Getting started

Introduction

biofilmFoam is an open-source toolbox designed for the simulation of biofilm growth at the micro-scale, coupledwith surrounding hydrodynamics. Built on the OpenFOAM environment, it leverages numerous features such as pre- and post-processing tools and parallel computing efficiency.

The current version of biofilmFoam is based on Eberl’s deterministic biofilm growth model. However, the toolbox is flexible and can also accommodate more recent biofilm models.

Source code

As a reminder, the source code can be found here.

The source code is organized in a classical OpenFOAM structure:

  • The doc/ directory contains the sources for the documentation.

  • The libraries/ directory contains the specific source code for timestep management.

  • The solvers/ directory contains the specific solvers.

  • The tutorials/ directory contains test and validation cases.

  • The utilities/ directory contains specific post-processing tools.

  • The allwclean script cleans (or purges) the binary directories.

  • The allwmake script compiles all elements of the package.

  • The changelog file describes information about successive versions.

  • The license file describes the GPL-3.0 license.

  • The readme.rst file contains essential information about the toolbox.

How to cite

Guibert et al, Micro-continuum modeling of biofilm growth coupled with hydrodynamics in OpenFOAM, SoftwareX, 2025.