Command options

Command options#

From phonopy v1.12.2, the command option names with underscores _ are replaced by those with dashes -. Those tag names are unchanged.

Some of command-line options are equivalent to respective setting tags:

When both of equivalent command-line option and setting tag are set simultaneously, the command-line option supersedes the setting tag. The configuration file is recommended to place at the first position for the mixed use of setting tags and command-line options, i.e.,

% phonopy-load --config setting.conf [OPTIONS]

Choice of force calculator#

Currently interfaces for VASP, WIEN2k, Quantum ESPRESSO (QE), ABINIT, Elk, SIESTA, CRYSTAL, TURBOMOLE, Fleur, CP2K and Questaal are prepared. These interfaces are invoked with --vasp, --wienk2, --qe, --abinit, --elk, --siesta, --crystal, --turbomole, --fleur, --cp2k and --qlm options, respectively. When no interface is specified, --vasp is selected as the default interface.

The details about these interfaces are found at Interfaces to calculators.

--abinit#

Abinit mode is invoked with this option.

--cp2k#

CP2K mode is invoked with this option.

--crystal#

CRYSTAL mode is invoked with this option.

--elk#

Elk mode is invoked with this option.

--fleur#

Fleur mode is invoked with this option.

--qe#

Quantum ESPRESSO mode is invoked with this option.

--siesta#

Siesta mode is invoked with this option.

--turbomole#

TURBOMOLE mode is invoked with this option.

--vasp#

With this option, the calculator name vasp will appear in phonopy.yaml type files.

--wien2k#

This option invokes the WIEN2k mode.

--qlm#

This option invokes the Questaal/LMTO mode.

Only the WIEN2k struct with the P lattice is supported. See more information Wien2k & phonopy calculation.

Input cell#

-c or --cell#

phonopy-load doesn’t have this option.

Unit cell crystal structure file is specified with this tag.

% phonopy -c POSCAR-unitcell [OPTIONS]

Without specifying this tag, default file name is searched in current directory. The default file names for the calculators are as follows:

Calculator

Default crystal structure file name

VASP

POSCAR

WIEN2k

case.struct

ABINIT

unitcell.in

PWscf

unitcell.in

Elk

elk.in

CRYSTAL

crystal.o

TURBOMOLE

control

Fleur

fleur.in

CP2K

unitcell.inp

Questaal/LMTO

site.lm

Create FORCE_SETS#

FORCE_SETS is a file containing the displacement-force dataset from which supercell force constants will be calculated. The command option -f or --fz is used to collect displacements in phonopy_disp.yaml and forces from force calculator results if the corresponding interface exists in phonopy.

When combined with the --sp or --save-params option, this enables writing the displacement-force dataset to phonopy_params.yaml. If the force calculator interface supports reading supercell potential energy (e.g., electronic total energy in the case of VASP), supercell energies are also stored in phonopy_params.yaml. These supercell energies can be used to develop machine learning potentials such as pypolymlp. See Create phonopy_params.yaml.

-f or --forces#

VASP interface#

FORCE_SETS file is created from phonopy_disp.yaml, which is an output file when creating supercells with displacements, and vasprun.xml’s, which are the VASP output files. phonopy_disp.yaml in the current directory is automatically read. The order of displacements written in phonopy_disp.yaml file has to correpond to that of vasprun.xml files.

% phonopy -f disp-001/vasprun.xml disp-002/vasprun.xml ...

Note

  • Site-projected wave function information (the same information as PROCAR) significantly increases the size of vasprun.xml. So parsing xml files generated this way incurs huge memory costs. Therefore, this is not recommended.

  • If there are many displacements, shell expansions are useful, e.g., disp-*/vasprun.xml, or disp-{001..128}/vasprun.xml (for zsh, and recent bash).

ABINIT interface#

FORCE_SETS file is created from phonopy_disp.yaml and ABINIT output files (*.out). In the reading of forces in ABINIT output files, forces in eV/Angstrom are read. The unit conversion factor is determined with this unit.

% phonopy -f disp-001/supercell.out disp-002/supercell.out ...

Quantum ESPRESSO interface#

FORCE_SETS file is created from phonopy_disp.yaml and QE-PW output files.

% phonopy -f disp-001/supercell.out disp-002/supercell.out ...

Here *.out files are the saved texts of standard outputs of PWscf calculations.

WIEN2k interface#

This is experimental support to generage FORCE_SETS. Insted of this, you can use the external tool called scf2forces to generate FORCE_SETS. scf2forces is found at http://www.wien2k.at/reg_user/unsupported/.

FORCE_SETS file is created from phonopy_disp.yaml, which is an output file when creating supercell with displacements, and case.scf’s, which are the WIEN2k output files. The order of displacements in phonopy_disp.yaml file and the order of case.scf’s have to be same. For WIEN2k struct file, only negative atom index with the P lattice format is supported.

% phonopy -f case_001/case_001.scf case_002/case_002.scf ...

For more information, Wien2k & phonopy calculation.

Elk interface#

FORCE_SETS file is created from phonopy_disp.yaml and Elk output files.

% phonopy -f disp-001/INFO.OUT disp-002/INFO.OUT ...

CRYSTAL interface#

FORCE_SETS file is created from phonopy_disp.yaml and CRYSTAL output files.

% phonopy -f supercell-001.o supercell-002.o ...

TURBOMOLE interface#

FORCE_SETS file is created from phonopy_disp.yaml and TURBOMOLE output files.

% phonopy -f supercell-001 supercell-002 ...

Fleur interface#

FORCE_SETS file is created from phonopy_disp.yaml and special Fleur FORCES output files.

% phonopy -f disp-001/FORCES disp-002/FORCES ...

CP2K interface#

FORCE_SETS file is created from phonopy_disp.yaml and CP2K output files, with:

% phonopy -f supercell-001-forces-1_0.xyz supercell-002-forces-1_0.xyz ...

Please note: the files containing the forces can be prefixed with the PROJECT_NAME as specified in the original CP2K input file.

Questaal/LMTO interface#

FORCE_SETS file is created from phonopy_disp.yaml and force files, with:

% phonopy --qlm -f supercell-001/force.lm supercell-002/force.lm ...

--fz#

phonopy-load doesn’t have this option.

--fz option is used to subtract residual forces frown the forces calculated for the supercells with displacements. Here the residual forces mean that the forces calculated for the perfect supercell for which the number of atoms has to be the same as those for the supercells with displacements. If the forces are accurately calculated by calculators, the residual forces should be canceled when plus-minus displacements are employed (see PM), that is the default option in phonopy. Therefore --fz option is expected to be useful when PM = .FALSE. is set in the phonopy setting file.

The usage of this option is almost the same as that of -f option except that one more argument is inserted at the front. Mind that --fz is exclusively used with -f option. The example for the VASP interface is shown below:

% phonopy --fz sposcar/vasprun.xml disp-001/vasprun.xml ...

where sposcar/vasprun.xml assumes the output file for the perfect supercell containing residual forces.

This option perhaps works for the other calculator interfaces than the VASP interface, but it is not tested yet. It would be appreciated if you report it to the phonopy mailing list when you find it does/doesn’t work for any other calculator interfaces.

Create FORCE_CONSTANTS#

--fc or --force_constants#

Currently this option supports only VASP output.

VASP output of force constants is imported from vasprun.xml and FORCE_CONSTANTS is created.

% phonopy --fc vasprun.xml

This FORCE_CONSTANTS can be used instead of FORCE_SETS. For more details, please refer VASP-DFPT & phonopy calculation.

Create phonopy_params.yaml#

phonopy_params.yaml thus created by --sp option contains the necessary information to run phonopy. Therefore only this file can be given to other user as the phonopy input file.

--sp or --save-params#

After running phonopy, displacement-force dataset or force constants and parameters for non-analytical term correction are written in phonopy_params.yaml if these data are used.

When using with -f, displacement-force dataset are stored in phonopy_params.yaml instead of FORCE_SETS. When BORN file is found in the current directory, the parameters are also stored in phonopy_params.yaml.

% phonopy --sp -f disp-001/vasprun.xml disp-002/vasprun.xml ...

Graph plotting#

-p#

Result is plotted.

% phonopy-load -p

-p -s#

Result is plotted (saved) to PDF file.

% phonopy-load -p -s

Log level#

-v or --verbose#

More detailed log are shown

-q or --quiet#

No log is shown.

Crystal symmetry#

--symmetry#

Using this option, various crystal symmetry information is just printed out and phonopy stops without going to phonon analysis.

% phonopy --symmetry

This tag can be used together with the --cell (-c), --abinit, --qe, --elk, --wien2k, --siesta, --crystal or --primitive-axes option.

After running this, BPOSCAR and PPOSCAR files are written, which are the symmetrized conventional unit cell and primitive cell, respectively, in the VASP style format.

Contents