Better ways to get back my optimized cell and structure

[Henrique Junior]

This is probably a silly question. I’m running a CELL_OPT and at the end of my calculation I’m trying to open the resulting .xyz in VESTA and manually entering the cell parameters but doing this is generating a messy result.

What is the best way to get my optimized call and structure so I can work on them?

Thanks in advance.

[Matthias Krack]

Hi

I can confirm your observation, but this is rather an issue for the VESTA mailing list.

You can use FORMAT dcd (or dcd_aligned_cell) in the section &TRAJECTORY to dump the coordinates, if you are just interested in visualization with VMD. The dcd format includes the cell information, but it is binary and VESTA cannot load files in dcd format. On the other hand, CP2K can only read but not write files in cif format currently. So you can only try to load the xyz file with VESTA and then you export the structure in cif format (or any other format which includes cell information), but this procedure seems not to work properly with VESTA, unfortunately.

Matthias

[James Dean]

Hello Henrique,

The way I've usually done this is by using OpenBabel to convert from XYZ to a VASP file, and then filling in the cell parameters in the VASP file via a script that reads the cp2k output to find the current cell parameters. Just make sure you save it as a ".vasp" file or VESTA won't know what to do with it.

As an alternative, if you're comfortable using Python, the Atomic Simulation Environment (ASE) is another way you'd be able to accomplish this, as it has tools for file I/O with both xyz and VASP formats.

Best,

James Dean

[Henrique Junior]

Thank you for the tips, guys.

I was able to get the same results using Avogadro 1.2:

* Open a blank canvas.

* Use the crystallography tools to generate your (empty) cell

* Paste the XYZ coordinates to populate the cell

* Save as .cif.

Thank you very much.