-
Notifications
You must be signed in to change notification settings - Fork 25
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Bugfix/240 #263
Bugfix/240 #263
Commits on Apr 11, 2018
-
Add zoo_graze terms to zooplankton_share_type
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.
Configuration menu - View commit details
-
Copy full SHA for d2fbb78 - Browse repository at this point
Copy the full SHA d2fbb78View commit details -
Include all grazing terms for ciso dtracer
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.
Configuration menu - View commit details
-
Copy full SHA for dbb7cd0 - Browse repository at this point
Copy the full SHA dbb7cd0View commit details
Commits on Apr 12, 2018
-
Sum zooplankton terms before putting in share
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.
Configuration menu - View commit details
-
Copy full SHA for 739f597 - Browse repository at this point
Copy the full SHA 739f597View commit details -
Remove auto_loss and auto_graze from share type
Instead of copying these into marbl_autotroph_share_type, just pass autotroph_secondary_species to marbl_ciso_set_interior_forcing().
Configuration menu - View commit details
-
Copy full SHA for 394deb0 - Browse repository at this point
Copy the full SHA 394deb0View commit details -
Use more of autotroph_secondary_species
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.
Configuration menu - View commit details
-
Copy full SHA for 53b4b0a - Browse repository at this point
Copy the full SHA 53b4b0aView commit details
Commits on Apr 13, 2018
-
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.
Configuration menu - View commit details
-
Copy full SHA for 6a9a3ec - Browse repository at this point
Copy the full SHA 6a9a3ecView commit details
Commits on Apr 16, 2018
-
All zoo references in ciso mod are zootot
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.
Configuration menu - View commit details
-
Copy full SHA for 08995f3 - Browse repository at this point
Copy the full SHA 08995f3View commit details -
Diagnostic changes from 08995f3 reflected in YAML
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
Configuration menu - View commit details
-
Copy full SHA for 9deb765 - Browse repository at this point
Copy the full SHA 9deb765View commit details
Commits on Apr 17, 2018
-
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)
Configuration menu - View commit details
-
Copy full SHA for 394e9c7 - Browse repository at this point
Copy the full SHA 394e9c7View commit details -
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.
Configuration menu - View commit details
-
Copy full SHA for 3d31170 - Browse repository at this point
Copy the full SHA 3d31170View commit details
Commits on Apr 18, 2018
-
Only compute R1[34]C_autotrophCaCO3 for calcifiers
No need to compute this ratio for autotrophs that do not have CaCO3 tracer
Configuration menu - View commit details
-
Copy full SHA for 91e40ae - Browse repository at this point
Copy the full SHA 91e40aeView commit details -
Pass tracer_local to ciso_set_interior_forcing()
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).
Configuration menu - View commit details
-
Copy full SHA for d700590 - Browse repository at this point
Copy the full SHA d700590View commit details -
DO13Ctot_loc was inadvertently pointing to DO14Ctot_loc
Configuration menu - View commit details
-
Copy full SHA for a284a46 - Browse repository at this point
Copy the full SHA a284a46View commit details
Commits on Apr 20, 2018
-
Code clean-up following review
* 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
Configuration menu - View commit details
-
Copy full SHA for d106c6d - Browse repository at this point
Copy the full SHA d106c6dView commit details