1D validation case

The configuration presented in this tutorial is located in the folder tutorials/biofilmFoam/1d-A/ and corresponds to the first 1D validation test case from the original work by Eberl et al.

This 1D configuration focuses on biofilm growth from a surface. The domain consists of 64 cells, with the biomass inoculum deposited at one end and the nutrient supplied by pure diffusion at the other end.

For all the test cases supplied, we use the dimensions and parameter values specified in the original work. The mesh is described in this file system/blockMeshDict, and each cell is 1.6 microns

convertToMeters 1.6e-6;

Model parameters are entered in the constant/transportProperties file

d1    1.6e-09;

mmax  60;

c0    4e-03;

mum   1.5e-05;

Yxs   0.045;

ms    3e-05;

Ks    3.5e-05;

eps   1e-05;

a     4;

b     4;

To run this case, the procedure is as follows

cd tutorials/biofilmFoam/1d-A/
blockMesh
setFields
biofilmFoam
postProcess -func sample

All steps are also specified in the tutorials/biofilmFoam/1d-A/run script. The generated folders contain the resulting fields at the output time steps. The simulation can be visualized using ParaView:

paraview 1d-A.foam

In this particular case, the results are sampled so as to have data in a format comparable to the reference paier. The script tutorials/biofilmFoam/1d-plot.py, from sampled data in postProcessing, reproduces the figure illustrating the evolution of biofilm growth over time

ln -s ../1d-plot.py
python3 1d-plot.py

The obtained image, reported below, illustrates time trends in nutrient concentration C and biomass M.

The other 1D test cases of this type (1d-B, 1d-C and 1d-D) available in the toolbox, can be used to handle elementary behaviours, namely the biofilm growth under non-symmetric, the biofilm growth under symmetric conditions and the merging of two colonies.