[Wannier] understanding the wannier function of Si

Yongsheng Zhang yshzhang88 at yahoo.com
Sun Oct 13 16:17:15 CEST 2019 

Dear all, 

 
I am trying to learnthe wannier90 code using the well-known Si compound, which is an example fromthe tutorial. “num_bands = 12 and num_wann = 8” and “initial projections: Si :sp3”. Everything looks fine: no any error message is generated and WF bandstructures are good agreement with the DFT band structures. However, when I visualize thegenerated 8 WF (name. xsf), there are two points against my intuitions. 
1.     The WF at each Si does looks like the sp3 hybridizations.But why the WF at the two inequilibrium  Siatoms does not look similar in shape and size. I believe it’s due to the DFT calculationaccuracy. However, with increasing the k-mesh from (4x4x4) to (6x6x6), it doesnot improve too much. 
2.     In principle, the sp3 hybridized functions at two inequilibriumSi sites form the covalence bonds. It means that the hybridized functions withthe same sign from the two Si atoms should “mix” with each other and form thecovalence bonds. However, from the current WF, it seems that the sp3 hybridizedfunctions with the opposite signs from the two Si atoms sit on the bond (see attachment).It is really confused me.
Please help me understanding the WFs of Si.The followings are the si.nscf and si.win file. Many thanks.
 

Best

Yongsheng Zhang

 

Si.nscf

 

&control

   calculation     =  'nscf'

   restart_mode    =  'from_scratch'

   prefix          =  'si'

   pseudo_dir      =  'pseudo/'

   outdir          =  'out/'

/

&system

   ibrav           =   0

   nat             =   2

   ntyp            =   1

   ecutwfc         =  25.0

   ecutrho         = 200.0

   nbnd = 12

/

&electrons

   conv_thr        =   1.0d-12

   diagonalization =  'cg'

   diago_full_acc = .true. 

/

ATOMIC_SPECIES

Si 28.  Si.pbe-n-van.UPF

ATOMIC_POSITIONS crystal

Si -0.25   0.75   -0.25

Si  0.00   0.00    0.00

CELL_PARAMETERS bohr

-5.1   0.0    5.1

 0.0   5.1    5.1

-5.1   5.1    0.0

K_POINTS crystal

64

 0.00000000  0.00000000  0.00000000 1.562500e-02 

 0.00000000  0.00000000  0.25000000 1.562500e-02 

 0.00000000  0.00000000  0.50000000 1.562500e-02 

 0.00000000  0.00000000  0.75000000 1.562500e-02 

 0.00000000  0.25000000  0.00000000 1.562500e-02 

 0.00000000  0.25000000  0.25000000 1.562500e-02 

  0.00000000 0.25000000  0.50000000  1.562500e-02 

 0.00000000  0.25000000  0.75000000 1.562500e-02 

 0.00000000  0.50000000  0.00000000 1.562500e-02 

 0.00000000  0.50000000  0.25000000 1.562500e-02 

 0.00000000  0.50000000  0.50000000 1.562500e-02 

 0.00000000  0.50000000  0.75000000 1.562500e-02 

 0.00000000  0.75000000  0.00000000 1.562500e-02 

 0.00000000  0.75000000  0.25000000 1.562500e-02 

 0.00000000  0.75000000  0.50000000 1.562500e-02 

 0.00000000  0.75000000  0.75000000 1.562500e-02 

 0.25000000  0.00000000  0.00000000 1.562500e-02 

 0.25000000  0.00000000  0.25000000 1.562500e-02 

 0.25000000  0.00000000  0.50000000 1.562500e-02 

 0.25000000  0.00000000  0.75000000 1.562500e-02 

 0.25000000  0.25000000  0.00000000 1.562500e-02 

 0.25000000  0.25000000  0.25000000 1.562500e-02 

 0.25000000  0.25000000  0.50000000 1.562500e-02 

 0.25000000  0.25000000  0.75000000 1.562500e-02 

 0.25000000  0.50000000  0.00000000 1.562500e-02 

 0.25000000  0.50000000  0.25000000 1.562500e-02 

 0.25000000  0.50000000  0.50000000 1.562500e-02 

 0.25000000  0.50000000  0.75000000 1.562500e-02 

 0.25000000  0.75000000  0.00000000 1.562500e-02 

 0.25000000  0.75000000  0.25000000 1.562500e-02 

 0.25000000  0.75000000  0.50000000 1.562500e-02 

 0.25000000  0.75000000  0.75000000 1.562500e-02 

 0.50000000  0.00000000  0.00000000 1.562500e-02 

 0.50000000  0.00000000  0.25000000 1.562500e-02 

 0.50000000  0.00000000  0.50000000 1.562500e-02 

 0.50000000  0.00000000  0.75000000 1.562500e-02 

 0.50000000  0.25000000  0.00000000 1.562500e-02 

 0.50000000  0.25000000  0.25000000 1.562500e-02 

 0.50000000  0.25000000  0.50000000 1.562500e-02 

 0.50000000  0.25000000  0.75000000 1.562500e-02 

 0.50000000  0.50000000  0.00000000 1.562500e-02 

 0.50000000  0.50000000  0.25000000 1.562500e-02 

 0.50000000  0.50000000  0.50000000 1.562500e-02 

 0.50000000  0.50000000  0.75000000 1.562500e-02 

 0.50000000  0.75000000  0.00000000 1.562500e-02 

 0.50000000  0.75000000  0.25000000 1.562500e-02 

 0.50000000  0.75000000  0.50000000 1.562500e-02 

 0.50000000  0.75000000  0.75000000 1.562500e-02 

 0.75000000  0.00000000  0.00000000 1.562500e-02 

 0.75000000  0.00000000  0.25000000 1.562500e-02 

 0.75000000  0.00000000  0.50000000 1.562500e-02 

 0.75000000  0.00000000  0.75000000 1.562500e-02 

 0.75000000  0.25000000  0.00000000 1.562500e-02 

 0.75000000  0.25000000  0.25000000 1.562500e-02 

 0.75000000  0.25000000  0.50000000 1.562500e-02 

 0.75000000  0.25000000  0.75000000 1.562500e-02 

 0.75000000  0.50000000  0.00000000 1.562500e-02 

 0.75000000  0.50000000  0.25000000 1.562500e-02 

 0.75000000  0.50000000  0.50000000 1.562500e-02 

 0.75000000  0.50000000  0.75000000 1.562500e-02 

 0.75000000  0.75000000  0.00000000 1.562500e-02 

 0.75000000  0.75000000  0.25000000 1.562500e-02 

 0.75000000  0.75000000  0.50000000 1.562500e-02 

 0.75000000  0.75000000  0.75000000 1.562500e-02

 

Si.win:

 

use_ws_distance = .true.

 

num_bands        =  12

num_wann         =  8

num_iter         = 100

 

dis_num_iter      = 100

dis_froz_max = 6.5

dis_win_max = 17

 

iprint           =   2

num_dump_cycles  =   10

num_print_cycles =   10

 

!! To plot the WFs

! restart                =  plot

wannier_plot           = true

wannier_plot_supercell =  3

! wannier_plot_list      = 1,5

 

!! To plot the WF interpolatedbandstructure

bands_plot      = .true.

bands_num_points = 200

 

begin kpoint_path

L 0.50000 0.50000 0.5000 G 0.00000  0.000000.0000

G 0.00000 0.00000 0.0000 X 0.50000  0.000000.5000

X 0.50000 -0.50000 0.0000 K 0.37500-0.37500 0.0000

K 0.37500 -0.37500 0.0000 G 0.00000  0.00000 0.0000

end kpoint_path

 

begin projections

Si : sp3

end projections

 

mp_grid =  4 4 4

begin kpoints

 0.00000000  0.00000000  0.00000000 

 0.00000000  0.00000000  0.25000000 

 0.00000000  0.00000000  0.50000000 

 0.00000000  0.00000000  0.75000000 

 0.00000000  0.25000000  0.00000000 

 0.00000000  0.25000000  0.25000000 

 0.00000000  0.25000000  0.50000000 

 0.00000000  0.25000000  0.75000000 

 0.00000000  0.50000000  0.00000000 

 0.00000000  0.50000000  0.25000000 

 0.00000000  0.50000000  0.50000000 

 0.00000000  0.50000000  0.75000000 

 0.00000000  0.75000000  0.00000000 

 0.00000000  0.75000000  0.25000000 

 0.00000000  0.75000000  0.50000000 

 0.00000000  0.75000000  0.75000000 

 0.25000000  0.00000000  0.00000000 

 0.25000000  0.00000000  0.25000000 

 0.25000000  0.00000000  0.50000000 

 0.25000000  0.00000000  0.75000000 

 0.25000000  0.25000000  0.00000000 

 0.25000000  0.25000000  0.25000000 

 0.25000000  0.25000000  0.50000000 

 0.25000000  0.25000000  0.75000000 

 0.25000000  0.50000000  0.00000000 

 0.25000000  0.50000000  0.25000000 

 0.25000000  0.50000000  0.50000000 

 0.25000000  0.50000000  0.75000000 

 0.25000000  0.75000000  0.00000000 

 0.25000000  0.75000000  0.25000000 

 0.25000000  0.75000000  0.50000000 

 0.25000000  0.75000000  0.75000000 

 0.50000000  0.00000000  0.00000000 

 0.50000000  0.00000000  0.25000000 

 0.50000000  0.00000000  0.50000000 

 0.50000000  0.00000000  0.75000000 

 0.50000000  0.25000000  0.00000000 

 0.50000000  0.25000000  0.25000000 

 0.50000000  0.25000000  0.50000000 

 0.50000000  0.25000000  0.75000000 

 0.50000000  0.50000000  0.00000000 

 0.50000000  0.50000000  0.25000000 

 0.50000000  0.50000000  0.50000000 

 0.50000000  0.50000000  0.75000000 

 0.50000000  0.75000000  0.00000000 

 0.50000000  0.75000000  0.25000000 

 0.50000000  0.75000000  0.50000000 

 0.50000000  0.75000000  0.75000000 

 0.75000000  0.00000000  0.00000000 

 0.75000000  0.00000000  0.25000000 

 0.75000000  0.00000000  0.50000000 

 0.75000000  0.00000000  0.75000000 

 0.75000000  0.25000000  0.00000000 

 0.75000000  0.25000000  0.25000000 

 0.75000000  0.25000000  0.50000000 

 0.75000000  0.25000000  0.75000000 

 0.75000000  0.50000000  0.00000000 

 0.75000000  0.50000000  0.25000000 

 0.75000000  0.50000000  0.50000000 

 0.75000000  0.50000000  0.75000000 

 0.75000000  0.75000000  0.00000000 

 0.75000000  0.75000000  0.25000000 

 0.75000000  0.75000000  0.50000000 

 0.75000000  0.75000000  0.75000000

end kpoints

 

begin atoms_frac

Si -0.25 0.75  -0.25

Si 0.00  0.00   0.00

end atoms_frac

 

begin unit_cell_cart

 bohr

-5.10  0.00   5.10

 0.00   5.10  5.10

-5.10  5.10   0.00

end unit_cell_cart

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