Benzene

In this example, how to visualize the wave functions is described by taking benzene as an example.

SCF calculation

A benzene molecule is placed in a cubic box with the cell edge of 15 Angstrom (28.3459032 Bohr). Cutoff energies of 36 Ry (GMAX=6) and 400 Ry (GMAXP=20) are used for the wave functions and the augmentation charge, respectively. Only the Gamma point was used for Brillouin zone sampling. pot.C_pbe6TM and pot.H_lda1 were used.

  • Input file (nfinp_scf)
         0     0     0     0     0     0 : i_ctrl(1:6) (dummy)
      6.00 20.00     2    12    12       : GMAX GMAXP NTYP NATM NATM2
        25     0                         : num_space_group type_bravis_lattice
      28.3459032  28.3459032  28.3459032 90.000 90.000 90.000 : a b c alpha beta gamma
         1     1     1     1     1     1 : K_mesh
         1     0                         : NCORD NINV
         -0.000000000000      2.647599670938      0.000002633351    1    1    1
         -2.292860266586      1.323707013877      0.000002742992    1    1    1
         -2.292860266586     -1.323707013877      0.000002742992    1    1    1
          0.000000000000     -2.647599670938      0.000002633351    1    1    1
          2.292860266586     -1.323707013877      0.000002742992    1    1    1
          2.292860266586      1.323707013877      0.000002742992    1    1    1
          0.000000000000      4.717073171214     -0.000006057411    1    1    2
         -4.085276621440      2.358661303430      0.000001383774    1    1    2
         -4.085276621440     -2.358661303430      0.000001383774    1    1    2
          0.000000000000     -4.717073171214     -0.000006057411    1    1    2
          4.085276621440     -2.358661303430      0.000001383774    1    1    2
          4.085276621440      2.358661303430      0.000001383774    1    1    2
      6.00  0.15 28.29     3     1  0.00 : type iatomn alfa amion iloc ivan zeta1
      1.00  0.15 28.29     3     1  0.00 : type iatomn alfa amion iloc ivan zeta1
         0     0     0     0     0       : icond inipos inivel ininos iniacc
         0     1                         : ipre ipri
       300   300     0    28000.00     0 : nmd1 nmd2 last_iter cpumax ifstop
         6     1                         : way_mix mimx_what
         0     8  0.80                   : iter_start KBXMIX  MIX_ALPHA
      0.60  0.50  0.60  0.70  1.00       : dtim1 dtim2 dtim3 dtim4 dtim
    500.00     4     1    0.10D-08       : dtio imdalg iexpl edelta
    0.0010    0.50D-03     0             : width forccr istress
    ggapbe           1                   : xctype kspin
         1.00                            : destm
       102                               : nbztyp
         4     4     4                   : (dummy)
         4     4     4                   : (dummy)
        18                               : keg
         1                               : nextst
         0                               : (dummy)
         2                               : imsd
         0                               : evaluate_eko_diff
         0                               : npdosao
         0  0.00                         : sm_n dopping

Wave function plot

Once converged charge density and wave functions are obtained, we are ready to calculate the wave functions in real space. We use FFT to transform the wave functions in reciprocal space to those in real space (this is why I name "wfnfft," where "wfn" stands for the wave function)

  • Input file (nfinp_wfnfft)
         0     0     0     0     0     0 : i_ctrl(1:6) (dummy)
      6.00 20.00     2    12    12       : GMAX GMAXP NTYP NATM NATM2
        25     0                         : num_space_group type_bravis_lattice
      28.3459032  28.3459032  28.3459032 90.000 90.000 90.000 : a b c alpha beta gamma
         1     1     1     1     1     1 : K_mesh
         1     0                         : NCORD NINV
         -0.000000000000      2.647599670938      0.000002633351    1    1    1
         -2.292860266586      1.323707013877      0.000002742992    1    1    1
         -2.292860266586     -1.323707013877      0.000002742992    1    1    1
          0.000000000000     -2.647599670938      0.000002633351    1    1    1
          2.292860266586     -1.323707013877      0.000002742992    1    1    1
          2.292860266586      1.323707013877      0.000002742992    1    1    1
          0.000000000000      4.717073171214     -0.000006057411    1    1    2
         -4.085276621440      2.358661303430      0.000001383774    1    1    2
         -4.085276621440     -2.358661303430      0.000001383774    1    1    2
          0.000000000000     -4.717073171214     -0.000006057411    1    1    2
          4.085276621440     -2.358661303430      0.000001383774    1    1    2
          4.085276621440      2.358661303430      0.000001383774    1    1    2
      6.00  0.15 28.29     3     1  0.00 : type iatomn alfa amion iloc ivan zeta1
      1.00  0.15 28.29     3     1  0.00 : type iatomn alfa amion iloc ivan zeta1
        15     0     0     0     0       : icond inipos inivel ininos iniacc
         0     1                         : ipre ipri
       300   300     0    28000.00     0 : nmd1 nmd2 last_iter cpumax ifstop
         6     1                         : way_mix mimx_what
         0     8  0.80                   : iter_start KBXMIX  MIX_ALPHA
      0.60  0.50  0.60  0.70  1.00       : dtim1 dtim2 dtim3 dtim4 dtim
    500.00     4     1    0.10D-08       : dtio imdalg iexpl edelta
    0.0010    0.50D-03     0             : width forccr istress
    ggapbe           1                   : xctype kspin
         1.00                            : destm
       102                               : nbztyp
         4     4     4                   : (dummy)
         4     4     4                   : (dummy)
        18                               : keg
         1                               : nextst
         0                               : (dummy)
         2                               : imsd
         0                               : evaluate_eko_diff
         0                               : npdosao
         0  0.00                         : sm_n dopping
    &PLOT
     IK      1
     IBAND_S 9
     IBAND_E 18
    &END
    Here to tell the wave functions to be plotted, we need to specify the k-point index (IK), starting band index (IBAND_S), and ending band index (IBAND_E) in the &PLOT block. By running this we obtain the following cube files for this example
    nfwfn_kpt0001_band0009.cube
    nfwfn_kpt0001_band0010.cube
    nfwfn_kpt0001_band0011.cube
    nfwfn_kpt0001_band0012.cube
    nfwfn_kpt0001_band0013.cube
    nfwfn_kpt0001_band0014.cube
    nfwfn_kpt0001_band0015.cube
    nfwfn_kpt0001_band0016.cube
    nfwfn_kpt0001_band0017.cube
    nfwfn_kpt0001_band0018.cube
    Note that the cube files generated by STATE are visualized by XCrySDen, but not by VESTA, possibly because the orgin of the volumeric data is shifted in STATE. Here let us use the utlitiy called mocube2moxsf (mocube2denxsf) to convert the cube file to XSF file. For example, to convert nfwfn_kpt0001_band0015.cube to the data in the XSF format, run the following (do NOT forget "-vesta" option"!)
    $ mocube2moxsf -vesta nfwfn_kpt0001_band0015.cube band0015
    and we get
    band0015_re.xsf
    band0015_im.xsf
    the former being the real part of the wave function, the latter, imaginary part. If you want to get the charge density corresponding to the specific state, type, for instance,
    $ mocube2dexsf -vesta nfwfn_kpt0001_band0015.cube band0015
    and get band0015.xsf. How to use mocube2moxsf and mocube2denxsf can be found by typing
    $ mocube2moxsf -h
トップ   編集 凍結 差分 バックアップ 添付 複製 名前変更 リロード   新規 一覧 単語検索 最終更新   ヘルプ   最終更新のRSS
Last-modified: 2019-11-28 (木) 21:52:47 (12d)