5.8 KiB
(input-output_files)=
Input / Output files
:depth: 3
:local:
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 {ref}file_format_compatibility
.
phono3py_disp.yaml
This is created with -d
option. See {ref}create_displacements_option
.
This file contains displacement dataset and crystal structure information.
(input-output_files_FORCES_FC3)=
FORCES_FC3
This is created with --cf3
option. See {ref}cf3_option
.
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 {ref}cf2_option
and
{ref}dim_fc2_option
.
The file formats (type-I and type-II) are same as those of FORCES_FC3
.
HDF5 files
kappa-*.hdf5
See the detail at {ref}kappa_hdf5_file
.
(fc3_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
{ref}--pa option <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,
(\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}.
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_file)=
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 {ref}fc3_hdf5_file
.
gamma-*.hdf5
Imaginary parts of self energies at harmonic phonon frequencies
(\Gamma_\lambda(\omega_\lambda)
= half linewidths) are stored in THz. See
{ref}write_gamma_option
.
gamma_detail-*.hdf5
Q-point triplet contributions to imaginary parts of self energies at phonon
frequencies (half linewidths) are stored in THz. See
{ref}write_detailed_gamma_option
.
Simple text file
gammas-*.dat
Imaginary parts of self energies with respect to frequency
\Gamma_\lambda(\omega)
are stored in THz. See {ref}ise_option
.
jdos-*.dat
Joint densities of states are stored in Thz. See {ref}jdos_option
.