Trajectories

Ouro plays any file ending in .traj as a 3D animation. These are ASE trajectory files, as written by ASE's optimizers and molecular dynamics, so a relaxation or MD run works as is.

What the viewer shows

The structure is drawn like a crystal or molecule, with a play button and a scrubber across the frames. Beside it:

• Energy per frame, from the calculator's results or atoms.info["energy"]
• Max force per frame, the largest force on any atom, when forces were saved
• Temperature per frame from the saved momenta, computed as ASE's get_temperature does, with the thermostat's target marked when the run recorded one
• Time in fs or ps for MD runs that recorded their time step

Click or drag on any plot to jump to that frame. Click the view, then press space to play or pause, ← → to step one frame, and shift with an arrow to jump a tenth of the run. Periodic structures are wrapped into the cell by default; turn that off to see atoms as stored. Bonds are found every frame from covalent radii, so they form and break as the atoms move. Click atoms to measure distances and angles, which follow the atoms through the run.

Writing a file

Attach a trajectory to an optimizer or dynamics run in ASE:

from ase.optimize import BFGS
 
opt = BFGS(atoms, trajectory="relax.traj")
opt.run(fmax=0.02)

Then upload it with the .traj extension:

from ouro import Ouro
 
ouro = Ouro()
ouro.files.create(
    name="Relaxation",
    description="BFGS relaxation of the strained cell",
    visibility="public",
    file_path="relax.traj",
)

Limits

The file is read in the browser. Long runs are sampled: the viewer loads up to 500 frames, and fewer for large systems (about 500,000 atom-frames in all), spread evenly across the run and always including the last frame. Only the sampled frames are downloaded. Trajectories in ASE's old pickle format need converting first with ase convert old.traj new.traj.