phonopy/example/Si-lammps

Si example using LAMMPS interface

The pair_style of polymlp is a LAMMPS module of the polynomial machine learning potentials provided at https://sekocha.github.io/lammps/index-e.html. For the silicon calculation found in the example directory, mlp.lammp of gtinv-289 was obtained from Polynomial Machine Learning Potential Repository at Kyoto University.

This example shows how to generate supercells from non-LAMMPS structure but the structure defined in yaml style format. This is not supported by usual phonopy command line interface. So a python script that runs this task using phonopy-API is provided in this example directory. See also the documentation of the phonopy LAMMPS interface.

1. Generate supercells using a python script

   % python generate_displacements.py
   

   The supercell-001 LAMMPS structure file follows the LAMMPS structure input format. The basis vectors are rotated from that defined in phonopy_disp.yaml. Therefore forces as obtained LAMMPS calculation have to be rotated back to the original coordinate system, which is performed automatically in the step 3.

2. Run LAMMPS

   % lmp_serial -in in.polymlp
   

   Suppose that the LAMMPS output file name is removed to lammps_forces_Si.0 after the LAMMPS calculation.

3. Make FORCE_SETS

   % phonopy -f lammps_forces_Si.0
           _
     _ __ | |__   ___  _ __   ___   _ __  _   _
    | '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |
    | |_) | | | | (_) | | | | (_) || |_) | |_| |
    | .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |
    |_|                            |_|    |___/
                                         2.18.0
   
   Compiled with OpenMP support (max 10 threads).
   Python version 3.11.0
   Spglib version 2.0.2
   
   Calculator interface: lammps
   Displacements were read from "phonopy_disp.yaml".
   1. Drift force of "lammps_forces_Si.0" to be subtracted
    -0.00000000  -0.00000000  -0.00000000
   Forces parsed from LAMMPS output were rotated by F=R.F(lammps) with R:
     0.00000 0.57735 0.57735
     0.70711 0.57735 0.57735
     0.70711 -0.57735 -0.57735
   "FORCE_SETS" has been created.
                    _
      ___ _ __   __| |
     / _ \ '_ \ / _` |
    |  __/ | | | (_| |
     \___|_| |_|\__,_|
   

   The rotation of forces is performed and the rotation matrix is found in last lines of the output.