Trajectory Playback
This tutorial covers loading and playing molecular dynamics (MD) trajectories and optimization paths.
Supported Formats
| Format | Extensions | Description |
|---|---|---|
| Extended XYZ | .extxyz | Multi-frame XYZ with lattice and per-atom properties |
| XYZ | .xyz | Simple multi-frame Cartesian coordinates |
| ASE Trajectory | .traj | ASE native binary format |
| HDF5 | .hdf5, .h5 | Hierarchical Data Format (multi-frame) |
| XDATCAR | XDATCAR | VASP MD trajectory |
| Compressed | .gz, .zip | Any of the above, compressed |
Loading a Trajectory
Drag and Drop
Drop a trajectory file onto the viewer. CatGo auto-detects the format and switches to trajectory mode.
File Picker
Use the Import button to browse for trajectory files.
From Optimization
After running a structure optimization, you can export the full optimization trajectory as a multi-frame extXYZ file, then reload it for analysis.
Playback Controls
Buttons
| Button | Action |
|---|---|
| Play / Pause | Start or pause playback |
| Previous | Go back one frame |
| Next | Advance one frame |
| FPS slider | Adjust playback speed |
Keyboard Shortcuts
| Key | Action |
|---|---|
| Space | Play / Pause |
| A | Previous frame |
| D | Next frame |
| Ctrl+A | Jump to first frame |
| Ctrl+D | Jump to last frame |
| J | Back 10 frames |
| L | Forward 10 frames |
| PageUp | Back 25 frames |
| PageDown | Forward 25 frames |
| 0-9 | Jump to percentage (0 = start, 5 = halfway, 9 = end) |
| + / = | Increase playback speed |
| - | Decrease playback speed |
| F | Toggle fullscreen |
Display Modes
The trajectory viewer supports multiple visualization layouts:
| Mode | Description |
|---|---|
| Structure + Scatter | 3D viewer alongside energy/force plots (default) |
| Structure + Histogram | 3D viewer with property distribution |
| Structure only | Full-size 3D viewer |
| Scatter only | Energy/force plots only |
| Histogram only | Property distribution analysis |
Plot Interaction
When the scatter plot is visible:
- Hover over a data point to preview that frame in the 3D viewer
- Click a data point to jump to that frame
- Plots show per-frame properties like energy, max force, volume, and temperature (when available in the trajectory metadata)
Information Pane
Press I to view trajectory metadata:
- File info (name, size, format)
- Frame count and indexing status
- Current structure info (atom count, formula, volume, density)
- Energy range across frames
- Force range across frames
- Volume change metrics
Large Trajectory Handling
CatGo uses intelligent loading strategies for large files:
| File Size | Strategy |
|---|---|
| Small (<25 MB text, <50 MB binary) | Load all frames into memory |
| Large (>25 MB text, >50 MB binary) | Indexed loading — frames loaded on demand |
For indexed trajectories:
- Frame byte offsets are pre-computed for fast seeking
- Only the current frame (plus a few prefetched frames) is in memory
- Plot metadata is extracted without loading full structures
Performance Settings
| Setting | Default | Description |
|---|---|---|
max_frames_in_memory | 1000 | Max frames kept in memory |
prefetch_frames | 5 | Frames pre-loaded ahead of current |
chunk_size | 1000 | Frames processed at once during parsing |
cache_parsed_data | true | Cache parsed frames for reuse |
Tips
- Use extXYZ for rich data — The extXYZ format supports per-frame and per-atom properties (energy, forces, stress, charges), which CatGo can plot.
- Loop playback is enabled by default. Disable it in settings for one-shot viewing.
- Pause on hover — Enable this setting to automatically pause when you hover over the controls, making it easier to interact with the UI.
- Hidden elements persist — If you hide an element type, it stays hidden across all frames.