def test_autoneb(asap3):
EMT = asap3.EMT
fmax = 0.02
# Pt atom adsorbed in a hollow site:
slab = fcc211('Pt', size=(3, 2, 2), vacuum=4.0)
add_adsorbate(slab, 'Pt', 0.5, (-0.1, 2.7))
# Fix second and third layers:
slab.set_constraint(FixAtoms(range(6, 12)))
# Use EMT potential:
slab.calc = EMT()
# Initial state:
qn = QuasiNewton(slab, trajectory='neb000.traj')
qn.run(fmax=fmax)
# Final state:
slab[-1].x += slab.get_cell()[0, 0]
slab[-1].y += 2.8
qn = QuasiNewton(slab, trajectory='neb001.traj')
qn.run(fmax=fmax)
# Stops PermissionError on Win32 for access to
# the traj file that remains open.
del qn
def attach_calculators(images):
for i in range(len(images)):
images[i].calc = EMT()
autoneb = AutoNEB(attach_calculators,
prefix='neb',
optimizer='BFGS',
n_simul=3,
n_max=7,
fmax=fmax,
k=0.5,
parallel=False,
maxsteps=[50, 1000])
autoneb.run()
nebtools = NEBTools(autoneb.all_images)
assert abs(nebtools.get_barrier()[0] - 0.937) < 1e-3
# Final state:
slab[-1].x += slab.get_cell()[0, 0]
slab[-1].y += 2.8
qn = QuasiNewton(slab, trajectory='neb001.traj')
qn.run(fmax=0.05)
# Stops PermissionError on Win32 for access to
# the traj file that remains open.
del qn
def attach_calculators(images):
for i in range(len(images)):
images[i].set_calculator(EMT())
autoneb = AutoNEB(attach_calculators,
prefix='neb',
optimizer='BFGS',
n_simul=3,
n_max=7,
fmax=0.05,
k=0.5,
parallel=False,
maxsteps=[50, 1000])
autoneb.run()
nebtools = NEBTools(autoneb.all_images)
assert abs(nebtools.get_barrier()[0] - 0.938) < 1e-3
nim = len(images)
n = size // nim # number of cpu's per image
j = rank // n # image number
assert nim * n == size
for i in range(nim):
ranks = range(i * n, (i + 1) * n)
if rank in ranks:
calc = getcalc(txt='neb%d.txt' % j, communicator=ranks)
images[i].set_calculator(calc)
autoneb = AutoNEB(attach_calculators,
prefix='neb',
n_simul=2,
parallel=True,
climb=True,
n_max=5,
optimizer='FIRE',
fmax=0.05,
k=0.5,
maxsteps=[25, 1000])
autoneb.run()
nebtools = NEBtools(autoneb.all_images)
barrier, delta_e = nebtools.get_barrier()
print('barrier', barrier)
ref = 0.74051020956857272 # 1.484 <- with better parameters
err = abs(barrier - ref)
assert err < 1e-3, 'barrier={}, expected={}, err={}'.format(barrier, ref, err)
qn.run(fmax=0.05)
# Final state:
slab[-1].x += slab.get_cell()[0, 0]
slab[-1].y += 2.8
qn = QuasiNewton(slab, trajectory='neb001.traj')
qn.run(fmax=0.05)
# Stops PermissionError on Win32 for access to
# the traj file that remains open.
del qn
def attach_calculators(images):
for i in range(len(images)):
images[i].set_calculator(EMT())
autoneb = AutoNEB(attach_calculators,
prefix='neb',
n_simul=3,
n_max=7,
fmax=0.05,
k=0.5,
parallel=False,
maxsteps=[50, 1000])
autoneb.run()
nebtools = NEBTools(autoneb.all_images)
assert abs(nebtools.get_barrier()[0] - 0.938) < 1e-3