diff --git a/example/AlN-LDA/README b/example/AlN-LDA/README deleted file mode 100644 index 5ba60b15..00000000 --- a/example/AlN-LDA/README +++ /dev/null @@ -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. diff --git a/example/AlN-LDA/README.md b/example/AlN-LDA/README.md new file mode 100644 index 00000000..19dcdeb2 --- /dev/null +++ b/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. diff --git a/example/Si-LDA/README b/example/Si-LDA/README deleted file mode 100644 index 9cfe9bbb..00000000 --- a/example/Si-LDA/README +++ /dev/null @@ -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 diff --git a/example/Si-LDA/README.md b/example/Si-LDA/README.md new file mode 100644 index 00000000..751ddffd --- /dev/null +++ b/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 +``` diff --git a/example/Si-PBE/README b/example/Si-PBE/README deleted file mode 100644 index 03c100af..00000000 --- a/example/Si-PBE/README +++ /dev/null @@ -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 diff --git a/example/Si-PBE/README.md b/example/Si-PBE/README.md new file mode 100644 index 00000000..89cd4195 --- /dev/null +++ b/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 +``` diff --git a/example/Si-QE/README b/example/Si-QE/README deleted file mode 100644 index 0f775895..00000000 --- a/example/Si-QE/README +++ /dev/null @@ -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 diff --git a/example/Si-QE/README.md b/example/Si-QE/README.md new file mode 100644 index 00000000..8f17a517 --- /dev/null +++ b/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 +``` diff --git a/example/zb-ZnTe-PBEsol/README b/example/zb-ZnTe-PBEsol/README deleted file mode 100644 index 5c5dc28b..00000000 --- a/example/zb-ZnTe-PBEsol/README +++ /dev/null @@ -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. diff --git a/example/zb-ZnTe-PBEsol/README.md b/example/zb-ZnTe-PBEsol/README.md new file mode 100644 index 00000000..154541ed --- /dev/null +++ b/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`.