mirror of https://github.com/phonopy/phonopy.git
Add an exmaple of phono3py
This commit is contained in:
Atsushi Togo
parent
05539e29d8
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8b0f49bee2
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Si
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1.0
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5.4335600309153529 0.0000000000000000 0.0000000000000000
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0.0000000000000000 5.4335600309153529 0.0000000000000000
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0.0000000000000000 0.0000000000000000 5.4335600309153529
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Si
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8
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Direct
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0.8750000000000000 0.8750000000000000 0.8750000000000000
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0.8750000000000000 0.3750000000000000 0.3750000000000000
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0.3750000000000000 0.8750000000000000 0.3750000000000000
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0.3750000000000000 0.3750000000000000 0.8750000000000000
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0.1250000000000000 0.1250000000000000 0.1250000000000000
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0.1250000000000000 0.6250000000000000 0.6250000000000000
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0.6250000000000000 0.1250000000000000 0.6250000000000000
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0.6250000000000000 0.6250000000000000 0.1250000000000000
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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 k-point mesh for the supercell, and PBE-sol. Silicon crystal is F-centre, so there is the transformation matrix from the conventinal unit cell to the primitive cell.
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To create fc3.hdf5 and fc2.hdf5,
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% phono3py --dim="2 2 2" --sym_fc3r --sym_fc2 --tsym -c POSCAR-unitcell
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Using 11x11x11 sampling mesh, lattice thermal conductivity is calculated by
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% phono3py --dim="2 2 2" --pa="0 1/2 1/2 1/2 0 1/2 1/2 1/2 0" -c POSCAR-unitcell --mesh="11 11 11" --fc3 --fc2 --thm --br
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kappa-m111111.hdf5 is written as the result. The lattice thermal conductivity is calculated as 108.9 W/m-K at 300 K. This becomes, with 19x19x19 sampling mesh, 123.2 W/m-K.
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Accumulated lattice thermal conductivity is calculated using 'kaccum' script.
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% kaccum --mesh="11 11 11" --pa="0 1/2 1/2 1/2 0 1/2 1/2 1/2 0" POSCAR-unitcell kappa-m111111.hdf5 |tee kaccum.dat
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The plot of this result is shown in Si-kaccum.png. It is found that most of the lattice thermal conductivity owes the phonon modes below 6 THz.
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fc2.hdf5 can be read by harmonic phonopy to rename it to force_constants.hdf5. The phonon band structure and DOS are watched by
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% cp fc2.hdf5 force_constants.hdf5
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% phonopy --dim="2 2 2" --pa="0 1/2 1/2 1/2 0 1/2 1/2 1/2 0" -c POSCAR-unitcell --mesh="19 19 19" --band="1/2 1/2 0 0 0 0 1/2 1/2 1/2" --hdf5 --readfc --thm -p
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Si-band-DOS.png shows this plot. The shape of phonon DOS below 6 THz is similar to the derivative of the accumulated lattice thermal conductivity, i.e., the heat is conductied by the low frequency longitudinal-acoustic-like modes.
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natom: 64
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num_first_displacements: 1
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num_second_displacements: 110
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num_displacements_created: 111
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first_atoms:
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- number: 1
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displacement:
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[ 0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00001
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second_atoms:
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- number: 1
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distance: 0.000000
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displacements:
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- [ 0.0212132034355964, 0.0212132034355964, 0.0000000000000000 ] # 00002
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- [ -0.0212132034355964, -0.0212132034355964, 0.0000000000000000 ] # 00003
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- number: 2
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||||
distance: 5.433560
|
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displacements:
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- [ 0.0212132034355964, 0.0212132034355964, 0.0000000000000000 ] # 00004
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- [ -0.0212132034355964, -0.0212132034355964, 0.0000000000000000 ] # 00005
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- number: 3
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distance: 5.433560
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displacements:
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- [ 0.0212132034355964, 0.0212132034355964, 0.0000000000000000 ] # 00006
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- [ -0.0212132034355964, -0.0212132034355964, 0.0000000000000000 ] # 00007
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- [ 0.0000000000000000, 0.0000000000000000, 0.0300000000000000 ] # 00008
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- number: 4
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distance: 7.684214
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displacements:
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- [ 0.0212132034355964, 0.0212132034355964, 0.0000000000000000 ] # 00009
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- [ -0.0212132034355964, -0.0212132034355964, 0.0000000000000000 ] # 00010
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- [ 0.0000000000000000, 0.0000000000000000, 0.0300000000000000 ] # 00011
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- number: 7
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distance: 7.684214
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displacements:
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- [ 0.0212132034355964, 0.0212132034355964, 0.0000000000000000 ] # 00012
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- [ -0.0212132034355964, -0.0212132034355964, 0.0000000000000000 ] # 00013
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- number: 8
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distance: 9.411202
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displacements:
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- [ 0.0212132034355964, 0.0212132034355964, 0.0000000000000000 ] # 00014
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- [ -0.0212132034355964, -0.0212132034355964, 0.0000000000000000 ] # 00015
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- number: 9
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distance: 3.842107
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displacements:
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- [ 0.0000000000000000, 0.0300000000000000, 0.0000000000000000 ] # 00016
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||||
- [ 0.0000000000000000, -0.0300000000000000, 0.0000000000000000 ] # 00017
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||||
- [ 0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00018
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- [ -0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00019
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- number: 10
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distance: 6.654725
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displacements:
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- [ 0.0000000000000000, 0.0300000000000000, 0.0000000000000000 ] # 00020
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- [ 0.0000000000000000, -0.0300000000000000, 0.0000000000000000 ] # 00021
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- [ 0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00022
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- [ -0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00023
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- number: 11
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distance: 3.842107
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displacements:
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- [ 0.0000000000000000, 0.0300000000000000, 0.0000000000000000 ] # 00024
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- [ 0.0000000000000000, -0.0300000000000000, 0.0000000000000000 ] # 00025
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- [ 0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00026
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- [ -0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00027
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- number: 12
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distance: 6.654725
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displacements:
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- [ 0.0000000000000000, 0.0300000000000000, 0.0000000000000000 ] # 00028
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- [ 0.0000000000000000, -0.0300000000000000, 0.0000000000000000 ] # 00029
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||||
- [ 0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00030
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- [ -0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00031
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- number: 17
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distance: 3.842107
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displacements:
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- [ 0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00032
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- [ -0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00033
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- [ 0.0000000000000000, 0.0300000000000000, 0.0000000000000000 ] # 00034
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- [ 0.0000000000000000, -0.0300000000000000, 0.0000000000000000 ] # 00035
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- [ 0.0000000000000000, 0.0000000000000000, 0.0300000000000000 ] # 00036
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- [ 0.0000000000000000, 0.0000000000000000, -0.0300000000000000 ] # 00037
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- number: 18
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distance: 3.842107
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displacements:
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- [ 0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00038
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- [ -0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00039
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||||
- [ 0.0000000000000000, 0.0300000000000000, 0.0000000000000000 ] # 00040
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||||
- [ 0.0000000000000000, -0.0300000000000000, 0.0000000000000000 ] # 00041
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- [ 0.0000000000000000, 0.0000000000000000, 0.0300000000000000 ] # 00042
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||||
- [ 0.0000000000000000, 0.0000000000000000, -0.0300000000000000 ] # 00043
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- number: 19
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||||
distance: 6.654725
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||||
displacements:
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||||
- [ 0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00044
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||||
- [ -0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00045
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||||
- [ 0.0000000000000000, 0.0300000000000000, 0.0000000000000000 ] # 00046
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||||
- [ 0.0000000000000000, -0.0300000000000000, 0.0000000000000000 ] # 00047
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||||
- [ 0.0000000000000000, 0.0000000000000000, 0.0300000000000000 ] # 00048
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- [ 0.0000000000000000, 0.0000000000000000, -0.0300000000000000 ] # 00049
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- number: 20
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||||
distance: 6.654725
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displacements:
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- [ 0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00050
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- [ -0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00051
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- [ 0.0000000000000000, 0.0300000000000000, 0.0000000000000000 ] # 00052
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- [ 0.0000000000000000, -0.0300000000000000, 0.0000000000000000 ] # 00053
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- [ 0.0000000000000000, 0.0000000000000000, 0.0300000000000000 ] # 00054
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- [ 0.0000000000000000, 0.0000000000000000, -0.0300000000000000 ] # 00055
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- number: 33
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distance: 7.058402
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displacements:
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- [ 0.0000000000000000, 0.0300000000000000, 0.0000000000000000 ] # 00056
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- [ 0.0000000000000000, -0.0300000000000000, 0.0000000000000000 ] # 00057
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- [ 0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00058
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- [ -0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00059
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- number: 34
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distance: 5.921085
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displacements:
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- [ 0.0000000000000000, 0.0300000000000000, 0.0000000000000000 ] # 00060
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- [ 0.0000000000000000, -0.0300000000000000, 0.0000000000000000 ] # 00061
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||||
- [ 0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00062
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- [ -0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00063
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- number: 35
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distance: 5.921085
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displacements:
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- [ 0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00064
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||||
- [ -0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00065
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||||
- [ 0.0000000000000000, 0.0300000000000000, 0.0000000000000000 ] # 00066
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- [ 0.0000000000000000, -0.0300000000000000, 0.0000000000000000 ] # 00067
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- [ 0.0000000000000000, 0.0000000000000000, 0.0300000000000000 ] # 00068
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||||
- [ 0.0000000000000000, 0.0000000000000000, -0.0300000000000000 ] # 00069
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- number: 36
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distance: 4.505270
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displacements:
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- [ 0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00070
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- [ -0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00071
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- [ 0.0000000000000000, 0.0300000000000000, 0.0000000000000000 ] # 00072
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- [ 0.0000000000000000, -0.0300000000000000, 0.0000000000000000 ] # 00073
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- [ 0.0000000000000000, 0.0000000000000000, 0.0300000000000000 ] # 00074
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- [ 0.0000000000000000, 0.0000000000000000, -0.0300000000000000 ] # 00075
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- number: 39
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distance: 4.505270
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displacements:
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- [ 0.0000000000000000, 0.0300000000000000, 0.0000000000000000 ] # 00076
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||||
- [ 0.0000000000000000, -0.0300000000000000, 0.0000000000000000 ] # 00077
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||||
- [ 0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00078
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- [ -0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00079
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- number: 40
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distance: 2.352801
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displacements:
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- [ 0.0000000000000000, 0.0300000000000000, 0.0000000000000000 ] # 00080
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- [ 0.0000000000000000, -0.0300000000000000, 0.0000000000000000 ] # 00081
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||||
- [ 0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00082
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||||
- [ -0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00083
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- number: 49
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||||
distance: 4.505270
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||||
displacements:
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- [ 0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00084
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||||
- [ -0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00085
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||||
- [ 0.0000000000000000, 0.0300000000000000, 0.0000000000000000 ] # 00086
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||||
- [ 0.0000000000000000, -0.0300000000000000, 0.0000000000000000 ] # 00087
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||||
- [ 0.0000000000000000, 0.0000000000000000, 0.0300000000000000 ] # 00088
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||||
- [ 0.0000000000000000, 0.0000000000000000, -0.0300000000000000 ] # 00089
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||||
- number: 50
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||||
distance: 5.921085
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||||
displacements:
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||||
- [ 0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00090
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||||
- [ -0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00091
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||||
- [ 0.0000000000000000, 0.0300000000000000, 0.0000000000000000 ] # 00092
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||||
- [ 0.0000000000000000, -0.0300000000000000, 0.0000000000000000 ] # 00093
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||||
- [ 0.0000000000000000, 0.0000000000000000, 0.0300000000000000 ] # 00094
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||||
- [ 0.0000000000000000, 0.0000000000000000, -0.0300000000000000 ] # 00095
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||||
- number: 51
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||||
distance: 2.352801
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||||
displacements:
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- [ 0.0000000000000000, 0.0300000000000000, 0.0000000000000000 ] # 00096
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- [ 0.0000000000000000, -0.0300000000000000, 0.0000000000000000 ] # 00097
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||||
- [ 0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00098
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||||
- [ -0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00099
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||||
- number: 52
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||||
distance: 4.505270
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displacements:
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- [ 0.0000000000000000, 0.0300000000000000, 0.0000000000000000 ] # 00100
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- [ 0.0000000000000000, -0.0300000000000000, 0.0000000000000000 ] # 00101
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- [ 0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00102
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||||
- [ -0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00103
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||||
- number: 53
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||||
distance: 5.921085
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displacements:
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- [ 0.0000000000000000, 0.0300000000000000, 0.0000000000000000 ] # 00104
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||||
- [ 0.0000000000000000, -0.0300000000000000, 0.0000000000000000 ] # 00105
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||||
- [ 0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00106
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||||
- [ -0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00107
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- number: 54
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||||
distance: 7.058402
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||||
displacements:
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- [ 0.0000000000000000, 0.0300000000000000, 0.0000000000000000 ] # 00108
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||||
- [ 0.0000000000000000, -0.0300000000000000, 0.0000000000000000 ] # 00109
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||||
- [ 0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00110
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- [ -0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00111
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lattice:
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- [ 10.867120061830706, 0.000000000000000, 0.000000000000000 ]
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- [ 0.000000000000000, 10.867120061830706, 0.000000000000000 ]
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- [ 0.000000000000000, 0.000000000000000, 10.867120061830706 ]
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atoms:
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- symbol: Si # 1
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position: [ 0.43750000000000, 0.43750000000000, 0.43750000000000 ]
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- symbol: Si # 2
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position: [ 0.93750000000000, 0.43750000000000, 0.43750000000000 ]
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- symbol: Si # 3
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position: [ 0.43750000000000, 0.93750000000000, 0.43750000000000 ]
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- symbol: Si # 4
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position: [ 0.93750000000000, 0.93750000000000, 0.43750000000000 ]
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||||
- symbol: Si # 5
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||||
position: [ 0.43750000000000, 0.43750000000000, 0.93750000000000 ]
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||||
- symbol: Si # 6
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position: [ 0.93750000000000, 0.43750000000000, 0.93750000000000 ]
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||||
- symbol: Si # 7
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||||
position: [ 0.43750000000000, 0.93750000000000, 0.93750000000000 ]
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||||
- symbol: Si # 8
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||||
position: [ 0.93750000000000, 0.93750000000000, 0.93750000000000 ]
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||||
- symbol: Si # 9
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||||
position: [ 0.43750000000000, 0.18750000000000, 0.18750000000000 ]
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- symbol: Si # 10
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||||
position: [ 0.93750000000000, 0.18750000000000, 0.18750000000000 ]
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- symbol: Si # 11
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||||
position: [ 0.43750000000000, 0.68750000000000, 0.18750000000000 ]
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||||
- symbol: Si # 12
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position: [ 0.93750000000000, 0.68750000000000, 0.18750000000000 ]
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||||
- symbol: Si # 13
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||||
position: [ 0.43750000000000, 0.18750000000000, 0.68750000000000 ]
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- symbol: Si # 14
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||||
position: [ 0.93750000000000, 0.18750000000000, 0.68750000000000 ]
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||||
- symbol: Si # 15
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||||
position: [ 0.43750000000000, 0.68750000000000, 0.68750000000000 ]
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||||
- symbol: Si # 16
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||||
position: [ 0.93750000000000, 0.68750000000000, 0.68750000000000 ]
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||||
- symbol: Si # 17
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||||
position: [ 0.18750000000000, 0.43750000000000, 0.18750000000000 ]
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||||
- symbol: Si # 18
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||||
position: [ 0.68750000000000, 0.43750000000000, 0.18750000000000 ]
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||||
- symbol: Si # 19
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||||
position: [ 0.18750000000000, 0.93750000000000, 0.18750000000000 ]
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||||
- symbol: Si # 20
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||||
position: [ 0.68750000000000, 0.93750000000000, 0.18750000000000 ]
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||||
- symbol: Si # 21
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||||
position: [ 0.18750000000000, 0.43750000000000, 0.68750000000000 ]
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||||
- symbol: Si # 22
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||||
position: [ 0.68750000000000, 0.43750000000000, 0.68750000000000 ]
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||||
- symbol: Si # 23
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||||
position: [ 0.18750000000000, 0.93750000000000, 0.68750000000000 ]
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||||
- symbol: Si # 24
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||||
position: [ 0.68750000000000, 0.93750000000000, 0.68750000000000 ]
|
||||
- symbol: Si # 25
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||||
position: [ 0.18750000000000, 0.18750000000000, 0.43750000000000 ]
|
||||
- symbol: Si # 26
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||||
position: [ 0.68750000000000, 0.18750000000000, 0.43750000000000 ]
|
||||
- symbol: Si # 27
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||||
position: [ 0.18750000000000, 0.68750000000000, 0.43750000000000 ]
|
||||
- symbol: Si # 28
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||||
position: [ 0.68750000000000, 0.68750000000000, 0.43750000000000 ]
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||||
- symbol: Si # 29
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||||
position: [ 0.18750000000000, 0.18750000000000, 0.93750000000000 ]
|
||||
- symbol: Si # 30
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||||
position: [ 0.68750000000000, 0.18750000000000, 0.93750000000000 ]
|
||||
- symbol: Si # 31
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||||
position: [ 0.18750000000000, 0.68750000000000, 0.93750000000000 ]
|
||||
- symbol: Si # 32
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||||
position: [ 0.68750000000000, 0.68750000000000, 0.93750000000000 ]
|
||||
- symbol: Si # 33
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||||
position: [ 0.06250000000000, 0.06250000000000, 0.06250000000000 ]
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||||
- symbol: Si # 34
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||||
position: [ 0.56250000000000, 0.06250000000000, 0.06250000000000 ]
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||||
- symbol: Si # 35
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||||
position: [ 0.06250000000000, 0.56250000000000, 0.06250000000000 ]
|
||||
- symbol: Si # 36
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||||
position: [ 0.56250000000000, 0.56250000000000, 0.06250000000000 ]
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||||
- symbol: Si # 37
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||||
position: [ 0.06250000000000, 0.06250000000000, 0.56250000000000 ]
|
||||
- symbol: Si # 38
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||||
position: [ 0.56250000000000, 0.06250000000000, 0.56250000000000 ]
|
||||
- symbol: Si # 39
|
||||
position: [ 0.06250000000000, 0.56250000000000, 0.56250000000000 ]
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||||
- symbol: Si # 40
|
||||
position: [ 0.56250000000000, 0.56250000000000, 0.56250000000000 ]
|
||||
- symbol: Si # 41
|
||||
position: [ 0.06250000000000, 0.31250000000000, 0.31250000000000 ]
|
||||
- symbol: Si # 42
|
||||
position: [ 0.56250000000000, 0.31250000000000, 0.31250000000000 ]
|
||||
- symbol: Si # 43
|
||||
position: [ 0.06250000000000, 0.81250000000000, 0.31250000000000 ]
|
||||
- symbol: Si # 44
|
||||
position: [ 0.56250000000000, 0.81250000000000, 0.31250000000000 ]
|
||||
- symbol: Si # 45
|
||||
position: [ 0.06250000000000, 0.31250000000000, 0.81250000000000 ]
|
||||
- symbol: Si # 46
|
||||
position: [ 0.56250000000000, 0.31250000000000, 0.81250000000000 ]
|
||||
- symbol: Si # 47
|
||||
position: [ 0.06250000000000, 0.81250000000000, 0.81250000000000 ]
|
||||
- symbol: Si # 48
|
||||
position: [ 0.56250000000000, 0.81250000000000, 0.81250000000000 ]
|
||||
- symbol: Si # 49
|
||||
position: [ 0.31250000000000, 0.06250000000000, 0.31250000000000 ]
|
||||
- symbol: Si # 50
|
||||
position: [ 0.81250000000000, 0.06250000000000, 0.31250000000000 ]
|
||||
- symbol: Si # 51
|
||||
position: [ 0.31250000000000, 0.56250000000000, 0.31250000000000 ]
|
||||
- symbol: Si # 52
|
||||
position: [ 0.81250000000000, 0.56250000000000, 0.31250000000000 ]
|
||||
- symbol: Si # 53
|
||||
position: [ 0.31250000000000, 0.06250000000000, 0.81250000000000 ]
|
||||
- symbol: Si # 54
|
||||
position: [ 0.81250000000000, 0.06250000000000, 0.81250000000000 ]
|
||||
- symbol: Si # 55
|
||||
position: [ 0.31250000000000, 0.56250000000000, 0.81250000000000 ]
|
||||
- symbol: Si # 56
|
||||
position: [ 0.81250000000000, 0.56250000000000, 0.81250000000000 ]
|
||||
- symbol: Si # 57
|
||||
position: [ 0.31250000000000, 0.31250000000000, 0.06250000000000 ]
|
||||
- symbol: Si # 58
|
||||
position: [ 0.81250000000000, 0.31250000000000, 0.06250000000000 ]
|
||||
- symbol: Si # 59
|
||||
position: [ 0.31250000000000, 0.81250000000000, 0.06250000000000 ]
|
||||
- symbol: Si # 60
|
||||
position: [ 0.81250000000000, 0.81250000000000, 0.06250000000000 ]
|
||||
- symbol: Si # 61
|
||||
position: [ 0.31250000000000, 0.31250000000000, 0.56250000000000 ]
|
||||
- symbol: Si # 62
|
||||
position: [ 0.81250000000000, 0.31250000000000, 0.56250000000000 ]
|
||||
- symbol: Si # 63
|
||||
position: [ 0.31250000000000, 0.81250000000000, 0.56250000000000 ]
|
||||
- symbol: Si # 64
|
||||
position: [ 0.81250000000000, 0.81250000000000, 0.56250000000000 ]
|
||||
Loading…
Reference in New Issue