deeptime.markov.tools.flux.coarsegrain

deeptime.markov.tools.flux.coarsegrain(F, sets)

Coarse-grains the flux to the given sets. See [1] .

Parameters:

• F ((n, n) ndarray or scipy.sparse matrix) – Matrix of flux values between pairs of states.

• sets (list of array-like of ints) – The sets of states onto which the flux is coarse-grained.

Notes

The coarse grained flux is defined as

\[fc_{I,J} = \sum_{i \in I,j \in J} f_{i,j} \]

Note that if you coarse-grain a net flux, it does n ot necessarily have a net flux property anymore. If want to make sure you get a netflux, use to_netflux(coarsegrain(F,sets)).

References

[1]

F. Noe, Ch. Schuette, E. Vanden-Eijnden, L. Reich and T. Weikl: Constructing the Full Ensemble of Folding Pathways from Short Off-Equilibrium Simulations. Proc. Natl. Acad. Sci. USA, 106, 19011-19016 (2009)