READMEs were changed to .md

example/AlN-LDA/README

@@ -1,60 +0,0 @@
-This is the example of the wurtzite-type AlN phono3py calculation. The
-VASP code was used with 500 eV and LDA as XC functional. The
-experimental lattice parameters were used and the internal positions
-of atoms were relaxed by calculation. The 3x3x2 and 5x5x3 supercells
-were chosen for fc3 and fc2. The 6x6x4, 2x2x2, 1x1x2 k-point sampling
-meshes with Gamma-centre in the basal plane and off-Gamma-centre along
-c-axis were employed for the unit cell, fc3 supercell, and fc2
-supercell, respectively. For the DFPT calculation of Born effective
-charges and dielectric constant, the 12x12x8 k-point sampling mesh
-with the similar shift was used.
-
-Perfect and displaced supercells were created by
-
-% phono3py --dim="3 3 2" -c POSCAR-unitcell -d
-
-Then the forces were calculated with the above settings. FORCES_FC3
-and FORCES_FC2 were created with subtracting residual forces of
-perfect supercell from all displaed supercell forces by
-
-% phono3py --cf3 disp-{00001..01254}/vasprun.xml --cfz disp-00000/vasprun.xml
-
-In the example directory, FORCES_FC3 is compressed to FORCES_FC3.lzma.
-After unzipping FORCES_FC3.lzma, to obtain fc3.hdf5 and normal fc2.hdf5,
-
-% phono3py --sym-fc
-
-Using 13x13x9 sampling mesh, lattice thermal conductivity is calculated by
-
-% phono3py --mesh="13 13 9" --fc3 --fc2 --br
-
-kappa-m13139.hdf5 is written as the result. The lattice thermal
-conductivity is calculated as k_xx=228.2 and k_zz=224.1 W/m-K at 300 K.
-
-With --nac option, non-analytical term correction is applied reading
-the Born effective charges and dielectric constant from BORN file:
-
-% phono3py --mesh="13 13 9" --fc3 --fc2 --br --nac
-
-This changes thermal conductivity at 300 K to k_xx=235.7 and
-k_zz=219.1. The shape of phonon band structure is important to
-fullfill energy and momentum conservations.
-
-Use of larger supercell of fc2 may change the shape of phonon band structure.
-To see it, first regenerate phono3py_disp.yaml with --dim-fc2 option,
-
-% phono3py --dim="3 3 2" --dim-fc2="5 5 3" -c POSCAR-unitcell -d
-
-To create force constants, FORCES_FC2 is needed.
-
-% phono3py --cf2 disp-{00001..00006}/vasprun.xml --cfz disp-00000/vasprun.xml
-
-Then re-create force constants and calculate thermal conductivity,
-
-% phono3py --sym-fc
-% phono3py --mesh="13 13 9" --fc3 --fc2 --br --nac
-
-k_xx=236.0 and k_zz=222.2 are obtained. In the case of this example,
-we can see that the larger fc2 supercell contributes little, which
-means that the 3x3x2 supercell was good enough to obtain a good shape
-of phonon band structure.

example/AlN-LDA/README.md

@@ -0,0 +1,65 @@
+This is the example of the wurtzite-type AlN phono3py calculation. The VASP code
+was used with 500 eV and LDA as XC functional. The experimental lattice
+parameters were used and the internal positions of atoms were relaxed by
+calculation. The 3x3x2 and 5x5x3 supercells were chosen for fc3 and fc2. The
+6x6x4, 2x2x2, 1x1x2 k-point sampling meshes with Gamma-centre in the basal plane
+and off-Gamma-centre along c-axis were employed for the unit cell, fc3
+supercell, and fc2 supercell, respectively. For the DFPT calculation of Born
+effective charges and dielectric constant, the 12x12x8 k-point sampling mesh
+with the similar shift was used.
+
+Then the forces were calculated with the above settings. `FORCES_FC3` and
+`FORCES_FC2` were created with subtracting residual forces of perfect supercell
+from all displaced supercell forces.
+
+Perfect and displaced supercells were created by
+
+```
+% phono3py --dim 3 3 2 -c POSCAR-unitcell -d
+```
+
+In the example directory, `FORCES_FC3` is compressed to `FORCES_FC3.lzma`. After
+unzipping `FORCES_FC3.lzma` (e.g., using `tar xvfz` or `tar xvfa`), to obtain
+`fc3.hdf5` and normal `fc2.hdf5`,
+
+```
+% phono3py --sym-fc
+```
+
+Using 13x13x9 sampling mesh, lattice thermal conductivity is calculated by
+
+```
+% phono3py --mesh 13 13 9 --fc3 --fc2 --br
+```
+
+`kappa-m13139.hdf5` is written as the result. The lattice thermal conductivity
+is calculated as k_xx=228.2 and k_zz=224.1 W/m-K at 300 K.
+
+With `--nac` option, non-analytical term correction is applied reading the Born
+effective charges and dielectric constant from `BORN` file:
+
+```
+% phono3py --mesh 13 13 9 --fc3 --fc2 --br --nac
+```
+
+This changes thermal conductivity at 300 K to k_xx=235.7 and k_zz=219.1. The
+shape of phonon band structure is important to fullfil energy and momentum
+conservations.
+
+Use of larger supercell of fc2 may change the shape of phonon band structure. To
+see it, first regenerate `phono3py_disp.yaml` with `--dim-fc2` option,
+
+```
+% phono3py --dim 3 3 2 --dim-fc2 5 5 3 -c POSCAR-unitcell -d
+```
+
+Then re-create force constants and calculate thermal conductivity,
+
+```
+% phono3py --sym-fc
+% phono3py --mesh="13 13 9" --fc3 --fc2 --br --nac
+```
+
+k_xx=236.0 and k_zz=222.2 are obtained. In the case of this example, we can see
+that the larger fc2 supercell contributes little, which means that the 3x3x2
+supercell was good enough to obtain a good shape of phonon band structure.

example/Si-LDA/README

@@ -1,24 +0,0 @@
-This is the example of silicon calculation. The supercell is 2x2x2 of the conventinal 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 LDA. Silicon crystal is F-centre, so there is the transformation matrix from the conventinal 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 --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 112.5 W/m-K at 300 K. This becomes, with 19x19x19 sampling mesh, 127.0 W/m-K.
-
-Accumulated lattice thermal conductivity is calculated using 'phono3py-kaccum' script.
-
-% phono3py-kaccum --pa="F" -c POSCAR-unitcell kappa-m111111.hdf5 |tee kaccum.dat
-
-
-The file 'vasprun_xmls.tar.lzma' in this example contains 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

example/Si-LDA/README.md

@@ -0,0 +1,42 @@
+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
+LDA. 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 auto
+```
+
+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 112.5 W/m-K at 300 K. This becomes, with 19x19x19 sampling
+mesh, 127.0 W/m-K.
+
+Accumulated lattice thermal conductivity is calculated using `phono3py-kaccum`
+script.
+
+```
+% phono3py-kaccum kappa-m111111.hdf5 |tee kaccum.dat
+```
+
+The file `vasprun_xmls.tar.lzma` in this example contains `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
+```

example/Si-PBE/README

@@ -1,24 +0,0 @@
-This is the example of silicon calculation. The supercell is 2x2x2 of the conventinal 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. Silicon crystal is F-centre, so there is the transformation matrix from the conventinal 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 --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 119.3 W/m-K at 300 K. This becomes, with 19x19x19 sampling mesh, 132.4 W/m-K.
-
-Accumulated lattice thermal conductivity is calculated using 'phono3py-kaccum' script.
-
-% phono3py-kaccum --pa="0 1/2 1/2 1/2 0 1/2 1/2 1/2 0" POSCAR-unitcell kappa-m111111.hdf5 |tee kaccum.dat
-
-
-The file 'vasprun_xmls.tar.lzma' in this example contains 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

example/Si-PBE/README.md

@@ -0,0 +1,42 @@
+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. 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 auto
+```
+
+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 119.3 W/m-K at 300 K. This becomes, with 19x19x19 sampling
+mesh, 132.4 W/m-K.
+
+Accumulated lattice thermal conductivity is calculated using `phono3py-kaccum`
+script.
+
+```
+% phono3py-kaccum kappa-m111111.hdf5 |tee kaccum.dat
+```
+
+The file `vasprun_xmls.tar.lzma` in this example contains `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
+```

example/Si-QE/README

@@ -1,20 +0,0 @@
-This is the example of silicon calculation. The supercell is 2x2x2 of the conventinal unit cell. The qe (pw) calculation was made to obtain forces with 50 Ry, 2x2x2 k-point mesh for the supercell, PBE, and the lattice parameters in Si.in. Silicon crystal is F-centre, so there is the transformation matrix from the conventinal unit cell to the primitive cell.
-
-phono3py_disp.yaml is generated by
-
-% phono3py --qe -d --dim="2 2 2" -c Si.in --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 118.9 W/m-K at 300 K. This becomes, with 19x19x19 sampling mesh, 129.9 W/m-K.
-
-
-The .out files for supercells are found in supercell_out.tar.lzma. If phono3py is properly installed, the following command should work.
-
-% phono3py --cf3 supercell_out/disp-{00001..00111}/Si.out

example/Si-QE/README.md

@@ -0,0 +1,34 @@
+This is the example of silicon calculation. The supercell is 2x2x2 of the
+conventional unit cell. The qe (pw) calculation was made to obtain forces with
+50 Ry, 2x2x2 k-point mesh for the supercell, PBE, and the lattice parameters in
+Si.in. 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 --qe -d --dim 2 2 2 -c Si.in --pa auto
+```
+
+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 118.9 W/m-K at 300 K. This becomes, with 19x19x19 sampling
+mesh, 129.9 W/m-K.
+
+The .out files for supercells are found in `supercell_out.tar.lzma`. If phono3py
+is properly installed, the following command should work.
+
+```
+% phono3py --cf3 supercell_out/disp-{00001..00111}/Si.out
+```

example/zb-ZnTe-PBEsol/README

@@ -1,3 +0,0 @@
-Zincblende ZnTe
-Forces and NAC params were calculated using VASP code.
-PBEsol, 500eV PW-cutoff, 2x2x2 supercell and 2x2x2 off-Gamma k-point mesh for supercells.

example/zb-ZnTe-PBEsol/README.md

@@ -0,0 +1,21 @@
+Zincblende ZnTe
+
+Forces and NAC params were calculated using VASP code. PBEsol, 500eV PW-cutoff,
+2x2x2 supercell and 2x2x2 off-Gamma k-point mesh for supercells.
+
+`phono3py_params_ZnTe.yaml` contains all needed information to calculate thermal
+conductivity.
+
+`fc3.hdf5` and `fc2.hdf5` are generated by
+
+```
+% phono3py-load phono3py_params_ZnTe.yaml
+```
+
+Lattice thermal conductivity at 300K is calculated as 46.5 W/m-K by
+
+```
+% phono3py-load phono3py_params_ZnTe.yaml --mesh 50 --br --ts 300
+```
+
+The 14x14x14 sampling mesh is chosen by `--mesh 50`.