This repository contains the OpenFOAM configurations and other code for the publication:

Kira Kiviat, David E. Block, Harishankar Manikantan, Simulation of bioreactor flow environments for large-scale animal cell culture conditions relevant to cultivated meat production, Biochemical Engineering Journal, 2025, https://doi.org/10.1016/j.bej.2025.109753.

Prerequisites

These cases are configured for use with OpenFOAM 10. The case setup scripts rely on PyFoam and Salome (used Salome 9.10.0). A docker image kkiviat/openfoam with the necessary software can be obtained from dockerhub.

If you are not using the docker image this way, you can configure the root directory in default.parameters in each case to point to the root directory of this repository. You may also need to change the path to Salome in scripts/run_salome_script.py.

Setup

Clone this repo into the OpenFOAM run directory. The scripts expect the path to be under OpenFOAM/openfoam-10/run/of-bioreactors. If you change this, you will need to update the project_root in the case's default.parameters.

Compile the strainRate function object, located under functionObjects/strainRate. To do so, you need to be in the docker image or have OpenFOAM installed.

cd functionObjects/strainRate
wmake

To use the docker image, run a command like this. This mounts the OpenFOAM directory under /data in the container, sets the user id to the current id to ensure access to the files, and sets the working directory to /data. Here <path_to_OpenFOAM_dir> refers to the OpenFOAM directory that is the parent of openfoam-10/run/of-bioreactors.

docker container run -ti --shm-size=1024M --rm -u $(id -u):$(id -g) -v <path_to_OpenFOAM_dir>:/data:z -w /data kkiviat/openfoam:10 bash

Note: The cases in this repo were run with the image kkiviat/openfoam:10. Version 10.1 is the same except that it has ParaView 5.12.1 installed instead of the default 5.10.

Configuring cases

Each case has a derivedParameters.py file which constructs a geometry configuration. Currently they all call a method in scripts/geometry_builder.py to construct a geometry based only on the case volume. Those functions can be modified or new ones added to define different geometries.

The operating conditions are specified in the default.parameters file in each case directory, including superficial gas velocity (v_s), agitation rate (RPM), bubble size, drag model, and more.

Running cases

To set up dictionaries from the templates:

sh init_params.sh

To set up the mesh:

sh set_up_mesh.sh

To set up the case to run on n processors:

sh set_up_case.sh <n>

To run the case and save output in log.solver:

mpirun -n <n> multiphaseEulerFoam -parallel &>> log.solver &

Building Docker image

The dockerfiles under docker/ are based on https://github.com/jakobhaervig/openfoam-dockerfiles

You can download the image from dockerhub via

docker pull kkiviat/openfoam:10

But if you want to build it locally, use

docker image build --no-cache -t openfoam:10 docker/openfoam
docker image build -t openfoam:10 docker/python

To include ParaView 5.12.1, also run

docker image build -t openfoam:10 docker/paraview512