bug report in BIO_fennel module

[tony1230]

I am running into a problem these days with LBCs in biological module. Without LBCs (dont use RadNud & Cla conditions) the case can run and the results seem okay. But when i switch the LBC to RadNud or Cla, something strange occurs. I have been strugling on this some days, but no solution.

For convenience and clear expression, i would like to show you with screenshots. Note, i dont define Carbon in my case, so there are 9 variables in total in biological modeling.Left panel in each screenshot is from file bio_Fennel.in in ROMS/External, and right panels are from output log files.

The tests seem so strange and i can not understand well and find a solution. So i take it as a bug for report.

- Shou

[arango]

Your first panel is completely illegal and a numerical absurdity; the western boundary is periodic and the eastern boundary closed for zooplankton and others. You better understand what periodicity is. Periodic boundary conditions works in pairs: west/east boundaries and south/north boundaries. ROMS corrected this by setting all boundary as periodic. Once you select periodic all the fields must be periodic.

You need to know what clamped means: the boundary condition values are always those specified.

You are incorrectly specifying the order of the biological variables in LBC(isTvar) when you change and commented stuff. You obviously do not know what you are doing. Use the compact specification for the biological tracers. If you don't know what that is check for information here in the forum. For example, you can study this posting.

[kate]

So, Hernan, you are saying that if it wants values for 9 bio tracers you'd better give it one line for all the same or nine lines with one each or else you have no idea what it will do? Giving it 11 lines for 9 tracers will give random results? Or 8 lines for 9 tracers will use the first line for all, is that it?

[arango]

Nope, what I am saying is that in a model like BIO_FENNEL with so many options for additional biological components, you need to know what the order of biological tracer is in idbio(:) and that's the order that you need follow in LBC(isTvar). If you don't know what that order is, you need to look at the code or specify the compact form. Then, you can check standard output for the order.

I never tested what would happen if you specify 11 values when you just need 9 values. I assume that it will pick the first 9 values but that needs to be checked in the debugger. If you only specify 5 values when you need 9, ROMS will persist the values for idbio(5) to indices 6, 7, 8, and 9.