Major WOMBAT-llite additions - variable sinking, CaCO3 dynamics, burial, updates to ecosystem model (#15)

* Added:
* Variable remineralisation rate (reminr) that increases as phytoplankton biomass increases and decreases with depth (emulating variable sinking rate of detritus)
* Fixed a bug in the calculation of the minimum Fe quota of phytoplankton that reduced their dFe limitation
* Added new diagnostics, particularly for terms contributing to the calculation of nutrient limitations

* Added:

* Zooplankton grazing of detritus, now we have additional diagnostics
* Bug fix of zooplankton excretion on Fe having the Fe2C quota of Zoo, not Phy

* Added:

* spatially variable sinking of detritus via "move_vertical" option
* hence, removed the spatially complex variations in remineralisation rates
* moved DIC and aDIC source/sink calculations into the nested timestep

* Trying to determine why Fe-limitation spreads too much across ocean. My changes are:

* new light diagnostics and chlorophyll light limitation diagnostic
* made zooplankton epsilon (prey capture coefficient) variable from zooepsmin to zooepsmax
* slowed dFe uptake by phytoplankton to min of 20% under darkness and nitrogen limitation
* made remineralisation of detritus quadratic rather than linear to allow more detrital aggregation in gyres

* Figured out why dFe was becoming so limiting:

* Missed the retuning of dFe back to a minimum concentration at every timestep. This happens under "Additional operations on dissolved iron"

Also took the opportunity to:

* Add N and C conservation of mass checks
* remove some unnecessary print statements
* reduce dFe scavenging rates
* Apply limitations to dFe uptake at night and when N is limiting
* increase zooplankton quadratic mortality but halve their linear mortality
* also reduced phytoplankton linear and quadratic mortality

* * Syntax corrections and removal of unnecessary code snippets
* Adjustment of zooepsmin and zooepsmax values from 0.025 - 0.5 to 0.01 - 0.1

* * minimum values of DIC and ALK within CO2 sys calculations
* Explicit ALK source and sink terms within nested timestep
* Variable epsilon of zooplankton with phy biomass and temp dependencies

* Problems with DIC air-sea flux solved: fix was to ensure upper and lower bounds on the DIC concentration that feeds into the omip2_co2calc subroutine. Setting upper and lower limits of the DIC that is fed into the subroutine does not preclude DIC concentrations from going higher or lower than those limits, but only ensures that the air-sea fluxes are reasonable.

* Updated some Fe cycling parameters to increase the loss rates of Fe in the interior, and also added a max to Alk in the CO2 flux calculations

* First pass of adding burial. Seems to work well so far.

* Computing omega_ara and omega_cal and added diagnostics to the output of the model

* Considering CaCO3 dynamics:

* Dissolution of CaCO3 based on detrital remin and saturation states of aragonite and calcite (Kwon et al., 2024)
* Precipation of CaCO3 based on HCO3- to H+ ratio (Lehmann et al., in prep)
* Sinking rate of material affected by ballasting, specifically CaCO3/Det ratio (Bach et al., 2016)

These feedbacks can be turned on and off using the "caco3_dynamics" logical

* Added dicp and dicr as new tracers (DIC preformed and DIC remineralised)
Removed adic as a tracer because CaCO3 dynamics mean that it is not appropriate

* Added sedimentary dissolution of CaCO3 dependent on Omega.
Also altered some of the parameters.

* Included a hard floor for DICp tracer == to dic_min parameter

* Included parameter control via the field_table on the dissolution of CaCO3 via saturation states (cal and ara) and detrius remin

* * Added "zooexcr" as an input parameter
* Added "fbury" as a diagnostic, rather than outputting det_sed_bury, detfe_sed_bury and caco3_sed_bury
* Fixed a minor bug in the "fbury" array, which involved the wrong units

* Added ballasting of CaCO3 to sinking rate

* * Increased the CFL criterion for vertically variable sinking, and made small edits to:
* remove background dissolution of CaCO3 in absence of detritus

* "conservetracers" logical option now active. Setting this to true means that any NO3 and Alkalinity that is lost through burial is added back to the ocean budget via a surface flux in exactly the same location.

* Updated the redistribution of tracer to be spread over the tile in question, rather than at the same exact lon,lat location.

* Added if statement to ensure no division by zero during conservetracers option (line 3269 in generic_WOMBATlite.F90)

* Altered the zooplankton grazing parameterisation. Simplified.

* Apply suggestions from code review

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

* Removed diagnostic wdet100 and defined diagnostics export_prod and export_inorg with the variable sinking rate

* Change default co2_calc to 'mocsy'

* Move flags caco3_dynamics, burial and conservetracers from field_table to namelist and rename to do_caco3_dynamics, do_burial, do_conserve_tracers

* Abort with mpp_error if ecosystem model is not conserving

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

Author: 10 people