The procedure of a Siesta-phonopy calculation is the following:
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.
xxx are numbers) give the perfect
supercell and supercells with displacements, respectively. In these
supercell files, lines only relevant to crystal structures are
disp.yaml is also created. This file contains
information on displacements. Perhaps the supercell files are
disp-xxx directories, then Siesta calculations are
executed in these directories.
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.
% phonopy --siesta -f disp-001/Si.FA ...
*.FA files are the forces files created by Siesta.
To run this command,
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
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]