Author Topic: Problem with Wigner-Seitz analisis: Predicts wrong number of V and interstitials  (Read 1281 times)

Xtof

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Hi all,

I am new to OVITO and I am experiencing some problems with the Wigner-Seitz analisis.
I am interested in determining vacancies and interstitials after cascades in solids, using the MD LAMMPS code.
To make a simple test, I created a box of 32x32x32 cells and periodic boundary conditions in LAMMPS. Then I selected an atom in the middle of the box and moved it by few cells.
This should create 1 vacancy and 1 interstitial.

Using OVITO, I upload the file with defects. Then I added the Wigner-Seitz defect analysis modifier. It asked me to upload the reference state, which I did,
by uploading file with the crystal after equilibrium. I set the boundary conditions of the simulation cell to periodic in OVITO. Then the Wigner-Seitz analysis gives 21 V and 21 interstitials.

Why such difference ?
Maybe there is something I did wrong, or missed something. Could you please give me some advice ?

Many thanks in advance and best regards,
Christophe

Alexander Stukowski

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Could you please attach the two simulation files (the reference and the displaced configuration) if they are not too large?

The steps that you describe sound correct. I am wondering whether the simulation cell size did change after you equilibrate the displaced system? In other words, did you use a barostat in LAMMPS to relax the box size? If yes, you probably have to activate the "Eliminate homogeneous cell deformation" option in the WS analysis modifier to account for the expansion/contraction of the lattice.

Another thing makes me suspicious: When you let LAMMPS write a dump file, OVITO should pick up the periodic boundary conditions automatically. No need to activate them explicitly in OVITO. Did you perhaps use some non-standard file format like XYZ, which doesn't store PBC flags and box size information? This would likely lead to artefacts at the box boundaries when performing the WS analysis.

Xtof

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Dear Alexander,

You were right. It is due to the file format. I also suspected something of that order because with some files, OVITO detects them is a LAMMPs dump, and with the files that exhibited a problem, they were not detected as LAMMPS dump.
Indeed, it was due to the way I dump the data into the xyz file.

If with LAMMPS you use:
write_dump      all custom crystal_eq.xyz x y z

Then the PBC flags are kept into the file.

You can do the following way (the way I was using):
write_dump      all xyz crystal_eq.xyz

This way I checked that the PBC flags are not written into the file, and OVITO does not detect it as a LAMMPS dump.
This was the problem.

Thanks a lot for your help !
With best regards,
Christophe