## Attachment 'N2Ru-Dissociation1.py'

```   1 from math import sqrt
2
3 from ASE import Atom, Slab
4 from ASE.Calculators.PairPotential import PairPotential
5 from ASE.Filters.Subset import Subset
6 from ASE.Dynamics.MDMin import MDMin
7 from ASE.IO.NetCDF import WriteNetCDF
8
9 # Find the initial and final states for the reaction.
10
11 # Set up a (3 x 3) two layer slab of Ru:
12 a = 2.70
13 c = 1.59 * a
14 bulk = Slab([Atom('Ru', (0, 0, 0), tag=1),
15              Atom('Ru', (1./3, 1./3, -0.5*c), tag=1)],
16             cell=(1, 1, 1))
17 bulk.SetUnitCell([(a,     0,              0),
18                   (a / 2, 3**0.5 * a / 2, 0),
19                   (0,     0,              1)])
20 slab = bulk.Repeat((4, 4, 1))
21
22 # Initial state.
24 x = a / 2
25 y = a * sqrt(3) / 6
26 z = 1.8
27 d = 1.10 # N2 bond length
28
29 # Molecular state parallel to the surface:
30 slab.extend([Atom('N', (x, y, z)),
31              Atom('N', (x + sqrt(3) * d / 2, y + d / 2, z))])
32
33 # Use a the PairPotential for the forces and energies:
34 slab.SetCalculator(PairPotential())
35
36 # We don't want to worry about the Ru degrees of freedom:
37 molecule = Subset(slab, indices=[-2, -1])
38
39 # Create a quickmin object, and relax the molecule until all force
40 # components are below 0.05 eV/Angstrom:
41 relax = MDMin(molecule, dt=0.08, fmax=0.05)
42 relax.Converge()
43 print 'initial state:', slab.GetPotentialEnergy()
44 WriteNetCDF(slab, 'N2.nc')
45
46 # Now the final state.
47 # Move the second N atom to a neighboring hollow site:
48 slab[-1].SetCartesianPosition((x + a, y, z))
49 relax.Converge()
50 print 'final state:  ', slab.GetPotentialEnergy()
51 WriteNetCDF(slab, '2N.nc')
```

## Attached Files

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• [get | view] (2005-11-17 10:40:35, 14.4 KB) [[attachment:2N.gif]]
• [get | view] (2005-11-17 10:38:37, 14.6 KB) [[attachment:N2.gif]]
• [get | view] (2005-11-17 10:37:12, 0.5 KB) [[attachment:N2.py]]
• [get | view] (2005-11-17 10:41:12, 1.5 KB) [[attachment:N2Ru-Dissociation1.py]]
• [get | view] (2006-09-27 15:11:52, 1.0 KB) [[attachment:N2Ru-Dissociation2-ANEB.py]]
• [get | view] (2005-11-17 10:41:40, 0.9 KB) [[attachment:N2Ru-Dissociation2.py]]
• [get | view] (2005-11-17 10:42:05, 1.0 KB) [[attachment:N2Ru-association.py]]
• [get | view] (2005-11-17 10:38:04, 1.1 KB) [[attachment:N2Ru-relax.py]]
• [get | view] (2005-11-17 10:37:43, 1.0 KB) [[attachment:N2Ru.py]]
• [get | view] (2006-09-05 08:56:57, 30.4 KB) [[attachment:aneb.jpeg]]
• [get | view] (2006-09-05 08:47:05, 23.2 KB) [[attachment:neb.jpeg]]
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