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jlopez141 / pyCSH

pyCSH: automated generation of realistic bulk calcium silicate hydrate (C-S-H) structures.
GNU General Public License v2.0
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molecule-tag and charge #4

Open dapang201 opened 1 month ago

dapang201 commented 1 month ago

Hello, I was ready to run your model in lammps today, but I was told that the atomic format does not meet the lammps specification because of the lack of molecle-tag. In addition, I would like to ask why the charge is zero. I look forward to your reply. e8bc03362eadf4cfface7a887dd7eaa image

casarziga commented 1 month ago

I guess you are talking about the atom_style

The atom_style style atomic needs the following columns in the 'Atoms' section: atom-ID atom-type x y z Therefore the data file you have has one column too many for the atomic style. I guess you could simply delete one of them (python pandas or so).

What you have here seems to be the atom_style charge: atom-ID atom-type charge x y z Therefore, you would need to specify in your lammps input file 'atom_style charge' and not 'atom_style atomic'

If you use pyCSH to make a data file which is compatible with the Erica force field, you will get a atom_style full format.

https://docs.lammps.org/read_data.html

dapang201 commented 1 month ago

Thank you very much for your help.