Add NaCl example

example/NaCl-alm/README.md

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+This is the example of NaCl calculation. The supercell is 2x2x2 of the
+conventional unit cell. The VASP calculation was made for force calculations
+with 500 eV, 2x2x2 off-Gamma-centre k-point sampling mesh for the supercell, and
+PBE-sol. For dielectric constant and Born effective charges were calculated in a
+similar calculation settings with `LEPSILON = .TRUE.` and 4x4x4 off-Gamma-centre
+k-point sampling mesh.
+
+200 supercells were generated with random displacements of 0.03 A displacement
+distance.
+
+```
+% phono3py -d --dim="2 2 2" -c POSCAR-unitcell --pa="F"
+```
+
+To create `fc3.hdf5` and `fc2.hdf5`,
+
+```
+% phono3py --sym-fc
+```
+
+Using 11x11x11 sampling mesh, lattice thermal conductivity is calculated by
+
+```
+% phono3py --mesh 11 11 11 --fc3 --fc2 --br
+```
+
+`kappa-m111111.hdf5` is written as the result. The lattice thermal conductivity
+is calculated as 109.0 W/m-K at 300 K. This becomes, with 19x19x19 sampling
+mesh, 123.2 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
+```
+
+![Si-kaccum.png](Si-kaccum.png)
+
+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
+```
+
+![Si-band-DOS.png](Si-band-DOS.png)
+
+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.xml`s 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 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 108.0 W/m-K, and with the 19x19x19 mesh, 125.4 W/m-K.