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VASP+phonopy (Fe2VAl-dfpt)

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■ Youtube動画:
基本的な使い方:https://www.youtube.com/watch?v=bKwjCIrvfSk
エラーが表示された場合:https://www.youtube.com/watch?v=5Y6tLWvlLJE
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■ phonon calculation for Fe2VAl (Primitive cell) by DFPT method
Need: POTCAR and POSCAR-unitcell
(Not need: KPOINT (for vasp verasion 5.3 and later)

# phonon dispersion (DFPT)
1. mkdir Fe2VAl-dfpt
2. cd Fe2*
3. cif2cell -p vasp --setup-all --vasp-format=5 --vasp-encutfac=1.0 --vasp-pseudo-libdr='/home/wien2k4/vasp/potpaw_PBE' --vasp-pseudo-priority="_d,_pv,_sv,_h,_s" --vasp-print-species --vasp-cartesian-lattice-vectors --print-symmetry-operations -f case.cif
4. gedit INCAR
-----INCAR----
   PREC = Accurate
#  ENCUT = 500
 IBRION = 8
  EDIFF = 1.0e-08
  IALGO = 38
 ISMEAR = 0; SIGMA = 0.1
  LREAL = .FALSE.
ADDGRID = .TRUE.
  LWAVE = .FALSE.
 LCHARG = .FALSE.
-------------
5. mv KPOINTS KPOINTS_
6. mv POSCAR POSCAR-unitcell
-----PSOCAR-unitcell----
Generated by cif2cell 1.2.10.  :  Failed to get author information, No journal information.
 1.0
  0.000000000000000   2.882550000000000   2.882550000000000
  2.882550000000000   0.000000000000000   2.882550000000000
  2.882550000000000   2.882550000000000   0.000000000000000
  Al  Fe   V
   1   2   1
Direct
  0.500000000000000   0.500000000000000   0.500000000000000
  0.250000000000000   0.250000000000000   0.250000000000000
  0.750000000000000   0.750000000000000   0.750000000000000
  0.000000000000000   0.000000000000000   0.000000000000000
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7. phonopy -d --dim="2 2 2" -c POSCAR-unitcell
8. mv SPOSCAR POSCAR
9. export OMP_NUM_THREADS=1
10. mpirun -np 6 $HOME/vasp/vasp.5.3/vasp
  gfortran + netlib case: mpirun.openmpi -np 4 $HOME/vasp/vasp.5.3/vasp
  vasp.5.4 + intel compiler + MKL case: mpirun -np 4 $HOME/vasp/vasp.5.4.1/bin/vasp_std
  vasp.5.4 + gfortran + netlib case: mpirun.openmpi -np 4 $HOME/vasp/vasp.5.4.1/bin/vasp_std
11. phonopy --fc vasprun.xml

# band dispersion
1. gedit band.conf
-----band.conf----G-X-K-G-L (same as xcrysden on WIEN2k)
DIM = 2 2 2
PRIMITIVE_AXIS = 1.0 0.0 0.0  0.0 1.0 0.0  0.0 0.0 1.0
BAND = 0.0 0.0 0.0  0.0 0.5 0.5  0.375 0.75 0.375  0.0 0.0 0.0  0.5 0.5 0.5
FORCE_CONSTANTS = READ
BAND_LABELS = $\Gamma$ X K $\Gamma$ L
BAND_POINTS = 51
GROUP_VELOCITY = .TRUE.
GV_DELTA_Q = 0.01
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* BANDの指定はWIEN2kでのTasks > Bandstructure > Generate k-mesh using Xcrysdenと同じ記号と数値にすればよい。上記の指定でunfoldingされる。group velocity (at gamma point) is shown in band.yaml
Youtube: https://www.youtube.com/watch?v=VvHgjCOoKhM
2. phonopy --dim="2 2 2" -c POSCAR-unitcell band.conf
3. cp $HOME/phonopy*/scripts/bandplot ./
4. bandplot


# other bandplot option
◆ bandplot -h
◆ bandplot --xlabel="" --ylabel="Frequency (THz)" --title="Fe2VAl" --fmin=0 --fmax=12
◆ bandplot --xlabel="" --ylabel="Frequency (THz)" --title="Fe2VAl" --fmin=0 --fmax=12 --dos=total_dos.dat
◆ bandplot --xlabel="" --ylabel="Frequency (THz)" --title="Fe2VAl" --fmin=0 --fmax=12 --dos=partial_dos.dat
if you want to get row data (for igor, origin, and other plot soft)
◆ bandplot --gnuplot > band_data.txt

Fig. band dispersion for G-X-K-G-L line with "bandplot --xlabel="" --ylabel="Frequency (THz)" --title="Fe2VAl" --fmin=0 --fmax=12 --dos=partial_dos.dat".

# TDOS and Cv (Specific heat)
1. gedit mesh.conf
-----mesh.conf-----
DIM = 2 2 2
MP = 16 16 16
FORCE_CONSTANTS = READ
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2. phonopy --dim="2 2 2" -c POSCAR-unitcell -p mesh.conf

3. phonopy --dim="2 2 2" -c POSCAR-unitcell -t -p mesh.conf


# PDOS
1. gedit pdos.conf
-----pdos.conf----plot pdos (Al, Fe, V, Total)-----
DIM = 2 2 2
MP = 16 16 16
PDOS = 1, 2 3, 4, 1 2 3 4
FORCE_CONSTANTS = READ
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Maybe, relate POSCAR-unitcell
-----POSCAR-unitcell----
  Al  Fe   V
   1   2   1
-------------
1=Al, 2=Fe, 3=Fe, V=4
2. phonopy --dim="2 2 2" -c POSCAR-unitcell -p pdos.conf

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■ benchmark
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Fe2VAl(primitive cell) DFPT calculation
Openmpi + intel compiler + MKL
mpirun -machinefile $HOME/machinefile -genv I_MPI_DEVICE sock -n 4 /home/student/vasp/vasp.5.3/vasp -r ssh
Intel(R) Core(TM) i7-4770 (8M Cache, 3.40 GHz, up to 3.90 GHz)
(cpu value $303.00 - $312.00)
Elapsed time (sec):      1171.669 = 19.5 min
Maximum memory used (kb):      248236. = 0.25 GB
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Hyper threading OFF (on BIOS)
※ Hyper threading OFFの有無を調べたが、計算速度に違いはない。加えて、PC安定に動作する(ハングアップしたりシャットダウンしたりする頻度が低下するわ)けではなかった(PCがハングアップしたりシャットダウンしたりしなくなるようにするにはそれよりも並列コア数を最大の半分くらいに指定したりHDDやメモリをクリーンにする方が効果がある)。
Fe2VAl(primitive cell) DFPT calculation
Openmpi + intel compiler + MKL
mpirun -machinefile $HOME/machinefile -genv I_MPI_DEVICE sock -n 4 /home/student/vasp/vasp.5.3/vasp -r ssh
Intel(R) Core(TM) i7-4770 (8M Cache, 3.40 GHz, up to 3.90 GHz)
(cpu value $303.00 - $312.00)
Elapsed time (sec):      1138.405 = 18.9 min
Maximum memory used (kb):      246372. = 0.25 GB
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Fe2VAl(primitive cell) DFPT calculation
intelmpi + intel compiler + MKL
mpirun -machinefile $HOME/machinefile -genv I_MPI_DEVICE sock -n 4 /home/student/vasp/vasp.5.3/vasp -r ssh
Intel(R) Core(TM) i7-4770S (8M Cache, 3.10 GHz, up to 3.90 GHz)
(cpu value $303.00 - $305.00)
Elapsed time (sec):      931.538 = 15.6 min
Maximum memory used (kb):      288624. = 0.29 GB
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Fe2VAl(primitive cell) DFPT calculation
intelmpi + intel compiler + MKL
mpirun -machinefile $HOME/machinefile -genv I_MPI_DEVICE sock -n 4 /home/student/vasp/vasp.5.3/vasp -r ssh
Intel(R) Xeon(R) E5-2640 v3 (20M Cache, 2.60 GHz, up to 3.40 GHz)
(cpu value $939.00 - $944.00)
Elapsed time (sec):      489.297 = 8.15 min
Maximum memory used (kb):      206484. = 0.21 GB
----------Results----------
Sorry, I didnt memorize second time (hh:mm:ss)
3.1 GB
start main + 3 part
Sat Nov 19 9:48:XX JST 2016, DAV, main, 17+3 cycle
Sat Nov 19 9:49:XX JST 2016, RMM, 1/3, 18 cycle
Sat Nov 19 9:53:XX JST 2016, RMM, 2/3, 18 cycle
Sat Nov 19 9:55:XX JST 2016, RMM, 3/3, 17 cycle
Sat Nov 19 9:57:XX JST 2016, END
primitive cell / about 9 min
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