ASE Manual Release 3.6.1.2825 CAMd - CampOS Wiki

ASE Manual, Release 3.6.1.2828
Note: For this reaction, the reaction coordinate is very simple: The x-coordinate of the Au atom. In such cases,
the NEB method is overkill, and a simple constraint method should be used like in this tutorial: Diffusion of gold
atom on Al(100) surface (constraint).
See Also:
• neb
• constraints
• Diffusion of gold atom on Al(100) surface (constraint)
• fcc100()
Parallelizing over images
Instead of having one process do the calculations for all three internal images in turn, it will be faster to have three
processes do one image each. This can be done like this:
from ase.io import read
from ase.constraints import FixAtoms
from ase.calculators.emt import EMT
from ase.neb import NEB
from ase.optimize import BFGS
from ase.io.trajectory import PickleTrajectory
from ase.parallel import rank, size
initial = read(’initial.traj’)
final = read(’final.traj’)
constraint = FixAtoms(mask=[atom.tag > 1 for atom in initial])
images = [initial]
j = rank * 3 // size # my image number
for i in range(3):
image = initial.copy()
if i == j:
image.set_calculator(EMT())
image.set_constraint(constraint)
images.append(image)
images.append(final)
36 Chapter 6. Tutorials