## 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]]
• [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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