Utilities

biomass

This post-processing tool enables the evaluation of the proportion of volume occupied by the biofilm phase. It generates a biomass.dat file that includes times and the corresponding percentages of volume occupied by the biofilm. Once the calculations are finished, type:

biomass

inoculumGenerator

This utility allows you to inoculate a surface with biomass. It randomly selects NBCELLS cells with a minimum of one side in contact with the PATCH surface. The utility is used with the following command

inoculumGenerator -patch PATCH -nbcells NBCELLS

It generates the file system/topoSetDict and the native OpenFOAM topoSet function creates the inoculum cells set. The biomass value (0.8 by default in all tutorials) is set in the 0/M file by the native OpenFOAM function setFields, via the associated dictionary setFieldsDict. Its use is therefore tracked by orders

topoSet
setFields

The tool also has optional arguments that allow you to define a spatial window from which to draw cells at random. An example can be found in tutorials/biofilmFoam/3d-A. For further information, type

inoculumGenerator -help

permeability

As with the biomass utility, this post-processing tool enables to evaluate the permeability of the domain by volume averaging. The biomass present is taken into account as a porous medium, with the effective permeability given in the 0/K file. It generates a permeability.dat file that includes times and the evaluated permeability. Once the calculations are finished, type:

permeability