the format of atomic positions in the output file

[luke419]

Hello,

Thank you for your answers, Francois.
I'd like to visualize the final atomic position of MD simulation.
In the output *.r file of MD simulation, the format of atomic positions and velocities is different from that of initial posistion file (named h2o64.i in the example) used in the ground state calculation.
Would you let me know how I can obtain the positions and/or velocities of the final structure in the format of h2o64.i so that I can convert qbox format to cif using utility?

Best regards,
Young

[fgygi]

Hello Young,

You can generate an xyz file for visualization of MD trajectories using the qbox_xyz.py python script provided in the util directory of the Qbox distribution. For example:

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$ qbox_xyz.py mdrun1.r > mdrun1.xyz

To get an xyz file from multiple MD runs, use:

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$ qbox_xyz.py mdrun1.r mdrun2.r > md.xyz

The xyz file can be visualized using tools such as VMD or Avogadro.

Note that if you simulate a liquid, molecules will diffuse away from the primitive unit cell. Qbox does not fold back atomic positions into the primitive unit cell. The reason is that this makes it possible to compute the diffusion coefficient from the root-mean-square displacement of atoms. If you want visualize all atoms folded in the primitive cell for one single snapshot, you must run a separate calculation in which you load the sample and use the fold_in_ws command, e.g.

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load restart.xml
fold_in_ws
run 0

Best,
Francois