Malgorzata Peszynska

This page maintains a list of code capsules that are available. Code capsules are prototypes of code for simulations various phenomena, typically modeled with differential equations. They come with a description of algortihm and data, and sometimes with graphs of solutions, so the user knows what to expect as output. We also provide references to the particular publicaitons where we used this or similar code.
We do not claim that the code capsules are written to emphasize efficiency. In contrast, they are written to emphasize portability, clarity, and modularity of the code. Users for whom the efficiency is crucial should port the code to a more efficient platform.

Code capsules and software with documentation.

  1. Biot 1d implementation on github (MATLAB and python).
    Developers: Naren Vohra, Malgorzata Peszynska.
    Link to Biot 1d on github. (Documentation included, with examples).
    Link to Biot1d on github in python.

  2. Coupled Biofilm-Nutrient model (2d-3d), with heterogeneous Brinkman flow model.
    Developers: Choah Shin; (early version by Malgorzata Peszynska).
    Link to choashin/BIO2020 github. (README included).

  3. Implementation of 1d Stefan problem using semismooth Newton approach, P0-P0 finite elements and doubling of variables.
    Developers: Malgorzata Peszynska.
    Link to code capsule.
    Used in GMPS14, #51, #77.
    N. Gibson, P. Medina, M. Peszynska, R. Showalter, Evolution of phase transitions in methane hydrate, J. Math. Anal. Appl. Volume 409, Issue 2 (2014), pp 816-833, doi=10.1016/j.jmaa.2013.07.023.

  4. (Not a capsule! Some documentation included.)
    Link to HybGe-Flow3D github.
    Developers: Timothy Costa and Joseph Umhoefer.
    Used in CKP18, #69,
    T. Costa, K. Kennedy, M. Peszynska, Hybrid three-scale model for evolving pore-scale geometries, Computational Geosciences, (2018) Volume 22: p. 925-950. https://doi.org/10.1007/s10596-018-9733-9 2018

  5. (First capsule, fpor educational purposes; with M. Renne)
    Link to mpesz fd1d github.
    Developers: Malgorzata Peszynska. Code editor: Michael Renne.
    Used in courses, and as a start for most student projects

(Some of) "this material is based upon work supported by the National Science Foundation under Grant Numbers listed at projects." Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.