# Setting tags#

Most of the setting tags have respective command-line options (Command options). 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]
```

For specifying real and reciprocal points, fractional values (e.g. `1/3`

) are
accepted. However fractional values must not have space among characters (e.g.
`1 / 3`

) are not allowed.

## Thermal displacements#

`TDISP`

, `TMAX`

, `TMIN`

, and `TSTEP`

#

Mean square displacements projected to Cartesian axes as a function of
temperature are calculated from the number of phonon excitations. The usages of
`TMAX`

, `TMIN`

, `TSTEP`

tags are same as those in
thermal properties tags. Phonon frequencies in
THz, which is the default setting of phonopy, are used to obtain the mean square
displacements, therefore physical units have to be set properly for it (see
Interfaces to calculators.) The result is given in \(\text{Angstrom}^2\)
and writen into `thermal_displacements.yaml`

. See the detail of the method,
Thermal displacement. These tags must be used with
Mesh sampling tags

Optionally, `FMIN`

tag (`--fmin`

option) with a small value is recommened to be
set when q-points at \(\Gamma\) point or near \(\Gamma\) point (e.g.
using very dense sampling mesh) are sampled to avoid divergence. `FMAX`

tag
(`--fmax`

option) can be used to specify an upper bound of phonon frequencies
where the phonons are considered in the summation. The projection is applied
along arbitrary direction using `PROJECTION_DIRECTION`

tag
(PROJECTION_DIRECTION).

`mesh.yaml`

or `mesh.hdf5`

is not written out from phonopy-1.11.14.

```
TDISP = .TRUE.
PROJECTION_DIRECTION = 1 1 0
```

`TDISPMAT`

, `TMAX`

, `TMIN`

, and `TSTEP`

#

Mean square displacement matrices are calculated. The definition is shown at
Thermal displacement. Phonon frequencies in THz, which is the default
setting of phonopy, are used to obtain the mean square displacement matrices,
therefore physical units have to be set properly for it (see
Interfaces to calculators.) The result is given in \(\text{Angstrom}^2\)
and written into `thermal_displacement_matrices.yaml`

where six matrix elements
are given in the order of xx, yy, zz, yz, xz, xy. In this yaml file,
`displacement_matrices`

and `displacement_matrices_cif`

correspond to
\(\mathrm{U}_\text{cart}\) and \(\mathrm{U}_\text{cif}\) defined at
Mean square displacement matrix, respectively.

Optionally, `FMIN`

tag (`--fmin`

option) with a small value is recommended to be
set when q-points at \(\Gamma\) point or near \(\Gamma\) point (e.g.
using very dense sampling mesh) are sampled to avoid divergence. `FMAX`

tag
(`--fmax`

option) can be used to specify an upper bound of phonon frequencies
where the phonons are considered in the summation.

The 3x3 matrix restricts distribution of each atom around the equilibrium position to be ellipsoid. But the distribution is not necessarily to be so.

`mesh.yaml`

or `mesh.hdf5`

is not written out from phonopy-1.11.14.

```
TDISPMAT = .TRUE.
```

`TDISPMAT_CIF`

#

This tag specifies a temperature (K) at which thermal displacement is calculated
and the mean square displacement matrix is written to the cif file
`tdispmat.cif`

with the dictionary item `aniso_U`

. Phonon frequencies in THz,
which is the default setting of phonopy, are used to obtain the mean square
displacement matrices, therefore physical units have to be set properly for it
(see Interfaces to calculators.) The result is given in
\(\textrm{Angstrom}^2\).

`mesh.yaml`

or `mesh.hdf5`

is not written out from phonopy-1.11.14.

```
TDISPMAT_CIF = 1273.0
```

## Specific q-points#

`QPOINTS`

#

When q-points are supplied, those phonons are calculated. Q-points are specified successive values separated by spaces and collected by every three values as vectors in reciprocal reduced coordinates.

```
QPOINTS = 0 0 0 1/2 1/2 1/2 1/2 0 1/2
```

With `QPOINTS = .TRUE.`

, q-points are read from `QPOITNS`

file (see the file
format at QPOINTS) in current directory phonons at the
q-points are calculated.

```
QPOINTS = .TRUE.
```

`WRITEDM`

#

```
WRITEDM = .TRUE.
```

Dynamical matrices \(D\) are written into `qpoints.yaml`

in the following
\(6N\times3N\) format, where *N* is the number of atoms in the primitive
cell.

The physical unit of dynamical matrix is
`[unit of force] / ([unit of displacement] * [unit of mass])`

, i.e., square of
the unit of phonon frequency before multiplying the unit conversion factor (see
FREQUENCY_CONVERSION_FACTOR).

and \(D_{jj'}\) is

where *j* and *j’* are the atomic indices in the primitive cell. The phonon
frequencies may be recovered from `qpoints.yaml`

by writing a simple python
script. For example, `qpoints.yaml`

is obtained for NaCl at
\(q=(0, 0.5, 0.5)\) by

```
phonopy --qpoints="0 1/2 1/2" --writedm
```

and the dynamical matrix may be used as

```
import yaml
import numpy as np
data = yaml.load(open("qpoints.yaml"))
dynmat = []
dynmat_data = data['phonon'][0]['dynamical_matrix']
for row in dynmat_data:
vals = np.reshape(row, (-1, 2))
dynmat.append(vals[:, 0] + vals[:, 1] * 1j)
dynmat = np.array(dynmat)
eigvals, eigvecs, = np.linalg.eigh(dynmat)
frequencies = np.sqrt(np.abs(eigvals.real)) * np.sign(eigvals.real)
conversion_factor_to_THz = 15.633302
print frequencies * conversion_factor_to_THz
```

## Non-analytical term correction#

`NAC`

#

Non-analytical term correction is applied to dynamical matrix. `BORN`

file has
to be prepared in the current directory. See BORN (optional) and
Non-analytical term correction. The default method is
`NAC_METHOD = GONZE`

after v1.13.0.

```
NAC = .TRUE.
```

`NAC_METHOD`

#

The method of non-analytical term correction is chosen by this tag between two,
`NAC_METHOD = GONZE`

(Correction by dipole-dipole interaction) and `NAC_METHOD = WANG`

(Interpolation scheme at general q-points with non-analytical term correction), and the default is the former after v1.13.0.

`Q_DIRECTION`

#

This tag is used to activate non-analytical term correction (NAC) at
\(\mathbf{q}\rightarrow\mathbf{0}\), i.e. practically \(\Gamma\)-point,
because NAC is direction dependent. With this tag, \(\mathbf{q}\) is
specified in the fractional coordinates of the reciprocal basis vectors. Only
the direction has the meaning. Therefore `Q_DIRECTION = 1 1 1`

and
`Q_DIRECTION = 2 2 2`

give the same result. This tag is valid for `QPOINTS`

,
`IRREPS`

, and `MODULATION`

tags.

Away from \(\Gamma\)-point, this setting is ignored and the specified
**q**-point is used as the **q**-direction.

```
QPOINTS = 0 0 0 NAC = .TRUE.
Q_DIRECTION = 1 0 0
```

## Group velocity#

`GROUP_VELOCITY`

#

Group velocities at q-points are calculated by using this tag. The group velocities are written into a yaml file corresponding to the run mode in Cartesian coordinates. The physical unit depends on physical units of input files and frequency conversion factor. Usually the phonon frequency is given in THz. Therefore, the physical unit of the group velocity written in the output files is [unit-of-distance.THz]. The distance units for different force calculators are listed at Physical unit system for calculator. For example, VASP [Angstrom.THz], and QE [au.THz].

```
GROUP_VELOCITY = .TRUE.
```

Technical details are shown at Group velocity.

`GV_DELTA_Q`

#

The reciprocal distance used for finite difference method is specified. The
default value is `1e-5`

for the method of non-analytical term correction by
Gonze *et al.*. In other case, unless this tag is specified, analytical
derivative is used instead of the finite difference method.

```
GV_DELTA_Q = 0.01
```

## Symmetry#

`SYMMETRY_TOLERANCE`

#

This is used to set geometric tolerance to find symmetry of crystal structure.
The default value is `1e-5`

. In general, it is not a good idea to loosen the
tolerance. It is recommended to symmetrize crystal structure before starting
phonon calculation, e.g., using --symmetry option.

```
SYMMETRY_TOLERANCE = 1e-3
```

`SYMMETRY`

#

P1 symmetry is enforced to the input unit cell by setting `SYMMETRY = .FALSE`

.

`MESH_SYMMETRY`

#

Symmetry search on the reciprocal sampling mesh is disabled by setting
`MESH_SYMMETRY = .FALSE.`

. In some case such as hexagonal systems or primitive
cells of cubic systems having F and I-centrings, the results with and without
mesh symmetry give slightly different values for those properties that can
employ mesh symmetry. This happens when the uniform sampling mesh made along
basis vectors doesn’t have the same crystallographic point group as the crystal
itself. This symmetry breaking may be also seen by the fact that `weight`

written in `mesh.yaml`

can be different from possible order of product group of
site-symmetry group and time reversal symmetry. Generally the difference becomes
smaller when increasing the sampling mesh numbers.

`FC_SYMMETRY`

#

**Changed at v1.12.3**

Previously this tag required a number for the iteration. From version 1.12.3, the way of symmetrization for translation invariance is modified and this number became unnecessary.

This tag is used to symmetrize force constants by translational symmetry and
permutation symmetry with `.TRUE.`

or `.FALSE.`

.

```
FC_SYMMETRY = .TRUE.
```

From the translation invariance condition,

where *i* and *j* are the atom indices, and \(\alpha\) and \(\beta\) are
the Cartesian indices for atoms *i* and *j*, respectively. When this condition
is broken, the sum gives non-zero value. This value is subtracted from the
diagonal blocks. Force constants are symmetric in each pair as

Mind that the other symmetries of force constants, i.e., the symmetry from
crystal symmetry or rotational symmetry, are broken to use `FC_SYMMETRY`

.

## Force constants#

`FORCE_CONSTANTS`

#

```
FORCE_CONSTANTS = READ
```

There are three values to be set, which are `READ`

and `WRITE`

, and `.FALSE.`

.
The default is `.FALSE.`

. When `FORCE_CONSTANTS = READ`

, force constants are
read from `FORCE_CONSTANTS`

file. With `FORCE_CONSTANTS = WRITE`

, force
constants calculated from `FORCE_SETS`

are written to `FORCE_CONSTANTS`

file.

The file format of `FORCE_CONSTANTS`

is shown
here.

`FULL_FORCE_CONSTANTS`

#

`FULL_FORCE_CONSTANTS = .TRUE.`

is used to compute full supercell constants
matrix. The default setting is `.FALSE.`

. By `.TRUE.`

or `.FALSE.`

, the array
shape becomes `(n_patom, n_satom, 3, 3)`

or `(n_satom, n_satom, 3, 3)`

,
respectively. The detail is found at FORCE_CONSTANTS and force_constants.hdf5.

`READ_FORCE_CONSTANTS`

#

`READ_FORCE_CONSTANTS = .TRUE.`

is equivalent to `FORCE_CONSTANTS = READ`

.

`WRITE_FORCE_CONSTANTS`

#

`WRITE_FORCE_CONSTANTS = .TRUE.`

is equivalent to `FORCE_CONSTANTS = WRITE`

.

`FC_CALCULATOR`

#

External force constants calculator can be used using this tag. Currently `ALM`

is supported. The phonopy’s default force constants calculator is based on
finite difference method, for which atomic displacements are made
systematically. The following is the list of the force constants calculator
currently possible to be invoked from phonopy.

`FC_CALCULATOR_OPTIONS`

#

To be written.

`ALM`

#

**New in v2.3** ALM (ttadano/ALM) is based on fitting
approach and any displacements set of atoms in supercell can be handled. For
example, random displacements generated by RANDOM_DISPLACEMENTS can
be used to compute force constants. To use ALM, its python module has to be
installed via conda-forge or building it. The installation instruction is found
here.

When ALM is used, please cite the paper: T. Tadano and S. Tsuneyuki, J. Phys.
Soc. Jpn. **87**, 041015 (2018).

```
FC_CALCULATOR = ALM
```

## Create animation file#

`ANIME_TYPE`

#

```
ANIME_TYPE = JMOL
```

There are `V_SIM`

, `ARC`

, `XYZ`

, `JMOL`

, and `POSCAR`

settings. Those may be
viewed by `v_sim`

, `gdis`

, `jmol`

(animation), `jmol`

(vibration), respectively.
For `POSCAR`

, a set of `POSCAR`

format structure files corresponding to
respective animation images are created such as `APOSCAR-000`

,
`APOSCAR-001`

,….

There are several parameters to be set in the `ANIME`

tag.

`ANIME`

#

**The format of ANIME tag was modified after ver. 0.9.3.3.**

#### For v_sim#

```
ANIME = 0.5 0.5 0
```

The values are the *q*-point to be calculated. An animation file of
`anime.ascii`

is generated.

#### For the other animation formats#

Phonon is only calculated at \(\Gamma\) point. So *q*-point is not necessary
to be set.

`anime.arc`

, `anime.xyz`

, `anime.xyz_jmol`

, or `APOSCAR-*`

are generated
according to the `ANIME_TYPE`

setting.

```
ANIME = 4 5 20 0.5 0.5 0
```

The values are as follows from left:

Band index given by ascending order in phonon frequency.

Magnitude to be multiplied. In the harmonic phonon calculation, there is no amplitude information obtained directly. The relative amplitude among atoms in primitive cell can be obtained from eigenvectors with the constraint of the norm or the eigenvectors equals one, i.e., number of atoms in the primitive is large, the displacements become small. Therefore this has to be adjusted to make the animation good looking.

Number of images in one phonon period.

(4-6) Shift of atomic points in reduced coordinate in real space. These values can be omitted and the default values are

`0 0 0`

.

For `anime.xyz_jmol`

, the first and third values are not used, however dummy
values, e.g. 0, are required.

## Create modulated structure#

`MODULATION`

#

The `MODULATION`

tag is used to create a crystal structure with displacements
along normal modes at q-point in the specified supercell dimension.

Atomic displacement of the *j*-th atom is created from the real part of the
eigenvectors with amplitudes and phase factors as

where \(A\) is the amplitude, \(\phi\) is the phase,
\(N_\mathrm{a}\) is the number of atoms in the supercell specified in this
tag and \(m_j\) is the mass of the *j*-th atom, \(\mathbf{q}\) is the
q-point specified, \(\mathbf{r}_{jl}\) is the position of the *j*-th atom in
the *l*-th unit cell, and \(\mathbf{e}_j\) is the *j*-th atom part of
eigenvector. Convention of eigenvector or dynamical matrix employed in phonopy
is shown in Dynamical matrix.

If several modes are specified as shown in the example above, they are
overlapped on the structure. The output filenames are `MPOSCAR`

and
`MPOSCAR-<number>`

. Each modulated structure of a normal mode is written in
`MPOSCAR-<number>`

where the numbers correspond to the order of specified sets
of modulations. `MPOSCAR`

is the structure where all the modulations are summed.
`MPOSCAR-orig`

is the structure without containing modulation, but the dimension
is the one that is specified. Some information is written into
`modulation.yaml`

.

#### Usage#

The first three (nine) values correspond to supercell dimension (supercell
matrix) like the DIM tag. The following values are used to
describe how the atoms are modulated. Multiple sets of modulations can be
specified by separating by comma `,`

. In each set, the first three values give a
Q-point in the reduced coordinates in reciprocal space. Then the next three
values are the band index from the bottom with ascending order, amplitude, and
phase factor in degrees. The phase factor is optional. If it is not specified, 0
is used.

Before multiplying user specified phase factor, the phase of the modulation
vector is adjusted as the largest absolute value,
\(\left|\mathbf{e}_j\right|/\sqrt{m_j}\), of element of 3N dimensional
modulation vector to be real. The complex modulation vector is shown in
`modulation.yaml`

.

```
MODULATION = 3 3 1, 1/3 1/3 0 1 2, 1/3 1/3 0 2 3.5
```

```
MODULATION = 3 3 1, 1/3 1/3 0 1 2, 1/3 0 0 2 2
```

```
MODULATION = 3 3 1, 1/3 1/3 0 1 1 0, 1/3 1/3 0 1 1 90
```

```
MODULATION = -1 1 1 1 -1 1 1 1 -1, 1/2 1/2 0 1 2
```

## Characters of irreducible representations#

`IRREPS`

#

Characters of irreducible representations (Irreps) of phonon modes are shown.
For this calculation, a primitive cell has to be used. If the input unit cell is
a non-primitive cell, it has to be transformed to a primitive cell using
`PRIMITIVE_AXES`

tag.

The first three values gives a *q*-point in reduced coordinates to be
calculated. The degenerated modes are searched only by the closeness of
frequencies. The frequency difference to be tolerated is specified by the fourth
value in the frequency unit that the user specified.

```
IRREPS = 0 0 0 1e-3
```

Symbols of Irreps for the 32 point group types at the \(\Gamma\) point are shown but not at non-\(\Gamma\) point.

`SHOW_IRREPS`

#

Irreducible representations are shown along with character table.

```
IRREPS = 1/3 1/3 0
SHOW_IRREPS = .TRUE.
```

`LITTLE_COGROUP`

#

Show irreps of little co-group (point-group of wavevector) instead of little group.

```
IRREPS = 0 0 1/8
LITTLE_COGROUP = .TRUE.
```

## Input/Output file control#

`FC_FORMAT`

, `READFC_FORMAT`

, `WRITEFC_FORMAT`

#

There are two file-formats to store force constants. Currently
text style (`TEXT`

) and hdf5 (`HDF5`

) formats are
supported. The default file format is the
text style. Reading and writing force constants are
invoked by FORCE_CONSTANTS tag. Using these tags,
the input/output formats are switched.

`FC_FORMAT`

affects to both input and output, e.g.

```
FORCE_CONSTANTS = WRITE
FC_FORMAT = HDF5
```

`READFC_FORMAT`

and `WRITEFC_FORMAT`

can be used to control input and output
formats separately, i.e., the following setting to convert force constants
format is possible:

```
READ_FORCE_CONSTANTS = .TRUE.
WRITE_FORCE_CONSTANTS = .TRUE.
WRITEFC_FORMAT = HDF5
```

`BAND_FORMAT`

, `MESH_FORMAT`

, `QPOINTS_FORMAT`

#

There are two file-formats to write the results of band structure, mesh, and
q-points calculations. Currently YAML (`YAML`

) and hdf5 (`HDF5`

) formats are
supported. The default file format is the YAML format. The file format is
changed as follows:

```
BAND_FORMAT = HDF5
```

```
MESH_FORMAT = HDF5
```

```
QPOINTS_FORMAT = HDF5
```

`HDF5`

#

The following output files are written in hdf5 format instead of their original
formats (in parenthesis) by `HDF5 = .TRUE.`

. In addition, `force_constants.hdf5`

is read with this tag.

`force_constants.hdf5`

(`FORCE_CONSTANTS`

)`mesh.hdf5`

(`mesh.yaml`

)`band.hdf5`

(`band.yaml`

)`qpoints.hdf5`

(`qpoints.yaml`

)

```
HDF5 = .TRUE.
```

`force_constants.hdf5`

#

With `--hdf5`

option and `FORCE_CONSTANTS = WRITE`

(`--writefc`

),
`force_constants.hdf5`

is written. With `--hdf5`

option and
`FORCE_CONSTANTS = READ`

(`--readfc`

), `force_constants.hdf5`

is read.

`mesh.hdf5`

#

In the mesh sampling calculations (see Mesh sampling tags), calculation
results are written into `mesh.hdf5`

but not into `mesh.yaml`

. Using this option
may reduce the data output size and thus writing time when `mesh.yaml`

is huge,
e.g., eigenvectors are written on a dense sampling mesh.

`qpoints.hdf5`

#

In the specific q-points calculations (QPOINTS), calculation results
are written into `qpoints.hdf5`

but not into `qpoints.yaml`

. With
WRITEDM, dynamical matrices are also stored in `qpoints.hdf5`

. Using
this option may be useful with large set of q-points with including eigenvector
or dynamical matrix output.

`band.hdf5`

#

In the band structure calculations (Band structure tags),
calculation results are written into `band.hdf5`

but not into `band.yaml`

.

`summary`

#

The following data may be optionally included in the summary yaml file called
`phonopy_disp.yaml`

/`phonopy.yaml`

in addition to other file output settings.
This happens at the end of the pre/post-process (after running the `phonopy`

script):

`force constants`

`force sets`

`dielectric constant`

`born effective charge`

`displacements`

`[all]`

Including all relevant data in a single output file allows for a human readable convenient file format.

`force constants`

#

The `--include-fc`

flag or setting `INCLUDE_FC = .TRUE.`

will cause the force
constants (if available) to be written as an entry in the yaml summary file. The
written force constants will reflect the required/available format used during
processing. So if `--full-fc`

is set the entire matrix will be written.

`force sets`

#

The `--include-fs`

flag or setting `INCLUDE_FS = .TRUE.`

will cause the force
sets (if available) to be written as an entry in the yaml summary file.

`dielectric constant`

and `born effective charge`

#

The `--include-born`

flag or setting `INCLUDE_BORN = .TRUE.`

will cause the born
effective charges and dielectric tensor (if available) to be written as an entry
in the yaml summary file. The values will only be written if non-analytical term
correction is set with the `--nac`

flag or by setting `NAC = .TRUE.`

.

This is more convenient than keeping track of the `BORN`

file created by the
user.

`displacements`

#

The `--include-disp`

flag or setting `INCLUDE_DISP = .TRUE.`

will cause
displacements data (if available) to be written as an entry in the yaml summary
file.

This is set by default when the `phonopy`

script is run in `displacements`

mode.

`all`

#

All available data covered by the other `include`

flags can be written to the
yaml summary file using the `--include-all`

flag or by setting
`INCLUDE_ALL = .TRUE.`

. Force constants are not stored when force sets are
stored.