phono3py/example/Si-PBEsol/README.md

This is the example of silicon calculation. The supercell is 2x2x2 of the conventional unit cell. The VASP calculation was made for force calculations with 300 eV, 2x2x2 off-Gamma-centre k-point sampling mesh for the supercell, and PBE-sol. Silicon crystal is F-centre, so there is the transformation matrix from the conventional unit cell to the primitive cell.

phono3py_disp.yaml is generated by

% phono3py -d --dim="2 2 2" -c POSCAR-unitcell --pa="F"

To create fc3.hdf5 and fc2.hdf5,

% phono3py-load

Using 11x11x11 sampling mesh, lattice thermal conductivity is calculated by

% phono3py-load --mesh 11 11 11 --br

kappa-m111111.hdf5 is written as the result. The lattice thermal conductivity is calculated as 109.1 W/m-K at 300 K. This becomes, with 19x19x19 sampling mesh, 124.4 W/m-K.

Accumulated lattice thermal conductivity is calculated using phono3py-kaccum script.

% phono3py-kaccum kappa-m111111.hdf5 |tee kaccum.dat

kaccum.dat is plotted using gnuplot by

gnuplot> p 'kaccum.dat' i 30 u 1:2 w l, 'kaccum.dat' i 30 u 1:8 w l

It is found that most of the lattice thermal conductivity owes the phonon modes below 6 THz.

fc2.hdf5 can be read by harmonic phonopy to rename it to force_constants.hdf5. The phonon band structure and DOS are plotted by

% ln -s fc2.hdf5 force_constants.hdf5
% phonopy --mesh 19 19 19 --band 1/2 1/2 0 0 0 0 1/2 1/2 1/2 --hdf5 --readfc -p

The shape of phonon DOS below 6 THz is similar to the derivative of the accumulated lattice thermal conductivity, i.e., the heat is conducted by the low frequency longitudinal-acoustic-like modes.

The file vasprun_xmls.tar.lzma in this example contains VASP output files of vasprun.xmls that are used to generate FORCES_FC3. To test the FORCES_FC3 generation, after decompressing this file, the following command is executed at current directory:

% phono3py --cf3 vasprun_xmls/disp-{00001..00111}/vasprun.xml

It is possible to combine different supercell sizes for fc2 and fc3, for which FORCES_FC2 is required. Displacements for fc2 and its dataset (phono3py_disp.yaml) can be created by

% phono3py -d --dim 2 2 2 --dim-fc2 4 4 4 -c POSCAR-unitcell --pa auto

In this example directory, the dataset is renamed to phono3py_disp_dimfc2.yaml. The result of the VASP force calculation is found at vasprun_xml_fc2/disp-fc2-00001/vasprun.xml. FORCES_FC2 is generated by

% phono3py -c phono3py_disp_dimfc2.yaml --cf2 vasprun_xml_fc2/disp-fc2-00001/vasprun.xml

A lattice thermal conductivity calculation is performed by, e.g.,

% phono3py-load phono3py_disp_dimfc2.yaml --mesh 11 11 11 --br --ts 300

The result is 107.9 W/m-K, and with the 19x19x19 mesh, 125.4 W/m-K.