https://github.com/axsk/tsqra.jl
tensorized sqra
https://github.com/axsk/tsqra.jl
paper sqra tensor zib
Last synced: 10 months ago
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tensorized sqra
- Host: GitHub
- URL: https://github.com/axsk/tsqra.jl
- Owner: axsk
- Created: 2023-08-23T14:34:18.000Z (almost 3 years ago)
- Default Branch: main
- Last Pushed: 2024-01-16T16:35:57.000Z (over 2 years ago)
- Last Synced: 2025-03-01T12:44:04.422Z (over 1 year ago)
- Topics: paper, sqra, tensor, zib
- Language: Jupyter Notebook
- Homepage:
- Size: 341 KB
- Stars: 1
- Watchers: 2
- Forks: 0
- Open Issues: 1
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Metadata Files:
- Readme: README.md
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README
# 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