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Hey Dougie! As I write the documentation, I am actually being forced to make certain updates to WOMBATmid (as I did for WOMBATlite). I'm expecting to make a few more commits to this branch therefore and perhaps we can therefore wait to merge with main until I come back and say it's ready. |
- Phytoplankton exude DOC with a NOSC of 0.0 - otehr processes, including cell lysis and hydrolysis of detritus give more negative values - bacterial consuming DOC shift the NOSC down towards more reducing compounds * Rewrote the N limitation section of bacterial growth to solve for Nlim analytically * Included an "in-code" computation of the bacterial C, O2, and anaerobic yields based on the relationship between NOSC and yield (Wang & Kuzyakov 2023 Global Change Biology)
* Added "regpp3d" as a new diagnostic for 3D regenerated primary production (NH4-based)
…in the code, rather than relying on input parameters * this means that the yields of bacteria on different substrates changes dynamically as DON:DOC and NOSC change * major update to bacterial N uptake partitioned between DON and NH4, with bacteria preferring DON to NH4 by 5-fold * results in actual limitation of bacterial growth by N sometimes, when DON:DOC is very low and when NH4 is low
… it vary between 0 and 1, rather than -1 and 0, since we are having issues initialising the field at -1
…% of the max yield on DON * Fixed the linear dependence of DON yield on NOSC
…ntation. More to come.
- renaming of some diagnostics (linear and quad mortality terms) - fix up of certain sections - removal of "sources and sinks" step, just calculations done within respective sections
…n some of the variable names causing problems
- checked that C, N and Si calculations conserve mass - reduced the depth of sediment over which organic carbon contributes to pore water DIC - checked source sink terms and updated them for ease of readability - added extra comments in the sinking routines - changed the N2O yield from ammonia oxidation to align with Kelly et al., 2024 - corrected the sediment bottom fluxes to align with having DOC and DON - bacterial use of DOC and DON now have separate kinetics
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Sinking and NOSC and bacterial yield calculations... Need to check what's already in main and what is not.