nlr-bird 0.0.55

Bio Reactor Design (BiRD): a toolbox to simulate and analyze different designs of bioreactors in OpenFOAM

Bio Reactor Design (BiRD)

Quick start

1. Follow the steps to install the python package (see Installation of python package for developers or Installation of python package for users below)
2. Follow the steps to install the BiRD OpenFOAM solver (see Installation of BiRD OpenFOAM solver (for developers and users) below)
3. Check that you can run any of the tutorial cases, for ex:

cd tutorial_cases/bubble_column_20L
bash run.sh

Installation of python package for developers (recommended)

conda create -c conda-forge --name bird python=3.14 paraview
conda activate bird
git clone https://github.com/NatLabRockies/BioReactorDesign.git
cd BioReactorDesign
pip install -e .

Installation of python package for developers (with pixi)

This requires installing pixi. If it is not available on your machine, follow Pixi Installation. Once installed, pixi does not require the conda environment creation and pip install gymnastics, and can be used as

git clone https://github.com/NREL/BioReactorDesign.git
cd BioReactorDesign
pixi shell

This will activate an environment for you (equivalent to pip install -e .) Alternatively to the pixi shell, in any directory of BiRD, you can use pixi run python myscript.py instead of python myscript.py.

Installation of python package for users

conda create -c conda-forge --name bird python=3.14 paraview
conda activate bird
pip install nlr-bird=={version}

We highly recommend that you specify the version explicitly as the library is still rapidly changing.

Installation of BiRD OpenFOAM solver (for developers and users)

1. Activate your OpenFOAM-9 environment (source <OpenFOAM-9 installation directory>/etc/<your-shell>rc)
2. cd OFsolvers/birdmultiphaseEulerFoam/
3. Compile ./Allwmake

Documentation

See the natlabrockies.github.io/BioReactorDesign.

References

Software record SWR 24-35

To cite BiRD, please use these articles on CO2 interphase mass transfer (open access link ) on aerobic bioreactors and on butanediol synthesis.

@article{hassanaly2025bayesian,
  title={Bayesian calibration of bubble size dynamics applied to CO2 gas fermenters},
  author={Hassanaly, Malik and Parra-Alvarez, John M and Rahimi, Mohammad J and Municchi, Federico and Sitaraman, Hariswaran},
  journal={Chemical Engineering Research and Design},
  volume={215},
  pages={312--328},
  year={2025},
  publisher={Elsevier}
}

@article{rahimi2018computational,
  title={Computational fluid dynamics study of full-scale aerobic bioreactors: Evaluation of gas--liquid mass transfer, oxygen uptake, and dynamic oxygen distribution},
  author={Rahimi, Mohammad J and Sitaraman, Hariswaran and Humbird, David and Stickel, Jonathan J},
  journal={Chemical Engineering Research and Design},
  volume={139},
  pages={283--295},
  year={2018},
  publisher={Elsevier}
}

@article{sitaraman2023reacting,
  title={A reacting multiphase computational flow model for 2, 3-butanediol synthesis in industrial-scale bioreactors},
  author={Sitaraman, Hariswaran and Lischeske, James and Lu, Yimin and Stickel, Jonathan},
  journal={Chemical Engineering Research and Design},
  volume={197},
  pages={38--52},
  year={2023},
  publisher={Elsevier}
}

Acknowledgments

This work was authored in part by the National Laboratory of the Rockies (NLR) for the U.S. Department of Energy (DOE) under Contract No. DE-AC36-08GO28308. This work was supported by funding from DOE Bioenergy Technologies Office (BETO) CO2RUe consortium. The research was performed using computational resources sponsored by the Department of Energy's Office of Critical Minerals and Energy Innovation (CMEI) and located at the National Laboratory of the Rockies. The views expressed in the article do not necessarily represent the views of the DOE or the U.S. Government. The U.S. Government retains and the publisher, by accepting the article for publication, acknowledges that the U.S. Government retains a nonexclusive, paid-up, irrevocable, worldwide license to publish or reproduce the published form of this work, or allow others to do so, for U.S. Government purposes.