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Input / Output files

Input / 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.

phono3py_disp.yaml#

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

This file contains displacement dataset and crystal structure information.

FORCES_FC3#

This is created with --cf3 option. See --cf3 (command option only).

There are two formats of FORCES_FC3. The type-I format is like that shown below

# File: 1
# 1       0.0300000000000000   0.0000000000000000   0.0000000000000000
  -0.6458483000    0.0223064300   -0.0143299700
   0.0793497000    0.0088413200   -0.0052766800
   0.0768176500   -0.0095501600    0.0057262300
  -0.0016552800   -0.0366684600   -0.0059480700
  -0.0023432300    0.0373490000    0.0059468600
   0.0143901800    0.0000959800   -0.0001100900
  -0.0019487200   -0.0553591300   -0.0113649500
   0.0143732700   -0.0000614400    0.0000502600
  -0.0020311400    0.0554678300    0.0115355100
...
# File: 1254
# 37      0.0000000000000000   0.0000000000000000  -0.0300000000000000
# 68      0.0000000000000000   0.0000000000000000  -0.0300000000000000
  -0.0008300600   -0.0004792400    0.0515596200
  -0.0133197900   -0.0078480800    0.0298334900
   0.0141518600   -0.0105405200    0.0106313000
   0.0153762500   -0.0072671600    0.0112864200
  -0.0134565300   -0.0076112400    0.0298334900
  -0.0019180000   -0.0011073600    0.0272454300
   0.0013945800    0.0169498000    0.0112864200
   0.0006578200    0.0003797900    0.0085617600
  -0.0020524300    0.0175261300    0.0106313000
   0.0019515200    0.0011267100   -0.2083651200
   0.0148675800   -0.0516285500   -0.0924200600
  -0.0168043800    0.0074232400   -0.0122506300
  -0.0128831200    0.0114004400   -0.0110906700
...

This file contains supercell forces. Lines starting with # is ignored when parsing. Each line gives forces of at atom in Cartesian coordinates. All forces of atoms in each supercell are written in the same order as the atoms in the supercell. All forces of all supercells are concatenated. If force sets are stored in a numpy array (forces) of the shape of (num_supercells, num_atoms_in_supercell, 3), this file is generated using numpy as follows:

np.savetxt("FORCES_FC3", forces.reshape(-1, 3))

The type-II format is the same as phonopy’s type-II format of FORCE_SETS.

FORCES_FC2#

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

The file formats (type-I and type-II) are same as those of FORCES_FC3.

HDF5 files#

kappa-*.hdf5#

See the detail at Details of kappa-*.hdf5 file.

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 --write-gamma (WRITE_GAMMA = .TRUE.).

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 Joint density of states (JDOS) and weighted-JDOS.

linewidth-*.dat#

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