Minimal energy path tools for atomistic systems
Minimum Energy Path Tools
This package contains various methods for finding the minimal energy path in atom simulations.
Currently the following methods are implemented:
Nudged elastic band method 
Climbing image nudged elastic band method 
How to use
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
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
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 (
 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.
 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.
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