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cmdtools

Python implementation of severals tools (PCCA, AJC, SQRA, P/Q estimation) for the analysis of dynamical systems from the transfer operator perspective.

https://github.com/zib-cmd/cmdtools

Science Score: 54.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 3 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (11.4%) to scientific vocabulary

Keywords

ajc package pcca python sqra zib
Last synced: 6 months ago · JSON representation ·

Repository

Python implementation of severals tools (PCCA, AJC, SQRA, P/Q estimation) for the analysis of dynamical systems from the transfer operator perspective.

Basic Info
  • Host: GitHub
  • Owner: zib-cmd
  • Language: Python
  • Default Branch: dev
  • Homepage:
  • Size: 3.49 MB
Statistics
  • Stars: 5
  • Watchers: 1
  • Forks: 0
  • Open Issues: 1
  • Releases: 2
Topics
ajc package pcca python sqra zib
Created almost 6 years ago · Last pushed about 1 year ago
Metadata Files
Readme Changelog Citation

README.md

Binder Documentation DOI

cmdtools

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

Installation

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]")

Note: It seems that pip has problems installing SLEPc. However, using conda you can install it with conda install -c conda-forge petsc slepc petsc4py slepc4py.

Contents

  • 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)

If you use cmdtools in your research, please cite our work.

Owner

  • Name: zib-cmd
  • Login: zib-cmd
  • Kind: organization

Citation (CITATION.bib) 

@misc{cmdtools,
  author    = {Alexander Sikorski and
               Renata Sechi and
               Luzie Helfmann},
  title     = {cmdtools},
  year      = {2021},
  url       = {https://github.com/zib-cmd/cmdtools},
  doi       = {10.5281/zenodo.4749330}
}

GitHub Events

Total
  • Release event: 3
  • Watch event: 1
  • Delete event: 1
  • Push event: 3
  • Create event: 2
Last Year
  • Release event: 3
  • Watch event: 1
  • Delete event: 1
  • Push event: 3
  • Create event: 2

Issues and Pull Requests

Last synced: 8 months ago

All Time
  • Total issues: 1
  • Total pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Total issue authors: 1
  • Total pull request authors: 0
  • Average comments per issue: 0.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • axsk (1)
Pull Request Authors
Top Labels
Issue Labels
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Packages

  • Total packages: 1
  • Total downloads:
    • pypi 637 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 2
  • Total maintainers: 1
pypi.org: cmdtools

A collection of tools relating to transfer operators

  • Versions: 2
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 637 Last month
Rankings
Dependent packages count: 10.1%
Dependent repos count: 21.5%
Stargazers count: 23.1%
Average: 25.3%
Forks count: 29.8%
Downloads: 41.9%
Maintainers (1)
axsk
Last synced: 6 months ago

Dependencies

docs/requirements.txt pypi
  • Sphinx >=3.0
requirements.txt pypi
  • matplotlib *
setup.py pypi
  • numpy *
  • scikit-learn *
  • scipy *
.github/workflows/python-publish.yml actions
  • actions/checkout v4 composite
  • actions/download-artifact v4 composite
  • actions/setup-python v5 composite
  • actions/upload-artifact v4 composite
  • pypa/gh-action-pypi-publish release/v1 composite