Input files¶
Setting file¶
A setting file contains phonopy settings which are summarized at Setting tags. This file is passed to phonopy as an argument, e.g.,
% phonopy phonopy.conf
where the filename is arbitrary.
Structure file (POSCAR)¶
Crystal structure is written in VASP’s manner (for Wien2k interface, see WIEN2k mode). The format is simple. The first line is for your comment, where you can write anything you want. The second line is the ratio for lattice parameters. You can multiply by this number. The third to fifth lines give the lattice parameters, a, b, and c for the respective lines. The sixth line contains the number of atoms for each atomic species, which have to correspond to the atomic positions in the order. The seventh line should be written as Direct. This means that the atomic positions are represented in fractional (reduced) coordinates. When you write chemicla symbols in the first line, they are read and those defined by the ATOM_NAME tag are overwritten.
Example of rutile-type silicon oxide crystal structure (1)¶
Si O
1.00000000000000
4.2266540199664249 0.0000000000000000 0.0000000000000000
0.0000000000000000 4.2266540199664249 0.0000000000000000
0.0000000000000000 0.0000000000000000 2.6888359272289208
2 4
Direct
0.0000000000000000 0.0000000000000000 0.0000000000000000
0.5000000000000000 0.5000000000000000 0.5000000000000000
0.3067891334429594 0.3067891334429594 0.0000000000000000
0.6932108665570406 0.6932108665570406 0.0000000000000000
0.1932108665570406 0.8067891334429594 0.5000000000000000
0.8067891334429594 0.1932108665570406 0.5000000000000000
The VASP 5.x style is also supported. Chemical symbols are inserted just before the line of the numbers of atoms. The chemical symbols in this line overwrite those defined by the ATOM_NAME tag and those defined by the first line of POSCAR.
Example of rutile-type silicon oxide crystal structure (2)¶
Stishovite
1.00000000000000
4.2266540199664249 0.0000000000000000 0.0000000000000000
0.0000000000000000 4.2266540199664249 0.0000000000000000
0.0000000000000000 0.0000000000000000 2.6888359272289208
Si O
2 4
Direct
0.0000000000000000 0.0000000000000000 0.0000000000000000
0.5000000000000000 0.5000000000000000 0.5000000000000000
0.3067891334429594 0.3067891334429594 0.0000000000000000
0.6932108665570406 0.6932108665570406 0.0000000000000000
0.1932108665570406 0.8067891334429594 0.5000000000000000
0.8067891334429594 0.1932108665570406 0.5000000000000000
Force file (FORCE_SETS)¶
This file gives sets of forces in supercells with finite atomic displacements. Each supercell involves one displaced atom. The first line is the number of atoms in supercell. The second line gives number of calculated supercells with displacements. Below the lines, sets of forces with displacements are written. In each set, firstly the atom number in supercell is written. Secondary, the atomic displacement in Cartesian coordinates is written. Below the displacement line, atomic forces in Cartesian coordinates are successively written. This is repeated for the set of displacements. Blank likes are simply ignored.
In the following example, the third line is the displaced atom number that corresponds to the atom number in the supercell created by phonopy. The fourth line gives the displacements in Cartesian coordinates. The lines below, the atomic forces in Cartesian coordinates are written. Once all the forces for a supercell have written, the next set of forces are written. This routine is repeated until the forces of all the displacements have been written.
See also VASP interface and WIEN2k interface for VASP and Wien2k users.
Example¶
48
2
1
0.0050650623043761 0.0000000000000000 0.0086223630086415
-0.0347116200 -0.0000026500 -0.0679795200
0.0050392400 -0.0015711700 -0.0079514600
0.0027380900 -0.0017851900 -0.0069206400
... (continue until all the forces for this displacement have written)
25
0.0050650623043761 0.0000000000000000 0.0086223630086415
-0.0017134500 -0.0001539800 0.0017333400
0.0013248100 0.0001984300 -0.0001203700
-0.0001310200 -0.0007955600 0.0003889300
... (continue until all the forces for this displacement have written)
FORCE_CONSTANTS¶
If force constants of a supercell are known, FORCES is not necessary to be prepared. Phonopy has interface to read and write FORCE_CONSTANTS. To read and write FORCE_CONSTANTS are controled by Force constants.
VASP users can use VASP DFPT interface to create FORCE_CONSTANTS from vasprun.xml.
Format¶
First line is for the number of atoms in supercell. Below second line, force constants between atoms are written by every four lines. In first line of the four lines, anything can be written, i.e., just ignored. Second to fourth lines of the four lines are for the second rank tensor of force constant in Cartesian coordinates, i.e.::
xx xy xz
yx yy yz
zx zy zz
Example¶
32
1 1
4.635786969900131 -0.000000000000000 -0.000000000000000
-0.000000000000000 4.635786969900130 -0.000000000000000
-0.000000000000000 -0.000000000000000 4.635786969900130
1 2
-0.246720998398056 -0.000000000000000 -0.000000000000000
-0.000000000000000 0.018256999881458 -0.000000000000000
-0.000000000000000 -0.000000000000000 0.018256999881458
...
1 32
0.002646999982813 0.018011999883049 -0.000000000000000
0.018011999883049 0.002646999982813 -0.000000000000000
-0.000000000000000 -0.000000000000000 0.035303999770773
2 1
-0.246720998398056 0.000000000000000 0.000000000000000
0.000000000000000 0.018256999881458 0.000000000000000
0.000000000000000 0.000000000000000 0.018256999881458
...
32 32
4.635786969900131 0.000000000000000 0.000000000000000
0.000000000000000 4.635786969900130 0.000000000000000
0.000000000000000 0.000000000000000 4.635786969900130
QPOINTS (optional)¶
Specific q-points are calculated using QPOINTS = .TRUE. tag and QPOINTS file. The file format of QPOINTS is as follows. The first line gives the number of q-points. Then the successive lines give q-points in reduced coordinate of reciprocal space of the input unit cell.
Example¶
512
-0.437500000000000 -0.437500000000000 -0.437500000000000
-0.312500000000000 -0.437500000000000 -0.437500000000000
-0.187500000000000 -0.437500000000000 -0.437500000000000
...
BORN (optional)¶
This file is used with the --nac option (nac_option).
Non-analytical term correction¶
To correct long range interaction of macroscopic electric field
induced by polarization of collective ionic motions near the
-point, non-analytical term is added to dynamical matrix
(Non-analytical term correction). At
, the dynamical matrix with
non-analytical term is given by,
![D_{\alpha\beta}(jj',\mathbf{q}\to \mathbf{0}) =
D_{\alpha\beta}^{\mathrm{N}}(jj',\mathbf{q}\to \mathbf{0})
+ \frac{4\pi}{\sqrt{m_j m_j}\Omega_0}
\frac{[\sum_{\gamma}q_{\gamma}Z^{*}_{j,\gamma\alpha}][\sum_{\gamma'}q_{\gamma'}Z^{*}_{j',\gamma'\beta}]}
{\sum_{\alpha\beta}q_{\alpha}\epsilon_{\alpha\beta}^{\infty} q_{\beta}}.](_images/math/41d34bd2cb992f0e581834da9b6c4159fecf3193.png)
Phonon frequencies at general q-points are interpolated by the method of Wang et al. (Interpolation scheme at general q-points with non-analytical term correction).
Format¶
In the first line, the first value is the unit conversion factor. For
VASP, it may be 27.2116 
0.52918.
In the second line, dielectric constant 
is specifed
in Cartesian coordinates. The nine values correspond to the tensor
elements of xx, xy, xz, yx, yy, yz, zx, zy, and zz.
From the third line, Born effective charges 
for the
independent atoms in the primitive cell have to be written in
Cartesian coordinates. The independent atoms can be found using the
--symmetry option. If PRIMITIVE_AXIS is supposed to be used to
calculate phonons, the option --primitive_axis has to be set
together with the --symmetry option.
Example¶
14.400
2.00 0.00 0.00 0.00 2.00 0.00 0.00 0.00 2.00
1.98 0.00 0.00 0.00 1.98 0.00 0.00 0.00 1.98
-0.99 0.00 0.00 0.00 -0.99 0.00 0.00 0.00 -0.99
...
Table Of Contents
- Input files