grid_style chemostat command
Syntax
grid_style nufeb/chemostat nsubs subID-1 subID-2 subID-3 ... scale
nsubs = # of substrates
subID-i = ID of ith substrate
scale = scale factor between mesh grid and simulation box
Examples
grid_style nufeb/chemostat 4 nh4 o2 no2 no3 4e-6
grid_style nufeb/chemostat 2 sub o2 1e-5
Description
Define substrates and Cartesian mesh in simulation box for use by other Ib processes. The grid_style assumes the micro-scale simulation box is a part of full-scale chemostat.
Substrates are growth media that are required by microbes for their metabolism. They are modelled as continuous fields in NUFEB due to their potential solubility. nsubs defines number of substrates available in the system, and subID assigns an unique string name to each of them. The substrate names are used as references by other commands. For example, in order to use fix nufeb/growth/aob command, three substrates must be defined in the grid_style to represent ammonium, oxygen and nitrite.
A mesh is a set cubic grids in space that is replicated infinitely in all dimensions. The scale parameter defines grid length, which must be consistent with the dimension of orthogonal simulation box to ensure a 3D cubic structured mesh. This means, for example, scale = 1e-5 is compatible with a 2e-4 x 1e-4 x 1e-4 simulation box, which generates a 20 x 10 x 10 cubic structured mesh. On the other hand, the scale cannot apply to a 2.05e-4 x 1e-4 x 1e-4 box as it is inconsistent with the x-dimension.
Similar to atoms, each grid is associated with a set of attributes including: substrate concentration, substrate utilisation rate, microbial growth rate, biomass density and diffusion coefficient. The values of these attributes can be accessed and/or changed by other Ib processes. For example, fix nufeb/growth/aob updates microbial growth rate and substrate utilisation rate, fix nufeb/diffusion_reaction alters substrate concentrations, and fix nufeb/diffusion_coeff updates diffusion coefficient based on biomass density. The grid_style also defines the global attributes boundary condition and bulk concentration for solving diffusion process or coupling with full-scale chemostat (e.g, fix reactor/solute_balance). Their values are initialised in grid_modify command.