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A collection of tools relating to transfer operators

Project description

Binder Documentation Status


This Python library implements a suite of tools used and/or developed in the Computational Molecular Design group of the Zuse Institute Berlin.


Install with 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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