(phonopy_gruneisen)=
# Calculation of mode Grüneisen parameters
## How to run
It is necessary to run three phonon calculations. One is calculated at the
equilibrium volume and the remaining two are calculated at the slightly larger
volume and smaller volume than the equilibrium volume. The unit cells at these
volumes have to be fully relaxed under the constraint of each volume.
Let files named `POSCAR-unitcell`, `FORCE_SETS` (or `FORCE_CONSTANTS` with
`--readfc` option), and optionally `BORN` stored in three different directories
named, e.g., `equiv`, `plus`, and `minus`.
The calculated results are written into the file `gruneisen.yaml`.
In the example directory, an example of silicon (`Si-gruneisen`) is prepared. A
calculation along paths in reciprocal space can be made by
```
% phonopy-gruneisen orig plus minus --dim="2 2 2" --pa="0 1/2 1/2 1/2 0 1/2 1/2 1/2 0" --band="1/2 1/4 3/4 0 0 0 1/2 1/2 1/2 1/2 0.0 1/2" -p -c POSCAR-unitcell
```
```{image} Si-gruneisen-band.png
:scale: 50
```
In this calculation, neighboring **q**-points in each band segment are connected
considering their phonon symmetry to treat band crossing correctly. Therefore
the phonon frequencies may not be ordered in `gruneisen.yaml`. In the plot (`-p`
option), the colors of phonon bands correspond to those of mode Grüneinen
parameters.
A calculation on a reciprocal mesh is made by
```
% phonopy-gruneisen orig plus minus --dim="2 2 2" --pa="0 1/2 1/2 1/2 0 1/2 1/2 1/2 0" --mesh="20 20 20" -p -c POSCAR-unitcell --color="RB"
```
```{image} Si-gruneisen-mesh.png
:scale: 50
```
In the plot (`-p` option), the colors of mode Grüneinen parameters are set for
band indices with ascending order of phonon frequencies.
Mode Grüneinen parameter may diverge around {math}`\Gamma`-point. In the above
example for band paths, mode Grüneinen parameters are calculated at
{math}`\Gamma`-point, but `phonopy-gruneisen` script avoids showing the values
on the plot. Instead the values at the neighboring **q**-points of
{math}`\Gamma`-point are used for the plot.
(gruneisen_calculators)=
## Force calculator interfaces
Options of force calculator interfaces such as `--abinit`, `--qe`, ... can be
specified for corresponding calculators and the crystal structure file format
should be different from that of the VASP format. An Abinit example is as
follows:
```
% phonopy-gruneisen orig plus minus --abinit --dim="2 2 2" --pa="0 1/2 1/2 1/2 0 1/2 1/2 1/2 0" --band="1/2 1/4 3/4 0 0 0 1/2 1/2 1/2 1/2 0.0 1/2" -p -c Si.in
```
(gruneisen_command_options)=
## Command options
If one of the force calculator options is specified, the interface mode is
changed to it. The unit conversion factor to THz is appropriately selected and
its crystal structure file format is accepted. If none of them is specified, as
the VASP interface mode is invoked as the default interface.
The following command options can be used for all interface modes. They work
similarly to those for `phonopy` script.
- `--dim`
- `--mp`, `--mesh`
- `--band`
- `--pa`, `--primitive_axis`
- `--readfc`
- `--band_points`
- `--nac`
- `--factor`
- `--nomeshsym`
- `-p`
- `-c`
- `-s`, `--save`
- `-o`
Currently `--pa="auto"` works but `--band="auto"` doesn't. The `--color` option
(`RB`, `RG`, `RGB`) is used to gradually change the marker colors with respect
to band indices. For the mesh-sampling plot, a few more options to control
matplotlib parameters are prepared.
## Method to calculate mode Grüneisen parameters
Mode Grüneisen parameter {math}`\gamma(\mathbf{q}\nu)` at the wave vector
{math}`\mathbf{q}` and band index {math}`\nu` is given by
```{math}
\gamma(\mathbf{q}\nu) =& -\frac{V}{\omega(\mathbf{q}\nu)}\frac{\partial
\omega(\mathbf{q}\nu)}{\partial V}\\
=&-\frac{V}{2[\omega(\mathbf{q}\nu)]^2}\left<\mathbf{e}(\mathbf{q}\nu)\biggl|
\frac{\partial D(\mathbf{q})} {\partial
V}\biggl|\mathbf{e}(\mathbf{q}\nu)\right>,
```
where {math}`V` is the volume, {math}`\omega(\mathbf{q}\nu)` is the phonon
frequency, {math}`D(\mathbf{q})` is the dynamical matrix, and
{math}`\mathbf{e}(\mathbf{q}\nu)` is the eigenvector. This is approximated by
the finite difference method:
```{math}
\gamma(\mathbf{q}\nu) \simeq -\frac{V}{2[\omega(\mathbf{q}\nu)]^2}
\left<\mathbf{e}(\mathbf{q}\nu)\biggl| \frac{\Delta D(\mathbf{q})} {\Delta
V}\biggl|\mathbf{e}(\mathbf{q}\nu)\right>.
```
The `phonopy-gruneisen` script requires three phonon calculations at
corresponding three volume points. One is for eigenvectors at the equilibrium
volume ({math}`V`) and the remaining two are for {math}`\Delta D(\mathbf{q})`
with slightly larger and smaller volumes than {math}`V`.