phonopy command

phonopy command#

The phonopy command runs the phonon calculation step of the workflow. It reads a phonopy.yaml-like file (phonopy-yaml format), constructs the phonon, and emits the requested property (band structure, mesh sampling, DOS, thermal properties, group velocity, …).

To prepare displacements and to convert calculator results into the phonopy input format (FORCE_SETS, FORCE_CONSTANTS) use phonopy-init command.

Example#

In the NaCl example for the VASP calculator,

% phonopy-init -d --dim 2 2 2 --pa auto -c POSCAR-unitcell
% phonopy-init --sp -f vasprun.xml-00{1,2}

In the NaCl-qe example for the QE calculator,

% phonopy-init --qe -d --dim 2 2 2 --pa auto -c NaCl.in
% phonopy-init --sp -f NaCl-00{1,2}.out

The first and second commands create phonopy_disp.yaml and phonopy_params.yaml, respectively.

Once the phonopy_xxx.yaml file is available, the phonon calculation is run as the post-process:

% phonopy --band auto -p phonopy_params.yaml

phonopy can read files with the following extensions: xz, lzma, gz, and bz2. Therefore when the file size of phonopy_params.yaml is large, it is recommended to compress it.

% xz phonopy_params.yaml
% phonopy --band auto -p phonopy_params.yaml.xz

Behaviour#

  • phonopy_xxx.yaml-like file (phonopy-yaml format) is always required, provided in either of two ways:

    1. phonopy_xxx.yaml-like file is given as the first argument of the command.

    2. phonopy_disp.yaml or phonopy.yaml is placed in the current directory. The search preference is phonopy_disp.yaml > phonopy.yaml.

  • The -c option (read crystal structure separately) does not exist — the crystal structure is read from the yaml file.

  • Use of command options is recommended, but a phonopy configuration file (Configuration file) can be read through --config option.

  • If parameters for non-analytical term correction (NAC) are found, NAC is automatically enabled. This can be disabled by --nonac option.

  • When force constants are calculated from displacements and forces dataset, force constants are automatically symmetrized. From phonopy v2.30.0, symfc is used for the symmetrization. From phonopy v2.41.0, symfc-projector is used to symmetrize force constants calculated by the finite difference approach. The old behavior of the symmetrization can be performed by --fc-calculator traditional option. The --no-sym-fc option can be used to calculate force constants in the traditional force constants calculator without symmetrization.

Relation to phonopy-load#

phonopy-load is the historical name of this command and is kept as a deprecated alias. It emits a warning and otherwise behaves identically to phonopy. Use phonopy in new scripts.