Can I regenerate a new structure file after adjustment of the atom coordinate in Ovito?

Victor_Hue · October 11, 2023, 9:34am

Hi. I’m using a software (Material Designs MedeA) to prepare a system structure file. Using Ovito, I can read the structure.dat in atom style full format. After some simulation in LAMMPS (which the input script will read the structure.dat to run the simulation), I have generated a trajectory file dump.deform.lammpstrj. I read the trajectory file in Ovito and plan to readjust the atom coordinate before the next simulation.

My question is: Is it possible to produce a new structure.dat file based on the adjusted trajectory coordinate in Ovito, so that my input script can read the new structure.dat to start a new simulation?

structure.dat (355.2 KB)
dump.deform.lammpstrj (6.9 MB)

Thanks.

kalcher · October 11, 2023, 9:51am

Yes, you can export the results of your OVITO pipeline evaluated at the animation frame of your choice to the LAMMPS data file format Exporting data — OVITO User Manual 3.9.2 documentation.
Does that answer your question?

kalcher · October 11, 2023, 10:17am

Here’s a short description of the workflow in the OVITO desktop application:

Import the data file (atom style full)
Add a Load Trajectory modifier to the pipeline to merge your trajectory file with the initial topology data.
Add more modifiers to alter the particle coordinates and/or cell shape (e.g. a Compute property, Python Script modifier or Affine Transformation modifier).
Use OVITO’s File → Export function to export the animation frame of your choice to LAMMPS data format (atom style full).

Victor_Hue · October 18, 2023, 9:58am

I see. Sorry for the late reply and thanks for the clear instruction!