Output files

The calculation results are written into files. Mostly the data are stored in HDF5 format, therefore how to read the data from HDF5 files is also shown.

Intermediate text files

The following files are not compatible with phonopy. But phonopy’s FORCE_SETS file can be created using phono3py command options from the following files. See the detail at File format compatibility with phonopy.

disp_fc3.yaml

This is created with -d option. See -d (CREATE_DISPLACEMENTS = .TRUE.).

disp_fc2.yaml

This is created with -d option with --dim_fc2 option. See --dim-fc2 (DIM_FC2).

FORCES_FC2

This is created with --cf2 option. See --cf2 (command option only) and --dim-fc2 (DIM_FC2).

HDF5 files

fc3.hdf5

Third order force constants (in real space) are stored in \(\mathrm{eV}/\text{Angstrom}^3\).

In phono3py, this is stored in the numpy array dtype='double' and order='C' in the shape of:

(num_atom, num_atom, num_atom, 3, 3, 3)

against \(\Phi_{\alpha\beta\gamma}(l\kappa, l'\kappa', l''\kappa'')\). The first three num_atom are the atom indices in supercell corresponding to \(l\kappa\), \(l'\kappa'\), \(l''\kappa''\), respectively. The last three elements are the Cartesian coordinates corresponding to \(\alpha\), \(\beta\), \(\gamma\), respectively.

If you want to import a supercell structure and its fc3, you may suffer from matching its atom index between the supercell and an expected unit cell. This may be easily dealt with by letting phono3py see your supercell as the unit cell (e.g., POSCAR, unitcell.in, etc) and find the unit (primitive) cell using –pa option. For example, let us assume your supercell is the 2x2x2 multiples of your unit cell that has no centring, then your --pa setting will be 1/2 0 0 0 1/2 0 0 1/2 0. If your unit cell is a conventional unit cell and has a centring, e.g., the face centring,

\[\begin{split}(\mathbf{a}_\text{p}, \mathbf{b}_\text{p}, \mathbf{c}_\text{p}) = (\mathbf{a}_\text{s}, \mathbf{b}_\text{s}, \mathbf{c}_\text{s}) \begin{pmatrix} \frac{{1}}{2} & 0 & 0 \\ 0 & \frac{{1}}{2} & 0 \\ 0 & 0 & \frac{{1}}{2} \end{pmatrix} \begin{pmatrix} 0 & \frac{{1}}{2} & \frac{{1}}{2} \\ \frac{{1}}{2} & 0 & \frac{{1}}{2} \\ \frac{{1}}{2} & \frac{{1}}{2} & 0 \end{pmatrix} = (\mathbf{a}_\text{s}, \mathbf{b}_\text{s}, \mathbf{c}_\text{s}) \begin{pmatrix} 0 & \frac{{1}}{4} & \frac{{1}}{4} \\ \frac{{1}}{4} & 0 & \frac{{1}}{4} \\ \frac{{1}}{4} & \frac{{1}}{4} & 0 \end{pmatrix}.\end{split}\]

So what you have to set is --pa="0 1/4 1/4  1/4 0 1/4  1/4 1/4 0".

fc2.hdf5

Second order force constants are stored in \(\mathrm{eV}/\text{Angstrom}^2\).

In phono3py, this is stored in the numpy array dtype='double' and order='C' in the shape of:

(num_atom, num_atom, 3, 3)

against \(\Phi_{\alpha\beta}(l\kappa, l'\kappa')\). More detail is similar to the case for fc3.hdf5.

gamma-*.hdf5

Imaginary parts of self energies at harmonic phonon frequencies (\(\Gamma_\lambda(\omega_\lambda)\) = half linewidths) are stored in THz. See Imaginary part of self energy.

gamma_detail-*.hdf5

Q-point triplet contributions to imaginary parts of self energies at phonon frequencies (half linewidths) are stored in THz. See --write-gamma-detail (WRITE_GAMMA_DETAIL = .TRUE.).

Simple text file

gammas-*.dat

Imaginary parts of self energies with respect to frequency \(\Gamma_\lambda(\omega)\) are stored in THz. See --ise (IMAG_SELF_ENERGY = .TRUE.).

jdos-*.dat

Joint densities of states are stored in Thz. See --jdos (JOINT_DOS = .TRUE.).