Find transition path on free energy surface by Nudged Elastic Band method

`neb` finds a transition path on free energy surface for a given pair of minima. For a 1D surface it simply takes the free energy profile between the two minima. For 2D surface it calculates the transition path by Nudged Elastic

neb(minims = minims, min1 = "A", min2 = "B", nbins = 20,
  nsteps = 100, step = 1, k = 0.2)

Arguments

minims

minima object.

min1

starting minimum identifier (can be letter or index, default "A").

min2

final minimum identifier (can be letter or index, default "B").

nbins

number of bins along Nudged Elastic Band (default 20).

nsteps

number of Nudged Elastic Band iterations (default 100).

step

Nudged Elastic Band iteration step (default 1).

k

Nudged Elastic Band toughness (default 0.2).

Value

NEB path

Examples

tfes<-fes(acealanme, imax=5000)
minima<-fesminima(tfes)
nebAD<-neb(minima, min1="A", min2="D", nsteps=20)
nebAD
#> path between minima:
#>   letter CV1bin CV2bin       CV1      CV2 free_energy
#> 1      A     79    235 -1.219677 2.624154   -58.22765
#>   letter CV1bin CV2bin       CV1       CV2 free_energy
#> 4      D    166    153 0.9239978 0.6036786   -54.17444