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Add Si PBE and LDA examples

This commit is contained in:
Atsushi Togo 2017-03-12 12:47:21 +09:00
parent f7f6945fc0
commit f9f85bc081
11 changed files with 15610 additions and 1 deletions
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example/Si-LDA/FORCES_FC3 Normal file
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example/Si-LDA/POSCAR-unitcell Normal file
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Si
1.0
5.4006797400000002 0.0000000000000000 0.0000000000000000
0.0000000000000000 5.4006797400000002 0.0000000000000000
0.0000000000000000 0.0000000000000000 5.4006797400000002
Si
8
Direct
0.8750000000000000 0.8750000000000000 0.8750000000000000
0.8750000000000000 0.3750000000000000 0.3750000000000000
0.3750000000000000 0.8750000000000000 0.3750000000000000
0.3750000000000000 0.3750000000000000 0.8750000000000000
0.1250000000000000 0.1250000000000000 0.1250000000000000
0.1250000000000000 0.6250000000000000 0.6250000000000000
0.6250000000000000 0.1250000000000000 0.6250000000000000
0.6250000000000000 0.6250000000000000 0.1250000000000000

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example/Si-LDA/README Normal file
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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 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.
To create fc3.hdf5 and fc2.hdf5,
% phono3py --dim="2 2 2" --sym_fc3r --sym_fc2 --tsym -c POSCAR-unitcell
Using 11x11x11 sampling mesh, lattice thermal conductivity is calculated by
% 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 --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 'kaccum' script.
% 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
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

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example/Si-LDA/disp_fc3.yaml Normal file
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natom: 64
num_first_displacements: 1
num_second_displacements: 110
num_displacements_created: 111
first_atoms:
- number: 1
displacement:
[ 0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00001
second_atoms:
- number: 1
distance: 0.000000
displacements:
- [ 0.0212132034355964, 0.0212132034355964, 0.0000000000000000 ] # 00002
- [ -0.0212132034355964, -0.0212132034355964, 0.0000000000000000 ] # 00003
- number: 2
distance: 5.400680
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- [ -0.0212132034355964, -0.0212132034355964, 0.0000000000000000 ] # 00005
- number: 3
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displacements:
- [ 0.0212132034355964, 0.0212132034355964, 0.0000000000000000 ] # 00006
- [ -0.0212132034355964, -0.0212132034355964, 0.0000000000000000 ] # 00007
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- number: 4
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- [ -0.0212132034355964, -0.0212132034355964, 0.0000000000000000 ] # 00010
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- [ 0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00018
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- number: 10
distance: 6.614455
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- [ 0.0000000000000000, -0.0300000000000000, 0.0000000000000000 ] # 00021
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- number: 12
distance: 6.614455
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- number: 17
distance: 3.818857
displacements:
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- number: 18
distance: 3.818857
displacements:
- [ 0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00038
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- number: 19
distance: 6.614455
displacements:
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- number: 20
distance: 6.614455
displacements:
- [ 0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00050
- [ -0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00051
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- number: 33
distance: 7.015689
displacements:
- [ 0.0000000000000000, 0.0300000000000000, 0.0000000000000000 ] # 00056
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- [ 0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00058
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- number: 34
distance: 5.885254
displacements:
- [ 0.0000000000000000, 0.0300000000000000, 0.0000000000000000 ] # 00060
- [ 0.0000000000000000, -0.0300000000000000, 0.0000000000000000 ] # 00061
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- number: 35
distance: 5.885254
displacements:
- [ 0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00064
- [ -0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00065
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- number: 36
distance: 4.478007
displacements:
- [ 0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00070
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- number: 39
distance: 4.478007
displacements:
- [ 0.0000000000000000, 0.0300000000000000, 0.0000000000000000 ] # 00076
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- number: 40
distance: 2.338563
displacements:
- [ 0.0000000000000000, 0.0300000000000000, 0.0000000000000000 ] # 00080
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- number: 49
distance: 4.478007
displacements:
- [ 0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00084
- [ -0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00085
- [ 0.0000000000000000, 0.0300000000000000, 0.0000000000000000 ] # 00086
- [ 0.0000000000000000, -0.0300000000000000, 0.0000000000000000 ] # 00087
- [ 0.0000000000000000, 0.0000000000000000, 0.0300000000000000 ] # 00088
- [ 0.0000000000000000, 0.0000000000000000, -0.0300000000000000 ] # 00089
- number: 50
distance: 5.885254
displacements:
- [ 0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00090
- [ -0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00091
- [ 0.0000000000000000, 0.0300000000000000, 0.0000000000000000 ] # 00092
- [ 0.0000000000000000, -0.0300000000000000, 0.0000000000000000 ] # 00093
- [ 0.0000000000000000, 0.0000000000000000, 0.0300000000000000 ] # 00094
- [ 0.0000000000000000, 0.0000000000000000, -0.0300000000000000 ] # 00095
- number: 51
distance: 2.338563
displacements:
- [ 0.0000000000000000, 0.0300000000000000, 0.0000000000000000 ] # 00096
- [ 0.0000000000000000, -0.0300000000000000, 0.0000000000000000 ] # 00097
- [ 0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00098
- [ -0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00099
- number: 52
distance: 4.478007
displacements:
- [ 0.0000000000000000, 0.0300000000000000, 0.0000000000000000 ] # 00100
- [ 0.0000000000000000, -0.0300000000000000, 0.0000000000000000 ] # 00101
- [ 0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00102
- [ -0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00103
- number: 53
distance: 5.885254
displacements:
- [ 0.0000000000000000, 0.0300000000000000, 0.0000000000000000 ] # 00104
- [ 0.0000000000000000, -0.0300000000000000, 0.0000000000000000 ] # 00105
- [ 0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00106
- [ -0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00107
- number: 54
distance: 7.015689
displacements:
- [ 0.0000000000000000, 0.0300000000000000, 0.0000000000000000 ] # 00108
- [ 0.0000000000000000, -0.0300000000000000, 0.0000000000000000 ] # 00109
- [ 0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00110
- [ -0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00111
lattice:
- [ 10.801359480000000, 0.000000000000000, 0.000000000000000 ]
- [ 0.000000000000000, 10.801359480000000, 0.000000000000000 ]
- [ 0.000000000000000, 0.000000000000000, 10.801359480000000 ]
atoms:
- symbol: Si # 1
position: [ 0.43750000000000, 0.43750000000000, 0.43750000000000 ]
- symbol: Si # 2
position: [ 0.93750000000000, 0.43750000000000, 0.43750000000000 ]
- symbol: Si # 3
position: [ 0.43750000000000, 0.93750000000000, 0.43750000000000 ]
- symbol: Si # 4
position: [ 0.93750000000000, 0.93750000000000, 0.43750000000000 ]
- symbol: Si # 5
position: [ 0.43750000000000, 0.43750000000000, 0.93750000000000 ]
- symbol: Si # 6
position: [ 0.93750000000000, 0.43750000000000, 0.93750000000000 ]
- symbol: Si # 7
position: [ 0.43750000000000, 0.93750000000000, 0.93750000000000 ]
- symbol: Si # 8
position: [ 0.93750000000000, 0.93750000000000, 0.93750000000000 ]
- symbol: Si # 9
position: [ 0.43750000000000, 0.18750000000000, 0.18750000000000 ]
- symbol: Si # 10
position: [ 0.93750000000000, 0.18750000000000, 0.18750000000000 ]
- symbol: Si # 11
position: [ 0.43750000000000, 0.68750000000000, 0.18750000000000 ]
- symbol: Si # 12
position: [ 0.93750000000000, 0.68750000000000, 0.18750000000000 ]
- symbol: Si # 13
position: [ 0.43750000000000, 0.18750000000000, 0.68750000000000 ]
- symbol: Si # 14
position: [ 0.93750000000000, 0.18750000000000, 0.68750000000000 ]
- symbol: Si # 15
position: [ 0.43750000000000, 0.68750000000000, 0.68750000000000 ]
- symbol: Si # 16
position: [ 0.93750000000000, 0.68750000000000, 0.68750000000000 ]
- symbol: Si # 17
position: [ 0.18750000000000, 0.43750000000000, 0.18750000000000 ]
- symbol: Si # 18
position: [ 0.68750000000000, 0.43750000000000, 0.18750000000000 ]
- symbol: Si # 19
position: [ 0.18750000000000, 0.93750000000000, 0.18750000000000 ]
- symbol: Si # 20
position: [ 0.68750000000000, 0.93750000000000, 0.18750000000000 ]
- symbol: Si # 21
position: [ 0.18750000000000, 0.43750000000000, 0.68750000000000 ]
- symbol: Si # 22
position: [ 0.68750000000000, 0.43750000000000, 0.68750000000000 ]
- symbol: Si # 23
position: [ 0.18750000000000, 0.93750000000000, 0.68750000000000 ]
- symbol: Si # 24
position: [ 0.68750000000000, 0.93750000000000, 0.68750000000000 ]
- symbol: Si # 25
position: [ 0.18750000000000, 0.18750000000000, 0.43750000000000 ]
- symbol: Si # 26
position: [ 0.68750000000000, 0.18750000000000, 0.43750000000000 ]
- symbol: Si # 27
position: [ 0.18750000000000, 0.68750000000000, 0.43750000000000 ]
- symbol: Si # 28
position: [ 0.68750000000000, 0.68750000000000, 0.43750000000000 ]
- symbol: Si # 29
position: [ 0.18750000000000, 0.18750000000000, 0.93750000000000 ]
- symbol: Si # 30
position: [ 0.68750000000000, 0.18750000000000, 0.93750000000000 ]
- symbol: Si # 31
position: [ 0.18750000000000, 0.68750000000000, 0.93750000000000 ]
- symbol: Si # 32
position: [ 0.68750000000000, 0.68750000000000, 0.93750000000000 ]
- symbol: Si # 33
position: [ 0.06250000000000, 0.06250000000000, 0.06250000000000 ]
- symbol: Si # 34
position: [ 0.56250000000000, 0.06250000000000, 0.06250000000000 ]
- symbol: Si # 35
position: [ 0.06250000000000, 0.56250000000000, 0.06250000000000 ]
- symbol: Si # 36
position: [ 0.56250000000000, 0.56250000000000, 0.06250000000000 ]
- symbol: Si # 37
position: [ 0.06250000000000, 0.06250000000000, 0.56250000000000 ]
- symbol: Si # 38
position: [ 0.56250000000000, 0.06250000000000, 0.56250000000000 ]
- symbol: Si # 39
position: [ 0.06250000000000, 0.56250000000000, 0.56250000000000 ]
- 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 ]

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example/Si-LDA/vasprun_xmls.tar.lzma Normal file
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Si
1.0
5.4662628900000003 0.0000000000000000 0.0000000000000000
0.0000000000000000 5.4662628900000003 0.0000000000000000
0.0000000000000000 0.0000000000000000 5.4662628900000003
Si
8
Direct
0.8750000000000000 0.8750000000000000 0.8750000000000000
0.8750000000000000 0.3750000000000000 0.3750000000000000
0.3750000000000000 0.8750000000000000 0.3750000000000000
0.3750000000000000 0.3750000000000000 0.8750000000000000
0.1250000000000000 0.1250000000000000 0.1250000000000000
0.1250000000000000 0.6250000000000000 0.6250000000000000
0.6250000000000000 0.1250000000000000 0.6250000000000000
0.6250000000000000 0.6250000000000000 0.1250000000000000

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example/Si-PBE/README Normal file
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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 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.
To create fc3.hdf5 and fc2.hdf5,
% phono3py --dim="2 2 2" --sym_fc3r --sym_fc2 --tsym -c POSCAR-unitcell
Using 11x11x11 sampling mesh, lattice thermal conductivity is calculated by
% 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 --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 'kaccum' script.
% 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
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

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example/Si-PBE/disp_fc3.yaml Normal file
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natom: 64
num_first_displacements: 1
num_second_displacements: 110
num_displacements_created: 111
first_atoms:
- number: 1
displacement:
[ 0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00001
second_atoms:
- number: 1
distance: 0.000000
displacements:
- [ 0.0212132034355964, 0.0212132034355964, 0.0000000000000000 ] # 00002
- [ -0.0212132034355964, -0.0212132034355964, 0.0000000000000000 ] # 00003
- number: 2
distance: 5.466263
displacements:
- [ 0.0212132034355964, 0.0212132034355964, 0.0000000000000000 ] # 00004
- [ -0.0212132034355964, -0.0212132034355964, 0.0000000000000000 ] # 00005
- number: 3
distance: 5.466263
displacements:
- [ 0.0212132034355964, 0.0212132034355964, 0.0000000000000000 ] # 00006
- [ -0.0212132034355964, -0.0212132034355964, 0.0000000000000000 ] # 00007
- [ 0.0000000000000000, 0.0000000000000000, 0.0300000000000000 ] # 00008
- number: 4
distance: 7.730463
displacements:
- [ 0.0212132034355964, 0.0212132034355964, 0.0000000000000000 ] # 00009
- [ -0.0212132034355964, -0.0212132034355964, 0.0000000000000000 ] # 00010
- [ 0.0000000000000000, 0.0000000000000000, 0.0300000000000000 ] # 00011
- number: 7
distance: 7.730463
displacements:
- [ 0.0212132034355964, 0.0212132034355964, 0.0000000000000000 ] # 00012
- [ -0.0212132034355964, -0.0212132034355964, 0.0000000000000000 ] # 00013
- number: 8
distance: 9.467845
displacements:
- [ 0.0212132034355964, 0.0212132034355964, 0.0000000000000000 ] # 00014
- [ -0.0212132034355964, -0.0212132034355964, 0.0000000000000000 ] # 00015
- number: 9
distance: 3.865232
displacements:
- [ 0.0000000000000000, 0.0300000000000000, 0.0000000000000000 ] # 00016
- [ 0.0000000000000000, -0.0300000000000000, 0.0000000000000000 ] # 00017
- [ 0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00018
- [ -0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00019
- number: 10
distance: 6.694777
displacements:
- [ 0.0000000000000000, 0.0300000000000000, 0.0000000000000000 ] # 00020
- [ 0.0000000000000000, -0.0300000000000000, 0.0000000000000000 ] # 00021
- [ 0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00022
- [ -0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00023
- number: 11
distance: 3.865232
displacements:
- [ 0.0000000000000000, 0.0300000000000000, 0.0000000000000000 ] # 00024
- [ 0.0000000000000000, -0.0300000000000000, 0.0000000000000000 ] # 00025
- [ 0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00026
- [ -0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] # 00027
- number: 12
distance: 6.694777
displacements:
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atoms:
- symbol: Si # 1
position: [ 0.43750000000000, 0.43750000000000, 0.43750000000000 ]
- symbol: Si # 2
position: [ 0.93750000000000, 0.43750000000000, 0.43750000000000 ]
- symbol: Si # 3
position: [ 0.43750000000000, 0.93750000000000, 0.43750000000000 ]
- symbol: Si # 4
position: [ 0.93750000000000, 0.93750000000000, 0.43750000000000 ]
- symbol: Si # 5
position: [ 0.43750000000000, 0.43750000000000, 0.93750000000000 ]
- symbol: Si # 6
position: [ 0.93750000000000, 0.43750000000000, 0.93750000000000 ]
- symbol: Si # 7
position: [ 0.43750000000000, 0.93750000000000, 0.93750000000000 ]
- symbol: Si # 8
position: [ 0.93750000000000, 0.93750000000000, 0.93750000000000 ]
- symbol: Si # 9
position: [ 0.43750000000000, 0.18750000000000, 0.18750000000000 ]
- symbol: Si # 10
position: [ 0.93750000000000, 0.18750000000000, 0.18750000000000 ]
- symbol: Si # 11
position: [ 0.43750000000000, 0.68750000000000, 0.18750000000000 ]
- symbol: Si # 12
position: [ 0.93750000000000, 0.68750000000000, 0.18750000000000 ]
- symbol: Si # 13
position: [ 0.43750000000000, 0.18750000000000, 0.68750000000000 ]
- symbol: Si # 14
position: [ 0.93750000000000, 0.18750000000000, 0.68750000000000 ]
- symbol: Si # 15
position: [ 0.43750000000000, 0.68750000000000, 0.68750000000000 ]
- symbol: Si # 16
position: [ 0.93750000000000, 0.68750000000000, 0.68750000000000 ]
- symbol: Si # 17
position: [ 0.18750000000000, 0.43750000000000, 0.18750000000000 ]
- symbol: Si # 18
position: [ 0.68750000000000, 0.43750000000000, 0.18750000000000 ]
- symbol: Si # 19
position: [ 0.18750000000000, 0.93750000000000, 0.18750000000000 ]
- symbol: Si # 20
position: [ 0.68750000000000, 0.93750000000000, 0.18750000000000 ]
- symbol: Si # 21
position: [ 0.18750000000000, 0.43750000000000, 0.68750000000000 ]
- symbol: Si # 22
position: [ 0.68750000000000, 0.43750000000000, 0.68750000000000 ]
- symbol: Si # 23
position: [ 0.18750000000000, 0.93750000000000, 0.68750000000000 ]
- symbol: Si # 24
position: [ 0.68750000000000, 0.93750000000000, 0.68750000000000 ]
- symbol: Si # 25
position: [ 0.18750000000000, 0.18750000000000, 0.43750000000000 ]
- symbol: Si # 26
position: [ 0.68750000000000, 0.18750000000000, 0.43750000000000 ]
- symbol: Si # 27
position: [ 0.18750000000000, 0.68750000000000, 0.43750000000000 ]
- symbol: Si # 28
position: [ 0.68750000000000, 0.68750000000000, 0.43750000000000 ]
- symbol: Si # 29
position: [ 0.18750000000000, 0.18750000000000, 0.93750000000000 ]
- symbol: Si # 30
position: [ 0.68750000000000, 0.18750000000000, 0.93750000000000 ]
- symbol: Si # 31
position: [ 0.18750000000000, 0.68750000000000, 0.93750000000000 ]
- symbol: Si # 32
position: [ 0.68750000000000, 0.68750000000000, 0.93750000000000 ]
- symbol: Si # 33
position: [ 0.06250000000000, 0.06250000000000, 0.06250000000000 ]
- symbol: Si # 34
position: [ 0.56250000000000, 0.06250000000000, 0.06250000000000 ]
- symbol: Si # 35
position: [ 0.06250000000000, 0.56250000000000, 0.06250000000000 ]
- symbol: Si # 36
position: [ 0.56250000000000, 0.56250000000000, 0.06250000000000 ]
- symbol: Si # 37
position: [ 0.06250000000000, 0.06250000000000, 0.56250000000000 ]
- symbol: Si # 38
position: [ 0.56250000000000, 0.06250000000000, 0.56250000000000 ]
- symbol: Si # 39
position: [ 0.06250000000000, 0.56250000000000, 0.56250000000000 ]
- 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 ]

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example/Si-PBE/vasprun_xmls.tar.lzma Normal file
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example/Si-PBEsol/README
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@ -1,4 +1,4 @@
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.
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-sol. Silicon crystal is F-centre, so there is the transformation matrix from the conventinal unit cell to the primitive cell.
To create fc3.hdf5 and fc2.hdf5,
@ -22,3 +22,8 @@ fc2.hdf5 can be read by harmonic phonopy to rename it to force_constants.hdf5. T
% 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
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.
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