[ase-users] Query about NEB

[Protik Das]

I used the procedure described in the example (
https://wiki.fysik.dtu.dk/ase/tutorials/neb/diffusion.html#diffusion-tutorial%29.)
for my calculation. For my case I used vasp as my calculator on 5 images.
But selecting Tools->NEB in ase-gui does not show any curve and the values
are all NaN. Also I tried the post processing script on the last 5 images.
That also shows an error. The way I coded the neb step is:

from ase.constraints import FixAtoms
from ase.calculators.vasp import Vasp
from ase.neb import NEB
from ase.optimize import BFGS
import ase.io.vasp as vp

initial = vp.read_vasp('start.vasp')
final = vp.read_vasp('end.vasp')

constraint = FixAtoms(mask=[atom.position[2] < z_thr for atom in initial])

calc1=Vasp(...)

fmax=0.05

images = [initial]
for i in range(3):
    image = initial.copy()
    image.set_calculator(calc1)
    image.set_constraint(constraint)
    images.append(image)

images.append(final)

neb = NEB(images)
neb.interpolate()
qn = BFGS(neb, trajectory='traj_neb.traj')
qn.run(fmax=fmax)

I tried post-processing with this code:

import matplotlib.pyplot as plt
from ase.neb import NEBTools
from ase.io import read

images = read('traj_neb.traj at -5:')
nebtools = NEBTools(images)

# Get the calculated barrier and the energy change of the reaction.
Ef, dE = nebtools.get_barrier()

And getting the following error:

---------------------------------------------------------------------------RuntimeError
                             Traceback (most recent call
last)<ipython-input-2-38055ba692ba> in <module>()      2       3 # Get
the calculated barrier and the energy change of the reaction.----> 4
Ef, dE = nebtools.get_barrier()      5       6 # # Get the barrier
without any interpolation between highest images.
C:\Users\Protik\Miniconda3\envs\ptk.pmg\lib\site-packages\ase\neb.py
in get_barrier(self, fit, raw)    536         without interpolation.
Set raw=True to get the raw energy of the    537         transition
state instead of the forward barrier."""--> 538         s, E, Sfit,
Efit, lines = self.get_fit()    539         dE = E[-1] - E[0]    540
      if fit:
C:\Users\Protik\Miniconda3\envs\ptk.pmg\lib\site-packages\ase\neb.py
in get_fit(self)    581         images = self._images    582         R
= [atoms.positions for atoms in images]--> 583         E =
[atoms.get_potential_energy() for atoms in images]    584         F =
[atoms.get_forces() for atoms in images]    585         A =
images[0].cell
C:\Users\Protik\Miniconda3\envs\ptk.pmg\lib\site-packages\ase\neb.py
in <listcomp>(.0)    581         images = self._images    582
R = [atoms.positions for atoms in images]--> 583         E =
[atoms.get_potential_energy() for atoms in images]    584         F =
[atoms.get_forces() for atoms in images]    585         A =
images[0].cell
C:\Users\Protik\Miniconda3\envs\ptk.pmg\lib\site-packages\ase\atoms.py
in get_potential_energy(self, force_consistent, apply_constraint)
675         """    676         if self._calc is None:--> 677
  raise RuntimeError('Atoms object has no calculator.')    678
if force_consistent:    679             energy =
self._calc.get_potential_energy(
RuntimeError: Atoms object has no calculator.

For your convenience I have attached the trajectory file. Any idea about
how I can fix this?
-- 
Protik Das,
ECE Graduate Student,
LATTE (http://latte.ece.ucr.edu),
University of California, Riverside.
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