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VASP+phonopy (Fe2VAl-dfpt, 2x2x2 primitive cell)

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■ phonon calculation for Fe2VTaAl (Primitive cell) by DFPT method
Need: POTCAR and POSCAR-unitcell
(Not need: KPOINT (for vasp verasion 5.3)

# make Fe2VTaAl (2x2x2 Primitive cell)
1. cif2cell -p vasp --setup-all --vasp-format=5 --vasp-encutfac=1.0 --vasp-pseudo-libdr='/home/wien2k2/vasp/potpaw_PBE' --vasp-pseudo-priority="_d,_pv,_sv,_h,_s" --vasp-print-species --vasp-cartesian-lattice-vectors --print-symmetry-operations  --supercell=[2,2,2] -f case.cif
2. VESTA > POSCAR > replate Ta for V(0.5 0.5 0.5) > case.cif
3. cif2cell -p vasp --setup-all --vasp-format=5 --vasp-encutfac=1.0 --vasp-pseudo-libdr='/home/wien2k2/vasp/potpaw_PBE' --vasp-pseudo-priority="_d,_pv,_sv,_h,_s" --vasp-print-species --vasp-cartesian-lattice-vectors --print-symmetry-operations  -f case.cif

# relaxation calculation
(see "VASP (relaxation)" on left column)

# DFPT calculation
1. mkdir Fe2VAl-dfpt
2. cd Fe2*
3. gedit POSCAR-unitcell
(Please, after relaxation, cp CONTCAR POSCAR-unitcell)
(following data is test)
-----PSOCAR-unitcell----
Generated by cif2cell 1.2.10.  :
   1.00000000000000     
     8.1024713612196866   -0.0000000000000000   -0.0000000000000000
     4.0512356806098433    7.0169460322521306   -0.0000000000000000
     4.0512356806098433    2.3389820107507102    6.6156401635006912
   Al   V    Fe   Ta
     8     7    16     1
Direct
  0.2500000000000000  0.2500000000000000  0.2500000000000000
  0.2482882837475219  0.7517117162524781  0.7517117162524781
  0.2482882837475219  0.2482882837475219  0.7517117162524781
  0.7517117162524781  0.7517117162524781  0.2482882837475219
  0.7517117162524781  0.2482882837475219  0.2482882837475219
  0.7500000000000000  0.7500000000000000  0.7500000000000000
  0.7517117162524781  0.2482882837475219  0.7517117162524781
  0.2482882837475219  0.7517117162524781  0.2482882837475219
  0.0000000000000000  0.0000000000000000 -0.0000000000000000
  0.0000000000000000  0.5000000000000000  0.5000000000000000
  0.0000000000000000  0.0000000000000000  0.5000000000000000
  0.5000000000000000  0.5000000000000000 -0.0000000000000000
  0.5000000000000000  0.0000000000000000 -0.0000000000000000
  0.5000000000000000  0.0000000000000000  0.5000000000000000
  0.0000000000000000  0.5000000000000000 -0.0000000000000000
  0.1250782077547379  0.1250782077547379  0.1250782077547379
  0.3729040419254014  0.3729040419254014  0.3729040419254014
  0.1187121257762041  0.6270959580745987  0.6270959580745987
  0.1250782077547379  0.1250782077547379  0.6247653767357861
  0.6270959580745987  0.6270959580745987  0.1187121257762041
  0.6247653767357861  0.1250782077547379  0.1250782077547379
  0.6270959580745987  0.6270959580745987  0.6270959580745987
  0.6270959580745987  0.1187121257762041  0.6270959580745987
  0.1250782077547379  0.6247653767357861  0.1250782077547379
  0.3752346232642139  0.8749217922452621  0.8749217922452621
  0.3729040419254014  0.3729040419254014  0.8812878742237960
  0.8749217922452621  0.8749217922452621  0.3752346232642139
  0.8812878742237960  0.3729040419254014  0.3729040419254014
  0.8749217922452621  0.8749217922452621  0.8749217922452621
  0.8749217922452621  0.3752346232642139  0.8749217922452621
  0.3729040419254014  0.8812878742237960  0.3729040419254014
  0.5000000000000000  0.5000000000000000  0.5000000000000000
-------------
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. phonopy -d --dim="2 2 2" -c POSCAR-unitcell
6. mv SPOSCAR POSCAR
7. mpirun -np 8 /home/wien2k3/vasp/vasp.5.3/vasp
8. phonopy --fc vasprun.xml
-----------
Intel(R) Xeon(R)  E5-2640 v3
mpirun -np 8 /home/wien2k3/vasp/vasp.5.3/vasp
Total CPU time used (sec):   118095.625
Elapsed time (sec):    64010.472
Maximum memory used (kb):     1322520.
-----------

# band dispersion
1. gedit band.conf
-----band.conf----G-X-K-G-L
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 is half as for 2x2x2 as for 1x1x1
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 --gnuplot
◆ 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

# TDOS and Cv (Specific heat)
1. gedit mesh.conf
-----mesh.conf-----
DIM = 2 2 2
MP = 16 16 16
FORCE_CONSTANTS = READ
-------------
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)-----
DIM = 2 2 2
MP = 16 16 16
PDOS = 1, 2 3, 4
FORCE_CONSTANTS = READ
-------------
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
------------------------------------------------------------------------------
------------------------------------------------------------------------------
■ recompile
Phonon calculation error case
---------
    internal error in SETUP_DEG_CLUSTERS: NB_TOT exceeds NMAX_DEG
    increase NMAX_DEG to          88
---------

1. cd $HOME/vasp.5.3
2. grep NMAX_DEG *.F
 You get "subrot_cluster.F:    INTEGER, PARAMETER :: NMAX_DEG=48"
-----
3. gedit subrot_cluster.F
-----before-----line 272 (Ctrl + i, 272)
    INTEGER, PARAMETER :: NMAX_DEG=48
-----after-----line 272
    INTEGER, PARAMETER :: NMAX_DEG=256
-----
4. make

 ※ VASPはCとFortranのプリプロセッサ(cppとfpp)を用いて、.Fの拡張子がついたファイルをコンパイルするPCの環境に合わせたものに書き換えて.f90の拡張子がついたものとして出力する。
上記のようにコードを書き換える場合には、.Fの拡張子を書き換えておくと安心できる。
(VASP copy automatically subrot_cluster.F to subrot_cluster.f90 for makefile)
動画:https://www.youtube.com/watch?v=5Y6tLWvlLJE
------------------------------------------------------------------------------
■ Benchmark
-----
□ Fe16V7Nb1Al8 (non-relaxed structure, 2x2x2 primitive cell)
Intel(R) Core(TM) i7-4770 CPU @ 3.40 GHz x 4 core, 8MB, 5GT/s, 84W
Memory 15.3 GiB
Ubuntu 12.04 (precise) 64-bit
Hyper threading: OFF
l_fcompxe_intel64_2013.5.192 + openmpi-1.6.5
(Use Openmpi + MKL{Scalapack and BLACS for Opnempi}, -axAVX,SSE4.2)
mpirun -np 2 /home/wien2k1/vasp/vasp.5.3/vasp
(INTEGER, PARAMETER :: NMAX_DEG=168) in subrot_cluster.F
Elapsed time (sec):   302868.753 = 84 hours = 3.5 days
Maximum memory used (kb):     3979780. = 4.0 GB

-----
□ Fe16V7Nb1Al8 (relaxed structure, 2x2x2 primitive cell)
Intel(R) Core(TM) i7-4770 CPU @ 3.40 GHz x 4 core, 8MB, 5GT/s, 84W
Memory 15.3 GiB
Ubuntu 12.04 (precise) 64-bit
Hyper threading: OFF
l_fcompxe_intel64_2013.5.192 + openmpi-1.6.5
(Use Openmpi + MKL{Scalapack and BLACS for Opnempi}, -axAVX,SSE4.2)
mpirun -np 2 /home/wien2k1/vasp/vasp.5.3/vasp
(INTEGER, PARAMETER :: NMAX_DEG=168) in subrot_cluster.F
Elapsed time (sec):   260127.608 = 72 hours = 3.0 days
Maximum memory used (kb):     3633476. = 3.6 GB

-----
□ Fe16V7Ta1Al8 (relaxed structure, 2x2x2 primitive cell)
Intel(R) Core(TM) i7-4770 CPU @ 3.40 GHz x 4 core, 8MB, 5GT/s, 84W
Memory 15.3 GiB
Ubuntu 12.04 (precise) 64-bit
Hyper threading: OFF
l_fcompxe_intel64_2013.5.192 + openmpi-1.6.5
(Use Openmpi + MKL{Scalapack and BLACS for Opnempi}, -axAVX,SSE4.2)
mpirun -np 2 /home/wien2k2/vasp/vasp.5.3/vasp
(INTEGER, PARAMETER :: NMAX_DEG=256) in subrot_cluster.F
defaults (PREC = Normal)
Elapsed time (sec):   254827.305 = 71 hours = 3.0 days
Maximum memory used (kb):     2898592. = 2.87GB
-----
□ Fe16V7Ta1Al8 (relaxed structure, 2x2x2 primitive cell)
Intel(R) Core(TM) i7-4770 CPU @ 3.40 GHz x 4 core, 8MB, 5GT/s, 84W
Memory 15.3 GiB
Ubuntu 12.04 (precise) 64-bit
Hyper threading: OFF
l_fcompxe_intel64_2013.5.192 + openmpi-1.6.5
(Use Openmpi + MKL{Scalapack and BLACS for Opnempi}, -axAVX,SSE4.2)
mpirun -np 2 /home/wien2k1/vasp/vasp.5.3/vasp
(INTEGER, PARAMETER :: NMAX_DEG=256) in subrot_cluster.F
PREC = Accurate
Elapsed time (sec):   308570.204 = 85 hours = 3.6 days
Maximum memory used (kb):     4003712. = 4.00GB

-----
□ Fe16V7Ta1Al8 (relaxed structure(PREC = High, EDIFF = 1.0e-08), 2x2x2 primitive cell)
Intel(R) Core(TM) i7-4770 CPU @ 3.40 GHz x 4 core, 8MB, 5GT/s, 84W
Memory 15.3 GiB
Ubuntu 12.04 (precise) 64-bit
Hyper threading: OFF
l_fcompxe_intel64_2013.5.192 + openmpi-1.6.5
(Use Openmpi + MKL{Scalapack and BLACS for Opnempi}, -axAVX,SSE4.2)
mpirun -np 2 /home/wien2k1/vasp/vasp.5.3/vasp
(INTEGER, PARAMETER :: NMAX_DEG=256) in subrot_cluster.F
PREC = Accurate
Elapsed time (sec):   306207.209 = 85 hours = 3.6 days
Maximum memory used (kb):     3946528. = 4.00GB
-----
□ Fe16V7Ta1Al8 (relaxed structure(PREC = High, EDIFF = 1.0e-08), 2x2x2 primitive cell)
Intel(R) Core(TM) i7-4770 CPU @ 3.40 GHz x 4 core, 8MB, 5GT/s, 84W
Memory 15.3 GiB
Ubuntu 12.04 (precise) 64-bit
Hyper threading: OFF
l_fcompxe_intel64_2013.5.192 + openmpi-1.6.5
(Use Openmpi + MKL{Scalapack and BLACS for Opnempi}, -axAVX,SSE4.2)
mpirun -np 2 /home/wien2k1/vasp/vasp.5.3/vasp
(INTEGER, PARAMETER :: NMAX_DEG=256) in subrot_cluster.F
PREC = High
Elapsed time (sec):   495448.914 = 137.6 hours = 5.7 days
Maximum memory used (kb):     4424432. = 4.42GB

-----
□ Fe16V7Ta1Al8 (non-relaxed structure, 2x2x2 primitive cell)
Intel(R) Xeon(R)  E5-2640 v3 @ 2.6GHz x 8 core, 20MB, 8GT/s, 90W
Hyper threading: OFF
parallel_studio_xe_2016_update4
(Use intelmpi + MKL{Scalapack and BLACS for intelmpi}, -axAVX2,AVX,SSE4.2)
mpirun -np 8 /home/wien2k3/vasp/vasp.5.3/vasp
(INTEGER, PARAMETER :: NMAX_DEG=256) in subrot_cluster.F
Total CPU time used (sec):   118095.625
User time (sec):   116682.165
System time (sec):     1413.457
Elapsed time (sec):    64010.472 = 17.8 hours = 0.74 days
Maximum memory used (kb):     1322520. = 1.3 GB

-----
□ Fe16V7Ta1Al8 (non-relaxed structure, 2x2x2 primitive cell)
Intel(R) Core(TM) i7-4770S @ 3.10 GHz x 4 core, 8MB, 5GT/s, 65W
Ubuntu 16.04 LTS
Memory 7.5 GiB
parallel_studio_xe_2016_update4
(Use intelmpi + MKL{Scalapack and BLACS for intelmpi}, -axAVX2,AVX,SSE4.2)
mpirun -machinefile $HOME/machinefile -env I_MPI_DEVICE sock -np 2 /home/student/vasp/vasp.5.3/vasp -r ssh
(INTEGER, PARAMETER :: NMAX_DEG=256) in subrot_cluster.F
Elapsed time (sec):   303475.296 = 84.3 h = 3.5 days
Maximum memory used (kb):     3565148. = 3.6 GB
-----
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