mep 0.0.1

Minimal energy path tools for atomistic systems

Minimum Energy Path Tools

Introduction

This package contains various methods for finding the minimal energy path in atom simulations.

Currently the following methods are implemented:

Nudged elastic band method [1]

Climbing image nudged elastic band method [2]

How to use

Regular NEB

from mep.optimize import ScipyOptimizer
from mep.path import Path
from mep.neb import NEB
from mep.models import LEPS

leps = LEPS() # Test model 
op = ScipyOptimizer(leps) # local optimizer for finding local minima
x0 = op.minimize([1, 4], bounds=[[0, 4], [-2, 4]]).x # minima one
x1 = op.minimize([3, 1], bounds=[[0, 4], [-2, 4]]).x # minima two


path = Path.from_linear_end_points(x0, x1, 101, 1)  # set 101 images, and k=1
neb =NEB(leps, path) # initialize NEB
history = neb.run(verbose=True) # run

The results will be like the following

Similar results can be obtained using the LEPS model with harmonics LEPSHarm

CI-NEB

Every thing is the same except that

neb =NEB(leps, path, climbing=True, n_climbs=1) # set one image for climbing
history = neb.run(verbose=True, n_steps=10, n_climb_steps=100) # run normal NEB for 10 steps and then switch to CINEB

For comparison, normal NEB using LEPSHarm potential with 5 images gives the following

With CI-NEB

We can see that using only 5 images, the CINEB gets Ea = 3.63 eV, the same as the one we ran with 101 images! With only normal NEB, however, this Ea value is substantially smaller (3.25 eV).

References

[1] Henkelman, G., & Jónsson, H. (2000). Improved tangent estimate in the nudged elastic band method for finding minimum energy paths and saddle points. The Journal of chemical physics, 113(22), 9978-9985.

[2] Henkelman, G., Uberuaga, B. P., & Jónsson, H. (2000). A climbing image nudged elastic band method for finding saddle points and minimum energy paths. The Journal of chemical physics, 113(22), 9901-9904.