Bugfix/240 #263
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Bugfix/240 #263
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Several tendencies in marbl_ciso_mod.F90 are missing zoo_graze terms; the first step to add them in is to make them accessible in the module via the share type.
Previously, marbl_ciso_mod.F90 computed tendencies without considering the possibility that zooplankton could be grazed, so no zoo_graze_* terms were included. The mass balance check did not catch this (even in a test run where zoo grazes itself) because the way the mass balance checks are constructed the missing terms all canceled each other out. I did confirm that adding some zoo_graze terms (but not all of them) triggered the error when zoo grazed itself and had no effect when zoo was not grazed.
marbl_ciso_mod.F90 only wants the sum of zooplankton terms like zoo_loss and zoo_graze (sum over all zooplankton species). Instead of sending each individual loss / grazing term, marbl_mod.F90 now does the sum in marbl_export_zooplankton_shared_variables(). Also, marbl_ciso_mod.F90 does not need x_graze_zoo so that field is not included in the share type.
Instead of copying these into marbl_autotroph_share_type, just pass autotroph_secondary_species to marbl_ciso_set_interior_forcing().
Cleaned up more variables that were available to marbl_ciso_mod.F90 via autotroph_secondary_species but were still being copied to marbl_autotroph_share_type. At this point, the only use of the share type is to copy tracer_local terms and there is already a plan to pass tracer_local instead.
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Part of some post-review code-cleanup - realized that the zooplankton_share_type and marbl_ciso_mod.F90 should be using zootot instead of zoo to signify this is a sum over zooplankton species. As a first pass, I changed zoo13Ctot and zoo14Ctot to zootot13C and zootot14C, respectively.
Since marbl_mod.F90 sums over all zooplankton when storing data in the zooplankton share type, those variables are now refered to as zootot: zoototC zootot_loss zootot_graze And so on. This is most pronounced in marbl_ciso_mod.F90, but also is apparent in the diagnostics module.
The changes to diagnostic names and metadata from the previous commit were not included in default_diagnostics.yaml, so GCMs were looking for CISO_zooC_d1[34]C instead of CISO_zoototC_d1[34]C
Expand autotroph_local_type to include carbon isotope elements, and then pass autotroph_local to marbl_ciso_set_interior() instead of copying data into the share type. Other related clean-ups: * marbl_autotroph_share_type is no longer needed * marbl_compute_autotroph_phyto_diatoms() does not need autotroph_local * marbl_ciso_mod.F90 no longer needs its own autotroph_local_type, so there is no longer a consistency check there (or a setup_autotroph_local, since that is taken care of in marbl_mod)
tracer_local is no longer restricted to the base tracers, it also contains carbon isotope tracers if ciso_on = .true. This fixes a bug in attempts to put carbon isotope fields in autotroph_local.
No need to compute this ratio for autotrophs that do not have CaCO3 tracer
Instead of copying some elements of tracer_local to interior_share and recomputing other elements in setup_local_column_tracers, just pass tracer_local (instead of tracers) to marbl_ciso_set_interior_forcing(). This means that some associate statements need to be updated to point to elements of tracer_local instead of marbl_interior_share_type (and some local variables are now associate statements instead of being computed in marbl_ciso_mod).
DO13Ctot_loc was inadvertently pointing to DO14Ctot_loc
* several "zooC" -> "total zooC" or "zoototC" in comments * R1[34]C_zooC -> R1[34]C_zoototC * autotroph consistency check has a single "if (ciso_on) then" block and checks for Ca1[34]CO3_ind instead of individual checks for all isotopic autotroph tracers * ciso_set_interior_forcing(): reordered arguments in interface so all intent(in)s are clumped together, followed by the (inout)s
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Added additional terms to
zooplankton_share_typeso thatmarbl_ciso_mod.F90could includezoo_grazeterms when computing tracer tendencies. This fixes #240 in the "quick fix" sense, but @klindsay28 and I talked about how it makes sense for me to take a little extra time to clean up the way some of this data is passed frommarbl_mod.F90tomarbl_ciso_mod.F90. Namely:autotroph_share_typeis a direct copy ofautotroph_secondary_species_type; why don't we pass that instead of doing unnecessary memory copies?marbl_ciso_mod.F90is only concerned with the sum over all zooplankton species, so this summation should be done as part of buildingzooplankton_share_typerather than done internal tomarbl_ciso_mod.F90. That would be consistent with howDOCtotis handled (summed inmarbl_mod.F90, treated as a single quantity throughoutmarbl_ciso_mod.F90)I'll add another comment when this is actually ready for review.