VASP & phono3py calculation#

Workflow#

Create POSCARs with displacements

This is the same way as usual phonopy:
```
% phono3py -d --dim 2 2 2 --pa F -c POSCAR-unitcell
```
phono3py_disp.yaml and POSCAR-xxxxx files are created.

If you want to use larger supercell size for second-order force constants (fc2) calculation than that for third-order force constants (fc3) calculation:
```
% phono3py -d --dim-fc2 4 4 4 --dim 2 2 2 --pa F -c POSCAR-unitcell
```
In this case, POSCAR_FC2-xxxxx files are also created.
Run VASP for supercell force calculations

To calculate forces on atoms in supercells, POSCAR-xxxxx (and POSCAR_FC2-xxxxx if they exist) are used as VASP (or any force calculator) calculations.

It is supposed that each force calculation is executed under the directory named disp-xxxxx (and disp_fc2-xxxxx), where xxxxx is sequential number.
Collect vasprun.xml’s

When VASP is used as the force calculator, force sets to calculate fc3 and fc2 are created as follows.
```
% phono3py --cf3 disp-{00001..00755}/vasprun.xml
```
where 0755 is an example of the index of the last displacement supercell. To perform this collection, phono3py_disp.yaml created at step 1 is required. Then FORCES_FC3 is created.

When you use larger supercell for fc2 calculation:
```
% phono3py --cf2 disp_fc2-{00001..00002}/vasprun.xml
```
phono3py_displ.yaml is necessary in this case and FORCES_FC2 is created.
Create fc2.hdf and fc3.hdf
```
% phono3py --sym-fc
```
--sym-fc symmetrizes fc3 and fc2. fc2.hdf5 and fc3.hdf5 are created from FORCES_FC3 (and optionally FORCES_FC2) and phono3py_disp.yaml. This step is not mandatory, but you can avoid calculating fc2 and fc3 at every run time when reading force constants from these files with --fc3 and --fc2 options.
Thermal conductivity calculation

An example of thermal conductivity calculation is:
```
% phono3py --mesh 11 11 11 --br
```
This calculation may take very long time. --thm invokes a tetrahedron method for Brillouin zone integration for phonon lifetime calculation, which is the default option. Instead, --sigma option can be used with the smearing widths.

In this command, phonon lifetimes at many grid points are calculated in series. The phonon lifetime calculation at each grid point can be separately calculated since they are independent and no communication is necessary at the computation. The procedure is as follows:

First run the same command with the addition option of --wgp:
```
% phono3py --fc3 --fc2 --mesh 11 11 11 --br --wgp
```
ir_grid_points.yaml is obtained. Irreducible q-points are found in this file. For example, the grid point indices of the irreducible q-points are printed by
```
% grep grid_point: ir_grid_points.yaml|awk '{printf("%d ", $3)}'
0 1 2 3 4 5 12 13 14 15 16 17 18 19 20 21 24 25 26 27 28 29 30 31 36 37 38 39 40 41 48 49 50 51 60 61 148 149 150 151 160 161 162 163 164 165 172 173 174 175 184 185 297 298 309 310
```
Phonon lifetimes on the first ten irreducible grid points are calculated and stored in files with --write-gamma option by:
```
% phono3py --mesh 11 11 11 --br --write-gamma --gp 0 1 2 3 4 5 12 13 14 15
```
After finishing distributed calculations at all irreducible grid points (0, 1, …, 310), run with --read-gamma option:
```
% phono3py --fc3 --fc2 --mesh 11 11 11 --br --read-gamma
```
Once this calculation runs without problem, separately calculated hdf5 files on grid points are no more necessary and may be deleted.

VASP & phono3py calculation

Contents

VASP & phono3py calculation#

Workflow#