def run(args, parser):
# Nothing will ever be stored in args.output; need to manually find
# if its supplied by checking extensions.
if args.filenames[-1].endswith('.pdf'):
args.output = args.filenames.pop(-1)
else:
args.output = 'nebplots.pdf'
images = Images()
images.read(args.filenames)
nebtools = NEBTools(images=images)
nebtools.plot_bands(constant_x=args.constant_x,
constant_y=args.constant_y,
nimages=args.n_images,
label=args.output[:-4])
final.positions[2:5] = initial.positions[[3, 4, 2]]
# Generate blank images.
images = [initial]
for i in range(9):
images.append(initial.copy())
for image in images:
image.calc = EMT()
images.append(final)
neb = NEB(images, climb=True)
neb.interpolate(method='idpp') #idpp插值，设置初猜
# set calculator
for atoms in images:
atoms.calc = EMT()
atoms.get_potential_energy()
# Optimize:
py_fname = os.path.splitext(sys.argv[0])[0]
traj_fname = "{}.traj".format(py_fname)
log_fname = "{}.log".format(py_fname)
optimizer = FIRE(neb, trajectory=traj_fname, logfile=log_fname)
optimizer.run(fmax=0.04)
neb_result = list(iread(traj_fname))
for i in neb_result:
#print(i.get_potential_energy())
pass
neb_result = NEBTools(neb_result)
neb_result.plot_bands(True, True, label=py_fname)
print(neb_result.get_barrier(), neb_result.get_fmax())
images = [initial]
for index in range(nimages - 2):
images += [initial.copy()]
images[-1].set_calculator(calc())
images += [final]
neb = NEB(images)
neb.interpolate()
dyn = BFGS(neb, trajectory='mep.traj')
dyn.run(fmax=fmax)
# Check climbing image.
neb.climb = True
dyn.run(fmax=fmax)
# Check NEB tools.
nt_images = ase.io.read('mep.traj', index='-{:d}:'.format(nimages))
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
# Plot one band.
nebtools.plot_band()
# Plot many (ok, 2) bands.
nt_images = ase.io.read('mep.traj', index='-{:d}:'.format(2 * nimages))
nebtools = NEBTools(nt_images)
nebtools.plot_bands()
def test_neb(plt):
from ase import Atoms
from ase.constraints import FixAtoms
import ase.io
from ase.neb import NEB, NEBTools
from ase.calculators.morse import MorsePotential
from ase.optimize import BFGS, QuasiNewton
def calc():
# Common calculator for all images.
return MorsePotential()
# Create and relax initial and final states.
initial = Atoms('H7',
positions=[(0, 0, 0), (1, 0, 0), (0, 1, 0), (1, 1, 0),
(0, 2, 0), (1, 2, 0), (0.5, 0.5, 1)],
constraint=[FixAtoms(range(6))],
calculator=calc())
dyn = QuasiNewton(initial)
dyn.run(fmax=0.01)
final = initial.copy()
final.calc = calc()
final.positions[6, 1] = 2 - initial.positions[6, 1]
dyn = QuasiNewton(final)
dyn.run(fmax=0.01)
# Run NEB without climbing image.
fmax = 0.05
nimages = 4
images = [initial]
for index in range(nimages - 2):
images += [initial.copy()]
images[-1].calc = calc()
images += [final]
neb = NEB(images)
neb.interpolate()
with BFGS(neb, trajectory='mep.traj') as dyn:
dyn.run(fmax=fmax)
# Check climbing image.
neb.climb = True
dyn.run(fmax=fmax)
# Check NEB tools.
nt_images = ase.io.read('mep.traj', index='-{:d}:'.format(nimages))
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
# Plot one band.
nebtools.plot_band()
# Plot many (ok, 2) bands.
nt_images = ase.io.read('mep.traj', index='-{:d}:'.format(2 * nimages))
nebtools = NEBTools(nt_images)
nebtools.plot_bands()
