Fms ocmip2 co2calc update #39
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* initial commit * add WOMBAT routines * bug fixes allocate/deallocate btf fields remove redundant diagnostics * enforce src info * add unit conversions * more bug fixes copy no3_orig and caco3_orig directly from corresponding fields spatially varying kmeuph * account for absorption of sw radiation with depth * keep only shortwave wavelengths < 710 nm sort out units * fix sinking bug by using internal sinking scheme fix bug in kmeuph calculation * fix fe units error * fix bug with wdet100 diagnostic * move sfc flux-related fields into WOMBAT type * update sediment tracers via pointers * rename to WOMBATlite * Address Pearse's review * Remove coupler fluxes from no3 and phy tracers * Fix bug in radbio_int100 diagnostic * Allow in update_from_coupler virtual flux adjustment due to salt flux restoring/adjustment * Apply MOM6 code style * Add ESM diagnostics
* Added "pchl" as a new tracer to WOMBATlite. Working fine. Currently mirrors the "phy" tracer. * New light attenuation scheme working. Considers blue, green and red light and their different attenuation given chlorophyll concentration. * Chlorophyll appears to be working well. Some outstanding issues but model is stable. Also converted all units of biomasses to carbon, rather than nitrogen. Altered some parameter coefficients as well, such as abio and alphabio. * Made 4 very slight changes to the code to account for Dougie Squire's review. All regarding syntax. No changes to equations. * Fixed a bug in the iron cycle, where I was previously making iron too limiting to phytoplankton. This will change a lot in the next branch focussed on iron cycle development though. I also took the opportunity to change the names of the parameters for WOMBAT-lite and their default values. * Made slight changes to (1) where we now calculate the mean light in the grid cell, not the mid point; (2) we save both the mid point and mean to diagnostic output (radmid and radbio); (3) renamed phy_lday to phy_leup because it makes more sense; (4) removed unecessary code snippets; (5) syntax changes for consistency --------- 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]>
* Introduced computations for dFe precipitation, scavenging and coagulation. These are not yet active within the dFe cycle, but will be made so in the next step. Diagnostics for precipitation, scavenging, ambiguous loss in shallow environments and coagulation are output from the model. These show that scavenging is absolutely minimal while ambiguous loss and coagulation are much larger sinks of dFe, which makes sense given that scavenging only occurs when free Fe is in excess of its solubility. I think... * Added FeIII precip, FeIII scavenging, dFe loss and coagulation onto detritus to the fe tracer source/sink term. Removed the previous use of scavening and background dFe concentrations. * phyfe, zoofe, and detfe have all been added as tracers now. They are currently mirroring phy, zoo and det * variable Fe2C ratios implemented in source and sink terms. Model stable. Also outputting new diagnostics of fesources and fesinks * Changes include: * Dynamic Fe uptake by phytoplankton and a quota model of their Fe limitation * diagnostic of phytoplannkton dFe uptake (phy_dfeupt) * Addition of chlorophyll and iron quotas as namelist inputs to the WOMBAT model, rather than hard-coded constants * Removed feloss as a diagnostic, increased fescaven and fecoag2det sinks of dFe. Rearranged the Fe chemistry part of the code to: * Calculate solubility of Fe3+ in solution first, * followed by estimate of colloidal iron, * equilibrium fraction of dFe into Fe' and Fe-L * then precip, scav, and coag * Following Tagliabue et al. (2023), made coagulation rate dependent on DOC and Phytoplankton biomass. Also added light as a means to increase free Fe. * Little clean up of the code * Removed unecessary call to wombat%kcoag_dfe * Included a three dimensional call and output of htotal and ahtotal arrays. The htotal array is being used to calculate pH within the biogeochemical code for iron chemistry calculation of free Fe solubility. * * added "zookz" as a new parameter controlling linear mortality (respiration) of zooplankton * no mortality/grazing of phy or zoo at concentrations less then 1e-3 mmol C m-3 * renamed f11,f21,etc. to readable arrays that are output as diagnostics (e.g., "phygrow", "zoograz") * rearranged code steps in biotic part * Fixed small bug in collection of tendency terms (Step 9) * Added "feIII", "felig", and "fecol" to diagnostic output. Made small syntax corrections given Dougie Squire's PR review. * Registered diagnostics of feIII, fecol and felig * Corrected long names of FeIII, felig and fecol --------- 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: Pearse Buchanan <[email protected]>
* Adding pressure effect to CO2 system calculations within ocmip2 option * Exposed omega_arag and omega_calc as outputs
Introduces a new optional argument to FMS_ocmip2_co2calc, called pcorr_ocmip2, that defaults to .false.
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Extended the ocmip2 co2 system calculations to be 3d with depth and pressure effects