`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]
kspacing = 0.2
kspacing_dense = 0.1
max_num_atoms = 100
symmetrize_cell = true

[vasp.incar]
encut = 400
ncore = 4

[vasp.phelel.incar]
kpar = 2
[vasp.phelel.scheduler]
ntasks = 48

[vasp.transport.scheduler]
ntasks = 144

[scheduler]
job_name = "PbTe"
partition = "short"
ntasks = 32
walltime = "12:00:00"
scheduler_template = '''#!/bin/bash
#SBATCH --job-name={job_name}
#SBATCH --partition={partition}
#SBATCH --ntasks={ntasks}
#SBATCH --time={walltime}
#SBATCH --output=%x-%j.out

source /opt/intel/oneapi/setvars.sh
mpirun -np ${{SLURM_NTASKS}} /usr/local/vasp/bin/vasp_std
'''

[init] gives the defaults of the command-line options of velph init (see [init]). max_num_atoms needs symmetrize_cell = true. [vasp.incar] gives the INCAR tags shared by the input sets, and velph init writes them in the INCAR tags of each input set (see [vasp.incar] and incar_unset).

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 init template "velph-tmpl.toml".
Space-group: Fm-3m
Crystal structure was standardized based on space-group-type Fm-3m.
Transformation matrix from conventional unit cell to primitive cell 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:
- [     6.400000000000001,     0.000000000000000,     0.000000000000000 ] # a
- [     0.000000000000000,     6.400000000000001,     0.000000000000000 ] # b
- [     0.000000000000000,     0.000000000000000,     6.400000000000001 ] # 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,  0.000000000000000,  0.000000000000000 ]
  mass: 127.600000
- symbol: Te # 6
  coordinates: [  0.500000000000000,  0.500000000000000,  0.500000000000000 ]
  mass: 127.600000
- symbol: Te # 7
  coordinates: [  0.000000000000000,  0.000000000000000,  0.500000000000000 ]
  mass: 127.600000
- symbol: Te # 8
  coordinates: [  0.000000000000000,  0.500000000000000,  0.000000000000000 ]
  mass: 127.600000
--------------------------------------------------------------------------------
Supercell of [phelel]: 64 atoms, supercell matrix [[2, 0, 0], [0, 2, 0], [0, 0, 2]].
Supercell of [phonopy]: 64 atoms, supercell matrix [[2, 0, 0], [0, 2, 0], [0, 0, 2]].
Supercell of [phono3py]: 64 atoms, supercell matrix [[2, 0, 0], [0, 2, 0], [0, 0, 2]].
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,

[velph]
version = "0.16.0"

[phelel]
supercell_dimension = [2, 2, 2]
amplitude = 0.03
diagonal = false
plusminus = true
nosym = false

# ...

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

# ...

[scheduler]
job_name = "PbTe"
partition = "short"
ntasks = 32
walltime = "12:00:00"
scheduler_template = """
#!/bin/bash
#SBATCH --job-name={job_name}
#SBATCH --partition={partition}
#SBATCH --ntasks={ntasks}
#SBATCH --time={walltime}
#SBATCH --output=%x-%j.out

source /opt/intel/oneapi/setvars.sh
mpirun -np ${{SLURM_NTASKS}} /usr/local/vasp/bin/vasp_std
"""

[symmetry]
tolerance = 1e-05
spacegroup_type = "Fm-3m"
primitive_matrix = [
  [0.0, 0.5, 0.5],
  [0.5, 0.0, 0.5],
  [0.5, 0.5, 0.0],
]

# ...

[scheduler] is that of the template, written as it is (see velph.toml-[scheduler] section).

Change directory to relax.

% velph relax generate
VASP input files were written in "relax/iter1".
% cd relax/iter1 && sbatch _job.sh && cd ../..
% velph relax generate
"relax/iter1" exists.
"relax/iter1/CONTCAR" was copied to "relax/iter2/POSCAR".
VASP input files were written 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 init template "velph-tmpl.toml".
Space-group: Fm-3m
Crystal structure was standardized based on space-group-type Fm-3m.
Transformation matrix from conventional unit cell to primitive cell 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,  0.000000000000000,  0.000000000000000 ]
  mass: 127.600000
- symbol: Te # 6
  coordinates: [  0.500000000000000,  0.500000000000000,  0.500000000000000 ]
  mass: 127.600000
- symbol: Te # 7
  coordinates: [  0.000000000000000,  0.000000000000000,  0.500000000000000 ]
  mass: 127.600000
- symbol: Te # 8
  coordinates: [  0.000000000000000,  0.500000000000000,  0.000000000000000 ]
  mass: 127.600000
--------------------------------------------------------------------------------
Supercell of [phelel]: 64 atoms, supercell matrix [[2, 0, 0], [0, 2, 0], [0, 0, 2]].
Supercell of [phonopy]: 64 atoms, supercell matrix [[2, 0, 0], [0, 2, 0], [0, 0, 2]].
Supercell of [phono3py]: 64 atoms, supercell matrix [[2, 0, 0], [0, 2, 0], [0, 0, 2]].
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,

[vasp.nac]
cell = "primitive"
[vasp.nac.incar]
ismear = 0
sigma = 0.01
ediff = 1e-08
encut = 400
prec = "accurate"
lreal = false
lwave = false
lcharg = false
lepsilon = true
[vasp.nac.kpoints]
mesh = [9, 9, 9]

[vasp.phelel.incar]
ismear = 0
sigma = 0.01
ediff = 1e-08
encut = 400
prec = "accurate"
lreal = false
lwave = false
lcharg = false
ncore = 4
elph_prepare = true
isym = 0
kpar = 2
[vasp.phelel.kpoints]
mesh = [3, 3, 3]
[vasp.phelel.scheduler]
ntasks = 48

# ...

NAC and phelel calculations,

% velph nac generate
VASP input files were written in "nac".
% cd nac && sbatch _job.sh && cd ..
% velph phelel init
Displacement distance: 0.03
Number of displacements: 4
NAC parameters are read from "nac/vasprun.xml".
"phelel/phelel_disp.yaml" was written.
Run "velph phelel generate" to write the VASP input files.
% velph phelel generate
VASP input files were written in "phelel/disp-000".
VASP input files were written in "phelel/disp-001".
VASP input files were written in "phelel/disp-002".
VASP input files were written in "phelel/disp-003".
VASP input files were written in "phelel/disp-004".
% for i in {000..004};do cd phelel/disp-$i; sbatch _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].
Found "phelel/disp-000/vaspout.h5".
Found "phelel/disp-001/vaspout.h5".
Found "phelel/disp-002/vaspout.h5".
Found "phelel/disp-003/vaspout.h5".
Found "phelel/disp-004/vaspout.h5".
Reading the VASP output files of 5 supercells...
Computing dV at grid points (dV evaluation method: shortest)...
Computed dV/du by displaced atom 1
Computing dV at grid points (dV evaluation method: shortest)...
Computed dV/du by displaced atom 33
Computing dDij/du and dqij/du of displaced atom 1...
Computing dDij/du and dqij/du of displaced atom 33...
"phelel/phelel_params.hdf5" was written.

The FFT mesh is the FFT grid of VASP on the primitive cell for encut and prec in the INCAR tags of the electron-phonon input sets (selfenergy and transport), here encut = 400 and prec = "accurate". VASP stops when its FFT grid differs from the mesh in phelel/phelel_params.hdf5, so these input sets have to give the same mesh. When they give different meshes, or when one of them does not give encut, velph phelel differentiate stops with an error. --encut gives ENCUT in place of encut of these input sets.

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#