v/v_ase-gui.svg)](https://pypi.org/project/v-ase-gui/)
[![Python versions](https://img.shields.io/pypi/pyversions/v_ase-gui.svg)](https://pypi.org/project/v-ase-gui/)
[![License](https://img.shields.io/badge/license-MIT-green.svg)](LICENSE)

`v_ase` brings ASE's convenient terminal and Python workflow together with
direct, Blender-style 3D structure editing. Open a structure or trajectory
with one command, inspect and measure it in a local browser, edit it manually
or let an external AI agent translate a natural-language request into verified
structure operations, then export publication images, videos, and reusable 3D
scenes.

![Phosphorene nanoribbon manipulation](https://raw.githubusercontent.com/lgyEthan/v_ase/main/docs/assets/github/readme_phosphorene_twist.gif)

The animation builds a phosphorene nanoribbon twist one ridge at a time. Each
amber box selects the remaining ridges, the Transform controls apply an exact
X-axis rotation, and the sequence reaches a 13.85 degree twist before the
completed structure is inspected from above and below.

| Work directly in v_ase | Included |
| --- | --- |
| Structures and trajectories | ASE-supported formats, live timeline, per-frame bonds |
| Geometry editing | Ordered selection, `G` move, `R` rotate, axis locks, numeric input |
| Scientific inspection | Distances, angles, torsions, displacement vectors, RDF, constraints |
| Volumetric fields | VASP and Cube/XSF grids, isosurfaces, density differences |
| Figure preparation | Appearance, bonds, lighting, exact preview, image/video export |
| Reproducible sessions | Self-contained `.vase` projects and reusable visual settings |
| Agent workflows | Semantic state/command API and a vendor-neutral AI skill |

## Quick Start

Install from PyPI:

```bash
python -m pip install v_ase-gui
```

Or install the current GitHub source:

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

Start an empty workspace or open a file:

```bash
v_ase gui
v_ase gui FILE
```

Examples:

```bash
v_ase gui POSCAR
v_ase gui trajectory.extxyz
v_ase gui relaxation.traj
v_ase gui project.vase
```

The default **View** mode is optimized for visualization, trajectories,
measurement, appearance, bonds, supercells, and export. Use the top-bar mode
switch or start directly in **Edit** when atomic coordinates must change:

```bash
v_ase gui structure.vasp --interactive
```

No Node.js installation or hosted account is required. Closing the v_ase
browser document releases the blocking terminal process.

## Common Tasks

| Goal | Action |
| --- | --- |
| Inspect a structure | Middle-drag to orbit, wheel to zoom, left-click to select |
| Edit coordinates | Enter **Edit**, select atoms, press `Esc` to focus the viewport, then use `G` or `R` |
| Measure geometry | Select 2, 3, or 4 atoms in the required order |
| Play a trajectory | Use the bottom timeline or `Space`; FPS and Skip update live |
| Plot an RDF | Use **Analysis > Radial Distribution Function** |
| View a charge or potential grid | Open CHGCAR/LOCPOT/PARCHG/Cube/XSF, then use **Analysis > Volumetric Data** |
| Style a figure | Use **Structure > Appearance/Bonding** and **View** |
| Repeat or wrap a cell | Use **Structure > Cell & Replication** |
| Save the whole session | Use **Export > v_ase Project** and choose compact `.vase` or browser-ready HTML |
| Reuse only the visual style | Use **Export > Save Settings** |
| Share an offline 3D view | Use **Export > Rendered media > HTML View**; the lightweight view-only file is the default |
| Hand the scene to an AI | Provide the bundled agent skill; the agent starts the CLI/API session itself |

> **Viewport tip:** after selecting atoms, press `Esc` to close the control
> panel before using `G` or `R`. The selection is preserved and keyboard focus
> returns to the 3D viewport.

## Work With An AI Agent

v_ase is the scientific application between you and an external AI Agent. It
does not interpret natural language itself: the Agent learns v_ase from the
bundled [v_ase Skill](#agent-setup), then controls the exact structure through
the CLI/API while you see the result in the normal GUI.

![Human and external AI agent working in one live v_ase document](https://raw.githubusercontent.com/lgyEthan/v_ase/main/docs/assets/github/readme_ai_collaboration.png)

1. **You → Agent:** describe the scientific result in ordinary language.
2. **Agent → v_ase:** the Agent sends exact, structured CLI/API commands.
3. **v_ase → you:** v_ase applies and validates the operations, then displays
   the live 3D document in the GUI.
4. **v_ase → Agent:** v_ase returns exact atoms, settings, and the current
   revision. GUI edits enter the same document, so the Agent continues from
   your latest work instead of overwriting it.

For example:

> From this pristine 6 x 6 graphene sheet, remove the carbon nearest the cell
> center, convert its three nearest neighbors to pyridinic nitrogen, add a
> `Li_site` atom 2.15 A above the vacancy, use a clean
> oblique studio-shadow view, and render a 4K image.

The agent preserves the three substituted sites as distinct `N_pyridinic` labels
and reports every committed edit to the same GUI session.

![Natural-language pyridinic N3 graphene edit](https://raw.githubusercontent.com/lgyEthan/v_ase/main/docs/assets/github/readme_ai_edit.gif)

The agent reads atom identities and coordinates directly instead of repeatedly
guessing from screenshots. This can reduce token use while preserving exact
indices, coordinates, and labels. The example assets are generated from
`ase.build.graphene`:

- [source graphene CIF](examples/readme_scene_assets/ai_graphene_source.cif)
- [intermediate pyridinic N3 CIF](examples/readme_scene_assets/ai_pyridinic_n3_graphene.cif)
- [final N3/Li-site CIF](examples/readme_scene_assets/ai_pyridinic_n3_li_graphene.cif)
- [ASE trajectory preserving labels](examples/readme_scene_assets/ai_pyridinic_n3_li_graphene.traj)

Codex, Claude Code, and GitHub Copilot names and marks belong to their
respective owners. They identify compatible external clients in the diagram;
no affiliation or endorsement is implied.

## Structure Manipulation

Use **Edit** when atom coordinates must change. Selection, measurement,
appearance, bonds, replication, wrapping, visual translation, and export
remain available in the default **View** mode.

### Select

- Left-click selects one atom; `Shift` + click extends or removes selection.
- Left-drag draws a visible selection box.
- Appearance rows select complete label groups without merging distinct labels.
- Ordered single-atom selections are retained for geometry measurement.

### Move

Press `G` after selecting atoms. Lock the move with `X`, `Y`, or `Z`, type an
exact displacement in angstrom, then confirm with left-click or `Enter`.
Configured ASE constraints remain authoritative when **Apply constraints** is
enabled.

### Rotate

Press `R` after selecting atoms. Choose **Selection COM**, **Active atom (last
selected)**, **Origin**, or **Unit-cell center** as the pivot, lock an axis if
needed, and enter an exact angle. To rotate around a particular atom, select
the moving atoms first and Shift-select the pivot atom last. For a panel-driven
edit, use **Structure > Transform > Exact selection rotation** to choose the
axis and angle, then click **Rotate Selection**. Both methods honor the current
constraint and undo settings. Every active rotation shows:

- the rotation axis through the chosen pivot;
- a neutral line fixed at the direction where the operation started;
- an amber line that follows the current structure;
- cyan candidate lines only when the commensurate guide is enabled.

#### Ferrocene: Use Fe As The Active Pivot

![Ferrocene pivot rotation](https://raw.githubusercontent.com/lgyEthan/v_ase/main/docs/assets/github/readme_ferrocene_pivot.gif)

Select the upper cyclopentadienyl ring first, then Shift-select Fe last. With
**Active atom (last selected)** enabled, Fe remains fixed at the exact rotation
pivot:

1. `R`, `Z` rotates the ring around the axis through Fe.
2. `R`, `X` folds the same ring around an X axis through Fe.

The active atom can be any selected atom; it does not need to coincide with the
global origin or the selection center.

#### Phosphorene: Build The Twist One Edit At A Time

![Cumulative phosphorene manipulation](https://raw.githubusercontent.com/lgyEthan/v_ase/main/docs/assets/github/readme_phosphorene_twist.gif)

The animation records a sequence of normal v_ase edits:

1. Keep the first puckered ridge fixed. Left-drag the visible amber box from
   the **second ridge through the end** of the ribbon, then release to commit
   the yellow outlined selection.
2. Open **Structure > Transform**, keep **Selection COM**, choose axis `X`,
   enter `1.538889` degrees, and click **Rotate Selection**.
3. Close the panel, left-drag a new box from the **third ridge through the
   end**, enter the same exact angle, and rotate again from the edited
   coordinates.
4. Continue advancing the box-selection boundary by one 12-atom ridge. After
   9 rotations, the final ridge is rotated by exactly 13.85 degrees.
5. Orbit the completed structure from above to below to inspect the full
   three-dimensional twist.

The amber box shows the current selection area, the yellow outline identifies
the atoms affected by the next edit, and bonds update after each rotation.

Black phosphorene has two puckered sublayers in one armchair unit cell. The
`5 x 6` model contains 10 puckered ridges with 12 atoms per ridge. Green and
purple distinguish the upper and lower P sublayers; both remain phosphorus in
the ASE structure.

The relaxed source coordinates come from the
[supporting information of Villegas et al.](https://www.rsc.org/suppdata/c6/cp/c6cp05566d/c6cp05566d1.pdf).
The 13.85 degree target is one of the H-APNR angles tabulated by
[Jang et al.](https://www.rsc.org/suppdata/c6/nr/c6nr04354b/c6nr04354b1.pdf),
and the green/purple sublayer convention follows published phosphorene
structure diagrams such as
[Zhang et al.](https://doi.org/10.1038/srep13927). The example demonstrates
geometry editing and is not an energy-minimized final structure.

#### Commensurate Atoms: Match Periodic 2D Cells

![Graphene hBN commensurate rotation](https://raw.githubusercontent.com/lgyEthan/v_ase/main/docs/assets/github/readme_commensurate.gif)

Enable **Structure > Transform > Commensurate atoms** to search bounded integer
supercells immediately. The search runs behind a staged progress display and
opens an interactive Plotly graph with two views:

| Graph | Meaning |
| --- | --- |
| **3D overview** | Rotation angle, common-cell area ratio, and maximum principal strain; a live plane follows the current rotation |
| **Paper strain projection** | Mean absolute strain versus the actual host-plus-guest atom count, with angle shown by color |

The graph's save icon exports the plotted angle, strain, host/guest integer
matrices, atom counts, surface notation, and method citations as CSV.
**Maximum strain** always uses the conservative maximum principal stretch;
switching graphs does not change accepted candidates. **Maximum area ratio**
defaults to `16` and is explicitly bounded at `128` so the interactive search
remains exhaustive instead of silently sampling a larger space.

Two workflows use the same bounded integer-boundary search:

| Workflow | Host | Guest / rotating component |
| --- | --- | --- |
| Same-lattice twist | Unselected atoms and the current periodic cell | Selected atoms using an independent copy of the same cell |
| Host/guest interface | The open structure | A second structure loaded with **Load guest structure** |

For the same-lattice graphene/hBN example, select the hBN layer before enabling
the workspace. For a separate host/guest calculation, v_ase rotates the entire
guest structure and its own cell together; it never silently substitutes the
host cell. **Apply residual strain to** chooses which lattice receives the
remaining in-plane deformation and defaults to the guest.

Cells-only preview is the default so the host cell, guest cell, and suggested
common cell remain readable while the guest rotates. Their vectors use
distinct colors. **Show preview atoms** adds the bounded supercell atoms plus
one primitive-cell halo, including bonds crossing the common-cell boundary.
The proposal reports both integer matrices, both area ratios, residual strain,
and notation such as `(sqrt(7) x sqrt(7)) R19.11 deg`.

Commensurate matching is deliberately restricted to two periodic vectors in
the global XY plane and rotation about global Z. This is the rigorously defined
2D interface workflow; ordinary free atom rotation remains available when the
workspace is off. **Set Suggested Cell as Structure** materializes the current
validated proposal only in Edit mode. Trajectories and active volumetric fields
remain preview-only because applying one inferred layer-specific cell to every
frame or sampled field would be ambiguous.

The boundary-matching method follows the published integer-supercell and
minimal-strain formulations in
[CellMatch](https://doi.org/10.1016/j.cpc.2015.08.038) and the
[optimal interface-supercell method](https://doi.org/10.1088/1361-648X/aa66f3).
A full same-lattice hexagonal regression follows the commensurate integer-cell
family in the
[twisted-bilayer graphene geometry](https://doi.org/10.1103/PhysRevB.86.155449).
A suggested cell is a geometric periodic match, not an electronic energy
minimum.

### Try A Separate Host And Guest

The repository includes a deterministic graphene/Cu(111) validation pair:

```bash
v_ase gui examples/commensurate_host_guest/graphene_host.extxyz
```

In **Structure > Transform > Commensurate atoms**, choose **Host / guest
interface**, load
[`cu111_guest.extxyz`](examples/commensurate_host_guest/cu111_guest.extxyz),
and keep guest strain `1%` with maximum area ratio `16`. The smallest match is
graphene `sqrt(13)` against Cu(111) `sqrt(12)` at `|16.10211375|` degrees.
The common cell contains 26 graphene atoms plus 12 Cu atoms. The
[example guide](examples/commensurate_host_guest/README.md) and
[`expected.json`](examples/commensurate_host_guest/expected.json) give the
exact maximum-principal and paper-style mean-strain values used by the tests.

The equations, numerical references, basis-invariance check, and measured
search bounds are collected in
[Commensurate Cell Scientific Validation](docs/commensurate_validation.md).

Normal `R` rotates selected atoms. **Cell Transform** is a separate periodic
operation that applies an integer matrix to the cell and every trajectory
frame. Display replication is separate again: it only repeats what is shown.
The common-cell equations, limits, and assumptions are documented in
[unit_cell_aware_rotate.md](docs/unit_cell_aware_rotate.md).

## Measurement And Analysis

![Ordered distance angle and torsion measurement](https://raw.githubusercontent.com/lgyEthan/v_ase/main/docs/assets/github/readme_measurement.gif)

The numbered `a1` to `a4` markers record selection order and are deliberately
different from atom indices.

| Ordered selection | Reported result |
| --- | --- |
| 1 atom | Label, element, position, force, charge, tag, magnetic moment |
| 2 atoms | Direct distance and minimum-image distance |
| 3 atoms | Angle `a1-a2-a3`, centered on `a2` |
| 4 atoms | Signed torsion `a1-a2-a3-a4` |
| 5 or more | Total count and per-label counts |

The connector, angle arc, torsion axis, and compact value badge stay attached
to the selected atoms. Hover information is independent, so moving the pointer
does not replace a saved measurement.

![Trajectory displacement analysis](https://raw.githubusercontent.com/lgyEthan/v_ase/main/docs/assets/github/readme_displacement.png)

For trajectories, **Analysis > Displacement** compares the current frame with
the previous frame or a chosen reference. Minimum-image correction, vector
scale, thickness, color, and 2D/3D style are configurable. Displayed
supercells repeat the vectors, and visual translation moves both endpoints
without changing the physical displacement.

### XY Registry Map

After choosing a periodic interface cell, select the layer or adsorbate that
should translate and open **Analysis > XY Registry Map**. Starting the analysis
without a selection produces a direct selection warning. v_ase scans one full
periodic XY cell on the requested fractional grid while a staged progress
display reports the active step.

The default **Short-contact score** is a dimensionless, covalent-radius-scaled
geometry proxy. **Bond-strain RMS** instead uses enabled interfacial pairwise
bond cutoffs and reports normalized bond-length mismatch for those pairs. Both
scores are lower-is-better geometric screening metrics, not energies. Validate
the proposed registry with an appropriate electronic-structure or force-field
calculation before drawing physical conclusions.

The Plotly heatmap marks the best grid point and the current translation. While
the map is active, `G` is constrained to the periodic XY plane and the marker
follows the move continuously in fractional coordinates. The graph's save icon
exports the complete fractional X/Y grid, metric values, selected indices, and
method notes as CSV. RDF, commensurate, and registry plots all expose the same
adjacent save icon.

### Volumetric Fields

Open a VASP `CHGCAR`, `CHG`, `PARCHG`, `LOCPOT`, or `ELFCAR` directly. Quantum
ESPRESSO and other electronic-structure codes can use Gaussian Cube or XSF
grid output:

```bash
v_ase gui CHGCAR
v_ase gui LOCPOT
v_ase gui charge-density.cube
v_ase gui charge-density.xsf
```

**Analysis > Volumetric Data** controls the dataset, isovalue, signed
positive/negative surfaces, mesh detail, field smearing, mesh smoothing,
colors, and isosurface opacity.
Opening a volumetric file, or adding the first scalar field, immediately shows
an isosurface at a valid default level. Drag **Isosurface opacity** to update
the current surface live without regenerating its mesh. Multiple compatible
datasets can be combined with coefficients such as `+1, -1, -1` for a
charge-density difference. Grid values stay in the local v_ase backend; the
browser receives only the generated surface mesh.
Signed mode treats the isovalue as a nonzero magnitude and renders the
positive and negative crossings that remain inside the displayed field range.

![Smooth signed benzene pi-field isosurfaces with live opacity control](https://raw.githubusercontent.com/lgyEthan/v_ase/main/docs/assets/github/readme_volumetric.png)

**Field smearing σ** applies a Gaussian filter measured in grid voxels before
the isosurface is extracted. Periodic directions wrap across the cell;
nonperiodic directions reflect at their boundary. **Mesh smoothing passes**
then reduce voxel stair-steps on the extracted mesh while keeping cell-boundary
vertices fixed. The source scalar field, its saved precision, integral, and
charge-density-difference inputs are never modified. Set either control to
`0` to disable that stage. Because field smearing can merge small features or
change the range crossed by an isovalue, use the smallest value that removes
visible grid artifacts and verify the resulting topology.

Choose the import precision before opening or adding a scalar field. **FP32**
is the lower-memory default; **FP64** preserves double-precision grid values
and uses twice the grid memory. The same choice is available from the CLI:

```bash
v_ase gui CHGCAR --volumetric-precision fp64
```

The Python API exposes the same choice:

```python
from v_ase.visualize import view

view("CHGCAR", volumetric_precision="fp64")
```

Visual translation and displayed cell replication move or repeat the
isosurface together with the atoms. **Set Supercell as Cell** repeats both the
ASE structure and periodic scalar grid exactly for diagonal integer
replications. A general non-diagonal cell matrix is rejected while scalar
grids are loaded because preserving that sampled field would require an
explicit interpolation choice.
After a materialized diagonal supercell, **Reset Coordinates** restores the
original atoms, cell, and scalar grid together; Undo/Redo keeps the same
atomic field pairing.

### Radial Distribution Function

**Analysis > Radial Distribution Function** plots the current frame in a
resizable Plotly drawer below the viewport. The total RDF is always included.
Pair curves default to the active bond-label pairs and can be switched to all
label pairs or total-only. Set the bin count and cutoff, then export exactly
the plotted columns as CSV.

RDF uses exact spherical shell volumes and ASE's periodic neighbor search in
the full triclinic cell. The requested cutoff is not limited to a `2 x 2 x 2`
replica or reduced at the unique minimum-image radius: v_ase includes every
periodic image whose distance falls inside the sphere and reports the image
span used. Bulk normalization is reported only for cells periodic in all three
directions; partial-PBC and finite systems require a separate boundary
correction and are rejected instead of returning a misleading bulk `g(r)`.

The dotted `g(r) = 1` reference makes the bulk limit explicit. In the
amorphous Cu-Zr example below, the broad short-range peak decays into a flat
long-range plateau rather than falling with the finite display cell.

![Amorphous Cu-Zr structure and RDF approaching the bulk limit](https://raw.githubusercontent.com/lgyEthan/v_ase/main/docs/assets/github/readme_rdf.png)

## Constraints

ASE remains authoritative when **Apply constraints** is enabled. Constraint
visualization is local to each atom rather than merged at a group center.

### FixedLine

A short cyan line passes through each constrained atom and remains visible
without selection. Starting `G` displays a longer guide through the atom's
original position while ASE restricts movement to that direction. FixedLine
does not use a ring or plane disc.

![FixedLine movement](https://raw.githubusercontent.com/lgyEthan/v_ase/main/docs/assets/github/readme_fixedline.gif)

```bash
v_ase gui examples/readme_scene_assets/fixedline.traj --interactive
```

### FixedPlane And FixScaled

Each constrained atom keeps its own local ring, crosshair, and normal marker.
When `G` starts, a larger translucent guide plane appears at that atom's
original position so the permitted surface remains visible while the atom
moves. Multiple selected atoms retain independent planes; no center-of-mass
plane is substituted.

VASP selective dynamics read as `FixScaled` are displayed from their allowed
fractional directions.

![FixedPlane movement and guide plane](https://raw.githubusercontent.com/lgyEthan/v_ase/main/docs/assets/github/readme_fixedplane.gif)

```bash
v_ase gui examples/readme_scene_assets/fixedplane.traj --interactive
```

### FixAtoms

Fixed atoms keep their element color but use a distinct constrained surface
treatment. They remain identifiable without looking selected.

### Hookean

Hookean constraints show their inactive cutoff and engaged state separately.
After the constrained distance passes `rt`, a shaded 3D helical spring appears
between the constrained atoms.

![Hookean constraint](https://raw.githubusercontent.com/lgyEthan/v_ase/main/docs/assets/github/readme_hookean.png)

![Hookean motion](https://raw.githubusercontent.com/lgyEthan/v_ase/main/docs/assets/github/readme_hookean.gif)

```bash
v_ase gui examples/readme_scene_assets/hookean.traj --interactive
```

## Relaxation

![Repulsive relaxation trajectory](https://raw.githubusercontent.com/lgyEthan/v_ase/main/docs/assets/github/readme_relaxation.gif)

**Structure > Relaxation** places every optimization step on a dedicated
timeline. A single loaded structure gains a relaxation movie after the first
run. If a source trajectory is already open, source and relaxation timelines
remain separate and the active timeline is clearly selected.

The included example starts from a deliberately compressed C60 geometry and
runs ASE FIRE with v_ase's repulsive fallback calculator:

- [crowded initial C60](examples/readme_scene_assets/crowded_c60_initial.cif)
- [relaxed C60](examples/readme_scene_assets/crowded_c60_relaxed.cif)
- [optimization trajectory](examples/readme_scene_assets/crowded_c60_relaxation.traj)

```bash
v_ase gui examples/readme_scene_assets/crowded_c60_initial.cif --interactive
```

The fallback calculator is intended for removing obvious close contacts, not
for predictive chemistry. Its cutoff scale and strength are editable. Attach a
scientific ASE calculator when the optimized energy or forces will be used as
physical results.

## Trajectories

Multi-frame inputs add a timeline below the viewport. Scrubbing updates the
frame continuously, selected atom indices persist when topology permits, FPS
changes apply during playback, and **Skip** advances by `skip + 1` source
frames per tick.

Bond topology is evaluated for each frame, so bonds form or break when a
pair crosses its cutoff. Appearance, pair settings, supercell display, camera,
and analysis settings remain active across the movie.

Video export uses FPS as playback speed. Optional `N x` interpolation creates
`(source_frames - 1) * N + 1` output frames. Minimum-image interpolation uses
periodic cells to avoid jumps across a boundary. Interpolation takes longer
because more frames are rendered.

## Appearance, Bonds, And Rendering

**Structure > Appearance** controls each stable atom label:

- ASE chemical TYPE and independent visual label;
- visibility and selection availability;
- color and radius;
- Standard, Metal, or Rubber material;
- all/partial/none selection checkbox.

View mode applies appearance by label. Edit mode can keep per-atom material
overrides. Relabeling does not reorder the table or merge otherwise distinct
atom types accidentally.

![Standard Metal and Rubber atom materials](https://raw.githubusercontent.com/lgyEthan/v_ase/main/docs/assets/github/readme_materials.png)

The comparison uses three identical Cu13 clusters with the same element color
and radius, so only the optical material changes:

| Material | Visual response | Typical use |
| --- | --- | --- |
| Standard | Balanced diffuse color and compact highlight | General structures and chemically neutral figures |
| Metal | Strong environment reflection and bright metallic highlight | Metals, electrodes, and reflective surfaces |
| Rubber | High roughness with broad, muted highlights | Soft visual grouping and low-glare nonmetal regions |

Materials affect rendering only. ASE elements, coordinates, calculators, and
constraints are unchanged.

![Pairwise Cu O bonds in a Cu2O(111) film on Cu(111)](https://raw.githubusercontent.com/lgyEthan/v_ase/main/docs/assets/github/readme_bonds.png)

**Structure > Bonding** provides automatic inference, explicit label-pair
cutoffs, and manual index pairs. A pair cutoff of zero disables that pair.
Changes apply immediately. Bonds support:

- cell-local or periodic minimum-image display;
- cylinder or flat 2D geometry;
- custom color or two half-bonds using the atom colors;
- configurable diameter;
- live formation and breaking during Edit transforms.

The top view shows a `6 x 6 Cu2O(111)` film on `7 x 7 Cu(111)`, with one
interfacial oxygen positioned over a substrate Cu top site.
The Cu(111) substrate uses a nearest-neighbor touching-sphere radius.
`Cu_oxide-O_oxide` and `Cu_substrate-O_oxide` bonds are enabled, while
`Cu_substrate-Cu_substrate`, `Cu_oxide-Cu_oxide`, cross-region Cu-Cu, and
O-O pairs are disabled. Dark metallic substrate Cu, bright standard-material
oxide Cu, and matte red oxide O separate the phases without changing ASE
elements. Each bond is split into the colors of its two endpoint atoms, so the
Cu-O connectivity remains readable without an unrelated custom bond color.
Separate oxide and substrate labels let each interaction be enabled or
assigned its own cutoff independently.

```bash
v_ase gui examples/readme_scene_assets/cu2o111_on_cu111_pairwise_bonds.traj
```

**View** controls projection, atomic scale, anti-aliasing, sphere smoothness,
background, 2D/3D display, grid, axes, unit cell, overlays, and cell material.
The **Axes** and **Unit Cell** switches update the working viewport
immediately; they are not export-only settings. Hiding world axes does not
remove the compact orientation gizmo. New documents use orthographic
projection and a true-white background.

The top-bar renderer switches between fast modeling light and Sun/soft-shadow
rendering. Sun source, target, intensity, and direction can be manipulated in
the viewport and carried into Blender export.

## Export And Save

| Command | Result |
| --- | --- |
| Export POSCAR | Current physical ASE structure in VASP format |
| Export ASE Pickle | ASE `Atoms`, labels, constraints, arrays, and a valid `SinglePointCalculator` |
| Export Image | PNG by default; JPEG, PDF, and lossless WebP from the exact preview frame |
| Export Video | Constant-frame-rate H.264 MOV or MPEG-4 AVI with optional interpolation |
| Export Blender | Optimized scene script with atoms, bonds, cell, camera, and Sun |
| Export 3DM | Instanced Rhino geometry, metadata, and saved camera views |
| Export OBJ | OBJ/MTL, camera, and metadata in a ZIP |
| Export HTML View | Offline, view-only 3D document; lightweight by default, with optional `.vase` recovery |
| Save `.vase` | Compact project with structure/trajectory and complete visual state |
| HTML Project | Browser-ready project with complete embedded `.vase` recovery by default |
| Save Settings | Reusable visual settings without coordinates |

Image, video, and HTML use one shared **Preview Area** composition. Its aspect
ratio, camera, crop, lighting, atom scale, and included overlays match the
saved output. HTML View defaults to grid off, axes on, and unit cell on; all
three overlays can be changed before saving.

The system save picker is opened before expensive rendering or scene
generation when the browser supports it. Canceling the picker cancels the
export. Chrome may then show **This site can view changes you make to this
file**. That message is Chrome's File System Access permission notice: v_ase
can write only to the destination selected in that picker. Browser code cannot
hide the notice while retaining destination selection before rendering.

Image export uses one determinate progress bar for rendering, pixel capture,
upload, encoding, download, and the final file write. It reports estimated
remaining time and reaches 100% once, only after the destination is complete.
Video export follows the same monotonic rule across all frames and encoding.
Every source frame is retained exactly once at `1x`; interpolation adds
in-between frames. Visible displacement vectors and other selected scene
overlays are recalculated for each rendered frame.

### Project Or Shareable HTML

Under **Export > v_ase Project**, use **Save .vase** for the smallest complete
project. It contains every loaded frame, coordinates, cells, PBC, labels,
constraints, safe calculator results, camera, appearance, bonds, lighting,
analysis, and export settings. It is self-contained and never references the
original input file.

Use **HTML Project** or **HTML View** when the result should open directly in a
browser. The save dialog shows the exact shared Preview Area crop and lets you
choose grid, axes, and unit-cell visibility. Every generated HTML:

- opens offline without v_ase, Python, a server, or a CDN;
- restores the saved camera, viewport styling, bonds, constraint overlays,
  displacement vectors, supercell, visual translation, and trajectory;
- allows orbit, pan, zoom, frame stepping, and movie playback;
- exposes no atom, structure, appearance, or project editing controls.

**HTML View** leaves **Embed editable .vase project** off by default and creates
the smaller view-only handoff. **HTML Project** enables it by default and stores
the complete `.vase` inside the same HTML. Embedded documents expose
**Download .vase**, and either command restores the full editable project:

```bash
v_ase gui project.vase
v_ase gui project.html
```

With project embedding disabled, the file is smaller and remains a portable
view-only document. It cannot be restored as an editable v_ase project. v_ase
reports this explicitly if that lightweight HTML is opened as input.

The exported frame is stored as an automatically optimized high-resolution
poster as well as an interactive 3D scene. The initial HTML surface contains
only that exact Preview Area crop: no v_ase logo, header, decorative border, or
page margin is included. This lets macOS Finder/Quick Look show the structure
without executing WebGL. In a browser, the first prepared WebGL frame replaces
the poster with a short cross-fade as soon as the first live frame is ready,
before camera input begins. Both surfaces occupy the same rectangle, so the
structure does not jump. View-only controls appear only after pointer or
keyboard activity.

HTML width and height inherit the image/video Preview Area. They define the
saved camera aspect and crop, not a fixed live WebGL resolution. The
interactive renderer automatically follows the browser size and display pixel
density.

HTML is larger than `.vase` because it contains the browser renderer and
immediately readable scene data. Embedding adds a Base64 copy of `.vase` on
top of that. Keep `.vase` as the compact editable source of truth.

Opening an ordinary structure in an existing tab keeps the current visual
settings; opening `.vase` or project-embedded HTML restores the saved project.

Rhino export requires the optional dependency:

```bash
python -m pip install "v_ase-gui[rhino]"
```

OBJ export has no optional Python dependency.

## Agent Setup

The AI agent runs separately from v_ase. Give it the complete
[v_ase Skill directory](https://github.com/lgyEthan/v_ase/tree/main/v_ase/skills/visualizing-atomic-structures-with-v-ase),
then describe the result you want. The agent starts the machine-readable v_ase
session, gives you the live GUI URL, and performs verified changes in that same
document.

The Skill is vendor-neutral and can be used by Codex, Claude Code, ChatGPT
desktop agents, Gemini-based agents, agentic IDEs, or another agent that can
run local commands.

```text
your natural-language request
  -> external AI agent + v_ase Skill
  -> v_ase structured CLI
  <-> the same live v_ase GUI you can watch and edit
```

`--cli` is not an embedded AI model. It is the structured connection the
external agent launches for itself. It exposes atomistic state and safe
operations, and reports committed GUI changes back to the agent. Revision
checks prevent an older agent command from silently replacing a newer human
edit.

### What To Give The AI

Prefer the complete skill directory. If the client accepts only individual
files, provide the following:

| Always provide | Add when the task needs it |
| --- | --- |
| [`SKILL.md`](v_ase/skills/visualizing-atomic-structures-with-v-ase/SKILL.md) | [`semantic-api.md`](v_ase/skills/visualizing-atomic-structures-with-v-ase/references/semantic-api.md) for live state, edits, camera, render, or export |
| [`agent-setup.md`](v_ase/skills/visualizing-atomic-structures-with-v-ase/references/agent-setup.md) | [`collaboration.md`](v_ase/skills/visualizing-atomic-structures-with-v-ase/references/collaboration.md) while a human and agent share the live GUI |
|  | [`workflows-and-examples.md`](v_ase/skills/visualizing-atomic-structures-with-v-ase/references/workflows-and-examples.md) for multi-step scientific workflows |
|  | [`cli-and-environments.md`](v_ase/skills/visualizing-atomic-structures-with-v-ase/references/cli-and-environments.md) for installation, server, WSL, or process handling |
|  | [`safety-and-errors.md`](v_ase/skills/visualizing-atomic-structures-with-v-ase/references/safety-and-errors.md) before destructive edits, relaxation, or file output |
|  | [`evaluation.md`](v_ase/skills/visualizing-atomic-structures-with-v-ase/references/evaluation.md) when changing or releasing v_ase itself |

For an AI client without a native skill loader, attach the files above and use:

```text
Read SKILL.md and agent-setup.md. Use v_ase's structured CLI to inspect and
edit the structure, give me the live GUI URL so I can watch or refine it, honor
newer GUI changes before continuing, and verify both scientific state and the
final rendered output.
```

The compatibility document
[`skills_v_ase.md`](v_ase/skills_v_ase.md) points existing integrations to the
same canonical skill and reference set.

### Install The Skill

Clients with skill-folder support should install the complete directory:

```bash
# Codex
cp -R v_ase/skills/visualizing-atomic-structures-with-v-ase "$CODEX_HOME/skills/"

# Claude Code, from a project root
mkdir -p .claude/skills
cp -R v_ase/skills/visualizing-atomic-structures-with-v-ase .claude/skills/
```

For another AI, use its documented local skill directory if it supports the
same `SKILL.md` convention. Otherwise attach the files listed above or make
them readable in the project and include the bootstrap instruction.

Detailed CLI fields and command examples live in the Skill references rather
than this user guide:

- [Agent setup](v_ase/skills/visualizing-atomic-structures-with-v-ase/references/agent-setup.md)
- [Live collaboration](v_ase/skills/visualizing-atomic-structures-with-v-ase/references/collaboration.md)
- [Semantic API](v_ase/skills/visualizing-atomic-structures-with-v-ase/references/semantic-api.md)

## Documents And File Opening

The top-bar **Open** button starts with the operating system file picker. A
selected file can:

1. replace the active document;
2. append structures to its current trajectory;
3. open in a new independent v_ase tab.

If the active document is empty, the selected file opens there immediately;
the destination chooser is shown only when a document already contains a
structure or trajectory.

The **+** beside the document tabs creates an empty independent document. Each
tab owns its structure, trajectory, camera, selection, history, settings,
calculator, and `.vase` output.

Adding `.vase` to an existing trajectory imports only its structures and keeps
the current tab's visual state. Replacing a tab or opening a new one restores
the complete `.vase` project.

## Python

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

atoms = molecule("H2O")
view(atoms)  # View mode
```

Inside Jupyter Notebook or JupyterLab, the same call automatically displays a
view-only interactive model directly below the cell:

```python
view(atoms)
```

The notebook output supports orbit, pan, zoom, and trajectory playback. After
importing `view`, use the `%v_ase` line magic to switch the default at any time:

```python
%v_ase inline
view(atoms)  # interactive output below this cell

%v_ase browser
editor = view(atoms, block=False)  # full interface in an external browser

%v_ase auto  # restore automatic Jupyter detection
```

`%load_ext v_ase.notebook` registers the same magic explicitly when needed.
Passing `notebook="inline"` / `True` or `notebook="browser"` / `False` to one
`view()` call overrides the current magic setting.

When retaining an inline handle, display it explicitly:

```python
from IPython.display import display

editor = view(atoms)
display(editor)
```

Return an edited ASE object:

```python
edited = view(atoms, viz_only=False)
print(edited.positions)
```

`view()` accepts one ASE `Atoms`, a sequence of frames, or a supported file
path. `view_edit()` remains a compatibility alias for Edit mode.

## File Formats

Common structure inputs include POSCAR/CONTCAR, VASP files, XDATCAR,
`vasprun.xml`, XYZ/extxyz, ASE `.traj`, LAMMPS dump/data, CIF, and `.vase`.
Volumetric inputs include VASP CHGCAR/CHG/PARCHG/LOCPOT/ELFCAR and Gaussian
Cube/XSF grids. ASE readers cover additional structure formats.

Use `--format` when an ambiguous filename does not identify the reader:

```bash
v_ase gui ABCD --format POSCAR
v_ase gui ABCD --format vasprun.xml
v_ase gui ABCD --format lammpstrj
v_ase gui ABCD --format data
v_ase gui ABCD --format CHGCAR
v_ase gui ABCD --format qe-cube
v_ase gui ABCD --format qe-xsf
```

Use `--index :` for every frame, `--index -1` for the last frame, or an integer
for one frame.

Repeated POSCAR/CONTCAR species blocks remain separate visual labels. For
example, `O Cu O` with counts `1 14 5` becomes `O1`, `Cu`, and `O2` while all
oxygen atoms remain ASE element `O`. Custom labels retain their complete text
when they are renamed or used for pair analysis.

## Controls

| Input | Action |
| --- | --- |
| Left click / Shift + click | Select / extend selection |
| Left drag | Box select |
| Middle drag | Orbit without inertia |
| Shift + middle drag | Pan |
| Wheel | Zoom |
| `G` / `R` | Move / rotate selected atoms |
| `X`, `Y`, `Z` during `G`/`R` | Lock transform axis |
| `X`, `Y`, `Z` otherwise | Align camera to an axis |
| Number keys | Exact move distance or rotation angle |
| `Enter` or left click | Confirm transform |
| `Esc` or right click | Cancel transform |
| `Ctrl+C`, `Ctrl+V` | Copy and paste atoms |
| `Ctrl+Z`, `Ctrl+Shift+Z` | Undo and redo structure and visualization-setting changes; camera navigation is excluded |
| `Delete` / `Backspace` | Delete selected atoms |
| `Space` | Play or pause the active timeline |
| Left / Right Arrow | Previous / next frame in the active timeline |
| `Tab` or `Esc` | Open a collapsed control panel |
| `Esc` with the panel open | Close it and return focus to the viewport |

The **?** button contains the complete shortcut table.

## Remote Servers

Install v_ase on both the local computer and remote host, then run one command
locally:

```bash
v_ase gui USER@SERVER:/absolute/path/to/STRUCTURE
```

An SSH config alias works:

```bash
v_ase gui physics:/absolute/path/to/trajectory.extxyz
```

v_ase selects private ports automatically, starts the backend beside the
remote file, creates the SSH tunnel, and opens the local browser. The source
file and full trajectory cache remain on the server; only the current frame
data required for local Three.js rendering crosses the tunnel. Use `ProxyJump`
in `~/.ssh/config` when a login node is required.

## Troubleshooting

<details>
<summary><code>v_ase</code> command is not found</summary>

Install and run with the same Python environment:

```bash
python -m pip install --upgrade v_ase-gui
python -m v_ase.cli --version
```

If the module command works but the console command does not, reactivate the
environment or add its Python scripts directory to `PATH`.

</details>

<details>
<summary>The browser does not open, or WSL prints <code>gio: ... Operation not supported</code></summary>

The terminal also prints the complete local URL. Ctrl+click it or copy the text
beginning with `http://` into Chrome, Edge, Firefox, or another browser. Keep
the terminal process running.

Example with sensitive session identifiers masked:

```text
(base) giyeok@DESKTOP-XXXX:~$ v_ase gui
gio: http://127.0.0.1:58039/workspace?workspace_id=xxxx&session_id=xxxx: Operation not supported
```

For better WSL performance, keep trajectories under the Linux filesystem
rather than `/mnt/c/...`.

</details>

<details>
<summary>A file is detected with the wrong format</summary>

Force the reader:

```bash
v_ase gui FILE --format POSCAR
v_ase gui FILE --format vasprun.xml
v_ase gui FILE --format lammpstrj
v_ase gui FILE --format data
```

</details>

<details>
<summary>Startup fails with <code>cannot import name 'read_vasp_configuration'</code></summary>

This was an ASE 3.23/3.24 compatibility defect in v_ase 0.1.1 through 0.1.5.
Upgrade v_ase in the same environment that provides the failing executable:

```bash
python -m pip install --upgrade "v_ase-gui>=0.1.6"
v_ase --version
```

v_ase 0.1.6 and later support the declared `ase>=3.23` range without making
ordinary structure loading depend on a newer VASP-internal helper.

</details>

<details>
<summary>Replicated supercell atoms cannot be selected</summary>

In **Edit**, displayed replicas are noneditable previews. Use
**Set Supercell as Cell** to create real ASE atoms and an editable larger cell.
In **View**, displayed replicas are selectable and participate in center,
distance, and other measurements.

</details>

<details>
<summary>Video export is unavailable or slow</summary>

Video export requires at least two frames and browser `MediaRecorder` support.
MOV/AVI conversion uses the bundled `imageio-ffmpeg`. Interpolation renders
additional frames and requires stable atom count, element, label, and ordering
between adjacent source frames. The selected FPS controls playback time:
72 frames at 30 FPS produce 2.40 seconds. The progress indicator reaches 100%
only after encoding and the destination write both finish.

</details>

<details>
<summary>Chrome says this site can view changes made to the saved file</summary>

This is a Chrome security notice for the File System Access API. v_ase opens
the system save picker before a costly image, video, Blender, or 3D scene export so
canceling does not waste time. It receives write access only to the file you
choose. Chrome does not allow a page to suppress this notice; using an ordinary
browser download would remove advance destination selection.

</details>

<details>
<summary>A large trajectory opens or plays slowly</summary>

- Keep the default View mode unless editing is required.
- Use `--stream-frames` when frame data should be loaded on demand.
- Keep browser hardware acceleration enabled.
- Close unused v_ase tabs; inactive tabs pause rendering but retain document
  state in memory.
- In WSL, keep data in the Linux filesystem.

</details>

<details>
<summary>RDF reports that fully periodic 3D boundaries are required</summary>

v_ase does not label a finite or partial-PBC histogram as a bulk RDF. Define a
valid 3D periodic cell for bulk `g(r)`, or use a method with the boundary
correction appropriate to the finite, slab, or wire geometry.

</details>

<details>
<summary>Volumetric datasets cannot be combined</summary>

Density differences require identical grid dimensions, cell vectors, origin,
PBC, endpoint convention, and units. Generate all component grids on the same
FFT mesh, or resample them deliberately before opening them in v_ase.

</details>

<details>
<summary>Installation fails while pip checks an unrelated package version</summary>

A package version reported as `None` usually belongs to a different incomplete
or manually installed distribution in that environment. Run
`python -m pip check`, repair that distribution, or use a clean environment:

```bash
python -m venv .venv
python -m pip install --upgrade pip
python -m pip install v_ase-gui
```

</details>

Run `v_ase --help` or `v_ase gui --help` for all CLI options. Report
reproducible problems at
[GitHub Issues](https://github.com/lgyEthan/v_ase/issues).
