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.

Importing trajectories from other codes

Click Import trajectory in the studio header to open a trajectory that was not produced by SIESTA. It accepts:

one multi-frame XYZ or extended-XYZ file (.xyz, .extxyz), or an .ANI file; with extended XYZ, the Lattice= cell of each frame is kept;
several single-structure files (.xyz, .cif, .fdf, .XV) selected together. They are sorted by name (image-2 before image-10) and played as one animation.

The visualizer does not read VASP (XDATCAR, vasprun.xml, OUTCAR) or ASE (.traj) files directly. Convert them to extended XYZ with ASE first:

from ase.io import read, write

# ASE trajectory, e.g. from a relaxation or an NEB run
images = read('neb.traj', index=':')

# or VASP output
images = read('XDATCAR', index=':')
# images = read('vasprun.xml', index=':')

write('trajectory.xyz', images, format='extxyz')

index=':' reads every frame; without it ASE returns only the last one. For an NEB run that wrote one .traj per image, read each file and pass the list of structures to write. Extra per-atom columns that ASE adds, such as forces or energies, are ignored.

The same file can also be opened with Analyze File, which shows it as an animated trajectory.

Orbital overlays