fixed colonies appearing at final size in first frame of GFP movie by using X from XAll2, also put RIKOAll2 so GFP baseline in movie only appears where RIKO is present. appeared to find source of checkerboard in diffusion term of C when C is very small, discovered this when adding in zeroing of C elements which were less than calculated consumption divided by area, so diffusion could not work on very small values as nodes under colony go to zero. But need to find deeper explanation for this, also it seems that colonies don't grow at all because not enough total carbon. Although at least now all carbon seems to be being drained to zero, but need to check whether there might be a bug in zeroing code
made many many changes. First, fixed checkerboarding by doing first diffusion update on concentrations, then consumption. Otherwise, we may have that colony nodes go to zero on combined diffusion plus consumption, then just diffusion on next step, which gives some nutrients to colony, then go to zero again on diffusion and consumption. This creates oscillations between zero and nonnegative at colony center, which propagates into checkeerboard. Also, to prevent diffusion stretching concentrations to very low values, as colonies keep consuming, made any concentration that is less than smallest consumption term spread across entire plate to be zero. Need to check whether this creates any issues. In overflow cell, fixed issue where as cell initially divides, internal iron and nitrogen are divided, because really they are proportions so biomass will compensate division of absolute iron and nitrogen. Also removed Yi and Ni terms in dYi/dt and dNi/dt from Hilary paper, since they seem to be due to dilution. Need to think through this. Changed dx and dy back to 1, kdecayX to 0, may need to think about that last part. Gave channel-specific min and max for movies. Finally, increased muMax by factor of four for casamino acids versus glycerol, used 3*10^8 for OD of 1, conversion factor of 1/3.7 to Tcam, to get a cell equals 1/(1*10^11) OD, actually seems to give reasonable results. However, now X in dR/dt and dL/dt is very small compared to kdecay, need to fix that.