Siesta & phonopy calculation

Siesta & phonopy calculation#

Supported Siesta tags#

Currently phonopy can read the siesta tags listed below. More tags may be supported on request.

AtomicCoordinatesFormat, ChemicalSpeciesLabel, AtomicCoordinatesFormat,
AtomicCoordinatesAndAtomicSpecies, LatticeVectors

How to run#

The procedure of a Siesta-phonopy calculation is the following:

  1. Read a Siesta input file and create supercells with --siesta option:

    % phonopy --siesta -d --dim="2 2 2" -c Si.fdf

    In this example, 2x2x2 supercells are created. supercell.fdf and supercell-xxx.fdf (xxx are numbers) give the perfect supercell and supercells with displacements, respectively. In these supercell files, lines only relevant to crystal structures are generated. phonopy_disp.yaml is also created. This file contains information on displacements. Perhaps the supercell files are stored in disp-xxx directories, then Siesta calculations are executed in these directories.

  2. Calculate forces on atoms in the supercells with displacements. Calculation specification tags have to be added to files. Crystal structure is not allowed to relax in the force calculations, because atomic forces induced by a small atomic displacement are what we need for the phonon calculation.

  3. Create FORCE_SETS by

    % phonopy --siesta -f disp-001/Si.FA ...

    Here *.FA files are the forces files created by Siesta. To run this command, phonopy_disp.yaml has to be located in the current directory because the atomic displacements are written into the FORCE_SETS file. An example is found in example/Si-siesta.

  4. Run post-process of phonopy with the Siesta input file for the unit cell used in the step 1:

    % phonopy --siesta -c Si.fdf -p band.conf


    % phonopy --siesta -c Si.fdf --dim="2 2 2" [other-OPTIONS] [setting-file]