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()
if 0: # verify that initial images make sense
from ase.visualize import view
view(neb.images)
for image in images:
image.set_calculator(MorsePotential())
dyn = BFGS(neb, trajectory='mep.traj') # , logfile='mep.log')
dyn.run(fmax=fmax)
for a in neb.images:
print(a.positions[-1], a.get_potential_energy())
neb.climb = True
dyn.run(fmax=fmax)
# Check NEB tools.
nt_images = read('mep.traj@-4:')
nebtools = NEBtools(nt_images)
nt_fmax = nebtools.get_fmax(climb=True)
Ef, dE = nebtools.get_barrier()
print(Ef, dE, fmax, nt_fmax)
assert nt_fmax < fmax
assert abs(Ef - 1.389) < 0.001
from ase.neb import NEBtools
from ase.io import read
images = read('neb.traj@-5:')
nebtools = NEBtools(images)
# Get the calculated barrier and the energy change of the reaction.
Ef, dE = nebtools.get_barrier()
# Get the barrier without any interpolation between highest images.
Ef, dE = nebtools.get_barrier(fit=False)
# Get the actual maximum force at this point in the simulation.
max_force = nebtools.get_fmax()
# Create a figure like that coming from ase-gui.
fig = nebtools.plot_band()
fig.savefig('diffusion-barrier.png')
# Create a figure with custom parameters.
from matplotlib import pyplot, rcParams
rcParams.update({'font.size': 10})
fig = pyplot.figure(figsize=(4.5, 3))
ax = fig.add_axes((0.15, 0.15, 0.8, 0.75))
nebtools.plot_band(ax)
fig.savefig('diffusion-barrier.png')
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()
if 0: # verify that initial images make sense
from ase.visualize import view
view(neb.images)
for image in images:
image.set_calculator(MorsePotential())
dyn = BFGS(neb, trajectory='mep.traj') # , logfile='mep.log')
dyn.run(fmax=fmax)
for a in neb.images:
print(a.positions[-1], a.get_potential_energy())
neb.climb = True
dyn.run(fmax=fmax)
# Check NEB tools.
nt_images = read('mep.traj@-4:')
nebtools = NEBtools(nt_images)
nt_fmax = nebtools.get_fmax(climb=True)
Ef, dE = nebtools.get_barrier()
print(Ef, dE, fmax, nt_fmax)
assert nt_fmax < fmax
assert abs(Ef - 1.389) < 0.001
from ase.neb import NEBtools
from ase.io import read
images = read("neb.traj@-5:")
nebtools = NEBtools(images)
# Get the calculated barrier and the energy change of the reaction.
Ef, dE = nebtools.get_barrier()
# Get the barrier without any interpolation between highest images.
Ef, dE = nebtools.get_barrier(fit=False)
# Get the actual maximum force at this point in the simulation.
max_force = nebtools.get_fmax()
# Create a figure like that coming from ase-gui.
fig = nebtools.plot_band()
fig.savefig("diffusion-barrier.png")
# Create a figure with custom parameters.
from matplotlib import pyplot, rcParams
rcParams.update({"font.size": 10})
fig = pyplot.figure(figsize=(4.5, 3))
ax = fig.add_axes((0.15, 0.15, 0.8, 0.75))
nebtools.plot_band(ax)
fig.savefig("diffusion-barrier.png")
images[-1].get_potential_energy()
dyn = BFGS(neb, trajectory='mep.traj', logfile='mep.log')
dyn.run(fmax=fmax)
for a in neb.images:
print(a.positions[-1], a.get_potential_energy())
results = [images[2].get_potential_energy()]
# Check NEB tools.
nt_images = [read('mep.traj', index=_) for _ in range(-4, 0)]
nebtools = NEBtools(nt_images)
nt_fmax = nebtools.get_fmax()
Ef, dE = nebtools.get_barrier()
assert nt_fmax < fmax
def run_neb_calculation(cpu):
images = [Trajectory('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(MorsePotential())
dyn = BFGS(neb)
