update dev/ncar#4
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- The strain component of viscosity had the order of bounding/scaling reversed in a previous commit. This doesn't seem to change answers but probably could in some special cases.
- The minimum viscsoity was only being applied in the strain component.
The minimum with KH_BG_MIN was not applied to the tension component.
This broke isotropy of the stress tensor.
- The parameter KH_BG_MIN defaults to 0.0 which would be harmless if
viscosities are always non-negative. However, when using backscatter
the viscosity is intentionally negative and this limiter was zeroing
out the backscatter, but only in the strain component.
- I've moved the min() function to before adding in the MEKE component
which is where negative viscosities might come from.
- This does not change answers in any tests BUT will change answers for
any backscatter experiments OR where KH_BG_MIN is non-zero.
- Delete unused supercritical bathymetry.
Added a new pointer, Kv_shear_Bu, to the vertvisc_type to describe the viscosity at the corner points. Also amended the comments describing TKE_turb to note that this now can be discretized at either the tracer or corner points. By default all answers are bitwise identical.
Check whether visc%Kv_shear_Bu is allocated, and if so add it to the viscosity. All answers are bitwise identical unless visc%Kv_shear_Bu is allocated.
Added a new subroutine, Calc_kappa_shear_vertex, to calculate the Jackson et al. stratified shear mixing at the cell corners, along with a new runtime parameter, VERTEX_SHEAR, to control wheter this is used, and a second new function, kappa_shear_at_vertex, to allow external queries of the setting of VERTEX_SHEAR. By default, all answers are bitwise identical, but there are two new interfaces and MOM_parameter_doc files have a new field.
Added code to calculate shear mixing at the cell verticies if VERTEX_SHEAR is true. Also added calls to allocate visc%Kv_visc_Bu and visc%TKE_turb in this case, including the addition of new restart fields. By default, all answers are bitwise identical, but several recently added interfaces are used. With this commit, the vertex mixing is fully available.
Added halo updates of vertex turbulence fields during initialization for reproducibility across restarts in non-symmetric memory mode. Also eliminated an unnecessary variable. All answers in test cases are bitwise identical.
Anisotropic horizontal viscosity
…into adcroft-bugfix-minimum-visc
Corrected a typo in the restart registration call for Kv_shear that was introduced with Hallberg-NOAA/MOM6@130a32b. This bug fix should restore the ability to reproduce across restarts.
Add vertex shear mixing
- turning on COMPUTED_VORTICITY makes things worse at outflow end.
Eliminated the file MOM_OCMIP2_CO2calc.F90, which is not being called by any MOM6 code. This file violates numerous MOM6 coding and licensing conventions, including some that break the automatic generation of documentation by MOM6, and it is an unused duplicate of capabilities that are found in the generic tracer code. All answers in test cases are bitwise identical.
- Split single declarations of multiple variables which leads to undocumented parameters.
- Split single declarations of multiple variables which leads to undocumented parameters.
- Doxygen comments in MOM_memory.h have to be specially formatted because of the ".h" extension (making it behave C-like) and it tooks some experimentation to find the one format that allows a comment to be split across multiple lines - Doxumentation of CPP macros only works for #define so the #undef lines have to be moved to the end. - Also reformatted config_src/dynamic/MOM_memory.h to look like a copy of config_src/dynamic_symmetric/MOM_memory.h, except for the one macro.
- The documentation for MOM_ice_shelf_dynamics said it was the thermodynamics - corrected. - All of the module doxumentatino was a complete copy of the MOM_ice_shelf module which caused conflicts with section and names and was incorrectly duplicated. This has been cut.
- Added section labels
- coord_adapt.F90, coord_rho.F90 and coord_slight.F90 each had single declaration lines for multiple variables leading to undocumented variables.
- Split single declarations of multiple variables which leads to undocumented parameters.
- Split single declarations of multiple variables which leads to undocumented parameters.
- Document a variable (e.g. Time) with the comment "!< Time" apparently is an error. Admittedly the comment gives no extra information than the variable name. I've changed the comment to "!< Model time".
sfc_state%melt_potential is now accumulated over time_in_thermo_cycle.
Conflicts: src/framework/MOM_restart.F90
Merge candidate 2018 07 16
Conflicts: src/core/MOM.F90 src/core/MOM_variables.F90
Add melt/freeze potential via MCT cap
add latitudinally varying background diffusivity
Improve melt potential calculation
Makes OBLD available to MCT (and other caps)
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Sep 2, 2021
Update CPT fork of MOM6 to latest (12/10/2020) from NOAA-GFDL
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Sep 2, 2021
Only write checksums from root PE MCT/NUOPC caps
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Nov 10, 2022
Correct a couple of typos in hor_visc
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