(setting_tags)= # Setting tags (configuration_file)= ## Configuration file Most of the setting tags have respective command-line options ({ref}`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., ```bash % phonopy --config setting.conf [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 (dimension_tag)= ### `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 {math}`\mathrm{M}_\mathrm{s}` with the unit cell. For example, ``` DIM = 0 1 1 1 0 1 1 1 0 ``` the supercell matrix is ```{math} \mathrm{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 {math}`\mathbf{a}_\mathrm{u}`, {math}`\mathbf{b}_\mathrm{u}`, and {math}`\mathbf{c}_\mathrm{u}`, those of supercell, {math}`\mathbf{a}_\mathrm{s}`, {math}`\mathbf{b}_\mathrm{s}`, {math}`\mathbf{c}_\mathrm{s}`, are determined by, ```{math} ( \mathbf{a}_\mathrm{s} \; \mathbf{b}_\mathrm{s} \; \mathbf{c}_\mathrm{s} ) = ( \mathbf{a}_\mathrm{u} \; \mathbf{b}_\mathrm{u} \; \mathbf{c}_\mathrm{u} ) \mathrm{M}_\mathrm{s} ``` Be careful that the axes in `POSCAR` is defined by three row vectors, i.e., {math}`( \mathbf{a}_\mathrm{u} \; \mathbf{b}_\mathrm{u} \; \mathbf{c}_\mathrm{u} )^T`. (primitive_axes_tag)= ### `PRIMITIVE_AXES` When specified, transformation from the input unit cell to the primitive cell is performed. With this, the primitive cell basis vectors are used as the coordinate system for the phonon calculation. The transformation matrix is specified by nine values. The first, second, and third three values give the rows of the 3x3 matrix as follows: ``` PRIMITIVE_AXES = 0.0 0.5 0.5 0.5 0.0 0.5 0.5 0.5 0.0 ``` Likewise, ``` PRIMITIVE_AXES = 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 {math}`\mathrm{M}_\mathrm{p}`. Let the matrix as, ```{math} \mathrm{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 {math}`\mathbf{a}_\mathrm{u}`, {math}`\mathbf{b}_\mathrm{u}`, and {math}`\mathbf{c}_\mathrm{u}`, those of supercell, {math}`\mathbf{a}_\mathrm{p}`, {math}`\mathbf{b}_\mathrm{p}`, {math}`\mathbf{c}_\mathrm{p}`, are determined by, ```{math} ( \mathbf{a}_\mathrm{p} \; \mathbf{b}_\mathrm{p} \; \mathbf{c}_\mathrm{p} ) = ( \mathbf{a}_\mathrm{u} \; \mathbf{b}_\mathrm{u} \; \mathbf{c}_\mathrm{u} ) \mathrm{M}\_\mathrm{p}. ``` {math}`\mathrm{M}_\mathrm{p}` is a change of basis matrix and so {math}`\mathrm{M}_\mathrm{p}^{-1}` must be an integer matrix. Be careful that {math}the axes in `POSCAR` is defined by three row vectors, i.e., {math}`( \mathbf{a}_\mathrm{u} \; \mathbf{b}_\mathrm{u} \; \mathbf{c}_\mathrm{u} )^T`. **New in v1.14.0** `PRIMITIVE_AXES = AUTO` is supported. This enables to choose the transformation matrix automatically. Since the choice of the primitive cell is arbitrary, it is recommended to use `PRIMITIVE_AXES = AUTO` to check if a possible transformation matrix exists or not. **Changed in v4.0** `PRIMITIVE_AXES = AUTO` is the default when `PRIMITIVE_AXES` is not specified. (primitive_axes_auto_magnetic)= #### Magnetic unit cells When the input unit cell has magnetic moments (see {ref}`magmom_tag`), the primitive cell is determined from the magnetic space group (MSG) detected by spglib. The behavior depends on the MSG type: - **Type-I, II, III** MSGs are handled using the so-called FSG (family space group). The primitive cell is determined as in the non-magnetic case and the input magnetic moments are preserved. - **Type-IV** MSGs are handled using the so-called XSG, the subgroup of the MSG obtained by removing the anti-translations (lattice translations combined with time reversal). The resulting primitive cell preserves the input magnetic moments and may be larger than the crystallographic primitive cell. A warning is emitted in this case. For example, antiferromagnetic bcc Cr (with moments `[1, -1]` on the two sites of the conventional cubic cell) is a Type-IV MSG: the body-center translation combined with time reversal is an anti-translation. The XSG is Pm-3m, so with `PRIMITIVE_AXES = AUTO` the primitive cell equals the 2-atom input cubic cell and the antiferromagnetic ordering is preserved. If a smaller primitive cell that ignores the magnetic ordering is desired (for example, in `phonopy` run mode where force constants are known to respect the higher non-magnetic symmetry), pass the centring of the FSG explicitly, e.g. `PRIMITIVE_AXES = I` for the bcc Cr example above. Note that this discards the input magnetic moments in the primitive cell, so it must not be used with `phonopy-init` when generating displacements for force calculations. See the references below for the definitions of FSG, XSG, and the MSG types. - [TODO: citation for IUCr ib5106] - [TODO: citation for IUCr ib5114] ### `ATOM_NAME` When a crystal structure format has no information about chemical symbols, this tag is used to specify chemical symbols. ``` ATOM_NAME = Si O ``` (eigenvectors_tag)= ### `EIGENVECTORS` When this tag is `.TRUE.`, eigenvectors are calculated. (mass_tag)= ### `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_tag)= ### `MAGMOM` Symmetry of spin such as magnetic moments is specified using this tag. The number of values has to be equal to the number of atoms, or its three times for non-collinear-like case, in **the input unit cell**, not the primitive cell or supercell. See also {ref}`primitive_axes_auto_magnetic` for how the primitive cell is determined when the input unit cell has magnetic moments. 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 ``` For non-collinear-like case, ``` MAGMOM = 0 0 1 0 0 1 0 0 -1 0 0 -1 ``` where the first three values as a vector is for the first atom, and so on. (cell_filename_tag)= ### `CELL_FILENAME` ``` CELL_FILENAME = POSCAR-unitcell ``` See {ref}`cell_filename_option`. (frequency_conversion_factor_tag)= ### `FREQUENCY_CONVERSION_FACTOR` **This tag was deprecated at v2.44.** ```{note} For unsupported force calculators, displacement-force dataset with displacements in Angstrom and forces in eV/Angstrom should be prepared to obtain frequencies in THz. ``` The following is the old documentation of the `FREQUENCY_CONVERSION_FACTOR` tag. This tag should be used to convert the phonon frequency unit to THz because if the frequency unit is different from THz, derived values like thermal properties and mean square displacements are wrongly calculated. Normally this tag is unnecessary to be specified because the default value is chosen for each force calculator, i.e., the default values for calculators are prepared to convert the frequency unit to THz. If no calculator is chosen, the factor for VASP is used. The default conversion factors are listed at {ref}`frequency_default_value_interfaces`. How to calculated these conversion factors is explained at {ref}`physical_unit_conversion`. ## Displacement creation tags (create_displacements_tag)= ### `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_tag)= ### `DISPLACEMENT_DISTANCE` Finite atomic displacement distance is set as specified value when creating supercells with displacements. The default displacement amplitude is 0.01 Angstrom, but when the `wien2k`, `abinit`, `Fleur` or `turbomole` 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_displacement_tag)= ### `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. (random_displacements_tag)= ### `RANDOM_DISPLACEMENTS` The number of random displacement supercells are created by the specified positive integer values. In each supercell, all atoms are displaced in random direction with a constant displacement distance specified by {ref}`displacement_distance_tag` tag. The random seed can be specified by {ref}`random_seed_tag` tag. To obtain force constants with random displacements and respective forces, an external force constants calculator is necessary. See {ref}`fc_calculator_tag`. See also {ref}`f_force_sets_option` for creating `FORCE_SETS` from a series of sueprcell calculation. ``` CREATE_DISPLACEMENTS = .TRUE. DIM = 2 2 2 RANDOM_DISPLACEMENTS = 20 DISPLACEMENT_DISTANCE = 0.03 ``` When `AUTO` is specified, the number of supercells to be generated is estimated using symfc. The default estimated number is four times the minimum number required to solve the normal equation under symmetry considerations. When `DISPLACEMENT_DISTANCE_MAX` is also specified, the default number becomes eight times the minimum required number. These factors (4 or 8) can be changed by `RD_NUMBER_ESTIMATION_FACTOR`. (displacement_distance_max_tag)= ### `DISPLACEMENT_DISTANCE_MAX` This is used along with `RANDOM_DISPLACEMENTS` but not with `RANDOM_DISPLACEMENT_TEMPERATURE`. The random displacements are generated with variation not only in direction, but also in distance, with distances randomly sampled uniformly between the values of `DISPLACEMENT_DISTANCE` and `DISPLACEMENT_DISTANCE_MAX`. (rd_number_estimation_factor_tag)= ### `RD_NUMBER_ESTIMATION_FACTOR` The default factor to generate supercells with symfc using `RANDOM_DISPLACEMENTS=AUTO` is changed to this value. See the default factor in {ref}`random_displacements_tag`. (random_displacement_temperature_tag)= ### `RANDOM_DISPLACEMENT_TEMPERATURE` This invokes generation of random displacements at a temperature specified by this tag. Collective displacements are randomly sampled from harmonic oscillator distribution functions of phonon modes. See more details at {ref}`random_displacements_at_temperatures`. An example of configure file for 2x2x2 supercell of NaCl conventional unit cell is as follows. ``` CREATE_DISPLACEMENTS = .TRUE. DIM = 2 2 2 PRIMITIVE_AXES = AUTO RANDOM_DISPLACEMENTS = 1000 RANDOM_DISPLACEMENT_TEMPERATURE = 300 FC_SYMMETRY = .TRUE. ``` The random displacements at a specified temperature are generated after phonon calculation, therefore a set of data for the phonon calculation is necessary. In the following example, `FORCE_SETS` of NaCl example is copied to an empty directory. Running following command, `phonopy_disp.yaml` is generated in the current directory. For example in `example/NaCl` directory, ```bash % mkdir rd && cd rd % cp ../FORCE_SETS % phonopy ../phonopy_disp.yaml --rd 1000 --rd-temperature 300 ``` See also {ref}`f_force_sets_option` for creating `FORCE_SETS` from a series of sueprcell calculation. Be careful that if `FORCE_SETS` exists in the current directory, it will be overwritten by creating new `FORCE_SETS`. To obtain force constants with random displacements and respective forces, an external force constants calculator is necessary. See {ref}`fc_calculator_tag`. Displacements thus generated are sensitive to acoustic sum rule. Tiny phonon frequency at Gamma point due to violation of acoustic sum rule can induce very large displacements. Therefore, it is safer to use this feature with `FC_SYMMETRY = .TRUE.` (this is a default setting for `phonopy` command) or a force constants calculator (see {ref}`fc_calculator_tag`) that enforces acoustic sum rule. It is also possible to ignore phonons with frequencies below cutoff frequency specified by {ref}`cutoff_frequency_tags` tag. Phonon frequencies of imaginary modes are treated as their absolute values. (random_seed_tag)= ### `RANDOM_SEED` The random seed used for creating random displacements by {ref}`random_displacements_tag` tag. The value has to be 32bit unsigned int. The random seed is useful for crating the same random displacements with using the same number. (band_structure_related_tags)= ## Band structure tags (band_tag)= ### `BAND` `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. 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_points_tag)= ### `BAND_POINTS` `BAND_POINTS` gives the number of sampling points including the path ends. The default value is `BAND_POINTS = 51`. (band_labels_tag)= ### `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. When LaTeX math style expression such as {math}`\Gamma` (`\Gamma`) is expected, it is probably necessary to place it between two $ characters. ``` BAND = 1/2 0 1/2 0 0 0 1/2 1/2 1/2 BAND_LABELS = X $\Gamma$ L ``` ```{image} band-labels.png :scale: 25 ``` 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_tag)= ### `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. ``` ```{image} band-connection.png :scale: 25 ``` (band_const_interval_tag)= ### `BAND_CONST_INTERVAL` When `BAND_CONST_INTERVAL = .TRUE.`, the number of q-points sampled in each band path segment is determined by the longest path segment, which uses the number specified by `BAND_POINTS`. This ensures similar distances between points across all segments. Consequently, the number of q-points in each band path segment is equal to or less than the value of `BAND_POINTS`. The default value is `.FALSE.`. ``` BAND = AUTO BAND_POINTS = 101 BAND_CONST_INTERVAL = .TRUE. ``` (mesh_sampling_tags)= ## Mesh sampling tags Mesh sampling tags are used commonly for calculations of thermal properties and density of states. (mesh_tag)= ### `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 {math}`\Gamma` center in two ways, ``` MESH = 8 8 8 GAMMA_CENTER = .TRUE. ``` ``` MESH = 8 8 8 MP_SHIFT = 1/2 1/2 1/2 ``` If only one float value is given, e.g., `MESH = 100.0`, {math}`\Gamma` centred sampling mesh is generated with the mesh numbers {math}`(N_{\mathbf{a}^*}, N_{\mathbf{b}^*}, N_{\mathbf{c}^*})` computed following the convention of the VASP automatic k-point generation, which is ```{math} N_{\mathbf{a}^*} = \max[1, \mathrm{nint}(l|\mathbf{a}^*|)], \; N_{\mathbf{b}^*} = \max[1, \mathrm{nint}(l|\mathbf{b}^*|)], \; N_{\mathbf{c}^*} = \max[1, \mathrm{nint}(l|\mathbf{c}^*|)], ``` where {math}`l` is the value to be specified. With this, `GAMMA_CENTER` is simply ignored, but `MP_SHIFT` works on top of the {math}`\Gamma` centred sampling mesh. ``` MESh = 100 ``` ### `MP_SHIFT` `MP_SHIFT` gives the shifts in direction along the corresponding reciprocal axes ({math}`a^*`, {math}`b^*`, {math}`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_tag)= ### `GAMMA_CENTER` Instead of employing the Monkhorst-Pack scheme for the mesh sampling, {math}`\Gamma` center mesh is used. The default value is `.FALSE.`. ``` GAMMA_CENTER = .TRUE. ``` (write_mesh_tag)= ### `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. ``` (dos_related_tags)= ## Phonon density of states (DOS) tags Phonon density of states (DOS) is calculated either with a linear tetrahedron method (default) or smearing method. Phonons are calculated on a sampling mesh, therefore these tags must be used with {ref}`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 {math}`3N_\mathrm{a}` states, where {math}`N_\mathrm{a}` is the number of atoms in the unit cell. Phonon-DOS is formally defined as ```{math} g(\omega) = \frac{1}{N} \sum_\lambda \delta(\omega - \omega_\lambda) ``` where {math}`N` is the number of unit cells and {math}`\lambda = (\nu, \mathbf{q})` with {math}`\nu` as the band index and {math}`\mathbf{q}` as the q-point. This is computed on a set of descritized sampling frequency points for which {math}`\omega` is specified arbitrary using {ref}`dos_range_tag`. The phonon frequencies {math}`\omega_\lambda` are obtained on a sampling mesh whose the number of grid points being {math}`N`. In the smearing method, the delta function is replaced by normal distribution (Gaussian function) with the standard deviation specified by {ref}`sigma_tag`. In the tetrahedron method, the Brillouin integration is made analytically within tetrahedra in reciprocal space. (dos_tag)= ### `DOS` This tag enables to calculate DOS. This tag is automatically set when `PDOS` tag or `-p` option. ``` DOS = .TRUE. ``` (dos_range_tag)= ### `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. {ref}`dos_fmin_fmax_tags` can be alternatively used to specify the minimum and maximum frequencies (the first and second values). (dos_fmin_fmax_tags)= ### `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_tag)= ### `PDOS` Projected DOS is calculated using this tag. The formal definition is written as ```{math} 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 {math}`j` is the atom indices and {math}`\hat{\mathbf{n}}` is the unit projection direction vector. Without specifying {ref}`projection_direction_tag` or {ref}`xyz_projection_tag`, PDOS is computed as sum of {math}`g^j(\omega, \hat{\mathbf{n}})` projected onto Cartesian axes {math}`x,y,z`, i.e., ```{math} g^j(\omega) = \sum_{\hat{\mathbf{n}} = \{x, y, z\}} g^j(\omega, \hat{\mathbf{n}}). ``` The atom indices {math}`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. `PDOS = AUTO` is supported To group symmetrically equivalent atoms automatically. ``` PDOS = AUTO ``` `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.` ({ref}`write_mesh_tag`). (projection_direction_tag)= ### `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_tag)= ### `XYZ_PROJECTION` PDOS is calculated using eigenvectors projected along x, y, and z Cartesian coordinates. The format of output file `projected_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 components of eigenvectors, respectively. ``` XYZ_PROJECTION = .TRUE. ``` (sigma_tag)= ### `SIGMA` A smearing method is used instead of a linear tetrahedron method. This tag also 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 ``` (debye_model_tag)= ### `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 {math}`D(\omega)=a\omega^2` where {math}`a` is the parameter and the Debye frequency is {math}`(9N/a)^{1/3}` where {math}`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. ``` (dos_moment_tag)= ### `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` ({math}`n` in the formula). Unless `MOMENT_ORDER` specified, the first and second moments are calculated. The moments for DOS are given as ```{math} 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 ```{math} 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}. ``` {math}`\omega_\text{min}` and {math}`\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 {math}`\epsilon < \omega < \infty`, where {math}`\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 {math}`\omega_\text{min}`. ``` MOMENT = .TRUE. MOMENT_ORDER = 3 ``` ## Thermal properties related tags See {ref}`cutoff_frequency_tags` on the treatment of the imaginary modes. (thermal_properties_tag)= ### `TPROP` Thermal properties, free energy, heat capacity, and entropy, are calculated from their statistical thermodynamic expressions (see {ref}`thermal_properties_expressions`). Thermal properties are calculated from phonon frequencies on a sampling mesh in the reciprocal space. Therefore these tags must be used with {ref}`mesh_sampling_tags` and their convergence with respect to the sampling mesh has to be checked. Usually this calculation is not computationally demanding, so the convergence is easily achieved with increasing the density of the sampling mesh. `-p` option can be used together to plot the thermal properties. Phonon frequencies in THz, which is the default setting of phonopy, are used to obtain the thermal properties, therefore physical units have to be set properly for it (see {ref}`calculator_interfaces`.) The calculated values are written into `thermal_properties.yaml`. The unit systems of free energy, heat capacity, and entropy are kJ/mol, J/K/mol, and J/K/mol, respectively, where 1 mol means {math}`\mathrm{N_A}\times` the primitive cell defined by {ref}`primitive_axes_tag` but may not corresppond to {math}`\mathrm{N_A}\times` formula unit, i.e. you have to divide the value by number of formula unit in the primitive cell defined by {ref}`primitive_axes_tag` by yourself. For example, in MgO (conventional) unit cell, if you want to compare with experimental results in kJ/mol, you have to divide the phonopy output by four. ``` TPROP = .TRUE. ``` (thermal_property_temperatures)= ### `TMIN`, `TMAX`, and `TSTEP` `TMIN`, `TMAX`, and `TSTEP` tags are used to specify the temperature range to be calculated. The default values of them are 0, 1000, and 10, respectively. ``` TPROP = .TRUE. TMAX = 2000 ``` (pretend_real_tags)= ### `PRETEND_REAL` This enables to take imaginary frequencies as real for thermal property calculation. This does give false thermal properties, therefore for a testing purpose only, when a small amount of imaginary branches obtained. ``` TPROP = .TRUE. PRETEND_REAL = .TRUE. ``` (cutoff_frequency_tags)= ### `CUTOFF_FREQUENCY` This is given by a real value and the default value is 0. This tag works as follows. Phonon thermal properties are computed as sum over phonon modes. See {ref}`thermal_properties_expressions`. When we treat imaginary frequencies as negative values by {math}`\text{sgn}(\nu^2) |\nu| \rightarrow \nu_\text{phonopy}`, all phonon modes with {math}`\nu_\text{phonopy}` smaller than this `CUTOFF_FREQUENCY` are simply excluded in the summation. In the `thermal_properties.yaml`, the total number of calculated phonon modes and the number of phonon modes included for the thermal property calculation are shown as `num_modes:` and `num_integrated_modes:`, respectively. ``` CUTOFF_FREQUENCY = 0.1 ``` (thermal_atomic_displacements_tags)= ## Thermal displacements (thermal_displacements_tag)= ### `TDISP` Mean square displacements projected to Cartesian axes as a function of temperature are calculated from the number of phonon excitations. 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 {ref}`calculator_interfaces`.) The result is given in {math}`\text{Angstrom}^2` and writen into `thermal_displacements.yaml`. See the detail of the method, {ref}`thermal_displacement`. These tags must be used with {ref}`mesh_sampling_tags` Optionally, `FMIN` tag (`--fmin` option) with a small value is recommened to be set when q-points at {math}`\Gamma` point or near {math}`\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 ({ref}`projection_direction_tag`). `TMAX`, `TMIN`, `TSTEP` tags are used to control temperature points at which the thermal displacements are calculated. `mesh.yaml` or `mesh.hdf5` is not written out from phonopy-1.11.14. ``` TDISP = .TRUE. PROJECTION_DIRECTION = 1 1 0 ``` (thermal_displacement_matrices_tag)= ### `TDISPMAT` Mean square displacement matrices are calculated. The definition is shown at {ref}`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 {ref}`calculator_interfaces`.) The result is given in {math}`\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 {math}`\mathrm{U}_\text{cart}` and {math}`\mathrm{U}_\text{cif}` defined at {ref}`thermal_displacement_matrix`, respectively. Optionally, `FMIN` tag (`--fmin` option) with a small value is recommended to be set when q-points at {math}`\Gamma` point or near {math}`\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. `TMAX`, `TMIN`, `TSTEP` tags are used to control temperature points at which the thermal displacement matrices are calculated. `mesh.yaml` or `mesh.hdf5` is not written out from phonopy-1.11.14. ``` TDISPMAT = .TRUE. ``` (thermal_displacement_cif_tag)= ### `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 {ref}`calculator_interfaces`.) The result is given in {math}`\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_tag)= ### `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 {ref}`QPOINTS`) in current directory phonons at the q-points are calculated. ``` QPOINTS = .TRUE. ``` (writedm_tag)= ### `WRITEDM` ``` WRITEDM = .TRUE. ``` Dynamical matrices {math}`D` are written into `qpoints.yaml` in the following {math}`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 {ref}`frequency_conversion_factor_tag`). ```{math} 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 {math}`D_{jj'}` is ```{math} 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 {math}`q=(0, 0.5, 0.5)` by ``` phonopy --qpoints="0 1/2 1/2" --writedm ``` and the dynamical matrix may be used as ```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_tag)= ### `NAC` Non-analytical term correction is applied to dynamical matrix. `BORN` file has to be prepared in the current directory. See {ref}`born_file` and {ref}`non_analytical_term_correction_theory`. The default method is `NAC_METHOD = GONZE` after v1.13.0. ``` NAC = .TRUE. ``` (nac_method_tag)= ### `NAC_METHOD` The method of non-analytical term correction is chosen by this tag between two, `NAC_METHOD = GONZE` ({ref}`reference_dp_dp_NAC`) and `NAC_METHOD = WANG` ({ref}`reference_wang_NAC`), and the default is the former after v1.13.0. (q_direction_tag)= ### `Q_DIRECTION` This tag is used to activate non-analytical term correction (NAC) at {math}`\mathbf{q}\rightarrow\mathbf{0}`, i.e. practically {math}`\Gamma`-point, because NAC is direction dependent. With this tag, {math}`\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 {math}`\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_tag)= ### `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 {ref}`interfaces-physical-units`. For example, VASP [Angstrom.THz], and QE [au.THz]. ``` GROUP_VELOCITY = .TRUE. ``` Technical details are shown at {ref}`group_velocity`. (gv_delta_q_tag)= ### `GV_DELTA_Q` The reciprocal distance used for the finite difference method is specified. Unless this tag is set, the analytical derivative of the dynamical matrix is used (including the Gonze-Lee non-analytical term correction, for which the analytical dipole-dipole derivative is now available). Set this tag to fall back to the finite-difference path with the given step. In earlier versions (v4.0.1 and earlier) the finite-difference path was used implicitly with `GV_DELTA_Q = 1e-5` whenever the Gonze-Lee non-analytical term correction was active. Set `GV_DELTA_Q = 1e-5` explicitly to reproduce that behavior. ``` GV_DELTA_Q = 0.01 ``` ## Symmetry (tolerance_tag)= ### `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 {ref}`symmetry_option` option. ``` SYMMETRY_TOLERANCE = 1e-3 ``` (symmetry_tag)= ### `SYMMETRY` P1 symmetry is enforced to the input unit cell by setting `SYMMETRY = .FALSE`. (nomeshsym_tag)= ### `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_tag)= ### `FC_SYMMETRY` ```{note} Starting with version 1.12.3, this tag was changed to a boolean (`.TRUE.` or `.FALSE.`), whereas it previously accepted an argument. ``` 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, ```{math} \sum_i \Phi_{ij}^{\alpha\beta} = 0, \;\;\text{for all $j$, $\alpha$, $\beta$}, ``` where _i_ and _j_ are the atom indices, and {math}`\alpha` and {math}`\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 ```{math} \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} ``` 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_tag)= ## 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 {ref}`here `. (full_force_constants_tag)= ### `FULL_FORCE_CONSTANTS` `FULL_FORCE_CONSTANTS = .TRUE.` is used to compute full supercell constants matrix. This may be used to enforce space group symmetry to existing force constants. 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 {ref}`file_force_constants`. (read_force_constants_tag)= ### `READ_FORCE_CONSTANTS` `READ_FORCE_CONSTANTS = .TRUE.` is equivalent to `FORCE_CONSTANTS = READ`. (write_force_constants_tag)= ### `WRITE_FORCE_CONSTANTS` `WRITE_FORCE_CONSTANTS = .TRUE.` is equivalent to `FORCE_CONSTANTS = WRITE`. (fc_calculator_tag)= ### `FC_CALCULATOR` External force constants calculator can be used using this tag. Currently `symfc` and `ALM` are 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_tag)= ### `FC_CALCULATOR_OPTIONS` To be written. (fc_calculator_symfc_tag)= #### `SYMFC` **New in v2.25** Symfc () is based on fitting approach and any displacements set of atoms in supercell can be handled. For example, random displacements generated by {ref}`random_displacements_tag` can be used to compute force constants. To use symfc, its python module has to be installed via conda-forge or pip. When symfc is used, please cite the manuscript: A. Seko and A. Togo, Phys. Rev. B, **110**, 214302 (2024) [[doi](https://doi.org/10.1103/PhysRevB.110.214302)] ```text FC_CALCULATOR = SYMFC ``` (fc_calculator_alm_tag)= #### `ALM` **New in v2.3** ALM () is based on fitting approach and any displacements set of atoms in supercell can be handled. For example, random displacements generated by {ref}`random_displacements_tag` 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](https://alm.readthedocs.io/en/develop/compile-with-conda-packages.html). When ALM is used, please cite the paper: T. Tadano and S. Tsuneyuki, J. Phys. Soc. Jpn. **87**, 041015 (2018). ``` FC_CALCULATOR = ALM ``` (animation_tag)= ## 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_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. ```{toctree} animation ``` #### For the other animation formats Phonon is only calculated at {math}`\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_tag)= ### `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 ```{math} \frac{A} { \sqrt{N_\mathrm{a}m_j} } \operatorname{Re} \left[ \exp(i\phi) \mathbf{e}_j \exp( i \mathbf{q} \cdot \mathbf{r}_{jl} ) \right], ``` where {math}`A` is the amplitude, {math}`\phi` is the phase, {math}`N_\mathrm{a}` is the number of atoms in the supercell specified in this tag and {math}`m_j` is the mass of the _j_-th atom, {math}`\mathbf{q}` is the q-point specified, {math}`\mathbf{r}_{jl}` is the position of the _j_-th atom in the _l_-th unit cell, and {math}`\mathbf{e}_j` is the _j_-th atom part of eigenvector. Convention of eigenvector or dynamical matrix employed in phonopy is shown in {ref}`dynacmial_matrix_theory`. If several modes are specified as shown in the example above, they are overlapped on the structure. The output filenames are `MPOSCAR` and `MPOSCAR-`. Each modulated structure of a normal mode is written in `MPOSCAR-` 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 {ref}`dimension_tag` 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, {math}`\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 ``` (irreducible_representation_related_tags)= ## Characters of irreducible representations (irreps_tag)= ### `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 {math}`\Gamma` point are shown but not at non-{math}`\Gamma` point. (show_irreps_tag)= ### `SHOW_IRREPS` Irreducible representations are shown along with character table. ``` IRREPS = 1/3 1/3 0 SHOW_IRREPS = .TRUE. ``` (little_cogroup_tag)= ### `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_tag)= ### `FC_FORMAT`, `READFC_FORMAT`, `WRITEFC_FORMAT` There are two file-formats to store force constants. Currently {ref}`text style` (`TEXT`) and hdf5 (`HDF5`) formats are supported. The default file format is the {ref}`text style`. Reading and writing force constants are invoked by {ref}`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_mesh_qpoints_format_tags)= ### `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_tag)= #### `BAND_FORMAT` When `HDF5` is set, calculated result is stored in `band.hdf5` instead of `band.yaml`. ``` BAND_FORMAT = HDF5 ``` (mesh_format_tag)= #### `MESH_FORMAT` When `HDF5` is set, calculated result is stored in `mesh.hdf5` instead of `mesh.yaml`. ``` MESH_FORMAT = HDF5 ``` (qpoints_format_tag)= #### `QPOINTS_FORMAT` When `HDF5` is set, calculated result is stored in `qpoints.hdf5` instead of `qpoints.yaml`. ``` QPOINTS_FORMAT = HDF5 ``` (hdf5_tag)= ### `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 {ref}`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 ({ref}`qpoints_tag`), calculation results are written into `qpoints.hdf5` but not into `qpoints.yaml`. With {ref}`writedm_tag`, 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 ({ref}`band_structure_related_tags`), calculation results are written into `band.hdf5` but not into `band.yaml`. (summary_tag)= ### The following data may be optionally included in the `phonopy.yaml` file that is written at the end of the pre/post-process (after running the `phonopy` script). (include_fc_tag)= #### `INCLUDE_FC` The `--include-fc` flag or setting `INCLUDE_FC = .TRUE.` will cause the force constants (if available) to be written as an entry in `phonopy.yaml` 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. (include_fs_tag)= #### `INCLUDE_FS` The `--include-fs` flag or setting `INCLUDE_FS = .TRUE.` will cause the force sets (if available) to be written as an entry in `phonopy.yaml`. (include_disp_tag)= #### `INCLUDE_DISP` The `--include-disp` flag or setting `INCLUDE_DISP = .TRUE.` will cause displacements data (if available) to be written as an entry in `phonopy.yaml` file. (include_all_tag)= #### `INCLUDE_ALL` All available data covered by the other `include` flags can be written to `phonopy.yaml` file using the `--include-all` flag or by setting `INCLUDE_ALL = .TRUE.`. Force constants are not stored when force sets are stored.