WOMBATmid - N cycle additions (#30)

* * Added NH4 tracer as an inert tracer
* Added sednh4 and sedo2 as extra diagnostics to the model

* * Added limitations by NH4 and NO3 to phytoplankton and diatom growth
* Added anammox to convert NH4 to NO3
* NH4 is now an activate BGC tracer with sources and sinks
NOTE: Still to correct Alkalinity effects to accommodate change in NH4 and NO3 sources and sinks

* * Corrected name of ammonia oxidation diagnostic from "anammox" to "ammox"

* * Bottom fluxes from sediment to NH4, not NO3 anymore
* Added virtual flux of NH4 due to salinity changes at surface
* do_conserve_tracers now points to NH4, not NO3
* Updated O2 stoichiometry to reflect the split of remin btw ammonification and nitrification
* Integrated changes in N cycle to alkalinity tracer (+ for NH4, - for NO3)

* * Added denitrification (NO3 loss) and anammox (NH4 loss) in low oxygen zones
* added logical flags for WOMBATmid: do_open_n_cycle, do_check_n_cycle, do_check_c_cycle

* * implicit routines for nitrogen fixation added (i.e., trichodesmium)

* * Altered the denitrification calculation to be dependent on f_det, not f_no3
* Altered the max growth rate parameters for anaerobic heterotrophs and anammox

* Update generic_tracers/generic_WOMBATmid.F90

Co-authored-by: Dougie Squire <[email protected]>

* Update generic_tracers/generic_WOMBATmid.F90

Co-authored-by: Dougie Squire <[email protected]>

* Update generic_tracers/generic_WOMBATmid.F90

Co-authored-by: Dougie Squire <[email protected]>

* Update generic_tracers/generic_WOMBATmid.F90

Co-authored-by: Dougie Squire <[email protected]>

* Update generic_tracers/generic_WOMBATmid.F90

Co-authored-by: Dougie Squire <[email protected]>

* Fix up merge of branch 'main'

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Co-authored-by: pearseb <[email protected]>
Co-authored-by: pearseb <[email protected]>
Co-authored-by: pearseb <[email protected]>
Co-authored-by: pearseb <[email protected]>
Co-authored-by: Dougie Squire <[email protected]>

Author: 6 people