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PWscf(XANES)

  ここではPWscfを用いたXANES 入力ファイルとその結果を掲載していく。
--------------------------------------------------------------------------------
CentOS6.4 (Final) 64-bit
プロセッサ: Intel® Core™ i7-2700K CPU @ 3.50GHz × 8
メモリ: 15.6 GiB
espresso-5.1
コンパイラ: ifort 13.1.1
VESTA v.2.1.6
-----
PAW: http://theossrv1.epfl.ch/Main/Pseudopotentials 

X-ray absorption lecture note :
http://cdsagenda5.ictp.it/askArchive.php?base=agenda&categ=a10125&id=a10125s1t6/lecture_notes
Xspectra: http://www.impmc.upmc.fr/~cabaret/Xspectra/Intro/intro.htm
XANES(SiO2): http://qe-forge.org/pipermail/pw_forum/2011-July/095650.html
ResearchGate: https://www.researchgate.net/topic/exafs
INPUT_XSPECTRA: http://code.google.com/p/ce-espresso/source/browse/trunk/Doc/INPUT_XSPECTRA?r=8
Other References: http://arxiv.org/pdf/1304.6251.pdf
-----
■ MgO

DOS (PWscf (upper side) and WIEN2k(under side))


□ Command
-----
export OMP_NUM_THREADS=1
mpirun -np 4 /home/vasp/espresso-5.1/bin/pw.x < input.pw
mpirun -np 4 /home/vasp/espresso-5.1/bin/pw.x < input_dos.pw
mpirun -np 4 /home/vasp/espresso-5.1/bin/projwfc.x  < input.pr.in
-----
Please, change vasp or username.

□ MgO (SCF)
input.pw
-----
 &CONTROL
                 calculation = 'scf' ,
                restart_mode = 'from_scratch' ,
                  pseudo_dir = '/home/vasp/espresso-5.1/PWscf_calc/MgO/' ,
 /
 &SYSTEM
                       ibrav = 2,
                   celldm(1) = 7.97426619678,
                         nat = 2,
                        ntyp = 2,
                     ecutwfc = 40 ,
                     ecutrho = 120 ,
                 occupations = 'tetrahedra' ,
                     degauss = 0.02 ,
                    smearing = 'fermi-dirac' ,
                       nspin = 2 ,
   starting_magnetization(1) = 1,
   starting_magnetization(2) = 1,
           tot_magnetization = -1 ,
            exxdiv_treatment = 'gygi-baldereschi' ,
 /
 &ELECTRONS
                    conv_thr = 1.0d-8 ,
                 mixing_beta = 0.7 ,
 /
ATOMIC_SPECIES
   Mg   24.30500  mg_pbe_v1.uspp.F.UPF
    O   15.99940  o_pbe_v1.2.uspp.F.UPF
ATOMIC_POSITIONS crystal
   Mg      0.000000000    0.000000000    0.000000000    
    O      0.500000000    0.500000000    0.500000000    
K_POINTS automatic
  4 4 4   1 1 1
-----

□ MgO (DOS)
input_dos.pw
-----
 &CONTROL
                 calculation = 'nscf' ,
                restart_mode = 'from_scratch' ,
                  pseudo_dir = '/home/vasp/espresso-5.1/PWscf_calc/MgO/' ,
 /
 &SYSTEM
                       ibrav = 2,
                   celldm(1) = 7.97426619678,
                         nat = 2,
                        ntyp = 2,
                     ecutwfc = 40 ,
                     ecutrho = 120 ,
                        nbnd = 30,
                 occupations = 'tetrahedra' ,
                     degauss = 0.02 ,
                    smearing = 'fermi-dirac' ,
                       nspin = 2 ,
   starting_magnetization(1) = 1,
   starting_magnetization(2) = 1,
           tot_magnetization = -1 ,
            exxdiv_treatment = 'gygi-baldereschi' ,
 /
 &ELECTRONS
                    conv_thr = 1.0d-8 ,
                 mixing_beta = 0.7 ,
 /
ATOMIC_SPECIES
   Mg   24.30500  mg_pbe_v1.uspp.F.UPF
    O   15.99940  o_pbe_v1.2.uspp.F.UPF
ATOMIC_POSITIONS crystal
   Mg      0.000000000    0.000000000    0.000000000    
    O      0.500000000    0.500000000    0.500000000    
K_POINTS automatic
  12 12 12   1 1 1
-----

□ input.pr.in
-----
 &PROJWFC
                     degauss = 0.006 ,
                      DeltaE = 0.03 ,
 /
-----

□ Fermi Energy
-----
input.pw.out
     the Fermi energy is    7.8143 ev
--
pwscf.pdos_tot ( find exiting first dosup < the Fermi energy is    10.9060 ev )
  8.110  0.311E-13  0.313E-13  0.308E-13  0.310E-13
  8.140  0.000E+00  0.000E+00  0.000E+00  0.000E+00
--
Fermi Energy = 7.8143 eV = 0.574496 Ry
-----

□ gnuplot (DOS plot)
-----
gnuplot
plot '/home/username/espresso-5.1/PWscf_calc/MgO/pwscf.pdos_tot' using ($1-7.8):($2*2) w l t "MgO PWscf USPP(GBRV)"
set xrange[-11:16]
set yrange[0:4]
set yzeroaxis
set xlabel "Energy / eV"
set ylabel "Density of State / eV"
replot
-----


-----
■ MgO (2x2x2)

PWscf (SCF: 2x2x2 k{5m10s}, NSCF: 3x3x3 k {17m43s}, XAS: 2x2x2 k{528 s})


PWscf (SCF: 2x2x2 k{5m10s}, XAS: 4x4x4 k{1h12m})






















PWscf (SCF: 2x2x2 k{5m10s}, NSCF: nbnd 320{9m25s}, XAS: 2x2x2 k{528 s})


PWscf (SCF: 2x2x2 k{5m10s}, XAS: 2x2x2 k{528 s})


□ Command
-----
export OMP_NUM_THREADS=1
mpirun -np 4 /home/vasp/espresso-5.1/bin/pw.x < input.pw
$HOME/espresso-5.1/XSpectra/tools/upf2plotcore.sh Mg.pbe-n-kjpaw_psl.0.3.0.UPF > Mg.wfc
mpirun -np 4 /home/vasp/espresso-5.1/bin/xspectra.x < prefix.xspectra.in
-----
Please, change vase.

----------
□ Mg 1s Core-hole PAW
1. Please, get paw: http://theossrv1.epfl.ch/Main/Pseudopotentials
2. cp Mg.in Mgc.in
3. gedit Mgc.in
   1s2 -> 1s1
   zval=2 -> zval=3

Mgc.in
-----
 &input
    title='Mg'
      zed=12
    config='1s1 2s2 2p6 3s2 3p0 3d0'
    iswitch=3,
    dft='PBE'
    nld=3,
        eminld=-4,
        emaxld=4,
        deld=0.01d0,
        rlderiv=1.85,
 /
 &inputp
   pseudotype=3,
   nlcc=.true.,
     new_core_ps = .true.
     rcore=1.2
   lloc=2,
   file_pseudopw='Mg.pbe-star1s-gipaw_kj.UPF'
   zval=3
   lpaw=.true.
     lnc2paw=.false.
     which_augfun ='BESSEL'
     rmatch_augfun= 1.80
     tm=.true.
   !bessel_vloc=.true.
   lgipaw_reconstruction=.true.
!nX n  l   occ   nrg   rmin   rcut
 /
5
3S  1  0  2.00  0.00  1.50  1.80
3S  1  0  0.00  2.00  1.50  1.80
3P  2  1  0.00  0.00  1.50  1.80
3P  2  1  0.00  2.00  1.50  1.80
3D  3  2  0.00  0.20  1.65  1.65
-----
4. /home/vasp/espresso-5.1/bin/ld1.x  < Mgc.in
-----------

□ MgO (2x2x2) (SCF)
input.pw (5m10s, 1.7 GB)
------
 &CONTROL
                 calculation = 'scf' ,
                restart_mode = 'from_scratch' ,
                  pseudo_dir = '/home/vasp/espresso-5.1/PWscf_calc/MgO/' ,
 /
 &SYSTEM
                       ibrav = 1,
                   celldm(1) = 15.9484,
                         nat = 64,
                        ntyp = 3,
                     ecutwfc = 50 ,
                     ecutrho = 200 ,
                 occupations = 'smearing' ,
                     degauss = 0.02 ,
                    smearing = 'gaussian' ,
                       nspin = 2 ,
   starting_magnetization(1) = 1,
   starting_magnetization(2) = 1,
   starting_magnetization(3) = 1,
           tot_magnetization = -1 ,
            exxdiv_treatment = 'gygi-baldereschi' ,
 /
 &ELECTRONS
                    conv_thr = 1.0d-8 ,
                 mixing_beta = 0.7 ,
 /
ATOMIC_SPECIES
   Mg   24.30500  Mg.pbe-n-kjpaw_psl.0.3.0.UPF
    O   15.99940  O.pbe-n-kjpaw_psl.0.1.UPF
  Mgc   24.30500  Mg.pbe-star1s-gipaw_kj.UPF
ATOMIC_POSITIONS crystal
  Mgc      0.000000000    0.000000000    0.000000000    
   Mg      0.000000000    0.250000000    0.250000000    
   Mg      0.250000000    0.000000000    0.250000000    
   Mg      0.250000000    0.250000000    0.000000000    
   Mg      0.500000000    0.500000000    0.000000000    
   Mg      0.500000000    0.000000000    0.000000000    
   Mg      0.000000000    0.500000000    0.500000000    
   Mg      0.000000000    0.000000000    0.500000000    
   Mg      0.500000000    0.500000000    0.500000000    
   Mg      0.500000000    0.000000000    0.500000000    
   Mg      0.000000000    0.500000000    0.000000000    
   Mg      0.500000000    0.750000000    0.250000000    
   Mg      0.500000000    0.250000000    0.250000000    
   Mg      0.000000000    0.750000000    0.750000000    
   Mg      0.000000000    0.250000000    0.750000000    
   Mg      0.500000000    0.750000000    0.750000000    
   Mg      0.500000000    0.250000000    0.750000000    
   Mg      0.000000000    0.750000000    0.250000000    
   Mg      0.750000000    0.500000000    0.250000000    
   Mg      0.750000000    0.000000000    0.250000000    
   Mg      0.250000000    0.500000000    0.750000000    
   Mg      0.250000000    0.000000000    0.750000000    
   Mg      0.750000000    0.500000000    0.750000000    
   Mg      0.750000000    0.000000000    0.750000000    
   Mg      0.250000000    0.500000000    0.250000000    
   Mg      0.750000000    0.750000000    0.000000000    
   Mg      0.750000000    0.250000000    0.000000000    
   Mg      0.250000000    0.750000000    0.500000000    
   Mg      0.250000000    0.250000000    0.500000000    
   Mg      0.750000000    0.750000000    0.500000000    
   Mg      0.750000000    0.250000000    0.500000000    
   Mg      0.250000000    0.750000000    0.000000000    
    O      0.250000000    0.250000000    0.250000000    
    O      0.250000000    0.000000000    0.000000000    
    O      0.000000000    0.250000000    0.000000000    
    O      0.000000000    0.000000000    0.250000000    
    O      0.750000000    0.750000000    0.250000000    
    O      0.750000000    0.250000000    0.250000000    
    O      0.250000000    0.750000000    0.750000000    
    O      0.250000000    0.250000000    0.750000000    
    O      0.750000000    0.750000000    0.750000000    
    O      0.750000000    0.250000000    0.750000000    
    O      0.250000000    0.750000000    0.250000000    
    O      0.750000000    0.500000000    0.000000000    
    O      0.750000000    0.000000000    0.000000000    
    O      0.250000000    0.500000000    0.500000000    
    O      0.250000000    0.000000000    0.500000000    
    O      0.750000000    0.500000000    0.500000000    
    O      0.750000000    0.000000000    0.500000000    
    O      0.250000000    0.500000000    0.000000000    
    O      0.500000000    0.750000000    0.000000000    
    O      0.500000000    0.250000000    0.000000000    
    O      0.000000000    0.750000000    0.500000000    
    O      0.000000000    0.250000000    0.500000000    
    O      0.500000000    0.750000000    0.500000000    
    O      0.500000000    0.250000000    0.500000000    
    O      0.000000000    0.750000000    0.000000000    
    O      0.500000000    0.500000000    0.250000000    
    O      0.500000000    0.000000000    0.250000000    
    O      0.000000000    0.500000000    0.750000000    
    O      0.000000000    0.000000000    0.750000000    
    O      0.500000000    0.500000000    0.750000000    
    O      0.500000000    0.000000000    0.750000000    
    O      0.000000000    0.500000000    0.250000000    
K_POINTS automatic
  2 2 2   1 1 1
------
nband default -> nbnd 320 case
input.pw (5m10s, 1.7 GB) -> (NSCF: nbnd 320, 9m25 s, 2.9 GB) -> prefix.xspectra.in ( 476.89 s, 1.5 GB)

□ space group
-----
input.pw.out
     48 Sym. Ops., with inversion, found
-----

□ number of electrons
-----
input.pw.out
number of electrons       =       257.00
-----

□ prefix.xspectra.in ( 1 core: 528 s, 4 core: 438.82 s , 1.2 GB)
-----
       &input_xspectra
       calculation='xanes_dipole',
       prefix='pwscf',
       xonly_plot=.false.,
       xniter=1000,
       xcheck_conv=50,
       xerror=0.001,

       x_save_file='prefix.xspectra.sav',

       ef_r=0.574496,

       xiabs=3,
       xepsilon(1)=1.0,
       xepsilon(2)=0.0,
       xepsilon(3)=0.0,
       /
       &plot
       xgamma=0.7,
       xnepoint=1000,
       xemin=-10.0,
       xemax=30.0,
       terminator=.true.,
       cut_occ_states=.true.,
       /
       &pseudos
       filecore='Mg.wfc',
       ! r_paw(1)=3.2,
       /
       &cut_occ
       cut_desmooth=0.1,
       cut_stepl=0.01,
       / 
       2 2 2 1 1 1
-----

□ gnuplot (XANES plot)
-----
gnuplot
plot '/home/username/espresso-5.1/PWscf_calc/MgO/xanes.dat' using ($1):($2) w l t "MgO PWscf xanes_dipole PAW(PSlibrary.0.3.1)"
set xrange[-10:30]
set yzeroaxis
set xlabel "Energy / eV"
set ylabel "Absorption / arb. unit"
replot
-----

--------------------------------------------------------------------------------
■ variables
  • calculation : 'xanes_dipole', Perform dipolar calculation. 'xanes_quadrupole', Perform quadrupolar calculation.
  • xonly_plot :(default .false.) .false. the continued fraction is calculated for each k-point and at the end written on the save file.
  • xniter : (default 2000) maximum number of iterations for lanczos.
  • xcheck_conv : (default 50) number of iterations between 2 convergence tests
  • xerror : (default 0.01) convergence threshold for lanczos calculation (eV)
  • xiabs : type of the absorbing atom, (ATOMIC_SPECIES in pwscf input)
  • xepsilon : (default 1.0 0.0 0.0) coordinates of the incident x-ray polarization vector
  • ef_r : Fermi energy in Rydberg. This value combined with the option cut_occupied_states can be used to exclude the occupied states in a smooth way from the final plot.
  • xgamma : (default 0.1) linewidth to be used in the spectrum (eV)
  • xnepoint : (default 1000) number of energy points in the plot of the XAS spectrum
  • xemin : (default 0.0) minimum energy in eV for the plot of the XAS spectrum
  • xemax : (default 10.0) maximum energy in eV for the plot of the XAS spectrum
  • terminator : (default .false.) .false. no terminator is used.
  • cut_occ_states : (default .false.) .false. the occupied states are visualized
  • filecore : core wavefunction file
  • r_paw(1) : (default 1.5*rc) paw radii to be used in paw reconstruction. A good choice to avoid linearly dependent projectors is 3*r_pseudo/2 or grater.
  • cut_desmooth : (default 0.01)  size of the interval near the fermi energy in which cross section is smoothed
  • cut_stepl : (default 0.01) integration initial step, lower side
--------------------------------------------------------------------------------

■ Carbon
-----------------------------
□ XANES:(下記にはCでの例を示す)
1)  case.ld1.in に下記を書き込む
(config で 1s1はCore-holeのため。2pは3sや3pを考慮するために1.5として少しイオンの状態にしている)
   ----------------------------------
       &INPUT
       iswitch = 3 ,
       zed = 6.0 ,
       config = '1s1 2s2 2p1.5 3s0 3p0' ,
       rel = 1 ,
       dft = 'PBE' ,
       /
       &InputP
       pseudotype = 2 ,
       file_pseudopw = 'C.pbe-cv1s-mt_gipaw.UPF' ,
       lloc = 1 ,
       tm = .true. ,
       lgipaw_reconstruction = .true. ,
       /
       2
       2S 2 0 2.000 0.000 1.50 1.50
       2P 2 1 1.500 0.000 1.50 1.50 
       &TEST
        /
       4
       2S 2 0 2.000 0.000 1.50 1.50
       3S 3 0 0.000 0.000 1.50 1.50
       2P 2 1 1.500 0.000 1.50 1.50 
       3P 3 1 0.000 0.000 1.50 1.50 
   ----------------------------------
   (iswitch = 3 は 擬ポテンシャルを生成するためのスイッチ)
   上記の file_pseudopw では利用に便利な名前を入力する。
   ./$HOME/espresso-4.2.1/bin/ld1.x <case.ld1.in> case.ld1.out
   上記のコマンドで擬ポテンシャルが作成される。
2) PWgui → Open → Open PW.X input
    Control
      Type of calculation (calculation): Self-Consistent-Field <scf>
    System をscfのときと同じように入力
     (コアホールを導入した場合にはスーパーセルにする。ecutwfcは通常より大きな値へ)
      Required variables
        Kinteic energy cutoff for ...... (ecutwfc): 40.0
      Optional variables
        Total system charge (tot_charge): 1.0
    Lattice & Atoms
      XANESを得たい原子に対して、作成した擬ポテンシャルを選択
      K-point をscfのときと同じように入力
4) Run
   上記で、XANESでの終状態の波動関数を得る
5) $HOME/espresso-4.2.1/bin/XSpectra/upf2plotcore.sh C.pbe-mt_gipaw.UPF > C.wfc
   この手順で始状態の波動関数を得る
6) prefix.xspectra.in を作成する
  ----------------------------------
       &input_xspectra
       calculation='xanes_dipole',
       prefix='pwscf',
       xonly_plot=.false.,
       xniter=1000,
       xcheck_conv=50,
       xerror=0.001,

       x_save_file='prefix.xspectra.sav',

       ef_r=${FERMI_LEVEL},

       xiabs=1,
       xepsilon(1)=1.0,
       xepsilon(2)=0.0,
       xepsilon(3)=0.0,
       /
       &plot
       xgamma=0.8,
       xnepoint=1000,
       xemin=-10.0,
       xemax=30.0,
       terminator=.true.,
       cut_occ_states=.true.,
       /
       &pseudos
       filecore='C.wfc',
       r_paw(1)=3.2,
       /
       &cut_occ
       cut_desmooth=0.1,
       cut_stepl=0.01,
       / 
       4 4 4 1 1 1
  ----------------------------------
最後の数値はK-pointである。SCF計算の時に入力したファイルを参考に値を入力すればよい。各入力データの意味は「X-ray absorption lecture note : 」を参照して下さい。時間があれば意味をここに書き加えます。
7) $HOME/espresso-4.2.1/bin/xspectra.x < prefix.xspectra.in > prefix.xspectra.out
8) xmgrace xanes.dat
--------------------------------------------------------------------------------
■ MgO (2x2x2) Retry




□ MgO (2x2x2) (SCF) (16m5s)
input.pw
------
 &CONTROL
                 calculation = 'scf' ,
                restart_mode = 'from_scratch' ,
                  pseudo_dir = '/home/vasp/espresso-5.1/PWscf_calc/MgO/' ,
 /
 &SYSTEM
                       ibrav = 1,
                   celldm(1) = 15.9484,
                         nat = 64,
                        ntyp = 3,
                     ecutwfc = 50 ,
                     ecutrho = 200 ,
                  tot_charge = 1.000000,
                 occupations = 'smearing' ,
                     degauss = 0.02 ,
                    smearing = 'gaussian' ,
                       nspin = 2 ,
   starting_magnetization(1) = 1,
   starting_magnetization(2) = 1,
   starting_magnetization(3) = 1,
           tot_magnetization = -1 ,
            exxdiv_treatment = 'gygi-baldereschi' ,
 /
 &ELECTRONS
                    conv_thr = 1.0d-8 ,
                 mixing_beta = 0.7 ,
 /
ATOMIC_SPECIES
   Mg   24.30500  Mg.pbe-n-kjpaw_psl.0.3.0.UPF
    O   15.99940  O.pbe-n-kjpaw_psl.0.1.UPF
  Mgc   24.30500  Mg.pbe-star1s-gipaw_kj.UPF
ATOMIC_POSITIONS crystal
  Mgc      0.000000000    0.000000000    0.000000000    
   Mg      0.000000000    0.250000000    0.250000000    
   Mg      0.250000000    0.000000000    0.250000000    
   Mg      0.250000000    0.250000000    0.000000000    
   Mg      0.500000000    0.500000000    0.000000000    
   Mg      0.500000000    0.000000000    0.000000000    
   Mg      0.000000000    0.500000000    0.500000000    
   Mg      0.000000000    0.000000000    0.500000000    
   Mg      0.500000000    0.500000000    0.500000000    
   Mg      0.500000000    0.000000000    0.500000000    
   Mg      0.000000000    0.500000000    0.000000000    
   Mg      0.500000000    0.750000000    0.250000000    
   Mg      0.500000000    0.250000000    0.250000000    
   Mg      0.000000000    0.750000000    0.750000000    
   Mg      0.000000000    0.250000000    0.750000000    
   Mg      0.500000000    0.750000000    0.750000000    
   Mg      0.500000000    0.250000000    0.750000000    
   Mg      0.000000000    0.750000000    0.250000000    
   Mg      0.750000000    0.500000000    0.250000000    
   Mg      0.750000000    0.000000000    0.250000000    
   Mg      0.250000000    0.500000000    0.750000000    
   Mg      0.250000000    0.000000000    0.750000000    
   Mg      0.750000000    0.500000000    0.750000000    
   Mg      0.750000000    0.000000000    0.750000000    
   Mg      0.250000000    0.500000000    0.250000000    
   Mg      0.750000000    0.750000000    0.000000000    
   Mg      0.750000000    0.250000000    0.000000000    
   Mg      0.250000000    0.750000000    0.500000000    
   Mg      0.250000000    0.250000000    0.500000000    
   Mg      0.750000000    0.750000000    0.500000000    
   Mg      0.750000000    0.250000000    0.500000000    
   Mg      0.250000000    0.750000000    0.000000000    
    O      0.250000000    0.250000000    0.250000000    
    O      0.250000000    0.000000000    0.000000000    
    O      0.000000000    0.250000000    0.000000000    
    O      0.000000000    0.000000000    0.250000000    
    O      0.750000000    0.750000000    0.250000000    
    O      0.750000000    0.250000000    0.250000000    
    O      0.250000000    0.750000000    0.750000000    
    O      0.250000000    0.250000000    0.750000000    
    O      0.750000000    0.750000000    0.750000000    
    O      0.750000000    0.250000000    0.750000000    
    O      0.250000000    0.750000000    0.250000000    
    O      0.750000000    0.500000000    0.000000000    
    O      0.750000000    0.000000000    0.000000000    
    O      0.250000000    0.500000000    0.500000000    
    O      0.250000000    0.000000000    0.500000000    
    O      0.750000000    0.500000000    0.500000000    
    O      0.750000000    0.000000000    0.500000000    
    O      0.250000000    0.500000000    0.000000000    
    O      0.500000000    0.750000000    0.000000000    
    O      0.500000000    0.250000000    0.000000000    
    O      0.000000000    0.750000000    0.500000000    
    O      0.000000000    0.250000000    0.500000000    
    O      0.500000000    0.750000000    0.500000000    
    O      0.500000000    0.250000000    0.500000000    
    O      0.000000000    0.750000000    0.000000000    
    O      0.500000000    0.500000000    0.250000000    
    O      0.500000000    0.000000000    0.250000000    
    O      0.000000000    0.500000000    0.750000000    
    O      0.000000000    0.000000000    0.750000000    
    O      0.500000000    0.500000000    0.750000000    
    O      0.500000000    0.000000000    0.750000000    
    O      0.000000000    0.500000000    0.250000000    
K_POINTS automatic
  3 3 3   1 1 1
------
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