### Run an example (standard)

Source: https://natlabrockies.github.io/BioReactorDesign/quickstart.html

Run a tutorial case after installing the python package and OpenFOAM solver.

```bash
cd tutorial_cases/bubble_column_20L
bash run.sh

```

--------------------------------

### Run an example (pixi)

Source: https://natlabrockies.github.io/BioReactorDesign/quickstart.html

Run a tutorial case using pixi after installing the python package and OpenFOAM solver.

```bash
cd tutorial_cases/bubble_column_20L
bash run_pixi.sh

```

--------------------------------

### Installation for users

Source: https://natlabrockies.github.io/BioReactorDesign/quickstart.html

Steps to install the BioReactorDesign python package for users.

```bash
conda create -c conda-forge --name bird python=3.14 paraview
conda activate bird
pip install nlr-bird

```

--------------------------------

### Installation for developers (pixi)

Source: https://natlabrockies.github.io/BioReactorDesign/quickstart.html

Steps to install the BioReactorDesign python package for developers using pixi.

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

```

--------------------------------

### Installation of BiRD OpenFOAM solver (compile)

Source: https://natlabrockies.github.io/BioReactorDesign/quickstart.html

Compile the BiRD OpenFOAM solver.

```bash
cd OFsolvers/birdmultiphaseEulerFoam/
./Allwmake

```

--------------------------------

### Install dependencies

Source: https://natlabrockies.github.io/BioReactorDesign/calibration_normal_beta.html

Commands to activate the environment, set the BIRD_DIR, and install additional dependencies for calibration.

```bash
conda activate bird
BIRD_DIR = `python -c "import bird; print(bird.BIRD_DIR)"`
cd ${BIRD_DIR}/../
pip install .[calibration]

```

--------------------------------

### Installation for developers (conda)

Source: https://natlabrockies.github.io/BioReactorDesign/quickstart.html

Steps to install the BioReactorDesign python package for developers using conda.

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

```

--------------------------------

### Installation of BiRD OpenFOAM solver (activate environment)

Source: https://natlabrockies.github.io/BioReactorDesign/quickstart.html

Activate the OpenFOAM-9 environment.

```bash
source <OpenFOAM-9 installation directory>/etc/<your-shell>rc

```

--------------------------------

### Setup environment and case folder

Source: https://natlabrockies.github.io/BioReactorDesign/python_interface_tut.html

This snippet shows how to activate the 'bird' environment, set the BIRD_HOME path, and navigate to the case directory.

```bash
conda activate bird
BIRD_HOME=`python -c "import bird; print(bird.BIRD_DIR)"
DCM_CASE=${BIRD_HOME}/postprocess/data_conditional_mean/
cd $DCM_CASE

```

--------------------------------

### Boundary Patch Shapes

Source: https://natlabrockies.github.io/BioReactorDesign/meshing.html

Example JSON configuration for defining boundary conditions with circular inlets.

```json
{
    "inlets": [
        {"type": "circle", "centx": 5.0, "centy": 0.0, "centz": 0.5, "radius": 0.4, "normal_dir": 1,"nelements": 50},
        {"type": "circle", "centx": 2.5, "centy": 0.0, "centz": 0.5, "radius": 0.4, "normal_dir": 1,"nelements": 50},
        {"type": "circle", "centx": 7.5, "centy": 0.0, "centz": 0.5, "radius": 0.4, "normal_dir": 1,"nelements": 50}
    ],
}
```

--------------------------------

### Setup environment and case path

Source: https://natlabrockies.github.io/BioReactorDesign/bubbleColumn.html

Commands to activate the 'bird' conda environment and set the BIRD_HOME and BCE_CASE environment variables.

```bash
conda activate bird
BIRD_HOME=`python -c "import bird; print(bird.BIRD_DIR)"
BCE_CASE=${BIRD_HOME}/../tutorial_cases/bubble_column_20L
```

--------------------------------

### Run Unit Tests with Conda

Source: https://natlabrockies.github.io/BioReactorDesign/contribute.html

Steps to activate the 'bird' conda environment, install pytest, set the BIRD_HOME environment variable, and run unit tests.

```bash
conda activate bird
pip install pytest
BIRD_HOME=`python -c "import bird; print(bird.BIRD_DIR))"
cd ${BIRD_HOME}/../
pytest .

```

--------------------------------

### Coarsening Configuration Example

Source: https://natlabrockies.github.io/BioReactorDesign/bubbleColumn.html

Configuration snippet for defining radial and vertical coarsening ratios to adjust mesh density.

```json
"Meshing": {
 ...
        "verticalCoarsening":[
                               {"ratio": 0.5, "direction": "+", "directionRef": "-"},
                               {"ratio": 1.0, "direction": "+", "directionRef": "-"},
                               {"ratio": 1.0, "direction": "+", "directionRef": "-"}
                             ],
        "radialCoarsening":  [
                               {"ratio": 1.0, "direction": "+", "directionRef": "-"},
                               {"ratio": 1.0, "direction": "+", "directionRef": "-"}
                             ]


```

--------------------------------

### Meshing Configuration Example

Source: https://natlabrockies.github.io/BioReactorDesign/bubbleColumn.html

Configuration snippet for defining the base mesh resolution in radial and vertical directions.

```json
"Meshing": {
        "NRSmallest": 4,
        "NVertSmallest": 12,


```

--------------------------------

### Run Regression Tests

Source: https://natlabrockies.github.io/BioReactorDesign/contribute.html

Steps to run regression tests, including sourcing OpenFOAM environment variables, activating the 'bird' conda environment, installing pytest, setting BIRD_HOME, and executing the regression test script.

```bash
source <OpenFOAM-9 installation directory>/etc/<your-shell>rc
conda activate bird
pip install pytest
BIRD_HOME=`python -c "import bird; print(bird.BIRD_DIR))"
cd ${BIRD_HOME}/../tutorial_cases
bash run_all.sh

```

--------------------------------

### Unrecognized Drag and Mass Transfer Model Error

Source: https://natlabrockies.github.io/BioReactorDesign/troubleshoot.html

An example of a FATAL ERROR message indicating an unrecognized dragModelType, suggesting the use of the wrong OpenFOAM solver.

```text
[6] --> FOAM FATAL ERROR:
[6] Unknown dragModelType type Grace

```

--------------------------------

### Run the entire tutorial

Source: https://natlabrockies.github.io/BioReactorDesign/bubbleColumn.html

Commands to navigate to the case directory and execute the main run script.

```bash
cd ${BCE_CASE}
bash run.sh
```

--------------------------------

### Run the tutorial with pixi

Source: https://natlabrockies.github.io/BioReactorDesign/bubbleColumn.html

Commands to navigate to the case directory and execute the run script when using pixi.

```bash
cd ${BCE_CASE}
bash run_pixi.sh
```

--------------------------------

### Generate Target Data

Source: https://natlabrockies.github.io/BioReactorDesign/calibration_bsd.html

Generates the target data for the calibration tutorial.

```bash
cd make_dataset
bash gen_target.sh
cd ..

```

--------------------------------

### Generate Dataset

Source: https://natlabrockies.github.io/BioReactorDesign/calibration_bsd.html

Commands to navigate to the dataset generation directory and execute the dataset generation script. This creates a file 'data/dataset.npz' containing BSD of simulations.

```bash
cd make_dataset
bash gen_dataset.sh
cd ..
```

--------------------------------

### Run Unit Tests with Pixi

Source: https://natlabrockies.github.io/BioReactorDesign/contribute.html

Steps to enter a Pixi shell, set the BIRD_HOME environment variable, and run unit tests.

```bash
pixi shell
BIRD_HOME=`python -c "import bird; print(bird.BIRD_DIR))"
cd ${BIRD_HOME}/../
pixi run test

```

--------------------------------

### Train Neural Net Surrogate

Source: https://natlabrockies.github.io/BioReactorDesign/calibration_bsd.html

Command to train a neural network surrogate model. This process generates a loss history plot ('loss.png') and model weights ('Modeltmp').

```bash
bash train_surrogate.sh
```

--------------------------------

### Apply Initial Conditions

Source: https://natlabrockies.github.io/BioReactorDesign/bubbleColumn.html

Commands to copy the initial condition folder and run the `setFields` utility.

```bash
cd ${BCE_CASE}
cp -r 0.orig 0
setFields -dict system/setFieldsDict
```

--------------------------------

### Check Generated Dataset

Source: https://natlabrockies.github.io/BioReactorDesign/calibration_bsd.html

Commands to navigate to the data directory and run a Python script to check the generated dataset, visualizing Bf and Cr values and their relation to runaway conditions.

```bash
cd data
python check_real.py -ter
cd ..
```

--------------------------------

### Calibrate with a surrogate

Source: https://natlabrockies.github.io/BioReactorDesign/calibration_normal_beta.html

Calibrate with a surrogate for alpha=5, beta=5.

```python
python tut_calibration.py -useNN --alpha 5 --beta 5

```

--------------------------------

### Calibrate with a surrogate

Source: https://natlabrockies.github.io/BioReactorDesign/calibration_normal_beta.html

Calibrate with a surrogate for alpha=2, beta=5.

```python
python tut_calibration.py -useNN --alpha 2 --beta 5

```

--------------------------------

### Running the BiRD multiphase solver

Source: https://natlabrockies.github.io/BioReactorDesign/bubbleColumn.html

Command to execute the BiRD multiphase solver.

```bash
cd ${BCE_CASE}
birdmultiphaseEulerFoam
```

--------------------------------

### Bioreactor Simulation Computations

Source: https://natlabrockies.github.io/BioReactorDesign/python_interface_tut.html

Demonstrates the computation of superficial gas velocity, reactor-averaged CO2 mass fraction, concentration, kLa, and bubble diameter. It also shows how fields are stored and reused.

```python
sup_vel, field_dict = compute_superficial_gas_velocity(
    field_dict=field_dict, **kwargs
)
print("fields stored = ", list(field_dict.keys()))
print(f"Superficial velocity = {sup_vel:.4g} m/s")

# Compute reactor-averaged CO2 mass fraction
y_ave_co2, field_dict = compute_ave_y_liq(
    species_name="CO2", field_dict=field_dict, **kwargs
)
print("fields stored = ", list(field_dict.keys()))
print(f"Reactor averaged YCO2 = {y_ave_co2:.4g}")

# Compute reactor-averaged CO2 concentration
c_ave_co2, field_dict = compute_ave_conc_liq(
    species_name="CO2",
    field_dict=field_dict,
    **kwargs,
)
print("fields stored = ", list(field_dict.keys()))
print(f"Reactor averaged [CO2] = {c_ave_co2:.4g} mol/m3")

kla, cstar, field_dict = compute_instantaneous_kla(
    species_names=["CO2"],
    field_dict=field_dict,
    **kwargs,
)
print("fields stored = ", list(field_dict.keys()))
print(f"Reactor averaged kLa = {kla['CO2']:.4g} h-1")
print(f"Reactor averaged cstar_co2 = {cstar['CO2']:.4g} mol/m3")

# Compute reactor-averaged bubble diameter
diam, field_dict = compute_ave_bubble_diam(
    field_dict=field_dict, **kwargs
)
print("fields stored = ", list(field_dict.keys()))
print(f"Reactor averaged bubble diameter = {diam:.4g} m")
```

--------------------------------

### Calibrate against Binary Breakup and Coalescence Data

Source: https://natlabrockies.github.io/BioReactorDesign/calibration_bsd.html

Python command to calibrate the model against target data obtained with binary breakup and coalescence.

```python
python tut_calibration.py
```

--------------------------------

### Calibrate against Ternary Breakup and Coalescence Data

Source: https://natlabrockies.github.io/BioReactorDesign/calibration_bsd.html

Python command to calibrate the model against target data obtained with ternary breakup and coalescence.

```python
python tut_calibration.py -ter
```

--------------------------------

### Setting up the constant diameter bubble model

Source: https://natlabrockies.github.io/BioReactorDesign/bubbleColumn.html

Commands to copy the template for the constant diameter bubble model to the main phaseProperties file.

```bash
cd ${BCE_CASE}
cp constant/phaseProperties_constantd constant/phaseProperties
```

--------------------------------

### Generating a mesh object file with OpenFOAM utility

Source: https://natlabrockies.github.io/BioReactorDesign/python_interface.html

Command to generate a mesh object file using OpenFOAM's writeMeshObj utility.

```bash
writeMeshObj -case {case_folder}
```

--------------------------------

### Perform early prediction

Source: https://natlabrockies.github.io/BioReactorDesign/uq.html

This script performs early prediction using a specified data file.

```python
python applications/early_prediction.py -df bird/postprocess/data_early

```

--------------------------------

### Compute kLa with uncertainty estimates

Source: https://natlabrockies.github.io/BioReactorDesign/uq.html

This script computes kLa with uncertainty estimates using Bayesian calibration and data bootstrapping. It takes input data file, time index, concentration index, and Monte Carlo simulations as arguments.

```python
python applications/compute_kla_uq.py -i bird/postprocess/data_kla/volume_avg.dat -ti 0 -ci 1 -mc 10

```

```text
Chopping index = 0
Chopping index = 1
Chopping index = 2
Chopping index = 3
Chopping index = 4
Doing data bootstrapping
      scenario 0
      scenario 1
      scenario 2
      scenario 3
For bird/postprocess/data_kla/volume_avg.dat with time index: 0, concentration index: 1
     kla = 324 +/- 2.446 [h-1]
     cstar = 0.3107 +/- 0.0006522 [mol/m3]
Without data bootstrap
     kla = 324.5 +/- 2.075 [h-1]
     cstar = 0.3105 +/- 0.0005444 [mol/m3]

```

--------------------------------

### Enforce Formatting with Pixi

Source: https://natlabrockies.github.io/BioReactorDesign/contribute.html

Commands to enforce code formatting, import sorting, and spell checks using Pixi.

```bash
pixi shell
pixi run lint-write
pixi run spell-write

```

--------------------------------

### Calibrate without a surrogate

Source: https://natlabrockies.github.io/BioReactorDesign/calibration_normal_beta.html

Calibrate without a surrogate for alpha=5, beta=5.

```python
python tut_calibration.py --alpha 5 --beta 5

```

--------------------------------

### Calibrate without a surrogate

Source: https://natlabrockies.github.io/BioReactorDesign/calibration_normal_beta.html

Calibrate without a surrogate for alpha=2, beta=5.

```python
python tut_calibration.py --alpha 2 --beta 5

```

--------------------------------

### Reading cell centers

Source: https://natlabrockies.github.io/BioReactorDesign/python_interface_tut.html

This snippet demonstrates how to read cell center coordinates using the `bird.utilities.ofio` module.

```python
# Set case folder
from pathlib import Path
case_folder = os.path.join(
    Path(__file__).parent,
)

from bird.utilities.ofio import *
cell_centers = read_cell_centers(case_folder=case_folder)

```

--------------------------------

### Calibrate Likelihood Uncertainty (Binary)

Source: https://natlabrockies.github.io/BioReactorDesign/calibration_bsd.html

Python command to calibrate the likelihood uncertainty against target data obtained with binary breakup and coalescence, using the '-cal_err' flag.

```python
python tut_calibration.py -cal_err
```

--------------------------------

### Activate Debug Logs

Source: https://natlabrockies.github.io/BioReactorDesign/troubleshoot.html

This code snippet shows how to activate debug logging in BiRD by setting the logger level to DEBUG at the beginning of a script.

```python
from bird import logger
logger.setLevel(level="DEBUG")

```

--------------------------------

### Calibrate Likelihood Uncertainty (Ternary)

Source: https://natlabrockies.github.io/BioReactorDesign/calibration_bsd.html

Python command to calibrate the likelihood uncertainty against target data obtained with ternary breakup and coalescence, using the '-cal_err' flag.

```python
python tut_calibration.py -ter -cal_err
```

--------------------------------

### Reading fields

Source: https://natlabrockies.github.io/BioReactorDesign/python_interface_tut.html

This snippet shows how to read scalar and vector fields like 'CO2.gas', 'alpha.gas', and 'U.liquid' at a specific time step.

```python
co2_gas, _ = read_field(case_folder, "80", field_name="CO2.gas")
alpha_gas, _ = read_field(case_folder, "80", field_name="alpha.gas")
u_liq, _ = read_field(case_folder, "80", field_name="U.liquid")
print("cell CO2 gas shape = ", co2_gas.shape)
print("cell alpha gas shape = ", alpha_gas.shape)
print("cell u liq shape = ", u_liq.shape)

```

--------------------------------

### Calibrate without a surrogate

Source: https://natlabrockies.github.io/BioReactorDesign/calibration_normal_beta.html

Calibrate without a surrogate for alpha=2, beta=5, calibrating likelihood uncertainty.

```python
python tut_calibration.py --alpha 2 --beta 5 -cal_err

```

--------------------------------

### Enforce Formatting with Nox

Source: https://natlabrockies.github.io/BioReactorDesign/contribute.html

Commands to automatically enforce code formatting, import sorting, and spell checks using Nox.

```bash
pip install nox
nox -s lint -- write
nox -s spell -- write

```

--------------------------------

### Block rectangular meshing

Source: https://natlabrockies.github.io/BioReactorDesign/meshing.html

Generates system/blockMeshDict for a block rectangular mesh and then constructs the mesh using OpenFOAM utilities.

```bash
root=`pwd`
caseFolder=bird/meshing/block_rect_cases_templates/case
mesh_temp=bird/meshing/block_rect_mesh_templates/loopReactor

python applications/write_block_rect_mesh.py -i $mesh_temp/input.json -o $caseFolder/system

```

```bash
cd $caseFolder
blockMesh
cd $root

```

--------------------------------

### Compute mean statistics with uncertainty

Source: https://natlabrockies.github.io/BioReactorDesign/uq.html

This script computes mean statistics with uncertainty for a time-series signal. It demonstrates averaging a discretized time-series signal and estimating statistical error.

```python
python applications/compute_time_series_mean.py

```

```text
2025-09-02 12:36:15,016 [DEBUG] bird: Making the time series equally spaced over time
2025-09-02 12:36:15,016 [DEBUG] bird: Time series already equally spaced
2025-09-02 12:36:15,016 [DEBUG] bird: T0 = 1.270553916086648
2025-09-02 12:36:15,016 [INFO] bird: Mean = 0.01 +/- 0.081

```

```text
2025-09-02 12:36:15,016 [DEBUG] bird: Making the time series equally spaced over time
2025-09-02 12:36:15,016 [DEBUG] bird: Time series already equally spaced
2025-09-02 12:36:15,030 [DEBUG] bird: T0 = 126.6515206796017
2025-09-02 12:36:15,030 [INFO] bird: Mean = 0.0001 +/- 0.08

```

--------------------------------

### BiRD Software Citations

Source: https://natlabrockies.github.io/BioReactorDesign/references.html

BibTeX entries for citing the BiRD software and related research on CO2 interphase mass transfer and butanediol synthesis.

```bibtex
@article{hassanaly2025inverse,
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}
}

```

--------------------------------

### Compute Gas Holdup

Source: https://natlabrockies.github.io/BioReactorDesign/python_interface_tut.html

This snippet demonstrates computing the gas holdup using the `compute_gas_holdup` function and storing intermediate fields.

```python
from bird.postprocess.post_quantities import *

# Compute Gas hold up
kwargs = {"case_folder": case_folder, "time_folder": "80"}
gh, field_dict = compute_gas_holdup(
    field_dict={"cell_centers": cell_centers}, **kwargs
)
print("fields stored = ", list(field_dict.keys()))
print(f"Gas Holdup = {gh:.4g}")

```

--------------------------------

### parse_yaml Function

Source: https://natlabrockies.github.io/BioReactorDesign/bird.utilities.html

Parses a YAML file into a Python dictionary.

```python
bird.utilities.parser.parse_yaml(_file_path : str_) -> dict
    
    Parse a yaml file into a dictionary 

    Parameters:
        
        file_path (_str_) – path to yaml file 

    Returns:
        
        inpt – Dictionary that contains the yaml file content 

    Return type:
        
        dict
```

--------------------------------

### Reading cell volumes with OpenFOAM utility

Source: https://natlabrockies.github.io/BioReactorDesign/python_interface.html

Command to generate a cell volume field using OpenFOAM's postProcess utility.

```bash
postProcess -func writeCellVolumes -time {time_folder} -case {case_folder}
```

--------------------------------

### Block cylindrical meshing

Source: https://natlabrockies.github.io/BioReactorDesign/meshing.html

Generates system/blockMeshDict for a block cylindrical mesh and then constructs the mesh using OpenFOAM utilities.

```bash
root=`pwd`
caseFolder=bird/meshing/block_cyl_cases_templates/case
mesh_temp=bird/meshing/block_cyl_mesh_templates/sideSparger

python applications/write_block_cyl_mesh.py -i $mesh_temp/input.json -t $mesh_temp/topology.json -o $caseFolder/system

```

```bash
cd $caseFolder
blockMesh
transformPoints "scale=(0.001 0.001 0.001)"
transformPoints "rotate=((0 0 1) (0 1 0))"
cd $root

```

--------------------------------

### Initial Conditions Definition

Source: https://natlabrockies.github.io/BioReactorDesign/bubbleColumn.html

Configuration for the `setFields` utility in OpenFOAM to define initial volume fractions for gas and liquid.

```plaintext
defaultFieldValues
(
    volScalarFieldValue alpha.gas 0.99
    volScalarFieldValue alpha.liquid 0.01
);

regions
(
    boxToCell
    {
        box (-1.0 -1.0 -1.0) (10 7 10);
        fieldValues
        (
            volScalarFieldValue alpha.gas 0.01
            volScalarFieldValue alpha.liquid 0.99
        );
    }
);
```

--------------------------------

### Generate stirred tank reactor mesh

Source: https://natlabrockies.github.io/BioReactorDesign/meshing.html

Generates a blockMeshDict for a stirred tank reactor using a Python script and then meshes the domain using OpenFOAM utilities.

```bash
inp=bird/meshing/stirred_tank_mesh_templates/base_tank/tank_par.yaml
out=bird/meshing/stirred_tank_case_templates/base/system/blockMeshDict

python applications/write_stirred_tank_mesh.py -i $inp -o $out

```

```bash
blockMesh -dict system/blockMeshDict
stitchMesh -perfect -overwrite inside_to_hub inside_to_hub_copy
stitchMesh -perfect -overwrite hub_to_rotor hub_to_rotor_copy
transformPoints "rotate=((0 0 1)(0 1 0))"

```

--------------------------------

### plot_stl Function

Source: https://natlabrockies.github.io/BioReactorDesign/bird.utilities.html

Plots a 2D STL file using Matplotlib, useful for checking boundary conditions.

```python
bird.utilities.stl_plotting.plot_stl(_stl_file : str_) -> Axes
    
    Plot a 2D STL file with matplotlib This is useful to check boundary condition definition with STL 

    Parameters:
        
        stl_file (_str_) – Name of the STL file to display 

    Returns:
        
        axes – Axes of the plot created 

    Return type:
        
        matplotlib.axes.Axes
```

--------------------------------

### bissection function

Source: https://natlabrockies.github.io/BioReactorDesign/bird.utilities.html

Solves a 1D non-linear equation using the bisection method. Useful for adjusting mesh grading for smooth mesh size variation.

```python
bird.utilities.mathtools.bissection(_fun_val : float_, _nonlin_fun : Callable_, _num_iter : int = 1000_, _x_min : float = 1e-06_, _x_max : float = 1000000.0_) → float
```

--------------------------------

### Generate mesh and topology

Source: https://natlabrockies.github.io/BioReactorDesign/bubbleColumn.html

Python command to generate the blockMeshDict file based on mesh and topology configuration.

```bash
python ${BIRD_HOME}/../applications/write_block_cyl_mesh.py -i system/mesh.json -t system/topology.json -o system
```

--------------------------------

### Generate STL patch mesh

Source: https://natlabrockies.github.io/BioReactorDesign/meshing.html

Generates an STL patch mesh using a Python script, with an option to visualize the STL mesh.

```bash
python applications/write_stl_patch.py -v

```

--------------------------------

### Updating global variables

Source: https://natlabrockies.github.io/BioReactorDesign/bubbleColumn.html

Commands to update global variables, including calculating inlet area, volumes, and running a Python script to write the correct globalVars file.

```bash
cd ${BCE_CASE}
postProcess -func "patchIntegrate(patch=\"inlet\", field=\"alpha.gas\")"
postProcess -func writeCellVolumes
writeMeshObj
python writeGlobalVars.py
```

--------------------------------

### parse_json Function

Source: https://natlabrockies.github.io/BioReactorDesign/bird.utilities.html

Parses a JSON file into a Python dictionary.

```python
bird.utilities.parser.parse_json(_file_path : str_) -> dict
    
    Parse a json file into a dictionary 

    Parameters:
        
        file_path (_str_) – path to json file 

    Returns:
        
        inpt – Dictionary that contains the json file content 

    Return type:
        
        dict
```

--------------------------------

### BlockMesh Generation Command

Source: https://natlabrockies.github.io/BioReactorDesign/bubbleColumn.html

Command to generate the mesh using the blockMesh utility in OpenFOAM.

```bash
blockMesh -dict system/blockMeshDict

```

--------------------------------

### Mesh Post-treatment Scaling

Source: https://natlabrockies.github.io/BioReactorDesign/bubbleColumn.html

Command to scale the mesh points, likely to adjust the reactor volume.

```bash
transformPoints "scale=(0.19145161188225573 0.19145161188225573 0.19145161188225573)"
```

--------------------------------

### Surface to Patch Conversion

Source: https://natlabrockies.github.io/BioReactorDesign/bubbleColumn.html

OpenFOAM commands to convert the generated STL patch into a boundary patch in the mesh, including renaming and copying mesh files.

```bash
cd ${BCE_CASE}/
surfaceToPatch -tol 1e-3 inlets.stl
export newmeshdir=$(foamListTimes -latestTime)
rm -rf constant/polyMesh/
cp -r $newmeshdir/polyMesh ./constant
rm -rf $newmeshdir
cp ${BCE_CASE}/constant/polyMesh/boundary /tmp
sed -i -e 's/inlets.stl/inlet/g' /tmp/boundary
cat /tmp/boundary > constant/polyMesh/boundary
```

--------------------------------

### Scale Points Transformation

Source: https://natlabrockies.github.io/BioReactorDesign/bubbleColumn.html

Command to transform points to convert units from mm to m.

```bash
transformPoints "scale=(0.001 0.001 0.001)"

```