Merge candidate 2018 07 16#76
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alperaltuntas merged 304 commits intoAug 3, 2018
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https://gitlab.gfdl.noaa.gov/ogrp/MOM6/pipelines/4655 passed first time. No timeouts!
- Moved setting of (constant) mod_Leith to outside of loops - Moved calculation of div_xx to after calculation of h_u,h_v - Used h_u,h_v in div_xx (avoids repeated computations) - Put calculation of div_xx, vort_xy into a conditional block - Aligned comments with code
- The logic for constructing viscosity involved nested if's and
alternate pathways.
- This refactor avoids large pathway branches and has not nested
if's, thereby simplifying the logic:
- The only case where extra steps occur are when Smagorinsky and
Leith are both disabled and better_bound is enabled. In this case
more conditionals are encountered sequentially.
- Added comments to:
- indicate contributions that are resolution scaled or not;
- indicate contributions that are additive rather than maxed.
- Added equations for anisotropic viscosity (yet to be implemented) - Also corrected missing factor of 1/2 in documentation of isotropic viscosity.
- Added parameters to control anisotropic viscosity - Added allocatable storage for factors in the anisotropic stress tensor - Set factors for i-oriented tensor - Actual viscosity not used yet
- Adds text to parameter_doc files in some OBC cases.
- The tension component of the stress tensor has an enhanced viscosity
made from an offset + a rotated component.
- The rotated component is often zero hence writing as ( 1 - stuff )
resolves to a constant offset where appropriate.
- Added run-time specification of n1,n2 for mode 0
- The logic for constructing viscosity involved nested if's and
alternate pathways.
- This refactor avoids large pathway branches and has not nested
if's, thereby simplifying the logic:
- The only case where extra steps occur are when Smagorinsky and
Leith are both disabled and better_bound is enabled. In this case
more conditionals are encountered sequentially.
- Added comments to:
- indicate contributions that are resolution scaled or not;
- indicate contributions that are additive rather than maxed.
Added the new module MOM_full_convection to homogenize temperature and salinity in regions of static instability. All answers are bitwise identical, but a new public interface has been added.
Cleaned up the MOM_kappa_shear code in preparation for adding the code to do the shear-mixing calculations at the vertices, includign dOxyGenizing the comments describing the elements of the Kappa_shear_CS, compacting some openMP directives, and eliminating duplicate comments describing arguments. All answers are bitwise identical.
Cleaned up the allocation and restart registry calls for the persistent elements of the visc type, including always setting visc%Kv_slow, as the comment indicated should be done but was not. The allocate calls now use safe_alloc_ptr and the restart registration calls avoid the use of a vardesc type. All answers are bitwise identical.
Doxygenize hor_visc_CS + refactor of horizontal_viscosity()
Doxygenize midas_vertmap
Refactored construction of Laplacian viscosity
- 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 dOxygen comments describing the whole MOM_variables and MOM_verticalGrid modules. All answers are bitwise identical.
Added dOxygen comments describing the whole MOM module and several subroutines within this module. All answers are bitwise identical.
Added dOxygen comments describing the whole module and removed duplicate older-style argument documentation comments from MOM_checksum_packages.F90. All answers are bitwise identical.
Added dOxygen comments describing the whole module and several routines in MOM_dynamics_unsplit.F90 and MOM_dynamics_unsplit_RK2.F90, and consolidated multiline comments with multiline declarations that dOxyGen would interpret incorrectly. All answers are bitwise identical.
Added dOxygen comments describing the whole MOM_transribe_grid module. All answers are bitwise identical.
…/vertical - Using an older version of doxygen detected a lot of modules which were missing the one-liner at the top.
Added dOxygen comments describing the various equation of state modules and the parameters used by these modules. All answers are bitwise identical.
Added dOxygen comments describing the various tracer package modules, including extended documentation at the end of these modules. All answers are bitwise identical.
Added dOxygen comments describing the various MOM6 framework modules, including extended documentation at the end of some of these modules. All answers are bitwise identical.
Even more doxy
module DoxyGenization in the MOM6/src/core directory
Module DoxyGenization in the EOS, tracer and framework code
- The duplicate files in solo_driver and coupled_driver cause conflicts when running doxygen. This configuration change avoids the duplicate files in coupled_driver.
- Using the older version of doxygen revealed numerous modules without either the header summary line or any doxumentation at all. The newer versions are deliberately silent on these omissions.
Fixes doxygen configuration and missing module one-liners
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Please keep this PR open until we get thumbs up from GFDL. |
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👍 |
Conflicts: src/framework/MOM_restart.F90
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I just fixed the conflict manually. @alperaltuntas, please merge this PR. |
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testing: aux_mom on cheyenne/intel, b4b
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update to gfdl 20210914
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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 merges the latest dev/master candidate into dev/ncar.
No answers change for MOM6-examples and MOM6-cases/cesm/T62_g16.