Attachment 'N2Ru-relax.py'

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   1 from ASE import Atom, Slab, Molecule
   2 from ASE.Calculators.PairPotential import PairPotential
   3 from ASE.Filters.Subset import Subset
   4 from ASE.Dynamics.MDMin import MDMin
   5 from ASE.Visualization.RasMol import RasMol
   6 
   7 
   8 a = 2.70
   9 c = 1.59 * a
  10 h = 1.85
  11 d = 1.10
  12 slab = Slab([Atom('Ru', (0, 0, 0)),
  13              Atom('Ru', (1/3., 1/3., -0.5*c), tag=1)])
  14 slab.SetUnitCell([(a, 0, 0),
  15                   (a / 2, 3**0.5 * a / 2, 0),
  16                   (0, 0, 1)])
  17 slab = slab.Repeat((4, 4, 1))
  18 slab.SetCalculator(PairPotential())
  19 subset = Subset(slab, mask=[a.GetTag() != 1 for a in slab])
  20 dyn = MDMin(subset, dt=0.08, fmax=0.05)
  21 dyn.Converge()
  22 e_slab = slab.GetPotentialEnergy()
  23 x = slab[0].GetCartesianPosition()[2] / (c / 2) * 100
  24 print 'Relaxation of the top layer: %f %%' % x
  25 
  26 molecule = Molecule([Atom('N', (0, 0, h)),
  27                      Atom('N', (0, 0, h + d))])
  28 molecule.SetCalculator(PairPotential())
  29 e_N2 = molecule.GetPotentialEnergy()
  30 
  31 slab.extend(molecule)
  32 
  33 subset = Subset(slab, mask=[a.GetTag() != 1 for a in slab])
  34 dyn = MDMin(subset, dt=0.08, fmax=0.05)
  35 dyn.Converge()
  36 
  37 print 'Adsorption energy:', e_slab + e_N2 - slab.GetPotentialEnergy()

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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