1 #!/usr/bin/env python
   2 
   3 import Numeric
   4 from ASE import Atom, ListOfAtoms
   5 from Dacapo import Dacapo
   6 from ASE.Utilities.Wannier import Wannier,CompositeWannierCells
   7 
   8 # Read the atoms for the DFT calculation of the scattering region 
   9 #(1 principal layer on each side of S must be included) 
  10 atoms1 = Dacapo.ReadAtoms("out_scatter_kpt-0.375x-0.375.nc",save_memory=True)
  11 # Read the atoms for the DFT calculation of the lead
  12 atoms2 = Dacapo.ReadAtoms("out_lead.nc",save_memory=True)
  13 
  14 calc1 = atoms1.GetCalculator()
  15 calc2 = atoms2.GetCalculator()
  16 
  17 # Initialize a Wannier object for the Wannier functions in S
  18 wannier1 = Wannier(numberofwannier=432,calculator=calc1,occupationenergy=3.0)
  19 wannier1.ReadZIBlochMatrix('zibloch_scatter.pickle')
  20 wannier1.ReadRotation('Wannier_scatter')
  21 
  22 # Initialize a Wannier object for the Wannier functions in the lead
  23 wannier2 = Wannier(numberofwannier=18,calculator=calc2,occupationenergy=3.0)
  24 wannier2.ReadZIBlochMatrix('zibloch_lead.pickle')
  25 wannier2.ReadRotation('Wannier_lead')
  26 
  27 # Setup cells describing 1 principal layer and the scattering region
  28 cell1=CompositeWannierCells.WannierCell(wannier2,atoms2,repeat=[1,3,3])
  29 cell2=CompositeWannierCells.WannierCell(wannier1,atoms1,repeat=[1,1,1])
  30 cell3=CompositeWannierCells.WannierCell(wannier2,atoms2,repeat=[1,3,3])
  31 
  32 # Glue the three regions together and specify the k-point
  33 container=CompositeWannierCells.CompositeWannierCell([cell1,cell2,cell3],kpoint=[-0.375,-0.375],executable='/home/niflheim/lhansen/thul/dacapo/dacapo.run')
  34 # Construct the Hamiltonian
  35 container.WriteHSMatrixToNetCDFFile('HS.nc')
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