Attachment 'N2Ru-Dissociation2-ANEB.py'

Download

   1 from math import sqrt
   2 
   3 import Numeric as num
   4 
   5 from ASE.Calculators.PairPotential import PairPotential
   6 from ASE.Filters.Subset import Subset
   7 from ASE.Dynamics.AdaptiveNudgedElasticBand import AdaptiveNudgedElasticBand
   8 from ASE.IO.NetCDF import ReadNetCDF
   9 import os
  10 
  11 # check that N2.nc and 2N.nc exists otherwise run
  12 # N2Ru-Dissociation1.py
  13 if not (os.path.exists('N2.nc') and os.path.exists('N2.nc')):
  14     os.system('python N2Ru-Dissociation1.py')
  15 
  16 initial = ReadNetCDF('N2.nc')
  17 final = ReadNetCDF('2N.nc')
  18 
  19 configs0 = [initial]
  20 for i in range(3):
  21     configs0.append(initial.Copy())
  22 configs0.append(final)
  23 
  24 configs = []
  25 for config in configs0:
  26     config.SetCalculator(PairPotential())
  27     configs.append(Subset(config, indices=[-2, -1]))
  28 
  29 
  30 # setup the Adaptive Nudged Elastic Band dynamics
  31 aneb = AdaptiveNudgedElasticBand(configs,prefix='aneb',linear_interpolation=True,maxlevels=1)
  32 
  33 aneb.Converge()
  34 
  35 # test the anebfit tool
  36 os.system('anebfit aneb')
  37 os.system('xmgrace aneb_-1.agr&')
  38 
  39 # clean up
  40 # os.system('rm aneb*conf*')

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] (2005-11-17 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]]
 All files | Selected Files: delete move to page copy to page

You are not allowed to attach a file to this page.