Auxiliary tools

A few auxiliary tools are prepared. They are stored in bin directory as well as phonopy.

phonopy-bandplot

Band structure is plotted reading phonopy output in band.yaml format. -o option with a file name is used to save the plot into a file in PDF format. A few more options are prepared and shown by -h option. If you specify more than two yaml files, they are plotted together.

phonopy-bandplot band.yaml

To obtain a simple text format data:

phonopy-bandplot --gnuplot band.yaml

phonopy-pdosplot

Partial density of states (PDOS) are plotted.

-i option is used as

phonopy-pdosplot -i '1 2 4 5, 3 6' -o 'pdos.pdf' partial_dos.dat

The indices and comma in ‘1 2 3 4, 5 6’ mean as follows. The indices are separated into blocks by comma (1 2 4 5 and 3 6). PDOS specified by the successive indices separated by space in each block are summed up. The PDOS of blocks are drawn simultaneously. Indices usually correspond to atoms. A few more options are prepared and shown by -h option.

phonopy-propplot

Thermal properties are plotted. Options are prepared and shown by -h option. If you specify more than two yaml files, they are plotted together.

phonopy-proplot thermal_properties_A.yaml thermal_properties_B.yaml

phonopy-dispmanager

This is used for two purposes.

The first argument is the displacement file (disp.yaml type). The default file name is disp.yaml.

-a, --amplitude, -s, -o, --overwite

-o is used to specify the output file name of the new displacement file and --overwrite is used to overwrite the displacement file.

-a is specified with an atom index and a direction of displacement as a character string. The first value is the atom index and remaining three values are for direction. --amplitude is used with -a and specify the displacement amplitude. An example is as follows:

phonopy-dispmanager disp.yaml -o disp-new.yaml -a "33 1 1 0" --amplitude 0.05

disp-new.yaml is created from disp.yaml with a new displacement of the thirty-third atom (index 33) with the direction of (1,1,0) with the amplitude of 0.05. The direction is defined against lattice vectors. The amplitude unit is same as the lattice vectors.

-s is specified with displacement indices. For example when there are four dependent displacements and only the first and third displacements are needed, phonopy-dispmanager is used like

phonopy-dispmanager disp.yaml -o disp-new.yaml -s "1 3"

-w

The option is used to create supercells with displacements in POSCAR format from a displacement file. DPOSCAR-xxx files are created.

--compatibility

The old style displacement file DISP is compared with disp.yaml whether the directions of the displacements are equivalent or not.

phonopy-vasp-born

This script is used to create a BORN style file from VASP output file of vasprun.xml. The first argument is a vasprun.xml file. If it is ommited, vasprun.xml at current directory are read. The Born effective charges and dielectric tensor are symmetrized as default. To prevent symmetrization, --nost option has to be specified.

phonopy-vasp-born
phonopy-vasp-born --nost

--dim

This is same as CELL_FILENAME.

--nost

Dielectric constant and Born effective charge tensors are not symmetrized.

--outcar

Read OUTCAR instead of vasprun.xml. Without specifying arguments, OUTCAR and POSCAR at current directory are read. POSCAR information is necessary in contrast to reading vasprun.xml where the unit cell structure is also read from it.

phonopy-vasp-born --outcar
phonopy-vasp-born --nost --outcar OUTCAR POSCAR