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Energy","sub_category":"Bioenergy","monthly_downloads":50,"total_dependent_repos":0,"total_dependent_packages":0,"readme":"# \u003cins\u003eBi\u003c/ins\u003eo \u003cins\u003eR\u003c/ins\u003eeactor \u003cins\u003eD\u003c/ins\u003eesign (BiRD) [![bird-CI](https://github.com/NatLabRockies/BioReactorDesign/actions/workflows/ci.yml/badge.svg)](https://github.com/NatLabRockies/BioReactorDesign/actions/workflows/ci.yml) [![bird-pyversion](https://img.shields.io/pypi/pyversions/NLR-bird.svg)](https://pypi.org/project/NLR-bird/) [![coverage](https://codecov.io/gh/NatlabRockies/BioReactorDesign/graph/badge.svg)](https://app.codecov.io/gh/nrel/bioreactordesign)  [![bird-pypi](https://badge.fury.io/py/nlr-bird.svg)](https://badge.fury.io/py/nlr-bird)\n\n## Quick start\n1. Follow the steps to install the python package (see `Installation of python package for developers` or `Installation of python package for users` below)\n2. Follow the steps to install the BiRD OpenFOAM solver (see `Installation of BiRD OpenFOAM solver (for developers and users)` below)\n3. Check that you can run any of the tutorial cases, for ex:\n\n```bash\ncd tutorial_cases/bubble_column_20L\nbash run.sh\n``` \n\n## Installation of python package for developers (recommended)\n\n```bash\nconda create -c conda-forge --name bird python=3.14 paraview\nconda activate bird\ngit clone https://github.com/NatLabRockies/BioReactorDesign.git\ncd BioReactorDesign\npip install -e .\n```\n\n## Installation of python package for developers (with `pixi`)\nThis requires installing `pixi`. If it is not available on your machine, follow [Pixi Installation](https://pixi.prefix.dev/latest/installation).\nOnce installed, `pixi` does not require the `conda` environment creation and `pip install` gymnastics, and can be used as\n\n```bash\ngit clone https://github.com/NREL/BioReactorDesign.git\ncd BioReactorDesign\npixi shell\n```\nThis will activate an environment for you (equivalent to `pip install -e .`)\nAlternatively to the `pixi shell`, in any directory of BiRD, you can use `pixi run python myscript.py` instead of `python myscript.py`.\n\n\n## Installation of python package for users\n\n```bash\nconda create -c conda-forge --name bird python=3.14 paraview\nconda activate bird\npip install nlr-bird=={version}\n```\n\nWe highly recommend that you specify the version explicitly as the library is still rapidly changing.\n\n## Installation of BiRD OpenFOAM solver (for developers and users)\n\n1. Activate your OpenFOAM-9 environment (`source \u003cOpenFOAM-9 installation directory\u003e/etc/\u003cyour-shell\u003erc`)\n2. `cd OFsolvers/birdmultiphaseEulerFoam/`\n3. Compile `./Allwmake`\n\n## Documentation\n\nSee the [natlabrockies.github.io/BioReactorDesign](https://natlabrockies.github.io/BioReactorDesign).\n\n\n## References\n\nSoftware record [SWR 24-35](https://www.osti.gov/biblio/2319227)\n\nTo cite BiRD, please use these articles on [CO2 interphase mass transfer](https://doi.org/10.1016/j.cherd.2025.01.034) (open access [link](https://arxiv.org/pdf/2404.19636) ) on [aerobic bioreactors](https://doi.org/10.1016/j.cherd.2018.08.033) and on [butanediol synthesis](https://doi.org/10.1016/j.cherd.2023.07.031).\n\n```\n@article{hassanaly2025bayesian,\n  title={Bayesian calibration of bubble size dynamics applied to CO2 gas fermenters},\n  author={Hassanaly, Malik and Parra-Alvarez, John M and Rahimi, Mohammad J and Municchi, Federico and Sitaraman, Hariswaran},\n  journal={Chemical Engineering Research and Design},\n  volume={215},\n  pages={312--328},\n  year={2025},\n  publisher={Elsevier}\n}\n\n@article{rahimi2018computational,\n  title={Computational fluid dynamics study of full-scale aerobic bioreactors: Evaluation of gas--liquid mass transfer, oxygen uptake, and dynamic oxygen distribution},\n  author={Rahimi, Mohammad J and Sitaraman, Hariswaran and Humbird, David and Stickel, Jonathan J},\n  journal={Chemical Engineering Research and Design},\n  volume={139},\n  pages={283--295},\n  year={2018},\n  publisher={Elsevier}\n}\n\n@article{sitaraman2023reacting,\n  title={A reacting multiphase computational flow model for 2, 3-butanediol synthesis in industrial-scale bioreactors},\n  author={Sitaraman, Hariswaran and Lischeske, James and Lu, Yimin and Stickel, Jonathan},\n  journal={Chemical Engineering Research and Design},\n  volume={197},\n  pages={38--52},\n  year={2023},\n  publisher={Elsevier}\n}\n```\n\n## Acknowledgments\n\nThis 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](https://www.energy.gov/eere/co2rue). 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.\n\n\n\n","funding_links":[],"readme_doi_urls":["https://doi.org/10.1016/j.cherd.2025.01.034","https://doi.org/10.1016/j.cherd.2018.08.033","https://doi.org/10.1016/j.cherd.2023.07.031"],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":[],"project_url":"https://ost.ecosyste.ms/api/v1/projects/298236","html_url":"https://ost.ecosyste.ms/projects/298236"}