A collection of tools relating to transfer operators
This Python library implements a suite of tools used and/or developed in the Computational Molecular Design group of the Zuse Institute Berlin.
pip install cmdtools
(If you want to use the SLEPc library for sparse Schur decompositions install cmdtools with the extra slepc, i.e.
pip install "cmdtools[slepc]")
pcca: An implementation of (generalized) PCCA⁺ using the Schur decomposition
ajc: A sparse implementation of the augmented jump chain
diffusionmaps: Diffusionmaps with sparse support and out of sample extensions
galerkin: Trajectory based estimation of the transfer operator using a Galerkin projection onto Gaussian RBFs
gillespie: Trajectory simulation from a generator
newton_generator: Multi-step estimation of the generator via the Newton polynomial
picking_algorithm: Given a set of datapoints, pick n points such that they are distributed as evenly / equidistant as possible
sqra: The Square Root approximation, estimating the generator for the diffusion in a given potential
voronoi: Voronoi clustering of trajectories and estimation of the transfer operator with different metrics and center strategies.
diffusion: A collection of dynamical systems (So far the double- and triple-well)
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