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(vasp_interface)=
# VASP & phonopy calculation
## Pre-process
The input structure of `POSCAR` ({ref}`this <example_POSCAR1>`) is used as an
example here. Most files are found at [SiO2-HP
example](https://github.com/phonopy/phonopy/tree/master/example/SiO2-HP/).
In the pre-process, supercell structures with (or without)
displacements are created from a unit cell fully considering crystal
symmetry.
To obtain supercells ({math}`2\times 2\times 3`) with displacements,
run phonopy,
```bash
% phonopy -d --dim 2 2 3 --pa auto
```
You should find the files, `SPOSCAR`, `phonopy_disp.yaml`, and
`POSCAR-{number}` as follows:
```bash
% ls
phonopy_disp.yaml POSCAR POSCAR-001 POSCAR-002 POSCAR-003 SPOSCAR
```
`SPOSCAR` is the perfect supercell structure, `phonopy_disp.yaml`
contains the information on displacements, and `POSCAR-{number}` are
the supercells with atomic displacements. `POSCAR-{number}`
corresponds to the different atomic displacements written in
`phonopy_disp.yaml`.
## Calculation of sets of forces
Force constants are calculated using the structure files
`POSCAR-{number}` (from forces on atoms) or using the `SPOSCAR`
file. In the case of VASP, the calculations for the finite
displacement method can be proceeded just using the
`POSCAR-{number}` files as `POSCAR` of VASP calculations. An
example of the `INCAR` is as follows:
```
PREC = Accurate
IBRION = -1
ENCUT = 500
EDIFF = 1.0e-08
ISMEAR = 0; SIGMA = 0.01
IALGO = 38
LREAL = .FALSE.
LWAVE = .FALSE.
LCHARG = .FALSE.
```
Be careful not to relax the structures. Then create `FORCE_SETS`
file using {ref}`vasp_force_sets_option`:
```bash
% phonopy -f disp-001/vasprun.xml disp-002/vasprun.xml disp-003/vasprun.xml
```
or
```bash
% phonopy -f disp-{001..003}/vasprun.xml
```
If you want to calculate force constants by VASP-DFPT directory, see
{ref}`vasp_dfpt_interface`.
## Post-process
In the post-process,
1. Force constants are calculated from the sets of forces
2. A part of dynamical matrix is built from the force constants
3. Phonon frequencies and eigenvectors are calculated from the
dynamical matrices with the specified *q*-points.
The density of states (DOS) is plotted by
```bash
% phonopy-load --mesh 20 20 20 -p
```
Thermal properties are calculated with the sampling mesh by
```bash
% phonopy-load --mesh 20 20 20 -t
```
You should check the convergence with respect to the mesh numbers.
Thermal properties can be plotted by
```bash
% phonopy-load --mesh 20 20 20 -t -p
```
Projected DOS is calculated and plotted by
```bash
% phonopy-load --mesh 20 20 20 --pdos "1 2, 3 4 5 6" -p
```
Band structure is plotted by
```bash
% phonopy-load --band "0.5 0.5 0.5 0.0 0.0 0.0 0.5 0.5 0.0 0.0 0.5 0.0" -p
```
In either case, by setting the `-s` option, the plot is going to be
saved in the PDF format. If you don't need to plot DOS, the (partial)
DOS is just calculated using the `--dos` option.
## Non-analytical term correction (Optional)
To activate non-analytical term correction, {ref}`born_file` is
required. This file contains the information of Born effective charge
and dielectric constant. These physical values are also obtained from
the first-principles calculations, e.g., by using VASP, pwscf, etc. In
the case of VASP, an example of `INCAR` will be as shown below
```
PREC = Accurate
IBRION = -1
NELMIN = 5
ENCUT = 500
EDIFF = 1.000000e-08
ISMEAR = 0
SIGMA = 1.000000e-02
IALGO = 38
LREAL = .FALSE.
LWAVE = .FALSE.
LCHARG = .FALSE.
LEPSILON = .TRUE.
```
In addition, it is recommended to increase the number of k-points to
be sampled. Twice the number for each axis may be a choice. After
running this VASP calculation, `BORN` file has to be created
following the `BORN` format ({ref}`born_file`). However for VASP, an
auxiliary tool is prepared, which is `phonopy-vasp-born`. There is
an option `--pa` for this command to set a transformation matrix
from supercell or unit cell with centring to the primitive cell. Since
this rutile-type SiO2 has the primitive lattice, it is unnecessary to
set this option. Running `phonopy-vasp-born` in the directory
containing `vasprun.xml` (or `OUTCAR`) of this VASP calculation:
```bash
% phonopy-vasp-born
# epsilon and Z* of atoms 1 3
3.2605670 0.0000000 0.0000000 0.0000000 3.2605670 0.0000000 0.0000000 0.0000000 3.4421330
3.7558600 0.3020100 0.0000000 0.3020100 3.7558600 0.0000000 0.0000000 0.0000000 3.9965200
-1.8783900 -0.5270900 0.0000000 -0.5270900 -1.8783900 0.0000000 0.0000100 0.0000100 -1.9987900
```
To employ symmetry constraints, `--st` option may used as follows:
```bash
% phonopy-vasp-born --st
# epsilon and Z* of atoms 1 3
3.2605670 0.0000000 0.0000000 0.0000000 3.2605670 0.0000000 0.0000000 0.0000000 3.4421330
3.7561900 0.3020100 0.0000000 0.3020100 3.7561900 0.0000000 0.0000000 0.0000000 3.9968733
-1.8780950 -0.5270900 0.0000000 -0.5270900 -1.8780950 0.0000000 0.0000000 0.0000000 -1.9984367
```
The values are slightly modified by symmetry, but we can see the
original values obtained directly from VASP was already very good.
To put `BORN` file in the current directly, non-analytical term correction is
activated.
|
