/usr/share/pyshared/ase/test/neb.py is in python-ase 3.6.0.2515-1.
This file is owned by root:root, with mode 0o644.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 | import threading
from ase.test import World
from ase.io import PickleTrajectory
from ase.neb import NEB
from ase.calculators.lj import LennardJones as Calculator
from ase.optimize import BFGS
fmax = 0.05
nimages = 3
print [a.get_potential_energy() for a in PickleTrajectory('H.traj')]
images = [PickleTrajectory('H.traj')[-1]]
for i in range(nimages):
images.append(images[0].copy())
images[-1].positions[6, 1] = 2 - images[0].positions[6, 1]
neb = NEB(images)
neb.interpolate()
for image in images[1:]:
image.set_calculator(Calculator())
dyn = BFGS(neb, trajectory='mep.traj')
dyn.run(fmax=fmax)
for a in neb.images:
print a.positions[-1], a.get_potential_energy()
results = [images[2].get_potential_energy()]
def run_neb_calculation(cpu):
images = [PickleTrajectory('H.traj')[-1]]
for i in range(nimages):
images.append(images[0].copy())
images[-1].positions[6, 1] = 2 - images[0].positions[6, 1]
neb = NEB(images, parallel=True, world=cpu)
neb.interpolate()
images[cpu.rank + 1].set_calculator(Calculator())
dyn = BFGS(neb)
dyn.run(fmax=fmax)
if cpu.rank == 1:
results.append(images[2].get_potential_energy())
w = World(nimages - 1)
ranks = [w.get_rank(r) for r in range(w.size)]
threads = [threading.Thread(target=run_neb_calculation, args=(rank,))
for rank in ranks]
for t in threads:
t.start()
for t in threads:
t.join()
print results
assert abs(results[0] - results[1]) < 1e-13
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