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:
--alm(FC_CALCULATOR = ALM)--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)--fc-symmetry(FC_SYMMETRY = .TRUE.)--fits-debye-model(DEBYE_MODEL = .TRUE.)--fmax(FMAX)--fmin(FMIN)--fpitch(FPITCH)--full-fc(FULL_FORCE_CONSTANTS)--gc,--gamma_center(GAMMA_CENTER)--gv,--group_velocity(GROUP_VELOCITY = .TRUE.)--gv-delta-q(GV_DELTA_Q)--hdf5(HDF5 = .TRUE.)--irreps(IRREPS)--include-fc(INCLUDE_FC = .TRUE.)--include-fs(INCLUDE_FS = .TRUE.)--include-born(INCLUDE_BORN = .TRUE.)--include-disp(INCLUDE_DISP = .TRUE.)--include-all(INCLUDE_ALL = .TRUE.)--lcg,--little_cogroup(LITTLE_COGROUP)--modulation(MODULATION)--moment(MOMENT = .TRUE.)--moment_order(MOMENT_ORDER)--mesh-format(MESH_FORMAT)--mp,--mesh(MPorMESH)--nac(NAC = .TRUE.)--nac-method(NAC_METHOD)--nosym(SYMMETRY = .FALSE.)--nomeshsym(MESH_SYMMETRY = .FALSE.)--nowritemesh(WRITE_MESH = .FALSE.)--pa,--primitive-axes(PRIMITIVE_AXES)--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)--tmin(TMIN)--tmax(TMAX)--tolerance(SYMMETRY_TOLERANCE)--tstep(TSTEP)--writedm(WRITEDM = .TRUE.)--writefc(WRITE_FORCE_CONSTANTS = .TRUE.)--writefc-format(WRITEFC_FORMAT)--xyz-projection(XYZ_PROJECTION = .TRUE.)
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 setting.conf [command-line-options]
Choice of force calculator¶
Currently interfaces for VASP, WIEN2k, Quantum ESPRESSO (QE), ABINIT,
Elk, SIESTA, CRYSTAL, TURBOMOLE and CP2K are prepared. These interfaces are invoked
with --vasp, --wienk2, --qe, --abinit, --elk,
--siesta, --crystal, --turbomole and --cp2k 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.
--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
--qe¶
Quantum ESPRESSO mode is invoked with this option. Usually this option
is used with --cell (-c) option or CELL_FILENAME tag to
read QE/PWscf input file that contains the unit cell crystal structure,
e.g.,
% phonopy --qe -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
--turbomole¶
TURBOMOLE mode is invoked with this option. Usually this option is used
with --cell (-c) option or CELL_FILENAME tag to read a TURBOMOLE
input file that contains the unit cell crystal structure, e.g.,
% phonopy --turbomole -c control band.conf
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
TURBOMOLE | control
CP2K | unitcell.inp
Create FORCE_SETS¶
-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 ...
Attention:
Site-projected wave function information (the same information as
PROCAR) siginificantly increases the size ofvasprun.xml. So parsing xml file uses huge memory space. It is recommendedto switch off to calculate it. If there are many displacements, shell expansions are useful, e.g.,
disp-*/vasprun.xml, ordisp-{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 ...
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.
--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.
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.