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…ed to figure out why the redistribution of residual does not fully conserve.
in MOM_tracer_registry.F90: MOM_tracer_chkinv. This routine calculates the global inventories of all tracers in the registry. Some of the debugging checksums in the offline tracer routines are updated to use this new function.
This primarily resulted from an error in the indexing when the fields were being updated. Now to test in OM4_05
Added a term proportional to the gradient of divergence to the Leith viscosity, which turns regular 2D Leith into Modified Leith.
Moved the calls to set_viscous_BBL out of the dynamics code and up into step_MOM, eliminating 4-way redundant calls and making the various algorithms more obviously similar. The answers are bitwise identical with 3 of the 4 dynamic solvers, but with MOM_dynamics_unsplit the time level of thicknesses used to calculate the bottom boundary layer properties are replaced with the initial thicknesses (like the other schemes), rather than the average of the initial thicknesses and the predicted thicknesses from the first (of perhaps several) step of the dynamics. All existing test cases are bitwise identical, but if SPLIT=FALSE and USE_RK2=FALSE, answers will change.
Eliminated calc_bbl and bbl_calc_time_interval from the vertvisc_type. Also renamed pass_kd_kv_turb to pass_kv_turb and added local variables inside of step_MOM to take the place of the variables that were eliminated, and added a new clock to step_MOM to record the time taken by calls to set_viscous_BBL. The unused module use statements for set_viscous_BBL were also eliminated from the MOM_dynamics modules. All answers are bitwise identical.
Moving set_viscous_BBL out of dynamics code Passes: https://gitlab.gfdl.noaa.gov/ogrp/MOM6/pipelines/1947
Runs fail with FATAL from PE 107: MPP_RESET_GROUP_UPDATE_FIELD_3D_: group%reset_index_s > group%nscalar etc. " .and. (.not.CS%thickness_diffuse_first .or. CS%t_dyn_rel_adv == 0)) " was removed in a previous update.
Corrected a bug when DIABATIC_FIRST=True in how the compensation for the difference between the dynamic sea surface height used by the barotropic solver and the height that the layers would have if net mass sources were applied gradually instead of abruptly at the start of the thermodynamic time step. This would change answers if both SPLIT and DIABATIC_FIRST are true and the value of BT_MASS_SOURCE_LIMIT > 0.0, but as there are currently no test cases that match these conditions, the answers are unchanged in all of the test cases. In cases where the answers do change, they are unambiguously better based on weaker high frequency gravity waves arising from coupling shocks.
…opass_fix Bugfix to reintroduce group halo pass check removed in 282a160
Corrected spelling errors and content errors in several of the comments describing subroutine arguments. All answers are bitwise identical.
Reverted to the simpler pass_var routines for the single 3-d variable h. This avoids the issue that triggered the recent pull request mom-ocean#520, and it should have no performance impacts. (In fact, by letting each call have its own halo size, it might lead to performance improvements in subsequent commits.) All answers are bitwise identical.
added Doxygen comments to all of the arguments to the subroutines in MOM_checksum_packages.F90. All the answers are bitwise identical.
Change to pass_var for h and correct barotropic mass source ...and it passed (no surprise): https://gitlab.gfdl.noaa.gov/ogrp/MOM6/pipelines/1956
added Doxygen comments to all of the subroutines in MOM_checksum_packages.F90. All the answers are bitwise identical.
Added Doxygen comments to all of the subroutines in the MOM_dynamics_legacy_split.F90. All the answers are bitwise identical.
Added Doxygen comments to all of the subroutines in the MOM_dynamics_unsplit.F90. All the answers are bitwise identical.
Added doxygen comments to all of the subroutines in MOM_dynamics_unsplit_RK2.F90
…line_tracer_updates # Conflicts: # src/core/MOM.F90
…anup code before PR
Added doxygen comments to all of the subroutines in MOM_interface_heights.F90. All the answers are bitwise identical.
… Hallberg-NOAA-dev/gfdl
The name "mod" had been used for various module name variables throughout the MOM6 code, but this can cause name-space conflicts with the mod intrinsic function, so "mod" has been renamed "mdl" throughout the MOM6 code. All answers are bitwise identical.
Renamed variables "mod" to "mdl" Passed: https://gitlab.gfdl.noaa.gov/ogrp/MOM6/pipelines/2054 (Initial fail seems to have been a stale file issue).
- VarMix was originally for a crude implementation of a Visbeck et al. diffusivity formula. It has become a catchall for resolution functions, stored slopes and length-scales. It infact has never contained an actual diffusivity. The meaning of the parameter USE_VARIABLE_MIXING was original "use Visbeck" but has really meant "allocate and calculate everything in this module even if not being used". This has now been cleaned up... - USE_VARIABLE_MIXING still exists but does nothing. - It will be made obsolete shortly. - Visbeck related fields (VarMix@L2v, ...) are allocated only if KhTh_Slope_Cff>0 or KhTr_Slope_Cff>0. - The Eady growth rates are now allocated and calculated if either of Visbeck or MEKE schemes are in use. - The field VarMix%Rd_dx_h is allocated and calculated if either the diagnostic is requested or the field needed "Passivity" or the resolution functions. - The wave speed VarMix%cg1 is calculated only if needed but which includes resolution fns, Rd_dx, and FGNV stream fn. - Closes mom-ocean#522. - Added logic in tracer_hordiff() to avoid referencing VarMix%L2v or VarMix%SN_v when VarMix%KhTh_Slope_Cff==0. - Added logic in tracer_hordiff() to avoid referencing VarMix%L2v or VarMix%SN_v when VarMix%KhTr_Slope_Cff==0. - This commit affects available_diags and MOM_parameter_doc for some experiments but does not changes answers.
- The third paper, in the series of Fox-Kemper et al., proposed upscaling the buoyancy gradients from the frontal scale to the grid-scale. To date this has been implemented as a globally constant upscaling indicated by the FOX_KEMPER_ML_RESTRAT parameter. This commit implements the upscaling as a function of grid-spacing, 1st-baroclinic deformation radius and a frontal length scale parameter, MLE_FRONT_LENGTH. - VarMix is now passed to mixedlayer_restrat since we need VarMix%Rd_dx. - Updated MLE doxumentation.
- For some reason we had "MLD" in the argument list but "Hml" in the subroutine code and declarations. This was breaking the CM4 compile.
- This fixes another occurrence of a keyword being used as a variable name. It is allowed but is rather poor practice and makes searching for the use of keywords and constructs somewhat harder.
- The forcing diagnostics were using array syntax than meant calculations were being made for points that could be invalid (uninitialized in halos)
- In order to call calculateBuoyancyFlux2d() along with the ePBL the KPP fields are all allocated but not all are needed. This allocates only those used.
- The resetting/zeroing and accumulation of diagnostic arrays within
extractFluxes1d() assumes the routine is called only once. With the
need for a buoyancy flux in ePBL, it is currently being called twice.
- This was leading to the "hdfs" diagnostic accumulating too much.
- I have added a flag to indicate to not calculate the diagnostic fields.
- A better solution will be to only call once but calculate a buoyancy
flux in extractFluxes1d() but this will require more coding since
the latter is dependent on the equation of state and needs a different
interpretation of mass fluxes.
- I checked that this changes "hdfs" but have not checked whether other
diagnostics were affected.
- Closes NOAA-GFDL/MOM6-examples#128 but I opened mom-ocean#543 to make a note that
we have more tidying up to do.
Re-factor of MOM_lateral_mixing_coeffs.F90 (VarMix)
Mle length scale
Fixed argument name to match declaration gen_trcr_col_physics()
…e-name Replace keyword variable name
Fix hdfs diagnostic
- A new local variable was missing from the openmp directives.
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Feature/runoff optional
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Merge in latest dev/gfdl updates
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+Add G%Rad_Earth_L and related code simplification
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Note that most of these commits are from previously squashed pull requests, and this PR is restoring them. - 6360dbb Merge branch 'main' into main_to_dev - bac8031 Merge pull request mom-ocean#1566 from jiandewang/EMC-FMS-mixed-mode-20220411 - e532d86 Merge pull request #88 from marshallward/missing_attrib_with_class_bugfix - d380f1d An alternate fix to class(*) issues with FMS 2022-01 - 8ecf333 Merge pull request #87 from jiandewang/feature/update-to-main-20220317 - ba37f94 Merge remote-tracking branch 'FSU/main' into feature/update-to-main-20220317 this is corresponding to MOM6 main 20220317 commit (hash # 399a7db) - 44313d9 Merge pull request #85 from jiandewang/feature/update-to-main-20220217 - 966707f Merge remote-tracking branch 'GFDL/main' into feature/update-to-main-20220217 this is corresponding to MOM6 main branch 20220217 commit (hash # 6f6d4d6), which originally based on GFDL-candidate-20220129 - 32c0e1e Merge pull request #81 from jiandewang/feature/update-to-main-20211220 - 9642b1d delete external/OCEAN_stochastic_phyiscs directory as Phil re-coded in external/stochastic_physics directory - e7c9ada solve minor conflict in mom_cap.F90 mom_ocean_model_nuopc.F90 and MOM_energetic_PBL.F90, add two new files: src/parameterizations/stochastic/MOM_stochastics.F90 and config_src/external/stochastic_physics/stochastic_physics.F90 - 90d5961 Merge pull request #78 from jiandewang/feature/update-to-GFDL-20211019 - fd02017 Merge remote-tracking branch 'GFDL/main' into feature/update-to-GFDL-20211019 - 36f17eb Merge pull request #72 from pjpegion/ocn_stoch_july2021 - a9a957e return a more accurate error message in MOM_stochasics - 56bb41e Merge branch 'ocn_stoch_july2021' of https://github.com/pjpegion/MOM6 into ocn_stoch_july2021 - ca2ae1c update to dev/emc - 14ca4a1 Merge pull request #76 from jiandewang/feature/update-to-GFDL-20210914 - 29016c2 Merge remote-tracking branch 'GFDL/main' into feature/update-to-GFDL-20210914 merge GFDL main 20210914 commit (hash # c09e199) - a8577df Merge branch 'NOAA-EMC:dev/emc' into ocn_stoch_july2021 - f8a8e4c update to gfdl 20210806 (#74) - 16e6af0 update to dev/emc - 237a510 add comments - 1b4273d revert logic wrt increments - 5b2040e add logic to remove incrments from restart if outside IAU window - c5f2b72 add write_stoch_restart_ocn to MOM_stochastics - bdf2dc7 doxygen cleanup - 8bc4acc move stochastics to external directory - a3fa3a1 Merge remote-tracking branch 'upstream/dev/emc' into ocn_stoch_july2021 - e4bc007 stochastic physics re-write - 202cbd4 update to dev/emc - 61717ee Merge remote-tracking branch 'origin/dev/emc' into ocn_stoch - 565e0bb remove debug statements - a4c0411 Merge remote-tracking branch 'upstream/dev/emc' into ocn_stoch - 689a73f remove PE_here from mom_ocean_model_nuopc.F90 - 8afe969 clean up of mom_ocean_model_nuopc.F90 - 25ed4fc revert MOM_domains.F90 - b8d9888 place stochastic array in fluxes container and make SPPT specific arrays allocatable - d984a7e remove stochastics container - eb88219 clean up of code for MOM6 coding standards - 6e3ea1b correct coupled_driver/ocean_model_MOM.F90 and other cleanup - 0b99c1f make stochastics optional - 85023f8 Merge remote-tracking branch 'upstream/dev/emc' into ocn_stoch - 80f9f44 clean up MOM_domains - 5443f8e remove blank link in MOM_diagnostics - 1727d9a re-write of stochastic code to remove CPP directives - 600ebf9 Merge remote-tracking branch 'upstream/dev/emc' into ocn_stoch - 6bb9d0b fix non stochastic ePBL calculation - 1d7ffa3 clean up code - 040e1f1 Merge pull request #13 from NOAA-EMC/dev/emc - 2cba995 Merge branch 'dev/emc' into ocn_stoch - 1dc0f4f Merge remote-tracking branch 'upstream/dev/emc' into dev/emc - 4bd9b9e clean up debug statements - 25ed5ef additions for stochy restarts - a2a374b add stochy_restart writing to mom_cap - 0c15f4c Update MOM_diabatic_driver.F90 - 167a62e Merge pull request #12 from pjpegion/dev/emc - bd477a9 Update MOM_diabatic_driver.F90 - 7212400 Update MOM_diabatic_driver.F90 - 7de295c cleanup of code and enhancement of ePBL perts - cd06356 Merge pull request #11 from NOAA-EMC/dev/emc - 9896d61 Merge pull request #9 from pjpegion/dev/emc_merge - 0a62737 Merge branch 'ocn_stoch' into dev/emc_merge - 3cad1ba Merge pull request #8 from NOAA-EMC/dev/emc - c2aa2a8 updates from dev/emc - 182ef34 additions for stochastic physics and ePBL perts - 671c714 Merge pull request #1 from NOAA-EMC/dev/emc
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This PR brings dev/ncar up to date with dev/master (as of 2017 July 21st).