Setting tags

Most of the setting tags have corresponding command-line options (Command 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.

Basic tags

DIM

The supercell is created from the input unit cell. When three integers are specified, a supercell elongated along axes of unit cell is created.

DIM = 2 2 3

In this case, a 2x2x3 supercell is created.

When nine integers are specified, the supercell is created by multiplying the supercell matrix M_\mathrm{s} with the unit cell. For example,

DIM = 0 1 1  1 0 1  1 1 0

the supercell matrix is

M_\mathrm{s} = \begin{pmatrix}
0 & 1 & 1 \\
1 & 0 & 1 \\
1 & 1 & 0
\end{pmatrix}

where the rows correspond to the first three, second three, and third three sets of numbers, respectively. When lattice parameters of unit cell are the column vectors of \mathbf{a}_\mathrm{u}, \mathbf{b}_\mathrm{u}, and \mathbf{c}_\mathrm{u}, those of supercell, \mathbf{a}_\mathrm{s}, \mathbf{b}_\mathrm{s}, \mathbf{c}_\mathrm{s}, are determined by,

( \mathbf{a}_\mathrm{s} \; \mathbf{b}_\mathrm{s} \; \mathbf{c}_\mathrm{s} )
=  ( \mathbf{a}_\mathrm{u} \; \mathbf{b}_\mathrm{u} \;
\mathbf{c}_\mathrm{u} ) M_\mathrm{s}

Be careful that the axes in POSCAR is defined by three row vectors, i.e., ( \mathbf{a}_\mathrm{u} \; \mathbf{b}_\mathrm{u}
\; \mathbf{c}_\mathrm{u} )^T.

PRIMITIVE_AXIS

PRIMITIVE_AXIS = 0.0 0.5 0.5  0.5 0.0 0.5  0.5 0.5 0.0

Likewise,

PRIMITIVE_AXIS = 0 1/2 1/2  1/2 0 1/2  1/2 1/2 0

The primitive cell for building the dynamical matrix is created by multiplying primitive-axis matrix M_\mathrm{p}. Let the matrix as,

M_\mathrm{p} = \begin{pmatrix}
0.0 & 0.5 & 0.5 \\
0.5 & 0.0 & 0.5 \\
0.5 & 0.5 & 0.0
\end{pmatrix}

where the rows correspond to the first three, second three, and third three sets of numbers, respectively.

When lattice parameters of unit cell (set by POSCAR) are the column vectors of \mathbf{a}_\mathrm{u}, \mathbf{b}_\mathrm{u}, and \mathbf{c}_\mathrm{u}, those of supercell, \mathbf{a}_\mathrm{p}, \mathbf{b}_\mathrm{p}, \mathbf{c}_\mathrm{p}, are determined by,

( \mathbf{a}_\mathrm{p} \; \mathbf{b}_\mathrm{p} \; \mathbf{c}_\mathrm{p} )
=  ( \mathbf{a}_\mathrm{u} \; \mathbf{b}_\mathrm{u} \;
\mathbf{c}_\mathrm{u} ) M_\mathrm{p}

Be careful that the axes in POSCAR is defined by three row vectors, i.e., ( \mathbf{a}_\mathrm{u} \; \mathbf{b}_\mathrm{u}
\; \mathbf{c}_\mathrm{u} )^T.

ATOM_NAME

Chemical symbols

ATOM_NAME = Si O

The number of chemical symbols have to be same as that of the numbers in the sixth line of POSCAR.

Chemical symbols read by phonopy are overwritten by those written in POSCAR. See POSCAR examples. In WIEN2k mode, you don’t need to set this tag, i.e., chemical symbols are read from the structure file.

EIGENVECTORS

When this tag is ‘.TRUE.’, eigenvectors are calculated. With -p option, partial density of states are calculated.

MASS

This tag is not necessary to use usually, because atomic masses are automatically set from the chemical symbols.

Atomic masses of a primitive cell are overwritten by the values specified. The order of atoms in the primitive cell that is defined by PRIMITIVE_AXIS tag can be shown using -v option. It must be noted that this tag does not affect to the symmetry search.

For example, when there are six atoms in a primitive cell, MASS is set as follows

MASS =   28.085 28.085 16.000 16.000 16.000 16.000

MAGMOM

Symmetry of spin such as collinear magnetic moments is considered using this tag. The number of values has to be equal to the number of atoms in the unit cell, not the primitive cell or supercell. If this tag is used with -d option (CREATE_DISPLACEMENTS tag), MAGMOM file is created. This file contains the MAGMOM information of the supercell used for VASP. Unlike MAGMOM in VASP, * can not be used, i.e., all the values (the same number of times to the number of atoms in unit cell) have to be explicitly written.

MAGMOM = 1.0 1.0 -1.0 -1.0

CELL_FILENAME

CELL_FILENAME = UPOSCAR

See Input cell.

FREQUENCY_CONVERSION_FACTOR

Unit conversion factor of frequency from input values to your favorite unit can be specified, but the use should be limited and it is recommended to use this tag to convert the frequency unit to THz in some exceptional case, for example, a special force calculator whose physical unit system is different from the default setting of phonopy is used. If the frequency unit is different from THz, though it works just for seeing results of frequencies, e.g., band structure or DOS, it doesn’t work for derived values like thermal properties and mean square displacements.

The default values for calculators are those to convert frequency units to THz. The default conversion factors for wien2k, abinit, pwscf, elk, and CRYSTAL are 3.44595, 21.49068, 108.9708, 154.1079, and 15.633302 respectively. These are determined following the physical unit systems of the calculators. How to calcualte these conversion factors is explained at Physical unit conversion.

Displacement creation tags

CREATE_DISPLACEMENTS

Supercells with displacements are created. This tag is used as the post process of phonon calculation.

CREATE_DISPLACEMENTS = .TRUE.
DIM = 2 2 2

DISPLACEMENT_DISTANCE

Finite atomic displacement distance is set as specified value when creating supercells with displacements. The default displacement amplitude is 0.01 \textrm{\AA}, but when the wien2k or abinit option is specified, the default value is 0.02 Bohr.

DIAG

When this tag is set .FALSE., displacements in diagonal directions are not searched, i.e. all the displacements are along the lattice vectors. DIAG = .FALSE. is recommended if one of the lattice parameter of your supercell is much longer or much shorter than the other lattice parameters.

PM

This tag specified how displacements are found. When PM = .FALSE., least displacements that can calculate force constants are found. This may cause less accurate result. When PM = .TRUE., all the displacements that are opposite directions to the least displacements are also found, which is called plus-minus displacements here. The default setting is PM = AUTO. Plus-minus displacements are considered with this tag. If the plus and minus displacements are symmetrically equivalent, only the plus displacement is found. This may be in between .FALSE. and .TRUE.. You can check how it works to see the file DISP where displacement directions on atoms are written.

Band structure tags

BAND and BAND_POINTS

BAND gives sampling band paths. The reciprocal points are specified in reduced coordinates. The given points are connected for defining band paths. When comma , is inserted between the points, the paths are disconnected.

BAND_POINTS gives the number of sampling points including the path ends. The default value is BAND_POINTS = 51.

An example of three paths, (0,0,0) to (1/2,0,1/2), (1/2,1/2,1) to (0,0,0), and (0,0,0) to (1/2,1/2,1/2), with 101 sampling points of each path are as follows:

BAND = 0 0 0  1/2 0 1/2,  1/2 1/2 1  0 0 0   1/2 1/2 1/2
BAND_POINTS = 101

BAND_LABELS

Labels specified are depicted in band structure plot at the points of band segments. The number of labels has to correspond to the number of band paths specified by BAND plus one.

BAND = 1/2 0 1/2   0 0 0   1/2 1/2 1/2
BAND_LABELS = X \Gamma L

bandlabels

The colors of curves are automatically determined by matplotlib. The same color in a band segment shows the same kind of band. Between different band segments, the correspondence of colors doesn’t mean anything.

BAND_CONNECTION

With this option, band connections are estimated from eigenvectors and band structure is drawn considering band crossings. In sensitive cases, to obtain better band connections, it requires to increase number of points calculated in band segments by the BAND_POINTS tag.

BAND = 1/2 0 1/2   0 0 0   1/2 1/2 1/2
BAND_POINTS = 101
BAND_CONNECTION = .TRUE.

bandconnection

Mesh sampling tags

Mesh sampling tags are used commonly for calculations of thermal properties and density of states.

MESH, MP, or MESH_NUMBERS

MESH numbers give uniform meshes in each axis. As the default behavior, the center of mesh is determined by the Monkhorst-Pack scheme, i.e., for odd number, a point comes to the center, and for even number, the center is shifted half in the distance between neighboring mesh points.

Examples of an even mesh with \Gamma center in two ways,

MESH = 8 8 8
GAMMA_CENTER = .TRUE.
MESH = 8 8 8
MP_SHIFT = 1/2 1/2 1/2

MP_SHIFT

MP_SHIFT gives the shifts in direction along the corresponding reciprocal axes (a^*, b^*, c^*). 0 or 1/2 (0.5) can be used as these values. 1/2 means the half mesh shift with respect to neighboring grid points in each direction.

GAMMA_CENTER

Instead of employing the Monkhorst-Pack scheme for the mesh sampling, \Gamma center mesh is used. The default value is .FALSE..

GAMMA_CENTER = .TRUE.

WRITE_MESH

With a dense mesh, with eigenvectors, without mesh symmetry, sometimes its output file mesh.yaml or mesh.hdf5 can be huge. However when those files are not needed, e.g., in (P)DOS calculation, WRITE_MESH = .FALSE. can disable to write out those files. With (P)DOS calculation, DOS output files are obtained even with WRITE_MESH = .FALSE.. The default setting is .TRUE..

WRITE_MESH = .FALSE.

Phonon density of states (DOS) tags

Phonon density of states (DOS) is calcualted either with smearing method (default) or tetrahedron method. Phonons are calculated on a sampling mesh, therefore these tags must be used with Mesh sampling tags. The physical unit of horizontal axis is that of frequency that the user employs, e.g., THz, and that of vertical axis is {no. of states}/({unit cell} x {unit of the horizontal axis}). If the DOS is integrated over the frequency range, it will be 3N_\mathrm{a} states, where N_\mathrm{a} is the number of atoms in the unit cell.

Phonon-DOS is formally defined as

g(\omega) = \frac{1}{N} \sum_\lambda \delta(\omega - \omega_\lambda)

where N is the number of unit cells and \lambda = (\nu,
\mathbf{q}) with \nu as the band index and \mathbf{q} as the q-point. This is computed on a set of descritized sampling frequency points for which \omega is specified arbitrary using DOS_RANGE. The phonon frequencies \omega_\lambda are obtained on a sampling mesh whose the number of grid points being N. In the smearing method, the delta function is replaced by normal distribution (Gaussian function) with the standard deviation specified by SIGMA. In the tetrahedron method, the Brillouin integration is made analytically within tetrahedra in reciprocal space.

DOS

This tag enables to calculate DOS. This tag is automatically set when PDOS tag or -p option.

DOS = .TRUE.

DOS_RANGE

DOS_RANGE = 0 40 0.1

Total and partial density of states are drawn with some parameters. The example makes DOS be calculated from frequency=0 to 40 with 0.1 pitch.

FMIN, FMAX, and FPITCH can be alternatively used to specify the minimum and maximum frequencies (the first and second values).

FMIN, FMAX, and FPITCH

The uniform frequency sampling points for phonon-DOS calculation are specified. FMIN and FMAX give the minimum, maximum frequencies of the range, respectively, and FPITCH gives the frequency pitch to be sampled. These three values are the same as those that can be specified by DOS_RANGE.

PDOS

Projected DOS is calculated using this tag. The formal definition is written as

g^j(\omega, \hat{\mathbf{n}}) = \frac{1}{N} \sum_\lambda
\delta(\omega - \omega_\lambda) |\hat{\mathbf{n}} \cdot
\mathbf{e}^j_\lambda|^2,

where j is the atom indices and \hat{\mathbf{n}} is the unit projection direction vector. Without specifying PROJECTION_DIRECTION or XYZ_PROJECTION, PDOS is computed as sum of g^j(\omega, \hat{\mathbf{n}}) projected onto Cartesian axes x,y,z, i.e.,

g^j(\omega) = \sum_{\hat{\mathbf{n}} = \{x, y, z\}} g^j(\omega,
\hat{\mathbf{n}}).

The atom indices j are specified by

PDOS = 1 2, 3 4 5 6

These numbers are those in the primitive cell. , separates the atom sets. In this example, atom 1 and 2 are summarized as one curve and atom 3, 4, 5, and, 6 are summarized as another curve.

EIGENVECTORS = .TRUE. and MESH_SYMMETRY = .FALSE. are automatically set, therefore the calculation takes much more time than usual DOS calculation. With a very dense sampling mesh, writing data into mesh.yaml or mesh.hdf5 can be unexpectedly huge. If only PDOS is necessary but these output files are unnecessary, then it is good to consider using WRITE_MESH = .FALSE. (WRITE_MESH).

PROJECTION_DIRECTION

Eigenvectors are projected along the direction specified by this tag. Projection direction is specified in reduced coordinates, i.e., with respect to a, b, c axes.

PDOS = 1, 2
PROJECTION_DIRECTION = -1 1 1

XYZ_PROJECTION

PDOS is calculated using eigenvectors projected along x, y, and z Cartesian coordinates. The format of output file partial_dos.dat becomes different when using this tag, where phonon-mode-frequency and x, y, and z components of PDOS are written out in the order:

frequency atom1_x atom1_y atom1_z atom2_x atom2_y atom2_z ...

With -p option, three curves are drawn. These correspond to sums of all projections to x, sums of all projections to y, and sums of all projections to z composents of eigenvectors, respectively.

XYZ_PROJECTION = .TRUE.

SIGMA

This tag specifies the smearing width. The unit is same as that used for phonon frequency. The default value is the value given by the difference of maximum and minimum frequencies divided by 100.

SIGMA = 0.1

TETRAHEDRON

Tetrahedron method is used instead of smearing method.

DEBYE_MODEL

By setting .TRUE., DOS at lower phonon frequencies are fit to a Debye model. By default, the DOS from 0 to 1/4 of the maximum phonon frequencies are used for the fitting. The function used to the fitting is D(\omega)=a\omega^2 where a is the parameter and the Debye frequency is (9N/a)^{1/3} where N is the number of atoms in unit cell. Users have to unserstand that this is not a unique way to determine Debye frequency. Debye frequency is dependent on how to parameterize it.

DEBYE_MODEL = .TRUE.

MOMEMT and MOMENT_ORDER

Phonon moments for DOS and PDOS defined below are calculated using these tags up to arbitrary order. The order is specified with MOMENT_ORDER (n in the formula). Unless MOMENT_ORDER specified, the first and second moments are calculated.

The moments for DOS are given as

M_n(\omega_\text{min}, \omega_\text{max})
&=\frac{\int_{\omega_\text{min}}^{\omega_\text{max}} \omega^n
g(\omega) d\omega} {\int_{\omega_\text{min}}^{\omega_\text{max}}
g(\omega) d\omega}.

The moments for PDOS are given as

M_n^j(\omega_\text{min}, \omega_\text{max})
&=\frac{\int_{\omega_\text{min}}^{\omega_\text{max}} \omega^n
g^j(\omega) d\omega} {\int_{\omega_\text{min}}^{\omega_\text{max}}
g^j(\omega) d\omega}.

\omega_\text{min} and \omega_\text{max} are specified :using ref:dos_fmin_fmax_tags tags. When these are not specified, the moments are computed with the range of \epsilon < \omega
< \infty, where \epsilon is a small positive value. Imaginary frequencies are treated as negative real values in this computation, therefore it is not a good idea to set negative \omega_\text{min}.

MOMENT = .TRUE.
MOMENT_ORDER = 3

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 \textrm{\AA}^2 and writen into thermal_displacements.yaml. See the detail of the method, Mean square displacement. These tags must be used with Mesh sampling tags

CUTOFF_FREQUENCY tag with a small value is recommened to be set when sampling \Gamma point or using very dense sampling mesh to avoid divergence.

The projection is applied along arbitrary direction using PROJECTION_DIRECTION tag (PROJECTION_DIRECTION).

TDISP = .TRUE.
PROJECTION_DIRECTION = 1 1 0

TDISPMAT, TMAX, TMIN, and TSTEP

Mean square displacement matricies are calculated. The definition is shown at Mean square displacement. Phonon frequencies in THz, which is the default setting of phonopy, are used to obtain the mean square displacement matricies, therefore physical units have to be set properly for it (see Interfaces to calculators.) The result is given in \textrm{\AA}^2 and writen 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.

CUTOFF_FREQUENCY tag with a small value is recommened to be set when sampling \Gamma point or using very dense sampling mesh to avoid divergence.

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

TDISPMAT = .TRUE.

TDISPMAT_CIF

This tag specifis 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 matricies, therefore physical units have to be set properly for it (see Interfaces to calculators.) The result is given in \textrm{\AA}^2.

TDISPMAT_CIF = 1273.0

CUTOFF_FREQUENCY

Frequencies lower than this cutoff frequency are not used to calculate thermal displacements.

Specific q-points

QPOINTS

When QPOINTS = .TRUE., QPOINTS file in your working directory is read, and the q-points written in this file are calculated.

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).

D =
\begin{pmatrix}
D_{11} & D_{12} & D_{13} & \\
D_{21} & D_{22} & D_{23} & \cdots \\
D_{31} & D_{32} & D_{33} & \\
& \vdots &  & \\
\end{pmatrix},

and D_{jj'} is

D_{jj'} =
\begin{pmatrix}
Re(D_{jj'}^{xx}) & Im(D_{jj'}^{xx}) & Re(D_{jj'}^{xy}) &
Im(D_{jj'}^{xy}) & Re(D_{jj'}^{xz}) & Im(D_{jj'}^{xz}) \\
Re(D_{jj'}^{yx}) & Im(D_{jj'}^{yx}) & Re(D_{jj'}^{yy}) &
Im(D_{jj'}^{yy}) & Re(D_{jj'}^{yz}) & Im(D_{jj'}^{yz}) \\
Re(D_{jj'}^{zx}) & Im(D_{jj'}^{zx}) & Re(D_{jj'}^{zy}) &
Im(D_{jj'}^{zy}) & Re(D_{jj'}^{zz}) & Im(D_{jj'}^{zz}) \\
\end{pmatrix},

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 --dim="2 2 2" --pa="0 1/2 1/2  1/2 0 1/2  1/2 1/2 0" --qpoints="0 1/2 1/2" --writedm

and the dynamical matrix may be used as

#!/usr/bin/env python

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.

NAC = .TRUE.

Q_DIRECTION

This tag is used to activate NAC at \mathbf{q}\rightarrow\mathbf{0}, i.e. practically \Gamma-point. Away from \Gamma-point, this setting is ignored and the specified q-point is used as the q-direction.

MESH = 1 1 1
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, but if VASP and the default settings (e.g., THz for phonon frequency) are simply used, then the physical unit will be Angstrom THz.

GROUP_VELOCITY = .TRUE.

Technical details are shown at Method.

GV_DELTA_Q

The reciprocal distance used for finite difference method is specified. The default value is 1e-4.

GV_DELTA_Q = 0.01

Symmetry

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..

FC_SYMMETRY

This tag is used to symmetrize force constants partly. The number of iteration of the following set of symmetrization applied to force constants is specified. The default value is 0. In the case of VASP, this tag is usually unnecessary to be specified.

FC_SYMMETRY = 1

From the translation invariance condition,

\sum_i \Phi_{ij}^{\alpha\beta} = 0, \;\;\text{for all $j$, $\alpha$, $\beta$},

where i and j are the atom indices, and \alpha and \beta are the Catesian indices for atoms i and j, respectively. Force constants are symmetric in each pair as

\Phi_{ij}^{\alpha\beta}
     = \frac{\partial^2 U}{\partial u_i^\alpha \partial u_j^\beta}
     = \frac{\partial^2 U}{\partial u_j^\beta \partial u_i^\alpha}
     = \Phi_{ji}^{\beta\alpha}

These symmetrizations break the symmetry conditions each other. Be careful that the other symmetries of force constants, i.e., the symmetry from crystal symmetry or rotational symmetry, are broken to force applying 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.

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:

  1. Band index given by ascending order in phonon frequency.
  2. 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.
  3. Number of images in one phonon period.
  4. (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

\frac{A} { \sqrt{N_\mathrm{a}m_j} } \operatorname{Re} \left[ \exp(i\phi)
\mathbf{e}_j \exp( \mathbf{q} \cdot \mathbf{r}_{jl} ) \right],

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.... 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 CELL_FILENAME 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 (IRs) 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_AXIS 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

Only the databases of IRs for a few point group types at the \Gamma point are implemented. If the database is available, the symbols of the IRs and the rotation operations are shown.

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.