Attachment 'setupham.py'

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   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')
  36 
  37 
  38 
  39 
  40 
  41 
  42 
  43                                       

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  • [get | view] (2005-11-10 12:53:31, 1.7 KB) [[attachment:Al_equation_of_state.py]]
  • [get | view] (2006-02-07 13:26:56, 5.2 KB) [[attachment:Al_murn.png]]
  • [get | view] (2005-11-10 12:52:32, 0.6 KB) [[attachment:CO_in_a_box.py]]
  • [get | view] (2005-11-10 12:52:58, 0.6 KB) [[attachment:CO_relaxed_in_a_box.py]]
  • [get | view] (2006-02-09 10:15:54, 0.5 KB) [[attachment:CO_vibrations.py]]
  • [get | view] (2006-02-07 13:34:52, 41.6 KB) [[attachment:HCo.jpg]]
  • [get | view] (2006-02-09 09:11:07, 1.7 KB) [[attachment:H_Co_ontop.py]]
  • [get | view] (2006-02-09 10:23:21, 3.0 KB) [[attachment:STM.py]]
  • [get | view] (2006-02-09 10:25:18, 3.4 KB) [[attachment:Wannier-Fe-bcc.py]]
  • [get | view] (2006-02-09 10:24:12, 1.9 KB) [[attachment:Wannier-Pt4.py]]
  • [get | view] (2006-02-09 10:24:44, 2.3 KB) [[attachment:Wannier-Ptwire.py]]
  • [get | view] (2006-02-09 10:23:48, 2.0 KB) [[attachment:Wannier-ethylene.py]]
  • [get | view] (2006-02-09 12:14:10, 1.5 KB) [[attachment:bee.py]]
  • [get | view] (2006-02-09 12:15:01, 1.5 KB) [[attachment:bee2.py]]
  • [get | view] (2006-02-07 13:39:49, 8.6 KB) [[attachment:dipole.gif]]
  • [get | view] (2006-02-09 10:16:22, 2.5 KB) [[attachment:electrostatic.py]]
  • [get | view] (2006-02-09 09:19:06, 1.8 KB) [[attachment:filter.py]]
  • [get | view] (2006-02-07 13:38:35, 51.2 KB) [[attachment:final.jpg]]
  • [get | view] (2006-02-07 13:36:15, 474.9 KB) [[attachment:h2o-hessian.png]]
  • [get | view] (2006-02-07 13:37:47, 10.7 KB) [[attachment:harris.gif]]
  • [get | view] (2006-02-09 10:06:30, 2.6 KB) [[attachment:harris.py]]
  • [get | view] (2006-02-07 13:38:12, 49.2 KB) [[attachment:initial.jpg]]
  • [get | view] (2006-02-09 10:14:38, 3.4 KB) [[attachment:neb.py]]
  • [get | view] (2006-02-07 13:39:08, 130.0 KB) [[attachment:nebpath.gif]]
  • [get | view] (2006-02-07 13:36:37, 82.3 KB) [[attachment:plottrajectory.gif]]
  • [get | view] (2006-02-09 10:05:51, 1.8 KB) [[attachment:plotwavefunction.py]]
  • [get | view] (2006-02-09 10:15:10, 1.9 KB) [[attachment:restart-neb.py]]
  • [get | view] (2006-02-09 10:38:41, 1.6 KB) [[attachment:setupham.py]]
  • [get | view] (2006-02-07 13:40:51, 84.3 KB) [[attachment:stm.jpg]]
  • [get | view] (2006-02-09 10:38:07, 3.3 KB) [[attachment:transport_1dmodel.py]]
  • [get | view] (2006-02-07 13:37:23, 69.9 KB) [[attachment:vtk.gif]]
  • [get | view] (2006-07-07 07:01:50, 108.7 KB) [[attachment:workfunction.pdf]]
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