Attachment 'Wannier-Pt4.py'

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   1 #!/usr/bin/env python
   2 
   3 # Localized Wannier orbitals for a Pt wire
   4 
   5 from Dacapo import Dacapo
   6 from ASE import Atom,ListOfAtoms
   7 from ASE.Visualization.RasMol import RasMol
   8 import os
   9 
  10 # check if we have already calculated the nc file
  11 if not os.path.isfile('pt4.nc'):
  12     
  13     # Pt wire
  14     lat = 2.41
  15     atoms = ListOfAtoms([
  16                         Atom('Pt', ([0*lat,2*lat,2*lat]),tag=0),
  17                         Atom('Pt', ([1*lat,2*lat,2*lat]),tag=0),
  18                         Atom('Pt', ([2*lat,2*lat,2*lat]),tag=0),
  19                         Atom('Pt', ([3*lat,2*lat,2*lat]),tag=0)],
  20                         cell=([4*lat,4*lat,4*lat]), periodic=True)
  21 
  22 
  23     # Dacapo calculator:
  24     calc = Dacapo(planewavecutoff=350, nbands=30, xc='PBE',out='pt4.nc')
  25 
  26     atoms.SetCalculator(calc)
  27 
  28     plot = RasMol(atoms.Repeat((2,2,2)))
  29     tot = atoms.GetPotentialEnergy()
  30 
  31 # Wannier part
  32 from Dacapo import Dacapo
  33 from ASE.Utilities.Wannier.Wannier import Wannier
  34 import Numeric as num
  35 
  36 atoms = Dacapo.ReadAtoms('pt4.nc')
  37 calc = atoms.GetCalculator()
  38 
  39 #Initialize Wannier class
  40 wannier = Wannier(numberofwannier=4*(5+1),calculator=calc) 
  41 
  42 # Perform localization 
  43 wannier.Localize()
  44 
  45 # Print the WF centers
  46 centers = wannier.GetCenters()
  47 for center in centers:
  48     print center
  49 
  50 
  51 centers = wannier.GetCentersAsAtoms()
  52 
  53 # plot centers together with atoms
  54 try:
  55     # first try with VMD
  56     from ASE.Visualization.VMD import VMD
  57     VMD(atoms,centers)
  58 except:
  59     from ASE.Visualization.RasMol import RasMol
  60     centers.extend(atoms)
  61     rasmol = RasMol(centers)
  62     
  63 
  64 # make a 3D isosurface plot using VTK
  65 from ASE.Visualization.VTK import VTKPlotElectronicState,VTKPlotAtoms
  66 
  67 state = wannier.GetElectronicState(10)
  68 
  69 plot = VTKPlotElectronicState(state)
  70 plot.SetRepresentationToIsoSurface2([3.0])
  71 atomsplot = VTKPlotAtoms(atoms,parent=plot) 
  72 plot.Update()
  73 atomsplot.RemoveAvatar(atomsplot.GetAvatars()[0])
  74 plot.Render()

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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]]
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  • [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]]
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  • [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]]
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  • [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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