phonopy/example/Ti-lammps

HCP Ti 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 HCP Ti calculation found in the example directory, mlp.lammp of gtinv-294 was obtained from Polynomial Machine Learning Potential Repository at Kyoto University.

1. Read a lammps input structure file and create supercells with

   % phonopy --lammps -c lammps_structure_Ti -d --dim 4 4 3
           _
     _ __ | |__   ___  _ __   ___   _ __  _   _
    | '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |
    | |_) | | | | (_) | | | | (_) || |_) | |_| |
    | .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |
    |_|                            |_|    |___/
                                         2.18.0
   
   Compiled with OpenMP support (max 10 threads).
   Python version 3.10.8
   Spglib version 2.0.2
   
   Calculator interface: lammps
   Crystal structure was read from "lammps_structure_Ti".
   Unit of length: angstrom
   Displacements creation mode
   Settings:
     Supercell: [4 4 3]
   Spacegroup: P6_3/mmc (194)
   Use -v option to watch primitive cell, unit cell, and supercell structures.
   
   "phonopy_disp.yaml" and supercells have been created.
   
   Summary of calculation was written in "phonopy_disp.yaml".
                    _
      ___ _ __   __| |
     / _ \ '_ \ / _` |
    |  __/ | | | (_| |
     \___|_| |_|\__,_|
   

2. Run LAMMPS

   % lmp_serial -in in.polymlp
   

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

3. Make FORCE_SETS

   % phonopy -f lammps_forces_Ti.0
           _
     _ __ | |__   ___  _ __   ___   _ __  _   _
    | '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |
    | |_) | | | | (_) | | | | (_) || |_) | |_| |
    | .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |
    |_|                            |_|    |___/
                                         2.18.0
   
   Compiled with OpenMP support (max 10 threads).
   Python version 3.10.8
   Spglib version 2.0.2
   
   Calculator interface: lammps
   Displacements were read from "phonopy_disp.yaml".
   1. Drift force of "lammps_forces_Ti.0" to be subtracted
    -0.00000000  -0.00000000   0.00000000
   Forces parsed from LAMMPS output were rotated by F=R.F(lammps) with R:
     1.00000 0.00000 0.00000
     0.00000 0.00000 0.00000
     0.00000 1.00000 1.00000
   "FORCE_SETS" has been created.
                    _
      ___ _ __   __| |
     / _ \ '_ \ / _` |
    |  __/ | | | (_| |
     \___|_| |_|\__,_|