def test_ethene_rotation(tmpdir):
tmpdir.chdir()
# Optimise molecule
initial = molecule('C2H6')
smart_cell(initial, vac=4.0, h=0.01)
initial.set_calculator(iEspresso(pw=300, dw=4000, kpts='gamma'))
qn = QuasiNewton(initial, 'initial.traj')
qn.run(fmax=0.01)
# Create final state
final = initial.copy()
final.positions[2:5] = initial.positions[[3, 4, 2]]
final.set_calculator(iEspresso(pw=300, dw=4000, kpts='gamma'))
final.get_potential_energy()
# Generate blank images
images = [initial]
nimage = 7
for i in range(nimage):
image = initial.copy()
image.set_calculator(iEspresso(pw=300, dw=4000, kpts='gamma'))
images.append(image)
images.append(final)
# Run IDPP interpolation
neb = NEBEspresso(images)
neb.interpolate('idpp')
# Run NEB calculation
qn = QuasiNewton(neb, logfile='ethane_linear.log', trajectory='neb.traj')
qn.run(fmax=0.05)
nt = NEBTools(neb.images)
print('fmax: ', nt.get_fmax())
print('Ef, dE: ', nt.get_barrier())
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
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
import matplotlib.pyplot as plt
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.
fig = plt.figure(figsize=(5.5, 4.0))
ax = fig.add_axes((0.15, 0.15, 0.8, 0.75))
nebtools.plot_band(ax)
fig.savefig('diffusion-barrier.png')
PySCF_simple(atoms=image, method='MP2', basis='6-31g*'))
neb = NEB(images, climb=True, k=0.6)
nebTools = NEBTools(images)
neb.interpolate('idpp')
print(" -> start neb run")
opt = FIRE(neb)
opt.run(fmax=0.05)
print(nebTools.get_barrier())
# get IRC data
Ef, dE = nebTools.get_barrier()
max_force = nebTools.get_fmax()
x, y, x_fit, y_fit, forces = nebTools.get_fit()
# save IRC data
np.save("x_claisen_mp2.npy", x)
np.save("y_claisen_mp2.npy", y)
np.save("x_claisen_fit_mp2.npy", x_fit)
np.save("y_claisen_fit_mp2.npy", y_fit)
# write NEB guess of interpolation
for i, image in enumerate(images):
out_name = "claisen_{:03d}.xyz".format(i)
io.write(out_name, image)
# plot IRC
y2 *= 23.06
# 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())
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()