[ase-users] NEB calculations - parallelization over images

[Isabela Man]

Dear AlI,
*I am trying to run a NEB calculation, using the attached script:*
 nimages = 3
parallel = True
climbing = False

### read initial and final state

initial = io.read('Cu2O_110_CuO_termination_CH3CH2O_NH2C6H5_vdW_r5.traj')
interpolate = False
n = size //(nimages-2) # number of cpu's per image
j = 1 + rank//n
assert (nimages-2) * n == size
images = [initial]
constraint = FixAtoms(mask = [atom.tag ==117 for atom in initial])
for i in range(1,nimages-1):
filename = id +'_'+str(i)
try:
atoms = io.read(filename+'.traj.bak')
print "Updated from traj file ",filename+'.traj.bak'
except:
atoms = initial.copy()
interpolate = True

ranks = np.arange((i-1)*n, i*n)

if rank in ranks:
poissonsolver = PoissonSolver()
correction = DipoleCorrection(poissonsolver,2)
mixer=Mixer(0.05, 5, weight=100.0)
calc = GPAW(h=0.2,
xc='RPBE',
txt=outid,
kpts=(2,2,1),
#eigensolver='cg',
#width=0.10,
occupations = FermiDirac(0.1),
#verbose=True,
mixer=mixer,
nbands = -30,
spinpol = False,
usesymm = False,
poissonsolver = correction) #calc.attach(calc.write,1,gpwdat)
atoms.set_calculator(calc)
atoms.set_constraint(constraint)
view(atoms)
images += [atoms]


images += [final]
view(images)
neb = NEB(images,parallel=parallel,climb=climbing)





After the first minimization step I get the following errors:
1. First log file is when I use  one traj file for all images.
2. Second log file is when I write separately traj files for each image.
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