I want to impose reflecting BCs at the non-periodic direction of my simulation box. To this end I need to use fix wall/reflect
Is there any way for direct inclusion of this command in PyIron?
Best regards
2 Answers
wall/reflect is currently not natively supported by pyiron, but if you know the LAMMPS command, you can include it for example via:
job.input.control['fix___fixname'] = 'all wall/reflect xlo EDGE xhi EDGE'
(I took the first example on the LAMMPS page you shared). If your LAMMPS input is not too complicated, this pyiron should be able to place this command in the appropriate position.
Sams's solution is definitely the easiest way if you just want to insert one fix. But you can even load full LAMMPS scripts inside pyiron, here is an example: https://github.com/jan-janssen/pyiron-free-energy/blob/master/free_energy.ipynb
The important part is to keep the read_data structure.inp and the include potential.inp to use the structure and interatomic potential defined by pyiron. Finally if you also copy the dump, dump_modify and thermo part you can use the pyiron parsers, otherwise you can always parse the output yourself, like I demonstrated in the above example.
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