PHONOPY

NAME

phonopy - manual page for phonopy 2.16.2

DESCRIPTION

usage: phonopy [-h] [--abacus] [--abinit] [--aims] [--cp2k] [--crystal]

[--dftb+] [--elk] [--qe] [--siesta] [--turbomole] [--vasp] [--wien2k] [--castep] [--fleur] [--alm] [--amplitude DISPLACEMENT_DISTANCE] [--anime ANIME [ANIME ...]] [--band BAND_PATHS [BAND_PATHS ...]] [--band-connection] [--band-const-interval] [--band-labels BAND_LABELS [BAND_LABELS ...]] [--band-format BAND_FORMAT] [--band-points BAND_POINTS] [--bi BAND_INDICES [BAND_INDICES ...]] [-c FILE] [--cutoff-freq CUTOFF_FREQUENCY] [--cutoff-radius CUTOFF_RADIUS] [-d] [--dense-svecs] [--dim SUPERCELL_DIMENSION [SUPERCELL_DIMENSION ...]] [--dm-decimals DYNAMICAL_MATRIX_DECIMALS] [--dos] [--eigvecs] [-f CREATE_FORCE_SETS [CREATE_FORCE_SETS ...]] [--factor FREQUENCY_CONVERSION_FACTOR] [--fc FILE] [--fc-calc-opt FC_CALCULATOR_OPTIONS] [--fc-decimals FORCE_CONSTANTS_DECIMALS] [--fc-format FC_FORMAT] [--fc-spg-symmetry] [--fc-symmetry] [--fits-debye-model] [--freq-scale FREQUENCY_SCALE_FACTOR] [--full-fc] [--fz CREATE_FORCE_SETS_ZERO [CREATE_FORCE_SETS_ZERO ...]] [--fmax FMAX] [--fmin FMIN] [--fpitch FPITCH] [--gc] [--gv] [--gv-delta-q GV_DELTA_Q] [--hdf5] [--hdf5-compression HDF5_COMPRESSION] [--hiphive] [--irreps IRREPS_QPOINT [IRREPS_QPOINT ...]] [--include-fc] [--include-fs] [--include-born] [--include-disp] [--include-all] [--legend] [--legacy-plot] [--lcg] [--loglevel LOGLEVEL] [--mass MASSES [MASSES ...]] [--magmom MAGMOMS [MAGMOMS ...]] [--mesh-format MESH_FORMAT] [--modulation MODULATION [MODULATION ...]] [--mp MESH_NUMBERS [MESH_NUMBERS ...]] [--moment] [--moment-order MOMENT_ORDER] [--nac] [--nac-method NAC_METHOD] [--nodiag] [--nomeshsym] [--nosym] [--nowritemesh] [-p] [--pa PRIMITIVE_AXES [PRIMITIVE_AXES ...]] [--pd PROJECTION_DIRECTION [PROJECTION_DIRECTION ...]] [--pdos PDOS [PDOS ...]] [--pm] [--pr] [--pt] [--qpoints QPOINTS [QPOINTS ...]] [--qpoints-format QPOINTS_FORMAT] [--q-direction NAC_Q_DIRECTION [NAC_Q_DIRECTION ...]] [-q] [--random-seed RANDOM_SEED] [--rd RANDOM_DISPLACEMENTS] [--readfc] [--readfc-format READFC_FORMAT] [--read-qpoints] [-s] [--sp] [--show-irreps] [--sigma SIGMA] [--symmetry] [-t] [--td] [--tdm] [--tdm-cif TEMPERATURE] [--temperature TEMPERATURE] [--tmax TMAX] [--tmin TMIN] [--tolerance SYMMETRY_TOLERANCE] [--trigonal] [--tstep TSTEP] [-v] [--wien2k-p1] [--writefc] [--writefc-format WRITEFC_FORMAT] [--writedm] [--xyz-projection] [filename ...]

Phonopy command-line-tool

positional arguments:

filename

Phonopy configure file

options:

-h, --help

show this help message and exit

--abacus

Invoke ABACUS mode

--abinit

Invoke Abinit mode

--aims

Invoke FHI-aims mode

--cp2k

Invoke CP2K mode

--crystal

Invoke CRYSTAL mode

--dftb+

Invoke dftb+ mode

	--elk		Invoke elk mode
	--qe		Invoke Quantum espresso (QE) mode

--siesta

Invoke Siesta mode

--turbomole

Invoke TURBOMOLE mode

--vasp

Invoke Vasp mode

--wien2k

Invoke Wien2k mode

--castep

Invoke CASTEP mode

--fleur

Invoke Fleur mode

--alm

Use ALM for generating force constants

--amplitude DISPLACEMENT_DISTANCE

Distance of displacements

--anime ANIME [ANIME ...]

Same as ANIME tag

--band BAND_PATHS [BAND_PATHS ...]

Same behavior as BAND tag

--band-connection

Treat band crossings

--band-const-interval

Band paths are sampled with similar interval.

--band-labels BAND_LABELS [BAND_LABELS ...]

Show labels at band segments

--band-format BAND_FORMAT

Band structure output file-format

--band-points BAND_POINTS

Number of points calculated on a band segment in the band structure mode

--bi BAND_INDICES [BAND_INDICES ...], --band-indices BAND_INDICES
[BAND_INDICES ...]

Band indices to be included to calcualte thermal properties

-c FILE, --cell FILE

Read unit cell

--cutoff-freq CUTOFF_FREQUENCY, --cutoff-frequency CUTOFF_FREQUENCY

Thermal properties are not calculated below this cutoff frequency.

--cutoff-radius CUTOFF_RADIUS

Out of cutoff radius, force constants are set zero.

-d, --displacement

Create supercells with displacements

--dense-svecs

Pair shortest vectors in supercell are stored in dense format.

--dim SUPERCELL_DIMENSION [SUPERCELL_DIMENSION ...]

Same behavior as DIM tag

--dm-decimals DYNAMICAL_MATRIX_DECIMALS

Decimals of values of decimals

--dos

Calculate (P)DOS

--eigvecs, --eigenvectors

Output eigenvectors

-f CREATE_FORCE_SETS [CREATE_FORCE_SETS ...], --force-sets
CREATE_FORCE_SETS [CREATE_FORCE_SETS ...]

Create FORCE_SETS

--factor FREQUENCY_CONVERSION_FACTOR

Frequency unit conversion factor

--fc FILE, --force-constants FILE

Create FORCE_CONSTANTS from vaspurn.xml. vasprun.xml has to be passed as argument.

--fc-calc-opt FC_CALCULATOR_OPTIONS, --fc-calculator-options
FC_CALCULATOR_OPTIONS

Options for force constants calculator as comma separated string with the style of key = values

--fc-decimals FORCE_CONSTANTS_DECIMALS

Decimals of values of force constants

--fc-format FC_FORMAT

Force constants input/output file-format

--fc-spg-symmetry

Enforce space group symmetry to force constants

--fc-symmetry, --sym-fc

Symmetrize force constants

--fits-debye-model

Fits total DOS to a Debye model

--freq-scale FREQUENCY_SCALE_FACTOR

Squared scale factor multiplied as fc2 * factorˆ2. Therefore frequency is changed but the contribution from NAC is not changed.

--full-fc

Calculate full supercell force constants matrix

--fz CREATE_FORCE_SETS_ZERO [CREATE_FORCE_SETS_ZERO ...], --force-sets-zero
CREATE_FORCE_SETS_ZERO [CREATE_FORCE_SETS_ZERO ...]

Create FORCE_SETS. disp.yaml in the current directory and vapsrun.xml’s for VASP or case.scf(m) for Wien2k as arguments are required. The first argument is that of the perfect supercell to subtract residual forces

--fmax FMAX

Maximum frequency used for DOS or moment calculation

--fmin FMIN

Minimum frequency used for DOS or moment calculation

--fpitch FPITCH

Frequency pitch used for DOS or moment calculation

--gc, --gamma-center

Set mesh as Gamma center

--gv, --group-velocity

Calculate group velocities at q-points

--gv-delta-q GV_DELTA_Q

Delta-q distance used for group velocity calculation

--hdf5

Use hdf5 for force constants

--hdf5-compression HDF5_COMPRESSION

hdf5 compression filter (default: gzip)

--hiphive

Use hiPhive for generating force constants

--irreps IRREPS_QPOINT [IRREPS_QPOINT ...], --irreps-qpoint IRREPS_QPOINT
[IRREPS_QPOINT ...]

A q-point where characters of irreps are calculated

--include-fc

Include force constants in phonopy.yaml

--include-fs

Include force sets in phonopy.yaml

--include-born, --include-nac-params

Include born effective charge and dielectric tensor in phonopy.yaml

--include-disp

Include displacements in phonopy.yaml

--include-all

Include all output file data in phonopy.yaml

--legend

Legend of plots is shown in thermal displacements

--legacy-plot

Legacy style band structure pl

--lcg, --little-cogroup

Show irreps of little co-group (or point-group of wave vector q) instead of little group

--loglevel LOGLEVEL

Log level

--mass MASSES [MASSES ...]

Same as MASS tag

--magmom MAGMOMS [MAGMOMS ...]

Same as MAGMOM tag

--mesh-format MESH_FORMAT

Mesh output file-format

--modulation MODULATION [MODULATION ...]

Same as MODULATION tag

--mp MESH_NUMBERS [MESH_NUMBERS ...], --mesh MESH_NUMBERS [MESH_NUMBERS
...]

Same behavior as MP tag

--moment

Calculate moment of phonon states distribution

--moment-order MOMENT_ORDER

Order of moment of phonon states distribution

--nac

Non-analytical term correction

--nac-method NAC_METHOD

Non-analytical term correction method: Gonze (default) or Wang

--nodiag

Set displacements parallel to axes

--nomeshsym

Symmetry is not imposed for mesh sampling.

--nosym

Symmetry is not imposed.

--nowritemesh

Do not write mesh.yaml or mesh.hdf5

-p, --plot

Plot data

--pa PRIMITIVE_AXES [PRIMITIVE_AXES ...], --primitive-axis PRIMITIVE_AXES
[PRIMITIVE_AXES ...], --primitive-axes PRIMITIVE_AXES [PRIMITIVE_AXES ...]

Same as PRIMITIVE_AXES tag

--pd PROJECTION_DIRECTION [PROJECTION_DIRECTION ...],
--projection-direction PROJECTION_DIRECTION [PROJECTION_DIRECTION ...]

Same as PROJECTION_DIRECTION tag

--pdos PDOS [PDOS ...]

Same as PDOS tag

--pm

Set plus minus displacements

--pr, --pretend-real

Use imaginary frequency as real for thermal property calculation. For a testing purpose only, when a small amount of imaginary branches obtained.

--pt, --projected-thermal-property

Output projected thermal properties

--qpoints QPOINTS [QPOINTS ...]

Calculate at specified q-points

--qpoints-format QPOINTS_FORMAT

Q-points output file-format

--q-direction NAC_Q_DIRECTION [NAC_Q_DIRECTION ...]

Direction of q-vector perturbation used for NAC at q->0, and group velocity for degenerate phonon mode in q-points mode

-q, --quiet

Print out smallest information

--random-seed RANDOM_SEED

Random seed by a 32 bit unsigned integer

--rd RANDOM_DISPLACEMENTS, --random-displacements RANDOM_DISPLACEMENTS

Number of supercells with random displacements

--readfc

Read FORCE_CONSTANTS

--readfc-format READFC_FORMAT

Force constants input file-format

--read-qpoints

Read QPOITNS

-s, --save

Save plot data in pdf

--sp, --save-params

Save parameters that can run phonopy in phonopy_params.yaml.

--show-irreps

Show IR-Reps along with characters

--sigma SIGMA

Smearing width for DOS

--symmetry

Check crystal symmetry

-t, --thermal-property

Output thermal properties

--td, --thermal-displacements

Output thermal displacements

--tdm, --thermal-displacement-matrix

Output thermal displacement matrices

--tdm-cif TEMPERATURE, --thermal-displacement-matrix-cif TEMPERATURE

Write cif with aniso_U for which temperature is specified

--temperature TEMPERATURE

A temperature point

--tmax TMAX

Maximum calculated temperature

--tmin TMIN

Minimum calculated temperature

--tolerance SYMMETRY_TOLERANCE

Symmetry tolerance to search

--trigonal

Set displacements of all trigonal axes

--tstep TSTEP

Calculated temperature step

-v, --verbose

Detailed information is shown.

--wien2k-p1

Assume Wien2k structs with displacements are P1

--writefc

Write FORCE_CONSTANTS

--writefc-format WRITEFC_FORMAT

Force constants output file-format

--writedm

Write dynamical matrices. This has to be used with QPOINTS setting (or --qpoints)

--xyz-projection

Project PDOS x, y, z directions in Cartesian coordinates