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 supercell-xxx.in 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

    or:

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