n1 = 0
for image in self.images:
n2 = n1 + self.N
positions[n1:n2] = image.get_positions()
n1 = n2
return positions
if __name__ == '__main__':
fmax = 1E-4
calc = Hotbit(potential='neb_model_1')
first = Atoms(symbols='H', positions=[(3.0, -1.3, 0.0)]) #,(0,0,0)])
first.set_calculator(calc)
md.quench_atoms(first, fmax=fmax)
print('first minimum:', first.get_positions()[0])
last = Atoms('H', [(0.77, 1.31, 0.0)]) #,(0,0,0)])
last.set_calculator(calc)
md.quench_atoms(last, fmax=fmax)
print('last minimum:', last.get_positions()[0])
images = [first.copy() for x in range(10)]
images.append(last)
bti = BTI(images, calc)
bti.initial_interpolation()
qn = ase.MDMin(bti, dt=0.05)
writer = md.TrajectoryWriter(images, name='test')
qn.attach(writer)
qn.run(fmax=fmax)
if __name__=='__main__':
fmax=1E-4
calc=Hotbit(potential='neb_model_1')
first=Atoms(symbols='H',positions=[(3.0,-1.3,0.0)]) #,(0,0,0)])
first.set_calculator(calc)
md.quench_atoms(first,fmax=fmax)
print 'first minimum:',first.get_positions()[0]
last=Atoms('H',[(0.77,1.31,0.0)]) #,(0,0,0)])
last.set_calculator(calc)
md.quench_atoms(last,fmax=fmax)
print 'last minimum:',last.get_positions()[0]
images=[first.copy() for x in range(10)]
images.append(last)
bti=BTI(images,calc)
bti.initial_interpolation()
qn=ase.MDMin(bti,dt=0.05)
writer=md.TrajectoryWriter(images,name='test')
qn.attach(writer)
qn.run(fmax=fmax)
