[ase-users] Running NEB in parallel

[Offermans Willem]

Dear ASE friends,

I like to run a NEB calculation in parallel.

I simply start with an example from the wiki:

https://wiki.fysik.dtu.dk/ase/tutorials/neb/diffusion.html#parallelizing-over-images-with-mpi

I have used mpi4py to support parallel calculation.

$cat neb.py:
<snip>
import mpi4py
from ase.io<http://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.parallel import rank, size, world
from ase.io<http://ase.io> import Trajectory

#initial = read('initial.traj')
#final = read('final.traj')

initial = Trajectory('initial.traj'.format(world.rank))[-1]
final = Trajectory('final.traj'.format(world.rank))[-1]

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)

neb = NEB(images, parallel=True)
neb.interpolate()
#qn = BFGS(neb, trajectory='neb.traj')
qn = BFGS(neb)
qn.run(fmax=0.05)
</snip>

mpirun -np 3 python neb.py

The job runs, if ``trajectory=‘neb.traj’``, is omitted. However, no output, except standard out, is obtained in this case.

How can I get output?

What am I doing wrong?


Met vriendelijke groeten,
Mit freundlichen Grüßen,


Willem Offermans
Researcher Electrocatalysis SCT
VITO NV | Boeretang 200 | 2400 Mol
Phone:+32(0)14335263 Mobile:+32(0)492182073

Willem.Offermans at Vito.be<mailto:Willem.Offermans at Vito.be>

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