## Attachment 'Wannier-Ptwire.py'

```   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('ptwire.nc'):
12     lat = 2.41
13     atoms = ListOfAtoms([
14           Atom('Pt', ([0*lat,2*lat,2*lat]),tag=0)],
15           cell=([lat,4*lat,4*lat]), periodic=True)
16
17     # Dacapo calculator:
18     calc = Dacapo(planewavecutoff=350, nbands=8,kpts=(15,1,1),xc='PBE',out='ptwire.nc')
19     atoms.SetCalculator(calc)
20
21     # Displace kpoints sligthly, so that the symmetry program in dacapo does
22     # not use inversion symmetry to reduce kpoints.
23     kpoints = calc.GetBZKPoints()
24     kpoints[:,0] += 2e-5
25     calc.SetBZKPoints(kpoints)
26
27 energy = atoms.GetPotentialEnergy()
28
29
30 # Wannier part
31 from ASE.Utilities.Wannier.Wannier import Wannier
32
34 calc = atoms.GetCalculator()
35
36 # Use 5 d-orbitals centered at the atom and 1 s-orbital centered at the Pt-Pt bond
37 # The radius of both types of orbitals is set to 0.4 Angstroms
38 initialwannier=[
39 [[0],2,0.4],
40 [[0.5,0.5,0.5],0,0.4]
41 ]
42
43 # Initialize the Wannier class
44 wannier = Wannier(numberofwannier=6,calculator=calc,occupationenergy=2.0,initialwannier=initialwannier)
45
46 # Perform the localization
47 wannier.Localize()
48
49 # Translate all the WFs to cell (1,0,0)
50 wannier.TranslateAllWannierFunctionsToCell([1,0,0])
51
52 # Band diagram
53 from ASE.Utilities.Wannier.HoppingParameters import HoppingParameters
54
56
57 # Get a band with 50 k-points
58 k,band=hop.GetBandDiagram(50,[0,0,0],[0.5,0,0])
59
60 # Plot the band using Gnuplot
61 import Gnuplot
62 plot=Gnuplot.Gnuplot()
63 plot('set data style lines')
64 plot.plot(Gnuplot.Data(k,band[0]),Gnuplot.Data(k,band[1]),Gnuplot.Data(k,band[2]),Gnuplot.Data(k,band[3]),Gnuplot.Data(k,band[4]),Gnuplot.Data(k,band[5]))
65
66 # Write the band diagram as a NetCDF file.
67 hop.WriteBandDiagramToNetCDFFile('ptband.nc',50,[0,0,0],[0.5,0,0])
68
69 # make a 3D isosurface plot using VTK
70 from ASE.Visualization.VTK import VTKPlotElectronicState,VTKPlotAtoms
71 state = wannier.GetElectronicState(0)
72
73 plot = VTKPlotElectronicState(state)
74 plot.SetRepresentationToIsoSurface2([0.1])
75 atomsplot = VTKPlotAtoms(atoms,parent=plot)
76 plot.Update()
77 atomsplot.RemoveAvatar(atomsplot.GetAvatars()[0])
78 plot.Render()
```

## Attached Files

To refer to attachments on a page, use attachment:filename, as shown below in the list of files. Do NOT use the URL of the [get] link, since this is subject to change and can break easily.
• [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]]
All files | Selected Files: delete move to page copy to page