. _command_options:

Command options

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

• --amplitude (DISPLACEMENT_DISTANCE)
• --anime (ANIME)
• --ct (CHARACTER_TABLE)
• --dim (DIM)
• --mp, --mesh (MP)
• --band (BAND)
• --band_points (BAND_POINTS)
• --band_connection (BAND_CONNECTION = .TRUE.)
• --eigvecs, --eigenvectors (EIGENVECTORS = .TRUE.)
• --fits_debye_model (DEBYE_MODEL = .TRUE.)
• --gc, --gamma_center (GAMMA_CENTER)
• --modulation (MODULATION)
• --nac (NAC = .TRUE.)
• --pa, --primitive_axis (PRIMITIVE_AXIS)
• --pd, --projection_direction (PROJECTION_DIRECTION)
• --readfc (FORCE_CONSTANTS = READ)
• --sigma (SIGMA)
• -t (TPROP)
• --td (TDISP)
• --tmin (TMIN)
• --tmax (TMAX)
• --tstep (TSTEP)
• --writedm (WRITEDM = .TRUE.)
• --writefc (FORCE_CONSTANTS = WRITE)

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

Help (-h or --help)

Review of options is shown.

Create FORCE_SETS

-f or --forces and --fz

VASP interface

FORCE_SETS file is created from disp.yaml, which is an output file when creating supercell 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 vapsrun.xml files .

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

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).

--fz option is used to subtract residual forces in the equilibrium supercell.

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

Usually the -f option is preferable to --fz.

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=case.struct -f case_001/case_001.scf case_002/case_002.scf ...

For more information, Wien2k & phonopy calculation.

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 supercell and displacements

--dim

This works same as specifying the tag DIM (DIM).

--displacement or -d

This has to be used with --dim option.

% phonopy -d --dim="2 2 1"

--amplitude

To specify this option is same as setting the DISPLACEMENT_DISTANCE tag (DISPLACEMENT_DISTANCE).

Create primitive cell

--primitive_axis or --pa

This is shortcut of the setting tag PRIMITIVE_AXIS.

Graph plotting

-p

Result is plotted.

% phonopy -p

-p -s

Result is plotted (saved) to PDF file.

% phonopy -p -s

Mesh numbers

--mp

Same as the setting tag MP.

Thermal properties

-t, --tmax, --tmin, --tstep

These correspond to TPROP, TMAX, TMIN, and TSTEP tags, respectively (Thermal properties related tags).

Thermal displacements

--td, --tmax, --tmin, --tstep, --pd

These correspond to TDISP, TMAX, TMIN, TSTEP, and PROJECTION_DIRECTION tags, respectively (thermal displacements tags).

% phonopy --td --pd="1 1 0"

Smearing width

--sigma

Same as the setting tag SIGMA.

Calculate DOS

--dos

Density of states are calculated using this option with MP tag. When -p option with MP tag is set, --dos is automatically set. Therefore this tag is used when you want to calculate DOS, but you don’t need to plot.

Unit conversion factor

--factor

Unit conversion factor of frequency from input values to your favorite unit is specified. The default value is that of VASP to THz, which is calculated by /() (=15.633302) in SI base unit. When the wien2k option is specified, the default value is changed to 3.44595, which is the factor to convert from Wien2k to THz.

When calculating thermal property, the factor to THz is required. Otherwise the calculated thermal properties have wrong units. In the case of band structure plot, any factor can be used, where the frequency is simply shown in the unit you specified.

% phonopy --factor=521.471

Non-analytical term correction

--nac

Non-analytical term correction. See NAC tag (Non-analytical term correction).

Group velocity

--gv or --group_velocity

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, --wien2k, or --primitive_axis option.

--nosym

P1 symmetry is enforced to the input unit cell.

--nomeshsym

Symmetry search on the reciprocal sampling mesh is disabled.

Input cell

-c or --cell

Phonopy searches the POSCAR file in the current directory. Using this tag, you can specify another filename than POSCAR as the input unit cell.

% phonopy --cell=UPOSCAR

--wien2k

This option with WIEN2k struct file, phonopy runs with the WIEN2k mode. In this mode, you don’t need to prepare POSCAR. The supercells with displacements in WIEN2k struct format are created using -d option. The physical unit is changed to mRydberg and Bohr. Only the WIEN2k struct with the P lattice is supported. See more information Wien2k & phonopy calculation.

% phonopy --wien2k=case.struct

Read and write FORCE_CONSTANTS

--readfc

This option activates FORCE_CONSTANTS = READ instead of reading FORCES.

% phonopy --readfc

--writefc

This option sets FORCE_CONSTANTS = WRITE.

% phonopy --writefc --dim="2 2 2"