mirror of https://github.com/phonopy/phono3py.git
91 lines
2.8 KiB
Markdown
91 lines
2.8 KiB
Markdown
This is the example of silicon calculation. The supercell is 2x2x2 of the
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conventional unit cell. The VASP calculation was made for force calculations
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with 300 eV, 2x2x2 off-Gamma-centre k-point sampling mesh for the supercell, and
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PBE-sol. Silicon crystal is F-centre, so there is the transformation matrix from
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the conventional unit cell to the primitive cell.
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`phono3py_disp.yaml` is generated by
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```
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% phono3py -d --dim="2 2 2" -c POSCAR-unitcell --pa="F"
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```
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To create `fc3.hdf5` and `fc2.hdf5`,
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```
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% phono3py-load
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```
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Using 11x11x11 sampling mesh, lattice thermal conductivity is calculated by
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```
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% phono3py-load --mesh 11 11 11 --br
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```
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`kappa-m111111.hdf5` is written as the result. The lattice thermal conductivity
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is calculated as 109.1 W/m-K at 300 K. This becomes, with 19x19x19 sampling
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mesh, 124.4 W/m-K.
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Accumulated lattice thermal conductivity is calculated using `phono3py-kaccum`
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script.
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```
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% phono3py-kaccum kappa-m111111.hdf5 |tee kaccum.dat
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```
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`kaccum.dat` is plotted using gnuplot by
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```
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gnuplot> p 'kaccum.dat' i 30 u 1:2 w l, 'kaccum.dat' i 30 u 1:8 w l
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```
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It is found that most of the lattice thermal conductivity owes the phonon modes
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below 6 THz.
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`fc2.hdf5` can be read by harmonic phonopy to rename it to force_constants.hdf5.
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The phonon band structure and DOS are plotted by
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```
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% ln -s fc2.hdf5 force_constants.hdf5
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% phonopy --mesh 19 19 19 --band 1/2 1/2 0 0 0 0 1/2 1/2 1/2 --hdf5 --readfc -p
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```
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The shape of phonon DOS below 6 THz is similar to the derivative of the
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accumulated lattice thermal conductivity, i.e., the heat is conducted by the low
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frequency longitudinal-acoustic-like modes.
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The file `vasprun_xmls.tar.lzma` in this example contains VASP output files of
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`vasprun.xml`s that are used to generate `FORCES_FC3`. To test the `FORCES_FC3`
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generation, after decompressing this file, the following command is executed at
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current directory:
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```
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% phono3py --cf3 vasprun_xmls/disp-{00001..00111}/vasprun.xml
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```
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It is possible to combine different supercell sizes for fc2 and fc3, for which
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`FORCES_FC2` is required. Displacements for fc2 and its dataset
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(`phono3py_disp.yaml`) can be created by
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```
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% phono3py -d --dim 2 2 2 --dim-fc2 4 4 4 -c POSCAR-unitcell --pa auto
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```
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In this example directory, the dataset is renamed to
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`phono3py_disp_dimfc2.yaml`. The result of the VASP force calculation is found
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at `vasprun_xml_fc2/disp-fc2-00001/vasprun.xml`. `FORCES_FC2` is generated by
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```
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% phono3py -c phono3py_disp_dimfc2.yaml --cf2 vasprun_xml_fc2/disp-fc2-00001/vasprun.xml
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```
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A lattice thermal conductivity calculation is performed by, e.g.,
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```
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% phono3py-load phono3py_disp_dimfc2.yaml --mesh 11 11 11 --br --ts 300
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```
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The result is 107.9 W/m-K, and with the 19x19x19 mesh, 125.4 W/m-K.
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