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update to main branch 20220217 commit#85

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jiandewang merged 195 commits intoNOAA-EMC:dev/emcNOAA-EMC/MOM6:dev/emcfrom jiandewang:feature/update-to-main-20220217jiandewang/MOM6:feature/update-to-main-20220217Copy head branch name to clipboardFeb 24, 2022

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Commits on Oct 1, 2021

• (+*)Fix MEKE advection bug

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Commits on Oct 5, 2021

• +Add BAROTROPIC_TIDAL_SAL_BUG to fix a tide bug

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Commits on Oct 8, 2021

• Merge branch 'dev/gfdl' into MEKE_advection_bugfix

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Commits on Oct 9, 2021

• Merge pull request mom-ocean#1506 from Hallberg-NOAA/MEKE_advection_bugfix

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• Merge branch 'dev/gfdl' into tidal_SAL_bugfix

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• Merge pull request mom-ocean#1508 from Hallberg-NOAA/tidal_SAL_bugfix

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Commits on Oct 11, 2021

• Particle API (mom-ocean#1504)

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Commits on Oct 12, 2021

• adds missing _ (mom-ocean#1519)

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• Working on boundary layer docs.

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• Done with EPBL docs?

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Commits on Oct 13, 2021

• Merge pull request mom-ocean#1510 from ESMG/esmg-docs

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Commits on Oct 14, 2021

• FMS1: Don't create IO domains for single-PE domain

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• User/wfc/remap scheme (mom-ocean#1503)

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• +*Change defaults for 3 parameters to better values (mom-ocean#1509)

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• +Add new parameter FATAL_INCONSISTENT_RESTART_TIME (mom-ocean#1511)

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Commits on Oct 15, 2021

• +(*)Fix bug when RES_SCALE_MEKE_VISC = True (mom-ocean#1512)

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• +Make 37 optional arguments in src/core mandatory

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• Refactored solo_driver/MOM_driver.F90

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Commits on Oct 19, 2021

• Merge branch 'dev/gfdl' into opt_args_in_core

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Commits on Oct 20, 2021

• Merge pull request mom-ocean#1523 from Hallberg-NOAA/opt_args_in_core

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• Merge branch 'main' into main_to_dev

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• Merge pull request mom-ocean#1529 from marshallward/main_to_dev

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• +Optional just_read_params args are now mandatory

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• +Argument cleanup in vertical parameterization code

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Commits on Oct 22, 2021

• Use FMS2 file_exists, remove domain args

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• fix low mode in tidal_mixing

  

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Commits on Oct 23, 2021

• +Eliminate unused arguments in diagnostics code

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Commits on Oct 25, 2021

• Merge branch 'dev/gfdl' into no_1pe_io_layout

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• Merge pull request mom-ocean#1522 from marshallward/no_1pe_io_layout

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• Always create single-threaded files in 1 PE runs

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• +Optional arg cleanup in horizontal param code

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Commits on Oct 26, 2021

• cpu_clock_id: synchro_flag arg changed to logical

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• Merge branch 'dev/gfdl' into fms2_file_exist

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• Merge pull request mom-ocean#1532 from marshallward/fms2_file_exist

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• Merge branch 'dev/gfdl' into sync_clock_flag

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• Merge pull request mom-ocean#1535 from marshallward/sync_clock_flag

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Commits on Oct 29, 2021

• Eliminate GET_ALL_PARAMS in hor_visc_init (mom-ocean#1536)

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Commits on Nov 5, 2021

• Add weighted d[uv]_dt_str diagnostics (mom-ocean#1539)

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Commits on Nov 9, 2021

• +Argument cleanup in vertical diffusivity code

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Commits on Nov 11, 2021

• +Move rotate_dyn_horgrid to MOM_dyn_horgrid module

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• +Reduce use of dyn_horgrid in initialize_MOM

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• (*)Fix compile-time issues with MOM_sum_driver.F90

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Commits on Nov 16, 2021

• Removed Travis-CI badge from README

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Commits on Nov 17, 2021

• (+) porous topography implementation (#3)

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• Disable clock sync of in-loop BML timers

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Commits on Nov 18, 2021

• Correct a couple of typos in hor_visc

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Commits on Nov 19, 2021

• Corrected the units of 124 variables

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• Horizontal viscosity pointer removal

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• MEKE pointer cleanup

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• Mixed layer pointer purge

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• Thickness diffusion pointer removal

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• Tidal forcing CS pointer removal

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• Internal tide pointer removal

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• Entrain diffusive pointer removal

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• Tidal mixing pointer cleanup

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• Geothermal heating pointer removal

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• Opacity pointer removal

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• Bulk mixed layer pointer removal

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• Energetic PBL pointer removal

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• Regularize layers pointer removal

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• CVMix convection pointer removal

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• MEKE_type pointer removal

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• Variable mixing pointer removal

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• Wave speed pointer removal

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• MOM_restart_cs pointer removal

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• Barotropic CS pointer removal

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• Wave structure CS pointer

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• ALE sponge pointer removal (partial)

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• MOM diagnostic pointer removal

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• set_visc_CS pointer removal

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• tidal_bay_obc_cs pointer removal

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• Equation of state pointer removal

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• CoriolisAdv_CS pointer removal

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• PressureForce CS pointer removal

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• MOM continuity CS pointer removal

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• MOM_open_boundary pointer removal

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• small fixes to porous topo code

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Commits on Nov 21, 2021

• Merge branch 'dev/gfdl' into hor_visc_typos

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• Merge pull request #4 from herrwang0/hor_visc_typos

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Commits on Nov 22, 2021

• Merge branch 'dev/gfdl' into no_more_pointers

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• Add initialization tests using CS%initialized

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• Merge pull request #5 from marshallward/no_more_pointers

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Commits on Nov 23, 2021

• Corrected the descriptions of 60 variables

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• Merge branch 'dev/gfdl' into initialized_tests

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• +Add G%Rad_Earth_L and related code simplification

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Commits on Nov 24, 2021

• preserve dimensions in porous topo interpolation

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• Remove Z_to_m rescaling in porous module

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• small bug fix

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• small bug fix 2

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• fix merge issue

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Commits on Nov 25, 2021

• Merge pull request #6 from Hallberg-NOAA/initialized_tests

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• Merge branch 'dev/gfdl' into more_unit_fixes

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Commits on Nov 26, 2021

• Merge pull request #7 from Hallberg-NOAA/more_unit_fixes

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• Merge branch 'dev/gfdl' into rescaled_Rad_Earth

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Commits on Nov 27, 2021

• Merge pull request #8 from Hallberg-NOAA/rescaled_Rad_Earth

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• (*)Fix rescaling when SPLIT_BOTTOM_STRESS = True

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Commits on Nov 28, 2021

• (*)Refactored and fixed pseudo_salt_tracer code

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• +Eliminate forcing%netSalt

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• +Clean up dimensional rescaling in write_u_accel

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• +Rescale fluxes passed to KPP_NonLocalTransport

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Commits on Nov 29, 2021

• Refactored DOME_initialize_sponges() (#12)

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• change conversion H_to_MKS to H_to_m for u/veffA

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• Merge branch 'dev/gfdl' into porous_topo_sjd

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• +Rescaled flux arguments to tracer_vertdiff()

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Commits on Nov 30, 2021

• Merge pull request #3 from sditkovsky/porous_topo_sjd

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• Bug fix for reading First_direction from restart

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• Expanded comments describing src/core code (NOAA-EMC#13)

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• Minor code cleanup in drivers/FMS_cap

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• Merge branch 'dev/gfdl' into refactor_pseudo_salt_tracer

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Commits on Dec 1, 2021

• Cleaned up whitespace leftover from porous topomerge.

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• Fix out-of-bounds k index in PPM flux

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Commits on Dec 2, 2021

• Testing: Codecov uploader update

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• Code cleanup in drivers/solo_driver forcing files

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• Merge branch 'dev/gfdl' into refactor_pseudo_salt_tracer

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Commits on Dec 4, 2021

• Merge pull request NOAA-EMC#16 from Hallberg-NOAA/refactor_pseudo_salt_tracer

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• Merge branch 'dev/gfdl' into tracer_sfc_flux_rescale

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• Bugfix: cpu clock sync error

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Commits on Dec 5, 2021

• Merge pull request NOAA-EMC#17 from Hallberg-NOAA/tracer_sfc_flux_rescale

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• Merge branch 'dev/gfdl' into bugfix_alternate_first_dir

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Commits on Dec 6, 2021

• Merge pull request NOAA-EMC#18 from herrwang0/bugfix_alternate_first_dir

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• Merge branch 'dev/gfdl' into new_codecov_uploader

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• Merge pull request NOAA-EMC#21 from marshallward/new_codecov_uploader

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• +Add the new routine unit_no_scaling_init

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• (*)Provide US arguments to 4 existing calls

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• +Make US arguments non-optional for 28 routines

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• Docs: Add NASA-GMAO to consortium figure

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Commits on Dec 7, 2021

• +Add post_product_[uv] and post_product_sum_[uv]

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• Use post_product_u for momentum budget diagnostics

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Commits on Dec 8, 2021

• +Rescale fluxes%net_mass_src and other diagnostics (NOAA-EMC#23)

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• +Rescale forcing arguments and revise ctrl_forcing (NOAA-EMC#25)

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Commits on Dec 9, 2021

• Merge branch 'dev/gfdl' into cpu_clock_sync_bugfix

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• +Remove clocks inside of j-loops

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• Deallocate eta_PF_start to avoid a memory leak

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• +Set find_salt_root if SHELF_THREE_EQN = .False.

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• +Obsolete ETA_TOLERANCE_AUX

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• (*)Fix extract_diabatic_member

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• Warn if opacity_from_chl is called without fluxes

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• Correct comments describing advect_tracer args

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• Update indexing of array passed to data_override.

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• Correct out of bounds index (por_face_areaU) bug

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• (*)Offline tracer read bug fix

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• +Refactored and rescaled the offline tracer code

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• Merge branch 'dev/gfdl' into cpu_clock_sync_bugfix

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• +(*)Revised offline tracer algorithms

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• Merge branch 'dev/gfdl' into offline_tracer_fix

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• Merge branch 'dev/gfdl' into mandatory_US_args

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• Merge pull request NOAA-EMC#29 from Hallberg-NOAA/mandatory_US_args

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• Merge branch 'dev/gfdl' into cpu_clock_sync_bugfix

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• Merge pull request NOAA-EMC#27 from marshallward/cpu_clock_sync_bugfix

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• Merge branch 'dev/gfdl' into consortium_fig_update

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• Merge pull request NOAA-EMC#31 from marshallward/consortium_fig_update

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• Eliminate unneeded diagnostic arrays

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• MOM_sponge cleanup

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• Use G%Rad_Earth_L in mct and NUOPC cap code

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• +Rescale some sea-surface height variables to [Z]

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• Correct the units in two comments

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• +Rescaled optics%opacity_band

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• Merge branch 'dev/gfdl' into opacity_rescale

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• +(*)Avoid segmentation faults if PEN_SW_NBANDS = 0

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• Ice dynamics (NOAA-EMC#35)

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• Adding temperature restore capability for SPEAR. (NOAA-EMC#36)

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Commits on Dec 19, 2021

• +Add US args and rescale dt arg to generic tracers

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• Corrected the unit documentation for 31 variables

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• +Rescale tides and ramp-up times

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• Merge branch 'main' into main_to_dev_gfdl

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• Merge pull request NOAA-EMC#47 from marshallward/main_to_dev_gfdl

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• (*)Removed problematic offline tracer lines

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• Fix badge URL for codecov

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• Merge branch 'dev/gfdl' into offline_tracer_fix

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• Merge branch 'dev/gfdl' into offline_tracer_fix

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Commits on Dec 23, 2021

• Bugfix - calculate density integrals in ALE mode w/ pressure_reconstruction=0

  

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• Update MOM_PressureForce_FV.F90

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• Correct comments describing generic_tracer args

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• Fixes an uninitialized logical in FMS_cap

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• Eliminate unneeded diagnostic arrays in CorAdCalc

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• Merge branch 'dev/gfdl' into opacity_rescale

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• Merge pull request NOAA-EMC#43 from Hallberg-NOAA/opacity_rescale

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• Merge branch 'dev/gfdl' into offline_tracer_fix

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• Deleted commented out offline tracer lines

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• (*)Use por_face_area in zonal_face_thickness

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• Merge branch 'dev/gfdl' into offline_tracer_fix

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• Merge pull request NOAA-EMC#37 from Hallberg-NOAA/offline_tracer_fix

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Commits on Jan 3, 2022

• Option to homogenize forces and fluxes (NOAA-EMC#51)

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Commits on Jan 6, 2022

• Hydrostatic initialization in ice cavities (NOAA-EMC#41)

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Commits on Jan 8, 2022

• Rewrite horizontal regridding to use netCDF wrapper functions (NOAA-EMC#48)

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Commits on Jan 10, 2022

• Clean up non-standard syntax and whitespace

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• Standardize code in calc_sfc_displacement

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Commits on Jan 24, 2022

• +(*)Change the remapping dzInterface argument sign

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Commits on Jan 25, 2022

• Avoid divide by zero in horizontal_viscosity() with better_bound_kh

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• Fix soft-conventional index capitalization in horizontal_viscosity()

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Commits on Jan 26, 2022

• Esmg docs (NOAA-EMC#57)

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Commits on Feb 8, 2022

• read_variable_2d modified to accept 3 or 4 dims

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Commits on Feb 16, 2022

• Diabatic driver: energetic_PBL -> ePBL, flag check

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Commits on Feb 17, 2022

• Merge pull request mom-ocean#1556 from NOAA-GFDL/dev-gfdl-main-candidate-2022-01-29

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• Merge remote-tracking branch 'GFDL/main' into feature/update-to-main-20220217

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