velph example#
NiTiSn#
POSCAR-unitcell, POTCAR, and velph-tmpl.toml are located in the current directory.
Initial POSCAR-unitcell,
Ti4Sn4Ni4
1.0
5.906882041566931 0.000000000000000 0.000000000000000
0.000000000000000 5.906882041566931 0.000000000000000
0.000000000000000 0.000000000000000 5.906882041566931
Ti Sn Ni
4 4 4
Direct
0.000000000000000 0.000000000000000 0.000000000000000
0.000000000000000 0.500000000000000 0.500000000000000
0.500000000000000 0.000000000000000 0.500000000000000
0.500000000000000 0.500000000000000 0.000000000000000
0.500000000000000 0.500000000000000 0.500000000000000
0.500000000000000 0.000000000000000 0.000000000000000
0.000000000000000 0.500000000000000 0.000000000000000
0.000000000000000 0.000000000000000 0.500000000000000
0.250000000000000 0.250000000000000 0.250000000000000
0.250000000000000 0.750000000000000 0.750000000000000
0.750000000000000 0.250000000000000 0.750000000000000
0.750000000000000 0.750000000000000 0.250000000000000
velph-tmpl.toml,
[init.options]
kspacing = 0.1
kspacing_dense = 0.2
max_num_atoms = 100
[vasp.incar]
encut = 520
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 = "TiNiSn"
mpirun_command = "mpirun"
vasp_binary = "/usr/local/vasp/bin/vasp_std"
pe = "vienna 32"
prepend_text = '''
source /opt/intel/oneapi/setvars.sh intel64 --config="/home/togo/.oneapi-config"
'''
append_text = ""
POTCAR choice,
PAW_PBE Ti_sv 26Sep2005
PAW_PBE Sn_d 06Sep2000
PAW_PBE Ni 02Aug2007
% velph init POSCAR_Ti4Sn4Ni4 relax --template-toml velph-tmpl.toml
Crystal structure file: "POSCAR_Ti4Sn4Ni4".
Velph template file: "velph-tmpl.toml".
Read crystal structure file "POSCAR_Ti4Sn4Ni4".
Read velph template file "velph-tmpl.toml".
Following options were found in "velph-tmpl.toml":
kspacing = "0.1"
kspacing_dense = "0.2"
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:
- [ 5.906882041566931, 0.000000000000000, 0.000000000000000 ] # a
- [ 0.000000000000000, 5.906882041566931, 0.000000000000000 ] # b
- [ 0.000000000000000, 0.000000000000000, 5.906882041566931 ] # c
points:
- symbol: Ti # 1
coordinates: [ 0.000000000000000, 0.000000000000000, 0.000000000000000 ]
mass: 47.867000
- symbol: Ti # 2
coordinates: [ 0.000000000000000, 0.500000000000000, 0.500000000000000 ]
mass: 47.867000
- symbol: Ti # 3
coordinates: [ 0.500000000000000, 0.000000000000000, 0.500000000000000 ]
mass: 47.867000
- symbol: Ti # 4
coordinates: [ 0.500000000000000, 0.500000000000000, 0.000000000000000 ]
mass: 47.867000
- symbol: Sn # 5
coordinates: [ 0.500000000000000, 0.500000000000000, 0.500000000000000 ]
mass: 118.710000
- symbol: Sn # 6
coordinates: [ 0.500000000000000, 0.000000000000000, 0.000000000000000 ]
mass: 118.710000
- symbol: Sn # 7
coordinates: [ 0.000000000000000, 0.500000000000000, 0.000000000000000 ]
mass: 118.710000
- symbol: Sn # 8
coordinates: [ 0.000000000000000, 0.000000000000000, 0.500000000000000 ]
mass: 118.710000
- symbol: Ni # 9
coordinates: [ 0.250000000000000, 0.250000000000000, 0.250000000000000 ]
mass: 58.693400
- symbol: Ni # 10
coordinates: [ 0.250000000000000, 0.750000000000000, 0.750000000000000 ]
mass: 58.693400
- symbol: Ni # 11
coordinates: [ 0.750000000000000, 0.250000000000000, 0.750000000000000 ]
mass: 58.693400
- symbol: Ni # 12
coordinates: [ 0.750000000000000, 0.750000000000000, 0.250000000000000 ]
mass: 58.693400
--------------------------------------------------------------------------------
[vasp.incar] (basic INCAR settings)
ismear = 0
sigma = 0.01
ediff = 1e-08
encut = 520
prec = accurate
lreal = False
lwave = False
lcharg = False
ncore = 4
[phelel]
supercell_dimension: [2 2 2]
[vasp.*.kpoints.mesh] (*kspacing=0.1)
selfenergy: [18 18 18]*
el_bands: [18 18 18]*
phelel: [5 5 5]*
relax: [11 11 11]*
nac: [18 18 18]*
[vasp.*.kpoints_dense.mesh] (*kspacing_dense=0.2)
selfenergy: [9 9 9]*
el_bands: [9 9 9]*
Created new folder "relax".
Initial settings were written to "relax/velph.toml".
Found "POTCAR".
PAW_PBE Ti_sv 26Sep2005
PAW_PBE Sn_d 06Sep2000
PAW_PBE Ni 02Aug2007
Max ENMAX in "POTCAR" is 274.61.
"POTCAR" was copied to "relax/POTCAR".
A directory relax is created and velph.toml is stored in it.
relax/velph.toml,
[phelel]
version = "0.6.0"
supercell_dimension = [2, 2, 2]
amplitude = 0.03
diagonal = true
plusminus = true
fft_mesh = [32, 32, 32]
# ...
[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 = 520
prec = "accurate"
lreal = false
lwave = false
lcharg = false
ncore = 4
[vasp.relax.kpoints]
mesh = [11, 11, 11]
# ...
[scheduler]
scheduler_name = "sge"
job_name = "TiNiSn"
mpirun_command = "mpirun"
vasp_binary = "/usr/local/vasp/bin/vasp_std"
pe = "vienna 32"
prepend_text = "source /opt/intel/oneapi/setvars.sh intel64 --config=\"/home/togo/.oneapi-config\"\n"
append_text = ""
[symmetry]
spacegroup_type = "F-43m"
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 = [
[ 5.906882041566931, 0.000000000000000, 0.000000000000000 ], # a
[ 0.000000000000000, 5.906882041566931, 0.000000000000000 ], # b
[ 0.000000000000000, 0.000000000000000, 5.906882041566931 ], # c
]
[[unitcell.points]] # 1
symbol = "Ti"
coordinates = [ 0.000000000000000, 0.000000000000000, 0.000000000000000 ]
[[unitcell.points]] # 2
symbol = "Ti"
coordinates = [ 0.000000000000000, 0.500000000000000, 0.500000000000000 ]
[[unitcell.points]] # 3
symbol = "Ti"
coordinates = [ 0.500000000000000, 0.000000000000000, 0.500000000000000 ]
[[unitcell.points]] # 4
symbol = "Ti"
coordinates = [ 0.500000000000000, 0.500000000000000, 0.000000000000000 ]
[[unitcell.points]] # 5
symbol = "Sn"
coordinates = [ 0.500000000000000, 0.500000000000000, 0.500000000000000 ]
[[unitcell.points]] # 6
symbol = "Sn"
coordinates = [ 0.500000000000000, 0.000000000000000, 0.000000000000000 ]
[[unitcell.points]] # 7
symbol = "Sn"
coordinates = [ 0.000000000000000, 0.500000000000000, 0.000000000000000 ]
[[unitcell.points]] # 8
symbol = "Sn"
coordinates = [ 0.000000000000000, 0.000000000000000, 0.500000000000000 ]
[[unitcell.points]] # 9
symbol = "Ni"
coordinates = [ 0.250000000000000, 0.250000000000000, 0.250000000000000 ]
[[unitcell.points]] # 10
symbol = "Ni"
coordinates = [ 0.250000000000000, 0.750000000000000, 0.750000000000000 ]
[[unitcell.points]] # 11
symbol = "Ni"
coordinates = [ 0.750000000000000, 0.250000000000000, 0.750000000000000 ]
[[unitcell.points]] # 12
symbol = "Ni"
coordinates = [ 0.750000000000000, 0.750000000000000, 0.250000000000000 ]
[primitive_cell]
lattice = [
[ 0.000000000000000, 2.953441020783465, 2.953441020783465 ], # a
[ 2.953441020783465, 0.000000000000000, 2.953441020783465 ], # b
[ 2.953441020783465, 2.953441020783465, 0.000000000000000 ], # c
]
[[primitive_cell.points]] # 1
symbol = "Ti"
coordinates = [ 0.000000000000000, 0.000000000000000, 0.000000000000000 ]
[[primitive_cell.points]] # 2
symbol = "Sn"
coordinates = [ 0.500000000000000, 0.500000000000000, 0.500000000000000 ]
[[primitive_cell.points]] # 3
symbol = "Ni"
coordinates = [ 0.250000000000000, 0.250000000000000, 0.250000000000000 ]
fft_mesh is calculated from encut value in the [vasp.selfenergy.incar] section.
Change directory to relax.
% velph relax generate
% cd relax/iter1
% qsub _job.sh
Structure optimization is done until stress becomes less than 0.1kB (0.01GPa). 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
Crystal structure file: "relax/relax/iter2/CONTCAR".
Velph template file: "velph-tmpl.toml".
Read crystal structure file "relax/relax/iter2/CONTCAR".
Read velph template file "velph-tmpl.toml".
Following options were found in "velph-tmpl.toml":
kspacing = "0.1"
kspacing_dense = "0.2"
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:
- [ 5.949975748250650, 0.000000000000000, 0.000000000000000 ] # a
- [ 0.000000000000000, 5.949975748250650, -0.000000000000000 ] # b
- [ 0.000000000000000, 0.000000000000000, 5.949975748250650 ] # c
points:
- symbol: Ti # 1
coordinates: [ 0.000000000000000, 0.000000000000000, 0.000000000000000 ]
mass: 47.867000
- symbol: Ti # 2
coordinates: [ 0.000000000000000, 0.500000000000000, 0.500000000000000 ]
mass: 47.867000
- symbol: Ti # 3
coordinates: [ 0.500000000000000, 0.000000000000000, 0.500000000000000 ]
mass: 47.867000
- symbol: Ti # 4
coordinates: [ 0.500000000000000, 0.500000000000000, 0.000000000000000 ]
mass: 47.867000
- symbol: Sn # 5
coordinates: [ 0.500000000000000, 0.500000000000000, 0.500000000000000 ]
mass: 118.710000
- symbol: Sn # 6
coordinates: [ 0.500000000000000, 0.000000000000000, 0.000000000000000 ]
mass: 118.710000
- symbol: Sn # 7
coordinates: [ 0.000000000000000, 0.500000000000000, 0.000000000000000 ]
mass: 118.710000
- symbol: Sn # 8
coordinates: [ 0.000000000000000, 0.000000000000000, 0.500000000000000 ]
mass: 118.710000
- symbol: Ni # 9
coordinates: [ 0.250000000000000, 0.250000000000000, 0.250000000000000 ]
mass: 58.693400
- symbol: Ni # 10
coordinates: [ 0.250000000000000, 0.750000000000000, 0.750000000000000 ]
mass: 58.693400
- symbol: Ni # 11
coordinates: [ 0.750000000000000, 0.250000000000000, 0.750000000000000 ]
mass: 58.693400
- symbol: Ni # 12
coordinates: [ 0.750000000000000, 0.750000000000000, 0.250000000000000 ]
mass: 58.693400
--------------------------------------------------------------------------------
[vasp.incar] (basic INCAR settings)
ismear = 0
sigma = 0.01
ediff = 1e-08
encut = 520
prec = accurate
lreal = False
lwave = False
lcharg = False
ncore = 4
[phelel]
supercell_dimension: [2 2 2]
[vasp.*.kpoints.mesh] (*kspacing=0.1)
selfenergy: [18 18 18]*
el_bands: [18 18 18]*
phelel: [5 5 5]*
relax: [11 11 11]*
nac: [18 18 18]*
[vasp.*.kpoints_dense.mesh] (*kspacing_dense=0.2)
selfenergy: [9 9 9]*
el_bands: [9 9 9]*
Created new folder "calc".
Initial settings were written to "calc/velph.toml".
Found "POTCAR".
PAW_PBE Ti_sv 26Sep2005
PAW_PBE Sn_d 06Sep2000
PAW_PBE Ni 02Aug2007
Max ENMAX in "POTCAR" is 274.61.
"POTCAR" was copied to "calc/POTCAR".
Change directory to calc.
% cd calc
velph.toml,
[phelel]
version = "0.6.0"
supercell_dimension = [2, 2, 2]
amplitude = 0.03
diagonal = true
plusminus = true
fft_mesh = [32, 32, 32]
[vasp.phelel.incar]
lwap = true
isym = 0
kpar = 2
ismear = 0
sigma = 0.01
ediff = 1e-08
encut = 520
prec = "accurate"
lreal = false
lwave = false
lcharg = false
ncore = 4
[vasp.phelel.kpoints]
mesh = [5, 5, 5]
[vasp.phelel.scheduler]
pe = "mpi* 48"
# ...
[vasp.nac]
cell = "primitive"
[vasp.nac.incar]
lepsilon = true
ismear = 0
sigma = 0.01
ediff = 1e-08
encut = 520
prec = "accurate"
lreal = false
lwave = false
lcharg = false
[vasp.nac.kpoints]
mesh = [18, 18, 18]
# ...
NAC and supercell calculations,
% velph nac generate
% cd nac; qsub _job.sh; cd ..
% velph phelel init
Found "nac" directory. Read NAC params.
"phelel/phelel_disp.yaml" was generated by phelel.
VASP input files will be generated by "velph phelel generate".
% velph supercell generate
VASP input files were generated in "supercell/disp-000".
VASP input files were generated in "supercell/disp-001".
VASP input files were generated in "supercell/disp-002".
VASP input files were generated in "supercell/disp-003".
VASP input files were generated in "supercell/disp-004".
VASP input files were generated in "supercell/disp-005".
VASP input files were generated in "supercell/disp-006".
% for i in {000..006};do cd phelel/disp-$i; qsub _job.sh; cd ../..;done
Using the VASP results of the supercell 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
Running finufft (eps=1.000e-06)...
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.yamlwhenphelel/phelel_disp.yamlis created byvelph phelel init.NAC data in
phelel/phelel_disp.yamlare transfered tophelel/phelel_params.hdf5byvelph 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.