Structure visualizer
The structure visualizer shows the atomic geometry from SIESTA output files in an interactive 3D viewer. It is useful for checking that a relaxation converged to the expected geometry or for visualizing a molecular dynamics trajectory.
Opening the visualizer
Pull an XV or ANI file from the cluster. The studio opens the structure visualizer automatically for these file types.
Controls
- Rotate — click and drag.
- Zoom — scroll wheel.
- Pan — hold Shift and drag.
- Periodic boundary conditions — toggle from the toolbar to show or hide the periodic images.
Trajectory playback
For ANI trajectory files, use the playback controls at the bottom of the viewer to step through the frames or play the animation. The step counter shows the current frame index.
Orbital overlays
Where orbital data is available, you can toggle orbital overlays from the viewer toolbar. Isovalue can be adjusted with the slider.