write('initial.traj', initial)
# Create final state
final = initial.copy()
final.positions[2:5] = initial.positions[[3, 4, 2]]
write('final.traj', final)
# Generate blank images
images = [initial]
nimage = 7
for i in range(nimage):
images.append(initial.copy())
images.append(final)
# Run IDPP interpolation
neb = NEB(images)
neb.interpolate()
calcs = NEBEspresso(neb, kpts='gamma', pw=300, dw=4000)
# Run NEB calculation
qn = QuasiNewton(neb, logfile='ethane_linear.log')
for j in range(nimage):
traj = Trajectory('neb%d.traj' % j, 'w', images[j + 1])
qn.attach(traj)
qn.run(fmax=0.05)
neb.write('%s-eval.xyz' % basename)
elif not opt.dry_run:
# Optimize:
if opt.optimizer == 'FIRE':
from ase.optimize.fire import FIRE
optimizer = FIRE(neb)
elif opt.optimizer == 'MDMin':
from ase.optimize import MDMin
optimizer = MDMin(neb)
else:
p.error('Unknown optimizer %s' % opt.optimizer)
if opt.write_traj is not None:
def write_traj():
global neb
n = 0
while os.path.exists('%s-band-%d.xyz' % (basename, n)):
n += 1
neb.write('%s-band-%d.xyz' % (basename, n))
optimizer.attach(write_traj, interval=opt.write_traj)
optimizer.run(fmax=opt.fmax)
if os.path.exists('%s-optimized.xyz' % basename):
os.unlink('%s-optimized.xyz' % basename)
neb.write('%s-optimized.xyz' % basename)
if opt.plot:
neb.plot(color=opt.plot_color, label=opt.plot_label)
t=traj): # store a reference to atoms in the definition.
"""Function to print the potential, kinetic and total energy."""
epot = a.get_potential_energy() / len(a)
ekin = a.get_kinetic_energy() / len(a)
stddev = hdt.evtokcal * a.calc.stddev
print('Step: %d Energy per atom: Epot = %.3feV Ekin = %.3feV (T=%3.0fK) '
'Etot = %.3feV'
' StdDev = %.3fKcal/mol/atom' %
(d.get_number_of_steps(), epot, ekin, ekin /
(1.5 * units.kB), epot + ekin, stddev))
# Attach the printer
dyn.attach(storeenergy, interval=250)
#dyn.attach(printenergy, interval=1)
# Run production
print('Running production...')
#start_time = time.time()
#for i in range(int(T)):
# print('Set temp:',i,'K')
# dyn.set_temperature(float(i) * units.kB)
# dyn.run(50)
mol.calc.nc_time = 0.0
dyn.set_temperature(T * units.kB)
start_time = time.time()
dyn.run(steps)
