[ase-users] Running NEB in parallel

[Jens Jørgen Mortensen]

Den 14/11/2018 kl. 11.39 skrev Offermans Willem via ase-users:
> 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?


You need the latest ASE-3.17 for "trajectory='neb.traj'" to work.


Jens Jørgen


>
> 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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