`velph` example#

PbTe#

POSCAR-unitcell, POTCAR, and velph-tmpl.toml are located in the current directory.

Initial POSCAR-unitcell,

Pb Te
00000000000000
4000000000000000    0.0000000000000000    0.0000000000000000
0000000000000000    6.4000000000000000    0.0000000000000000
0000000000000000    0.0000000000000000    6.4000000000000000
  Pb              Te
   4
Direct
0000000000000000    0.0000000000000000    0.0000000000000000
0000000000000000    0.5000000000000000    0.5000000000000000
5000000000000000    0.0000000000000000    0.5000000000000000
5000000000000000    0.5000000000000000    0.0000000000000000
5000000000000000    0.5000000000000000    0.5000000000000000
5000000000000000    0.0000000000000000    0.0000000000000000
0000000000000000    0.5000000000000000    0.0000000000000000
0000000000000000    0.0000000000000000    0.5000000000000000

velph-tmpl.toml,

[init.options]
kspacing = 0.2
kspacing_dense = 0.1
max_num_atoms = 100

[vasp.incar]
encut = 400
ncore = 4

[vasp.phelel.incar]
kpar = 2
[vasp.phelel.scheduler]
pe = "mpi* 48"

[vasp.transport.scheduler]
pe = "mpi* 144"

[scheduler]
scheduler_name = "sge"
job_name = "PbTe"
mpirun_command = "mpirun"
vasp_binary = "/usr/local/vasp/bin/vasp_std"
pe = "vienna 32"
prepend_text = '''
source /opt/intel/oneapi/setvars.sh
'''
append_text = ""

POTCAR choice,

  PAW_PBE Pb 08Apr2002
  PAW_PBE Te 08Apr2002

% velph init POSCAR-unitcell relax --template-toml velph-tmpl.toml
Read crystal structure file "POSCAR-unitcell".
Read velph template file "velph-tmpl.toml".
Following options were found in "velph-tmpl.toml":
  kspacing = "0.2"
  kspacing_dense = "0.1"
  max_num_atoms = "100"
The command options were prefered to [init.options] in "velph-tmpl.toml".
Found a primitive cell whose transformation matrix is
  [ 0.000  0.500  0.500]
  [ 0.500  0.000  0.500]
  [ 0.500  0.500  0.000]
Supercell is generated with respect to the cell below.
--------------------------------------------------------------------------------
lattice:
- [     6.400000000000000,     0.000000000000000,     0.000000000000000 ] # a
- [     0.000000000000000,     6.400000000000000,     0.000000000000000 ] # b
- [     0.000000000000000,     0.000000000000000,     6.400000000000000 ] # c
points:
- symbol: Pb # 1
  coordinates: [  0.000000000000000,  0.000000000000000,  0.000000000000000 ]
  mass: 207.200000
- symbol: Pb # 2
  coordinates: [  0.000000000000000,  0.500000000000000,  0.500000000000000 ]
  mass: 207.200000
- symbol: Pb # 3
  coordinates: [  0.500000000000000,  0.000000000000000,  0.500000000000000 ]
  mass: 207.200000
- symbol: Pb # 4
  coordinates: [  0.500000000000000,  0.500000000000000,  0.000000000000000 ]
  mass: 207.200000
- symbol: Te # 5
  coordinates: [  0.500000000000000,  0.500000000000000,  0.500000000000000 ]
  mass: 127.600000
- symbol: Te # 6
  coordinates: [  0.500000000000000,  0.000000000000000,  0.000000000000000 ]
  mass: 127.600000
- symbol: Te # 7
  coordinates: [  0.000000000000000,  0.500000000000000,  0.000000000000000 ]
  mass: 127.600000
- symbol: Te # 8
  coordinates: [  0.000000000000000,  0.000000000000000,  0.500000000000000 ]
  mass: 127.600000
--------------------------------------------------------------------------------
[vasp.incar] (basic INCAR settings)
  ismear = 0
  sigma = 0.01
  ediff = 1e-08
  encut = 400
  prec = accurate
  lreal = False
  lwave = False
  lcharg = False
  ncore = 4
[phelel]
  supercell_dimension: [2 2 2]
[vasp.*.kpoints.mesh] (*kspacing=0.2)
  selfenergy: [9 9 9]*
  transport: [9 9 9]*
  el_bands: [9 9 9]*
  phonopy: [2 2 2]*
  phono3py: [2 2 2]*
  phelel: [2 2 2]*
  relax: [5 5 5]*
  nac: [9 9 9]*
[vasp.*.kpoints_dense.mesh] (*kspacing_dense=0.1)
  selfenergy: [17 17 17]*
  transport: [17 17 17]*
  el_bands: [17 17 17]*
Created new folder "relax".
Initial settings were written to "relax/velph.toml".
Found "POTCAR".
  PAW_PBE Pb 08Apr2002
  PAW_PBE Te 08Apr2002
  Max ENMAX in "POTCAR" is 174.982.
"POTCAR" was copied to "relax/POTCAR".

A directory relax is created and velph.toml is stored in it.

relax/velph.toml,

[phelel]
version = "0.8.2"
supercell_dimension = [2, 2, 2]
amplitude = 0.03
diagonal = false
plusminus = true
fft_mesh = [30, 30, 30]

# ...

[vasp.relax]
cell = "unitcell"
[vasp.relax.incar]
ediffg = -1e-06
ibrion = 2
isif = 3
nsw = 10
ismear = 0
sigma = 0.01
ediff = 1e-08
encut = 400
prec = "accurate"
lreal = false
lwave = false
lcharg = false
ncore = 4
[vasp.relax.kpoints]
mesh = [5, 5, 5]

# ...

[scheduler]
scheduler_name = "sge"
job_name = "PbTe"
mpirun_command = "mpirun"
vasp_binary = "/usr/local/vasp/bin/vasp_std"
pe = "vienna 32"
prepend_text = "source /opt/intel/oneapi/setvars.sh\n"
append_text = ""

[symmetry]
spacegroup_type = "Fm-3m"
tolerance = 1e-05
primitive_matrix = [
  [  0.000000000000000,  0.500000000000000,  0.500000000000000 ],
  [  0.500000000000000,  0.000000000000000,  0.500000000000000 ],
  [  0.500000000000000,  0.500000000000000,  0.000000000000000 ],
]

[unitcell]
lattice = [
  [     6.400000000000000,     0.000000000000000,     0.000000000000000 ], # a
  [     0.000000000000000,     6.400000000000000,     0.000000000000000 ], # b
  [     0.000000000000000,     0.000000000000000,     6.400000000000000 ], # c
]
[[unitcell.points]]  # 1
symbol = "Pb"
coordinates = [  0.000000000000000,  0.000000000000000,  0.000000000000000 ]
[[unitcell.points]]  # 2
symbol = "Pb"
coordinates = [  0.000000000000000,  0.500000000000000,  0.500000000000000 ]
[[unitcell.points]]  # 3
symbol = "Pb"
coordinates = [  0.500000000000000,  0.000000000000000,  0.500000000000000 ]
[[unitcell.points]]  # 4
symbol = "Pb"
coordinates = [  0.500000000000000,  0.500000000000000,  0.000000000000000 ]
[[unitcell.points]]  # 5
symbol = "Te"
coordinates = [  0.500000000000000,  0.500000000000000,  0.500000000000000 ]
[[unitcell.points]]  # 6
symbol = "Te"
coordinates = [  0.500000000000000,  0.000000000000000,  0.000000000000000 ]
[[unitcell.points]]  # 7
symbol = "Te"
coordinates = [  0.000000000000000,  0.500000000000000,  0.000000000000000 ]
[[unitcell.points]]  # 8
symbol = "Te"
coordinates = [  0.000000000000000,  0.000000000000000,  0.500000000000000 ]
[primitive_cell]
lattice = [
  [     0.000000000000000,     3.200000000000000,     3.200000000000000 ], # a
  [     3.200000000000000,     0.000000000000000,     3.200000000000000 ], # b
  [     3.200000000000000,     3.200000000000000,     0.000000000000000 ], # c
]
[[primitive_cell.points]]  # 1
symbol = "Pb"
coordinates = [  0.000000000000000,  0.000000000000000,  0.000000000000000 ]
[[primitive_cell.points]]  # 2
symbol = "Te"
coordinates = [  0.500000000000000,  0.500000000000000,  0.500000000000000 ]

Change directory to relax.

% velph relax generate
VASP input files were made in "relax/iter1".
% cd relax/iter1 && qsub _job.sh && cd ../..
% velph relax generate
"relax/iter1" exists.
"relax/iter1/CONTCAR" will be as new "POSCAR".
VASP input files were made in "relax/iter2".

Structure optimizations (iter1, iter2, …) may be repeated until stress becomes less than a target value, e.g., 0.1kB (0.01GPa). Then, go back to the top directory and start supercell calculation.

% velph init --template-toml velph-tmpl.toml `ls relax/relax/iter*/CONTCAR|tail -n 1` calc
Read crystal structure file "relax/relax/iter2/CONTCAR".
Read velph template file "velph-tmpl.toml".
Following options were found in "velph-tmpl.toml":
  kspacing = "0.2"
  kspacing_dense = "0.1"
  max_num_atoms = "100"
The command options were prefered to [init.options] in "velph-tmpl.toml".
Found a primitive cell whose transformation matrix is
  [ 0.000  0.500  0.500]
  [ 0.500  0.000  0.500]
  [ 0.500  0.500  0.000]
Supercell is generated with respect to the cell below.
--------------------------------------------------------------------------------
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
- symbol: Pb # 2
  coordinates: [  0.000000000000000,  0.500000000000000,  0.500000000000000 ]
  mass: 207.200000
- symbol: Pb # 3
  coordinates: [  0.500000000000000,  0.000000000000000,  0.500000000000000 ]
  mass: 207.200000
- symbol: Pb # 4
  coordinates: [  0.500000000000000,  0.500000000000000,  0.000000000000000 ]
  mass: 207.200000
- symbol: Te # 5
  coordinates: [  0.500000000000000,  0.500000000000000,  0.500000000000000 ]
  mass: 127.600000
- symbol: Te # 6
  coordinates: [  0.500000000000000,  0.000000000000000,  0.000000000000000 ]
  mass: 127.600000
- symbol: Te # 7
  coordinates: [  0.000000000000000,  0.500000000000000,  0.000000000000000 ]
  mass: 127.600000
- symbol: Te # 8
  coordinates: [  0.000000000000000,  0.000000000000000,  0.500000000000000 ]
  mass: 127.600000
--------------------------------------------------------------------------------
[vasp.incar] (basic INCAR settings)
  ismear = 0
  sigma = 0.01
  ediff = 1e-08
  encut = 400
  prec = accurate
  lreal = False
  lwave = False
  lcharg = False
  ncore = 4
[phelel]
  supercell_dimension: [2 2 2]
[vasp.*.kpoints.mesh] (*kspacing=0.2)
  selfenergy: [8 8 8]*
  transport: [8 8 8]*
  el_bands: [8 8 8]*
  phonopy: [2 2 2]*
  phono3py: [2 2 2]*
  phelel: [2 2 2]*
  relax: [5 5 5]*
  nac: [8 8 8]*
[vasp.*.kpoints_dense.mesh] (*kspacing_dense=0.1)
  selfenergy: [17 17 17]*
  transport: [17 17 17]*
  el_bands: [17 17 17]*
Created new folder "calc".
Initial settings were written to "calc/velph.toml".
Found "POTCAR".
  PAW_PBE Pb 08Apr2002
  PAW_PBE Te 08Apr2002
  Max ENMAX in "POTCAR" is 174.982.
"POTCAR" was copied to "calc/POTCAR".

Change directory to calc.

% cd calc

velph.toml,

[phelel]
version = "0.8.2"
supercell_dimension = [2, 2, 2]
amplitude = 0.03
diagonal = false
plusminus = true
fft_mesh = [30, 30, 30]

[vasp.phelel.incar]
lwap = true
isym = 0
kpar = 2
ismear = 0
sigma = 0.01
ediff = 1e-08
encut = 400
prec = "accurate"
lreal = false
lwave = false
lcharg = false
ncore = 4
[vasp.phelel.kpoints]
mesh = [2, 2, 2]
[vasp.phelel.scheduler]
pe = "mpi* 48"

# ...

[vasp.nac]
cell = "primitive"
[vasp.nac.incar]
lepsilon = true
ismear = 0
sigma = 0.01
ediff = 1e-08
encut = 400
prec = "accurate"
lreal = false
lwave = false
lcharg = false
[vasp.nac.kpoints]
mesh = [8, 8, 8]

# ...

NAC and phelel calculations,

% velph nac generate
VASP input files were made in "nac".
% cd nac && qsub _job.sh && cd ..
% velph phelel init
Found "nac" directory. Read NAC params.
"phelel/phelel_disp.yaml" was generated.
VASP input files will be generated by "velph phelel generate".
% velph phelel generate
VASP input files were generated in "phelel/disp-000".
VASP input files were generated in "phelel/disp-001".
VASP input files were generated in "phelel/disp-002".
VASP input files were generated in "phelel/disp-003".
VASP input files were generated in "phelel/disp-004".
% for i in {000..004};do cd phelel/disp-$i; qsub _job.sh; cd ../..;done

Using the VASP results of the phelel calculations, derivatives of properties are computed using the phelel code. The results are stored in a newly created file phelel/phelel_params.hdf5. This process creates only phelel/phelel_params.hdf5 and is invoked by the following velph command:

% velph phelel differentiate
FFT mesh: [30 30 30].
Running finufft (eps=1.000e-06)...
Running finufft (eps=1.000e-06)...
"phelel/phelel_params.hdf5" has been made.

NAC parameters in phelel/phelel_params.hdf5 comes from phelel/phelel_disp.yaml, i.e.,

NAC parameters are stored in phelel/phelel_disp.yaml when phelel/phelel_disp.yaml is created by velph phelel init.
NAC data in phelel/phelel_disp.yaml are transfered to phelel/phelel_params.hdf5 by velph phelel differentiate.

Therefore, nac calculation has to exist in the initial step velph phelel init. If the nac calculation is performed after the supercell calculation, velph phelel init and velph phelel differentiate have to be re-executed to store the NAC parameters in phelel/phelel_params.hdf5.

velph example

Contents

`velph` example#

PbTe#

velph example

Contents

velph example#

PbTe#

`velph` example#