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:

  • --amplitude (DISPLACEMENT_DISTANCE)
  • --anime (ANIME)
  • --band (BAND)
  • --band-connection (BAND_CONNECTION = .TRUE.)
  • --band-format (BAND_FORMAT)
  • --band-labels (BAND_LABELS)
  • --band-points (BAND_POINTS)
  • --cutoff-freq (CUTOFF_FREQUENCY)
  • -c, --cell (CELL_FILENAME)
  • -d (CREATE_DISPLACEMENTS = .TRUE.
  • --dim (DIM)
  • --dos (DOS = .TRUE.)
  • --eigvecs, --eigenvectors (EIGENVECTORS = .TRUE.)
  • --factor (FREQUENCY_CONVERSION_FACTOR)
  • --fits-debye-model (DEBYE_MODEL = .TRUE.)
  • --fmax (FMAX)
  • --fmin (FMIN)
  • --fpitch (FPITCH)
  • --gc, --gamma_center (GAMMA_CENTER)
  • --gv, --group_velocity (GROUP_VELOCITY = .TRUE.)
  • --gv-delta-q (GV_DELTA_Q)
  • --hdf5 (HDF5 = .TRUE.)
  • --irreps (IRREPS)
  • --lcg, --little_cogroup (LITTLE_COGROUP)
  • --modulation (MODULATION)
  • --moment (MOMENT = .TRUE.)
  • --moment_order (MOMENT_ORDER)
  • --mesh-format (MESH_FORMAT)
  • --mp, --mesh (MP or MESH)
  • --nac (NAC = .TRUE.)
  • --nosym (SYMMETRY = .FALSE.)
  • --nomeshsym (MESH_SYMMETRY = .FALSE.)
  • --nowritemesh (WRITE_MESH = .FALSE.)
  • --pa, --primitive-axis (PRIMITIVE_AXIS)
  • --pd, --projection-direction (PROJECTION_DIRECTION)
  • --pdos (PDOS)
  • --pr, --pretend-real (PRETEND_REAL = .TRUE.)
  • --q-direction (Q_DIRECTION)
  • --qpoints (QPOINTS)
  • --qpoints-format (QPOINTS_FORMAT)
  • --readfc (READ_FORCE_CONSTANTS = .TRUE.)
  • --readfc-format (READFC_FORMAT)
  • --read-qpoints (QPOINTS = .TRUE.)
  • --show-irreps (SHOW_IRREPS)
  • --sigma (SIGMA)
  • -t (TPROP)
  • --td (TDISP)
  • --tdm (TDISPMAT)
  • --tdm-cif (TDISPMAT_CIF)
  • --thm, --tetrahedron-method (TETRAHEDRON)
  • --tmin (TMIN)
  • --tmax (TMAX)
  • --tstep (TSTEP)
  • --writedm (WRITEDM = .TRUE.)
  • --writefc (WRITE_FORCE_CONSTANTS = .TRUE.)
  • --writefc-format (WRITEFC_FORMAT)
  • --xyz-projection (XYZ_PROJECTION = .TRUE.)

When both of command-line option and setting tag for the same purpose are set simultaneously, the command-line options overide the setting tags.

Choice of force calculator

Currently interfaces for VASP, Wien2k, Pwscf, Abinit, and Elk are prepared. Wien2k, Pwscf, Abinit, Elk and CRYSTAL interfaces are invoked with --wienk2, --pwscf, --abinit, --elk and --crystal options, respectively, and if none of these options or --vasp option is specified, VASP mode is invoked.

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

--wien2k

Behavior is changed at phonopy 1.9.2.

This option invokes the WIEN2k mode.In this mode. Usually this option is used with --cell (-c) option or CELL_FILENAME tag to read WIEN2k crystal structure file.

% phonopy --wien2k -c NaCl.struct band.conf

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

For previous versions than 1.9.1.3, this option is used as

% phonopy --wien2k=NaCl.struct band.conf   (version <= 1.9.1.3)

--abinit

Abinit mode is invoked with this option. Usually this option is used with --cell (-c) option or CELL_FILENAME tag to read Abinit main input file that contains the unit cell crystal structure, e.g.,

% phonopy --abinit -c NaCl.in band.conf

--pwscf

Pwscf mode is invoked with this option. Usually this option is used with --cell (-c) option or CELL_FILENAME tag to read Pwscf input file that contains the unit cell crystal structure, e.g.,

% phonopy --pwscf -c NaCl.in band.conf

--siesta

Siesta mode is invoked with this option. Usually this option is used with --cell (-c) option or CELL_FILENAME tag to read a Siesta input file that contains the unit cell crystal structure, e.g.,

% phonopy --siesta -c Si.fdf band.conf

--elk

Elk mode is invoked with this option. Usually this option is used with --cell (-c) option or CELL_FILENAME tag to read Elk input file that contains the unit cell crystal structure, e.g.,

% phonopy --elk -c elk-unitcell.in band.conf

--crystal

CRYSTAL mode is invoked with this option. Usually this option is used with --cell (-c) option or CELL_FILENAME tag to read a CRYSTAL input file that contains the unit cell crystal structure, e.g.,

% phonopy --crystal -c crystal.o band.conf

--vasp

This doesn’t change the default behaviour, but vasp will appear as the calculator such as in band.yaml:

calculator: vasp
nqpoint: 204
...

Input cell

-c or --cell

Unit cell crystal structure file is specified with this tag.

% phonopy --cell=POSCAR-unitcell band.conf

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

VASP   | POSCAR
Wien2k | case.struct
Abinit | unitcell.in
Pwscf  | unitcell.in
Elk    | elk.in
CRYSTAL| crystal.o

Create FORCE_SETS

-f or --forces

VASP interface

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

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

Attention:

  • Site-projected wave function information (the same information as PROCAR) siginificantly increases the size of vasprun.xml. So parsing xml file uses huge memory space. It is recommended
  • to switch off to calculate it. 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 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 --abinit -f disp-001/supercell.out disp-002/supercell.out  ...

Pwscf interface

FORCE_SETS file is created from disp.yaml and Pwscf output files.

% phonopy --pwscf -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 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 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 --wien2k -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 disp.yaml and Elk output files.

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

CRYSTAL interface

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

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

--fz

--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.

Graph plotting

-p

Result is plotted.

% phonopy -p

-p -s

Result is plotted (saved) to PDF file.

% phonopy -p -s

Log level

-v or --verbose

More detailed log are shown

-q or --quiet

No log is shown.

Crystal symmetry

--tolerance

The specified value is used as allowed tolerance to find symmetry of crystal structure. The default value is 1e-5.

% phonopy --tolerance=1e-3

--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, --pwscf, --elk, --wien2k, --crystal or --primitive_axis option.