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2

Atomsk You can use this software to play with the structure and then, generate de coordinate file for you program. Atomsk is a free, Open Source command-line program dedicated to the creation, manipulation, and conversion of data files for atomic-scale simulations. It supports the file formats used by many programs, including: Visualization and analysis ...


4

You can either use python or MATLAB to generate the coordinates, or even use the built in tools in LAMMPS. To do this in LAMMPS, you only need to follow three steps. Use the lattice command to define the lattice type (diamond for Silicon) "https://docs.lammps.org/lattice.html". Use the region command to define a region with the desired dimensions....


5

I don't think you can build a nanoparticle using Avogadro, I personally use ASE which is a python package that can output a lot of different formats (xyz, cif, vasp, ...) You can directly output LAMMPS format using ASE or you can use Atomsk to convert whatever format to LAMMPS. By doing that you will obtain a "lammps-data" file, which needs to be ...


7

Your problem comes from the line: fix 11 A print v_com "coords of center of mass" file cdm.dat As per the documentation, the correct syntax is: fix ID group-ID print N string keyword value ... Where it will print every N timesteps. So you are asking LAMMPS to print the same message every v_com timesteps. And LAMMPS is respectfully ...


4

Resetting the atom IDs with the reset_atom_ids command can help with that. You can read more about it here. For the older version of LAMMPS, you may try reset_ids instead.


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