env_State and env_Sum Files
The env_State files contain a description of the concentration grid (2D or 3D) for different simulation components that are represented on a grid, including: each solute, the current rate of each reaction, the total biomass in each grid element, and a measure of the total biomass in the system. Also included in the output files are the mean, standard deviation, and maximum thickness of the biofilm/liquid interface.
The units for each concentration are included in the unit attribute. The values within each solute mark-up describe the 1D array of K-values for each I and J index. In general, you do not have to work with these files directly because there are Matlab routines pre-made for reading these values in.
To load the solute grids into Matlab, you may follow the same procedure as for the agents, but instead use the following function:
s = loadSolute(nFile,true)
As before, the variable s is an array of structures, with the name, resolution, and data fields. A routine to display the solutes is also available:
displaySolute(s)
This routine will create plots displaying the concentration for each solute, the reaction rates, and the biomass amounts. If the grids represent 3D simulations, two 2D plots will be created, one averaging the y-direction, the other one averaging the z-direction. In addition, another plot displaying the profile along the x-direction is created.
The env_Sum files are similar to the env_State files, but contain information about the solute concentrations in the different bulk compartments:
For each bulk mark-up, there are solute and uptake_rate mark-ups describing the concentration and rate of change for each solute in that bulk.