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Merge pull request #52 from phonopy/refactoring
(refactoring) Clear separation of phonopy instances for phelel and for extra phonon
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generated by phonopy | ||
1.00000000000000 | ||
6.4405958992591392 0.0000000000000000 0.0000000000000000 | ||
0.0000000000000000 6.4405958992591392 0.0000000000000000 | ||
0.0000000000000000 0.0000000000000000 6.4405958992591392 | ||
Pb Te | ||
4 4 | ||
Direct | ||
0.0000000000000000 0.0000000000000000 0.0000000000000000 | ||
0.0000000000000000 0.5000000000000000 0.5000000000000000 | ||
0.5000000000000000 0.0000000000000000 0.5000000000000000 | ||
0.5000000000000000 0.5000000000000000 0.0000000000000000 | ||
0.5000000000000000 0.5000000000000000 0.5000000000000000 | ||
0.5000000000000000 0.0000000000000000 0.0000000000000000 | ||
0.0000000000000000 0.5000000000000000 0.0000000000000000 | ||
0.0000000000000000 0.0000000000000000 0.5000000000000000 | ||
|
||
0.00000000E+00 0.00000000E+00 0.00000000E+00 | ||
0.00000000E+00 0.00000000E+00 0.00000000E+00 | ||
0.00000000E+00 0.00000000E+00 0.00000000E+00 | ||
0.00000000E+00 0.00000000E+00 0.00000000E+00 | ||
0.00000000E+00 0.00000000E+00 0.00000000E+00 | ||
0.00000000E+00 0.00000000E+00 0.00000000E+00 | ||
0.00000000E+00 0.00000000E+00 0.00000000E+00 | ||
0.00000000E+00 0.00000000E+00 0.00000000E+00 |
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# PbTe example | ||
|
||
Conventional unit cell of rocksalt-type PbTe crystal structure is stored in | ||
`POSCAR-unitcell`. This structure is relaxed with 400 eV cutoff energy and | ||
PBEsol XC functional. More detail of the relaxation calculation is found in | ||
`velph-tmpl.toml`. | ||
|
||
2x2x2 supercell of the unit cell and the supercells with displacements are | ||
generated by | ||
|
||
``` | ||
% phelel -d --dim 2 2 2 -c POSCAR-unitcell --pa auto --pm | ||
``` | ||
|
||
By this command, following files are created. `phelel_disp.yaml` contains | ||
crystal structure information and `SPOSCAR`, `POSCAR-001`, `POSCAR-002`, | ||
`POSCAR-003`, `POSCAR-004` files are the perfect supercell and supercells with | ||
four different displacements, respectively. | ||
|
||
Let's assume that these supercell calculations are executed in `disp-000`, | ||
`disp-001`, `disp-002`, `disp-003`, and `disp-004`. After the VASP calculations | ||
(`LWAP=.TRUE.` or `ELPH_PREPARE=.TRUE.` in `INCAR` is necessary), phelel | ||
computes derivatives of local potential and PAW strengths with respect to | ||
displacements by | ||
|
||
``` | ||
% phelel --cd disp-{000..004} | ||
``` | ||
|
||
The result is stored in `phelel_params.hdf5`. |
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phelel: | ||
version: "0.7.0" | ||
calculator: vasp | ||
symmetry_tolerance: 1.00000e-05 | ||
configuration: | ||
cell_filename: "POSCAR-unitcell" | ||
create_displacements: ".true." | ||
pm: ".true." | ||
primitive_axes: "auto" | ||
dim: "2 2 2" | ||
|
||
physical_unit: | ||
atomic_mass: "AMU" | ||
length: "angstrom" | ||
|
||
space_group: | ||
type: "Fm-3m" | ||
number: 225 | ||
Hall_symbol: "-F 4 2 3" | ||
|
||
primitive_matrix: | ||
- [ 0.000000000000000, 0.500000000000000, 0.500000000000000 ] | ||
- [ 0.500000000000000, 0.000000000000000, 0.500000000000000 ] | ||
- [ 0.500000000000000, 0.500000000000000, 0.000000000000000 ] | ||
|
||
supercell_matrix: | ||
- [ 2, 0, 0 ] | ||
- [ 0, 2, 0 ] | ||
- [ 0, 0, 2 ] | ||
|
||
primitive_cell: | ||
lattice: | ||
- [ 0.000000000000000, 3.220297949629569, 3.220297949629569 ] # a | ||
- [ 3.220297949629569, 0.000000000000000, 3.220297949629569 ] # b | ||
- [ 3.220297949629569, 3.220297949629569, 0.000000000000000 ] # c | ||
points: | ||
- symbol: Pb # 1 | ||
coordinates: [ 0.000000000000000, 0.000000000000000, 0.000000000000000 ] | ||
mass: 207.200000 | ||
- symbol: Te # 2 | ||
coordinates: [ 0.500000000000000, 0.500000000000000, 0.500000000000000 ] | ||
mass: 127.600000 | ||
reciprocal_lattice: # without 2pi | ||
- [ -0.155265136276448, 0.155265136276448, 0.155265136276448 ] # a* | ||
- [ 0.155265136276448, -0.155265136276448, 0.155265136276448 ] # b* | ||
- [ 0.155265136276448, 0.155265136276448, -0.155265136276448 ] # c* | ||
|
||
unit_cell: | ||
lattice: | ||
- [ 6.440595899259139, 0.000000000000000, 0.000000000000000 ] # a | ||
- [ 0.000000000000000, 6.440595899259139, 0.000000000000000 ] # b | ||
- [ 0.000000000000000, 0.000000000000000, 6.440595899259139 ] # c | ||
points: | ||
- symbol: Pb # 1 | ||
coordinates: [ 0.000000000000000, 0.000000000000000, 0.000000000000000 ] | ||
mass: 207.200000 | ||
reduced_to: 1 | ||
- symbol: Pb # 2 | ||
coordinates: [ 0.000000000000000, 0.500000000000000, 0.500000000000000 ] | ||
mass: 207.200000 | ||
reduced_to: 1 | ||
- symbol: Pb # 3 | ||
coordinates: [ 0.500000000000000, 0.000000000000000, 0.500000000000000 ] | ||
mass: 207.200000 | ||
reduced_to: 1 | ||
- symbol: Pb # 4 | ||
coordinates: [ 0.500000000000000, 0.500000000000000, 0.000000000000000 ] | ||
mass: 207.200000 | ||
reduced_to: 1 | ||
- symbol: Te # 5 | ||
coordinates: [ 0.500000000000000, 0.500000000000000, 0.500000000000000 ] | ||
mass: 127.600000 | ||
reduced_to: 5 | ||
- symbol: Te # 6 | ||
coordinates: [ 0.500000000000000, 0.000000000000000, 0.000000000000000 ] | ||
mass: 127.600000 | ||
reduced_to: 5 | ||
- symbol: Te # 7 | ||
coordinates: [ 0.000000000000000, 0.500000000000000, 0.000000000000000 ] | ||
mass: 127.600000 | ||
reduced_to: 5 | ||
- symbol: Te # 8 | ||
coordinates: [ 0.000000000000000, 0.000000000000000, 0.500000000000000 ] | ||
mass: 127.600000 | ||
reduced_to: 5 | ||
|
||
supercell: | ||
lattice: | ||
- [ 12.881191798518278, 0.000000000000000, 0.000000000000000 ] # a | ||
- [ 0.000000000000000, 12.881191798518278, 0.000000000000000 ] # b | ||
- [ 0.000000000000000, 0.000000000000000, 12.881191798518278 ] # c | ||
points: | ||
- symbol: Pb # 1 | ||
coordinates: [ 0.000000000000000, 0.000000000000000, 0.000000000000000 ] | ||
mass: 207.200000 | ||
reduced_to: 1 | ||
- symbol: Pb # 2 | ||
coordinates: [ 0.500000000000000, 0.000000000000000, 0.000000000000000 ] | ||
mass: 207.200000 | ||
reduced_to: 1 | ||
- symbol: Pb # 3 | ||
coordinates: [ 0.000000000000000, 0.500000000000000, 0.000000000000000 ] | ||
mass: 207.200000 | ||
reduced_to: 1 | ||
- symbol: Pb # 4 | ||
coordinates: [ 0.500000000000000, 0.500000000000000, 0.000000000000000 ] | ||
mass: 207.200000 | ||
reduced_to: 1 | ||
- symbol: Pb # 5 | ||
coordinates: [ 0.000000000000000, 0.000000000000000, 0.500000000000000 ] | ||
mass: 207.200000 | ||
reduced_to: 1 | ||
- symbol: Pb # 6 | ||
coordinates: [ 0.500000000000000, 0.000000000000000, 0.500000000000000 ] | ||
mass: 207.200000 | ||
reduced_to: 1 | ||
- symbol: Pb # 7 | ||
coordinates: [ 0.000000000000000, 0.500000000000000, 0.500000000000000 ] | ||
mass: 207.200000 | ||
reduced_to: 1 | ||
- symbol: Pb # 8 | ||
coordinates: [ 0.500000000000000, 0.500000000000000, 0.500000000000000 ] | ||
mass: 207.200000 | ||
reduced_to: 1 | ||
- symbol: Pb # 9 | ||
coordinates: [ 0.000000000000000, 0.250000000000000, 0.250000000000000 ] | ||
mass: 207.200000 | ||
reduced_to: 1 | ||
- symbol: Pb # 10 | ||
coordinates: [ 0.500000000000000, 0.250000000000000, 0.250000000000000 ] | ||
mass: 207.200000 | ||
reduced_to: 1 | ||
- symbol: Pb # 11 | ||
coordinates: [ 0.000000000000000, 0.750000000000000, 0.250000000000000 ] | ||
mass: 207.200000 | ||
reduced_to: 1 | ||
- symbol: Pb # 12 | ||
coordinates: [ 0.500000000000000, 0.750000000000000, 0.250000000000000 ] | ||
mass: 207.200000 | ||
reduced_to: 1 | ||
- symbol: Pb # 13 | ||
coordinates: [ 0.000000000000000, 0.250000000000000, 0.750000000000000 ] | ||
mass: 207.200000 | ||
reduced_to: 1 | ||
- symbol: Pb # 14 | ||
coordinates: [ 0.500000000000000, 0.250000000000000, 0.750000000000000 ] | ||
mass: 207.200000 | ||
reduced_to: 1 | ||
- symbol: Pb # 15 | ||
coordinates: [ 0.000000000000000, 0.750000000000000, 0.750000000000000 ] | ||
mass: 207.200000 | ||
reduced_to: 1 | ||
- symbol: Pb # 16 | ||
coordinates: [ 0.500000000000000, 0.750000000000000, 0.750000000000000 ] | ||
mass: 207.200000 | ||
reduced_to: 1 | ||
- symbol: Pb # 17 | ||
coordinates: [ 0.250000000000000, 0.000000000000000, 0.250000000000000 ] | ||
mass: 207.200000 | ||
reduced_to: 1 | ||
- symbol: Pb # 18 | ||
coordinates: [ 0.750000000000000, 0.000000000000000, 0.250000000000000 ] | ||
mass: 207.200000 | ||
reduced_to: 1 | ||
- symbol: Pb # 19 | ||
coordinates: [ 0.250000000000000, 0.500000000000000, 0.250000000000000 ] | ||
mass: 207.200000 | ||
reduced_to: 1 | ||
- symbol: Pb # 20 | ||
coordinates: [ 0.750000000000000, 0.500000000000000, 0.250000000000000 ] | ||
mass: 207.200000 | ||
reduced_to: 1 | ||
- symbol: Pb # 21 | ||
coordinates: [ 0.250000000000000, 0.000000000000000, 0.750000000000000 ] | ||
mass: 207.200000 | ||
reduced_to: 1 | ||
- symbol: Pb # 22 | ||
coordinates: [ 0.750000000000000, 0.000000000000000, 0.750000000000000 ] | ||
mass: 207.200000 | ||
reduced_to: 1 | ||
- symbol: Pb # 23 | ||
coordinates: [ 0.250000000000000, 0.500000000000000, 0.750000000000000 ] | ||
mass: 207.200000 | ||
reduced_to: 1 | ||
- symbol: Pb # 24 | ||
coordinates: [ 0.750000000000000, 0.500000000000000, 0.750000000000000 ] | ||
mass: 207.200000 | ||
reduced_to: 1 | ||
- symbol: Pb # 25 | ||
coordinates: [ 0.250000000000000, 0.250000000000000, 0.000000000000000 ] | ||
mass: 207.200000 | ||
reduced_to: 1 | ||
- symbol: Pb # 26 | ||
coordinates: [ 0.750000000000000, 0.250000000000000, 0.000000000000000 ] | ||
mass: 207.200000 | ||
reduced_to: 1 | ||
- symbol: Pb # 27 | ||
coordinates: [ 0.250000000000000, 0.750000000000000, 0.000000000000000 ] | ||
mass: 207.200000 | ||
reduced_to: 1 | ||
- symbol: Pb # 28 | ||
coordinates: [ 0.750000000000000, 0.750000000000000, 0.000000000000000 ] | ||
mass: 207.200000 | ||
reduced_to: 1 | ||
- symbol: Pb # 29 | ||
coordinates: [ 0.250000000000000, 0.250000000000000, 0.500000000000000 ] | ||
mass: 207.200000 | ||
reduced_to: 1 | ||
- symbol: Pb # 30 | ||
coordinates: [ 0.750000000000000, 0.250000000000000, 0.500000000000000 ] | ||
mass: 207.200000 | ||
reduced_to: 1 | ||
- symbol: Pb # 31 | ||
coordinates: [ 0.250000000000000, 0.750000000000000, 0.500000000000000 ] | ||
mass: 207.200000 | ||
reduced_to: 1 | ||
- symbol: Pb # 32 | ||
coordinates: [ 0.750000000000000, 0.750000000000000, 0.500000000000000 ] | ||
mass: 207.200000 | ||
reduced_to: 1 | ||
- symbol: Te # 33 | ||
coordinates: [ 0.250000000000000, 0.250000000000000, 0.250000000000000 ] | ||
mass: 127.600000 | ||
reduced_to: 33 | ||
- symbol: Te # 34 | ||
coordinates: [ 0.750000000000000, 0.250000000000000, 0.250000000000000 ] | ||
mass: 127.600000 | ||
reduced_to: 33 | ||
- symbol: Te # 35 | ||
coordinates: [ 0.250000000000000, 0.750000000000000, 0.250000000000000 ] | ||
mass: 127.600000 | ||
reduced_to: 33 | ||
- symbol: Te # 36 | ||
coordinates: [ 0.750000000000000, 0.750000000000000, 0.250000000000000 ] | ||
mass: 127.600000 | ||
reduced_to: 33 | ||
- symbol: Te # 37 | ||
coordinates: [ 0.250000000000000, 0.250000000000000, 0.750000000000000 ] | ||
mass: 127.600000 | ||
reduced_to: 33 | ||
- symbol: Te # 38 | ||
coordinates: [ 0.750000000000000, 0.250000000000000, 0.750000000000000 ] | ||
mass: 127.600000 | ||
reduced_to: 33 | ||
- symbol: Te # 39 | ||
coordinates: [ 0.250000000000000, 0.750000000000000, 0.750000000000000 ] | ||
mass: 127.600000 | ||
reduced_to: 33 | ||
- symbol: Te # 40 | ||
coordinates: [ 0.750000000000000, 0.750000000000000, 0.750000000000000 ] | ||
mass: 127.600000 | ||
reduced_to: 33 | ||
- symbol: Te # 41 | ||
coordinates: [ 0.250000000000000, 0.000000000000000, 0.000000000000000 ] | ||
mass: 127.600000 | ||
reduced_to: 33 | ||
- symbol: Te # 42 | ||
coordinates: [ 0.750000000000000, 0.000000000000000, 0.000000000000000 ] | ||
mass: 127.600000 | ||
reduced_to: 33 | ||
- symbol: Te # 43 | ||
coordinates: [ 0.250000000000000, 0.500000000000000, 0.000000000000000 ] | ||
mass: 127.600000 | ||
reduced_to: 33 | ||
- symbol: Te # 44 | ||
coordinates: [ 0.750000000000000, 0.500000000000000, 0.000000000000000 ] | ||
mass: 127.600000 | ||
reduced_to: 33 | ||
- symbol: Te # 45 | ||
coordinates: [ 0.250000000000000, 0.000000000000000, 0.500000000000000 ] | ||
mass: 127.600000 | ||
reduced_to: 33 | ||
- symbol: Te # 46 | ||
coordinates: [ 0.750000000000000, 0.000000000000000, 0.500000000000000 ] | ||
mass: 127.600000 | ||
reduced_to: 33 | ||
- symbol: Te # 47 | ||
coordinates: [ 0.250000000000000, 0.500000000000000, 0.500000000000000 ] | ||
mass: 127.600000 | ||
reduced_to: 33 | ||
- symbol: Te # 48 | ||
coordinates: [ 0.750000000000000, 0.500000000000000, 0.500000000000000 ] | ||
mass: 127.600000 | ||
reduced_to: 33 | ||
- symbol: Te # 49 | ||
coordinates: [ 0.000000000000000, 0.250000000000000, 0.000000000000000 ] | ||
mass: 127.600000 | ||
reduced_to: 33 | ||
- symbol: Te # 50 | ||
coordinates: [ 0.500000000000000, 0.250000000000000, 0.000000000000000 ] | ||
mass: 127.600000 | ||
reduced_to: 33 | ||
- symbol: Te # 51 | ||
coordinates: [ 0.000000000000000, 0.750000000000000, 0.000000000000000 ] | ||
mass: 127.600000 | ||
reduced_to: 33 | ||
- symbol: Te # 52 | ||
coordinates: [ 0.500000000000000, 0.750000000000000, 0.000000000000000 ] | ||
mass: 127.600000 | ||
reduced_to: 33 | ||
- symbol: Te # 53 | ||
coordinates: [ 0.000000000000000, 0.250000000000000, 0.500000000000000 ] | ||
mass: 127.600000 | ||
reduced_to: 33 | ||
- symbol: Te # 54 | ||
coordinates: [ 0.500000000000000, 0.250000000000000, 0.500000000000000 ] | ||
mass: 127.600000 | ||
reduced_to: 33 | ||
- symbol: Te # 55 | ||
coordinates: [ 0.000000000000000, 0.750000000000000, 0.500000000000000 ] | ||
mass: 127.600000 | ||
reduced_to: 33 | ||
- symbol: Te # 56 | ||
coordinates: [ 0.500000000000000, 0.750000000000000, 0.500000000000000 ] | ||
mass: 127.600000 | ||
reduced_to: 33 | ||
- symbol: Te # 57 | ||
coordinates: [ 0.000000000000000, 0.000000000000000, 0.250000000000000 ] | ||
mass: 127.600000 | ||
reduced_to: 33 | ||
- symbol: Te # 58 | ||
coordinates: [ 0.500000000000000, 0.000000000000000, 0.250000000000000 ] | ||
mass: 127.600000 | ||
reduced_to: 33 | ||
- symbol: Te # 59 | ||
coordinates: [ 0.000000000000000, 0.500000000000000, 0.250000000000000 ] | ||
mass: 127.600000 | ||
reduced_to: 33 | ||
- symbol: Te # 60 | ||
coordinates: [ 0.500000000000000, 0.500000000000000, 0.250000000000000 ] | ||
mass: 127.600000 | ||
reduced_to: 33 | ||
- symbol: Te # 61 | ||
coordinates: [ 0.000000000000000, 0.000000000000000, 0.750000000000000 ] | ||
mass: 127.600000 | ||
reduced_to: 33 | ||
- symbol: Te # 62 | ||
coordinates: [ 0.500000000000000, 0.000000000000000, 0.750000000000000 ] | ||
mass: 127.600000 | ||
reduced_to: 33 | ||
- symbol: Te # 63 | ||
coordinates: [ 0.000000000000000, 0.500000000000000, 0.750000000000000 ] | ||
mass: 127.600000 | ||
reduced_to: 33 | ||
- symbol: Te # 64 | ||
coordinates: [ 0.500000000000000, 0.500000000000000, 0.750000000000000 ] | ||
mass: 127.600000 | ||
reduced_to: 33 | ||
|
||
displacements: | ||
- atom: 1 | ||
displacement: | ||
[ 0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] | ||
- atom: 1 | ||
displacement: | ||
[ -0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] | ||
- atom: 33 | ||
displacement: | ||
[ 0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] | ||
- atom: 33 | ||
displacement: | ||
[ -0.0300000000000000, 0.0000000000000000, 0.0000000000000000 ] |
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[init.options] | ||
max_num_atoms = 600 | ||
phono3py_max_num_atoms = 100 | ||
|
||
[vasp.incar] | ||
encut = 400 | ||
ncore = 4 | ||
gga = "PS" | ||
|
||
[vasp.relax.kpoints] | ||
mesh = [8, 8, 8] | ||
shift = [0.5, 0.5, 0.5] | ||
|
||
[vasp.nac.kpoints] | ||
mesh = [16, 16, 16] | ||
|
||
[vasp.el_bands.kpoints] | ||
mesh = [16, 16, 16] | ||
[vasp.el_bands.kpoints_opt] | ||
line = 51 | ||
[vasp.el_bands.kpoints_dense] | ||
mesh = [32, 32, 32] | ||
|
||
[vasp.phelel.incar] | ||
kpar = 2 | ||
ediff = 1e-7 | ||
ncore = 8 | ||
[vasp.phelel.kpoints] | ||
mesh = [2, 2, 2] | ||
shift = [0.5, 0.5, 0.5] | ||
[vasp.phelel.scheduler] | ||
scheduler_name = "custom" | ||
scheduler_template = '''#!/bin/bash | ||
#QSUB2 core 192 | ||
#QSUB2 mpi 192 | ||
#QSUB2 smp 1 | ||
#QSUB2 wtime 48:00:00 | ||
#PBS -N {job_name} | ||
cd $PBS_O_WORKDIR | ||
{prepend_text} | ||
{mpirun_command} {vasp_binary} | ||
{append_text} | ||
''' | ||
job_name = "PbTe" | ||
mpirun_command = "mpijob" | ||
vasp_binary = "/home/togo/src/vasp-tmp1-atztogo/bin/vasp_std" | ||
prepend_text = ''' | ||
. /etc/profile.d/modules.sh | ||
module load comp3h | ||
module load hdf5/1.14.3-inteloneapi22u3 | ||
''' | ||
append_text = "" | ||
|
||
[vasp.phono3py.incar] | ||
kpar = 2 | ||
addgrid = true | ||
[vasp.phono3py.kpoints] | ||
mesh = [4, 4, 4] | ||
shift = [0.5, 0.5, 0.5] | ||
[vasp.phono3py.scheduler] | ||
pe = "mpi* 48" | ||
|
||
[vasp.phono3py.phonon.incar] | ||
kpar = 2 | ||
addgrid = true | ||
[vasp.phono3py.phonon.kpoints] | ||
mesh = [2, 2, 2] | ||
shift = [0.5, 0.5, 0.5] | ||
|
||
[vasp.transport.incar] | ||
kpar = 6 | ||
[vasp.transport.scheduler] | ||
pe = "mpi* 144" | ||
|
||
[scheduler] | ||
scheduler_name = "sge" | ||
job_name = "PbTe" | ||
mpirun_command = "mpirun" | ||
vasp_binary = "/home/togo/phelel/vasp-tmp1-atztogo/bin/vasp_std" | ||
pe = "vienna 32" | ||
prepend_text = ''' | ||
source /opt/intel/oneapi/setvars.sh --config="/home/togo/.oneapi-config" | ||
''' | ||
append_text = "" |
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