Need help for constructing CIf file to lammps data file of clay

OVITO
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1

Hello everyone,

I am working on simulation of CO₂ adsorption in montmorillonite clay using GCMC in LAMMPS. I have built the clay model in Material Studio and converted the CIF file to LAMMPS format using Ovito, but the generated LAMMPS data file is not working correctly. As I am new in lammps, I can’t understand what the problem and how can I solve it.

This CIf file created by MS.

1100106 (2) (0 0 1).cif (67.0 KB)

And this is the converted lammps data file.

mt1_final_fixed.data (49.5 KB)

Thank you in advance for your help!

2

You are not likely to get help if you don’t post in the correct category.
This looks like a question about OVITO and not about the Materials Project.

5

Hi,

I imported your CIF file into OVITO and exported it as a LAMMPS data file. The resulting file appears to be valid and loads correctly in OVITO.

However, the data file you provided cannot be opened in OVITO and seems to be invalid. I noticed that your file includes the header “(written by ASE)”, while the one generated by OVITO includes the header “# LAMMPS data file written by OVITO Pro 3.12.1”. This suggests that some additional post-processing may have been performed on the file.

Could it be that this post-processing step introduced the error?

After some investigation, I found that your file is missing a required empty line after the “Atoms” keyword. Adding this newline allows OVITO to read your file.

Your data file:

(written by ASE)

608 atoms
4 atom types

0.0      21.002800000000001  xlo xhi
0.0      18.549600727819278  ylo yhi
0.0      26.756799999999998  zlo zhi
    -9.8503766769848244                       0                       0  xy xz yz

Atoms
     1   4      7.6104013327901949      18.474660340878888      6.1013531039999993
     2   4       2.034189671282606      9.1998599769692504      6.1013531039999993
...

OVITO output:

# LAMMPS data file written by OVITO Pro 3.12.1

608 atoms
4 atom types

0.0 21.0028 xlo xhi
0.0 18.5496007278 ylo yhi
0.0 26.7568 zlo zhi
-9.850376677 0.0 0.0 xy xz yz

Atoms  # atomic

1 1 7.6104013328 18.4746603409 6.101353104
2 1 2.0341896713 9.199859977 6.101353104
...