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TSQRA

Tensorized SqRA as described in [1]. Contains the application to an artifical 9-dimensional pentane (heavy atoms only after removing symmetries) on a regular grid of 10^9 cells. The original force-fields and code by L. Donati were used as a reference and are contained in the python directory.

Core functionality

  • eigen.jl:: Krylov eigensolver computing the TSQRA spectrum.
  • apply_a.jl: Different implementations for the application of the adjacency operator A
  • tensorops.jl: Application of Q, AE, .. and modal_sum!() for construction of the whole tensor from lower-order tensors
  • pentane.jl: Forcefields and computation of the two pentane subsystems, the whole system etc.
  • experiments.jl: Compute the sensivity analysis of the eigenvalues wrt. to interaction strength.

See also

The supplementary material to [1], found at https://github.com/zib-cmd/article-tsqra contains a KISS implementation, as well as the python notebooks to create the article's data.

References

[1] A. Sikorski, A. Niknejad, M. Weber, L. Donati. Tensor-SqRA: Modeling the Transition Rates of Interacting Molecular Systems in terms of Potential Energies. https://arxiv.org/abs/2311.09779. 2023