Inconsistencies in env_State files

[roughhawkbit]

An email from Gavin in Edinburgh:

Just a quick query regarding the env state files. There is a little scene setting before the question, so apologies.

So the conentration of solutes (glucose and oxygen)in each grid element is given.
Also the pressure in each grid element is given.
Then the growth rate is given. Now the elements of growth rate correspond to the species elements (biomass) i.e. for each grid element in which there is an agent there is a corresponding growth rate for that grid element.

Where I am getting confused is the meaning of the "total biomass" column. Here the grid elements do not correspond to those of the agents. That is to say, there are entries for total biomass in grid elements that contain no biomass.
Why is this ?

The grid elements of the "total biomass" do correspond to those elements of the pressure ?

Also all the uptake rates in the env_Sum files are zero. Is this correct ?

[roughhawkbit]

I've compared the MyHeterotroph and totalBiomass grids from the example protocol single_species_single_substrate_2D.xml. As this is a single species simulation, the two should be the same but they're not. As far as I can see, there are three kinds of inconsistency:

1. numbers being very similar, with differences of order ~10^(-12)
   • these are probably rounding errors caused by slightly different ways of calculation: low priority
2. chunks of grid in one but not the other
   • I think these are caused by the padding being put in different places: medium priority
3. numbers indicative of an agent being present in the totalBiomass grid, corresponding to zeros in the MyHeterotroph grid
   • the most worrying... could be a sign that the effect of detachment is only being applied to one of the grids: high priority