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Dev master candidate 2018 04 22#912

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adcroft merged 225 commits intodev/mastermom-ocean/MOM6:dev/masterfrom dev-master-candidate-2018-04-22mom-ocean/MOM6:dev-master-candidate-2018-04-22Copy head branch name to clipboardApr 25, 2019

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Commits on May 3, 2018

• Merge pull request #3 from NOAA-GFDL/dev/gfdl

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Commits on Aug 17, 2018

• Updates to idealized hurricane routine for non-SCM (full domain) simulations

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Commits on Sep 5, 2018

• Effort to decimate the diag output at runtime

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Commits on Sep 10, 2018

• Merge branch 'dev/gfdl' into user/bgr/ideal_hurricane_config

  

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Commits on Sep 18, 2018

• Diag decimation prototype, coarsening by a factor of 2

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Commits on Sep 19, 2018

• Diag decimation prototype, works for native and _z

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Commits on Sep 27, 2018

• Diag decimation prototype, requesting in diag_table

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• Diag decimation prototype, requesting in diag_table

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Commits on Oct 1, 2018

• Diag decimation prototype, fixing memory leaks

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Commits on Oct 4, 2018

• Diag decimation prototype, aggregating methods

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Commits on Oct 5, 2018

• Diag decimation prototype, fixed masks and cleanup

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Commits on Oct 10, 2018

• Diag decimation prototype, fix masks for non-native grids

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• Numerous modifications to improve Ideal hurricane config and wave functionality in such cases.

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• Merge branch 'dev/gfdl' into user/bgr/ideal_hurricane_config

  

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Commits on Oct 14, 2018

• Updates to use the new idealized_hurricane test case.

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• Renaming SCM_idealized_hurricane.F90 to Idealized_Hurricane.F90

  

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• Updates to idealized hurricane code style.

  

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Commits on Oct 15, 2018

• Diag decimation prototype, first attemp at general algorithm

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Commits on Oct 17, 2018

• Merge branch 'dev/gfdl' into user/bgr/ideal_hurricane_config

  

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• Add missing logical condition for v_extensive

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• Trailing whitespace

  

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Commits on Oct 18, 2018

• Diag decimation prototype, decimation algorithm extension

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Commits on Oct 19, 2018

• Merge pull request #861 from nikizadehgfdl/patch-1

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• Rescale ISOMIP MIN_THICKNESS via get_param

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• +Changed the units of Kd_add from m2 s-1 to Z2 s-1

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• +Refactored Kelvin_set_OBC_data

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Commits on Oct 21, 2018

• Corrected scaling in hchksum calls for Kd_int

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• Corrected scaling in hchksum call for g_prime

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• +Added handling of underflows in kappa_shear

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• Merge branch 'dev/gfdl' into test_depth_units

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Commits on Oct 22, 2018

• Merge branch 'user/bgr/ideal_hurricane_config' of https://github.com/breichl/MOM6 into breichl-user/bgr/ideal_hurricane_config

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• Merge branch 'breichl-user/bgr/ideal_hurricane_config' into dev/gfdl

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• Merge branch 'dev/gfdl' into test_depth_units

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• Fixes bug (crash) if Langmuir number output is enabled but waves CS is not associated

  

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• Corrected chksum rescaling for e in thickness_diffuse

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• Recast SCM_CVMix_tests_TS_init to work in units of Z

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• +Recast MOM_wave_interface to work in units of Z

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Commits on Oct 23, 2018

• Diag decimation, fixed the decimated fields indices

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• Merge pull request #863 from breichl/user/bgr/KPP-LToutput_bugfix

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• Fix a typo in the description of USE_LEGACY_DIABATIC_DRIVER

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• Add missing register* and safe_alloc* for wd

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• Merge branch 'dev/gfdl' into nikizadeh_diag_decimation

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• Corrected openMP directive errors in recent commit

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Commits on Oct 24, 2018

• (*)Fixed dimensional scaling for Boussinesq Flather

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• Add missing diag_id check before post_data

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• Merge pull request #868 from nikizadehgfdl/patch-2

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Commits on Oct 25, 2018

• Diag decimation, check the commensurate condition

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• Merge pull request #864 from Hallberg-NOAA/test_depth_units

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• Merge pull request #866 from Hallberg-NOAA/fix_openMP

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• Merge pull request #867 from Hallberg-NOAA/fix_OBC_rescaling

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• Merge branch 'fix_wd_register' of https://github.com/gustavo-marques/MOM6 into gustavo-marques-fix_wd_register

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• Merge branch 'gustavo-marques-fix_wd_register' into dev/gfdl

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Commits on Oct 26, 2018

• (*)Fixed bugs in EBT mode wave speed calculation

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• Rescale values reported by PointAccel

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• +Add conversion argument to register_static_field

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• +Rescale depth inside of MEKE_lengthScales_0d

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• Simplify MOM_diagnostics code

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• Recast MOM_sum_output to work in units of Z

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• Use local variables to rescale in MOM_Point_Accel

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• Diagnostics downsampling, implement suggestions in reviews

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• Merge pull request #873 from NOAA-GFDL/dev-master-candidate-2018-10-15

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• Diagnostics downsampling, fix the issue for symmetric case

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Commits on Oct 29, 2018

• +Find diapyc_energy_req column height changes in Z

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• Find energetic_PBL column height changes in Z

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Commits on Oct 30, 2018

• Downsample Diagnostics, fix symmetric memory case

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• +Added m_to_Z arg to horiz_interp_and_extrap_tracer

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• +Recast MOM_ALE_sponge to work in units of Z

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Commits on Nov 1, 2018

• +Recast MOM_diag_to_Z to work in units of Z

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• Clarified comments in Idealized_Hurricane

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Commits on Nov 2, 2018

• Combined scaling factors in build_adapt_column

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• Corrected comments in build_sigma_column

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• Diagnostics Downsample, implement Hallberg's suggestion

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• +Pass max_depth to initialize_regridding in Z

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• Corrected comments in build_zlike_column

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• Set coord_adapt and coord_slight parameters in H

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• Calculate height-related diagnostics in Z

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• Merge branch 'dev/gfdl' into test_depth_units

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Commits on Nov 6, 2018

• +Add MOM_unit_scaling module

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• +Replace GV%m_to_Z with US%m_to_Z

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• +Replace GV%Z_to_m with US%Z_to_m

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• +Pass unit_scale_type argument to step_MOM_thermo

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• Corrected openMP directives

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• Rescale HMIX_SFC_PROP via get_param

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• Update cache dir for /lustre/f2

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• Merge branch 'dev/master' into dev/gfdl

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• Added parameter in Neverland_initialization which allows to remove continents

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• Merge branch 'fix_EBT_wave_speed' of https://github.com/Hallberg-NOAA/MOM6 into Hallberg-NOAA-fix_EBT_wave_speed

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• Merge branch 'Hallberg-NOAA-fix_EBT_wave_speed' into dev/gfdl

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• Merge branch 'test_depth_units' of https://github.com/Hallberg-NOAA/MOM6 into Hallberg-NOAA-test_depth_units

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• Merge branch 'Hallberg-NOAA-test_depth_units' into dev/gfdl

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• Merge branch 'dev/master' of https://github.com/NOAA-GFDL/MOM6 into dev/gfdl

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• +Added run-time parameters for benchmark test case

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• +Added a run-time parameter for circle_obcs

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• +Added the INTERFACE_IC_QUANTA runtime parameter

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• +Added run-time parameters for sloshing test case

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• Added a comment in USER_initialize_thickness

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Commits on Nov 7, 2018

• Merge branch 'dev/gfdl' of https://github.com/MFJansen/MOM6 into MFJansen-dev/gfdl

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• Merge branch 'dev/gfdl' into use_unit_scaling_type

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• Merge branch 'use_unit_scaling_type' into document_user_params

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• Merge branch 'MFJansen-dev/gfdl' into dev/gfdl

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• Merge branch 'use_unit_scaling_type' of https://github.com/Hallberg-NOAA/MOM6 into Hallberg-NOAA-use_unit_scaling_type

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• Merge branch 'Hallberg-NOAA-use_unit_scaling_type' into dev/gfdl

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• Merge branch 'dev/gfdl' into document_user_params

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Commits on Nov 8, 2018

• Merge branch 'Hallberg-NOAA-document_user_params' into dev/gfdl

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• Corrected an openMP directive

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• +Recast ice_shelf code to work in units of Z

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Commits on Nov 9, 2018

• +Changed units of ustar from m/s to Z/s

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• Split excessively long lines

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Commits on Nov 12, 2018

• Merge pull request #877 from Hallberg-NOAA/document_user_params

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• modified: src/parameterizations/lateral/MOM_MEKE.F90

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Commits on Nov 13, 2018

• +Changed units of fluxes%ustar_shelf to Z/s

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• Merge branch 'dev/gfdl' into rescale_ustar

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• modified: src/parameterizations/lateral/MOM_MEKE.F90

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• modified: src/parameterizations/lateral/MOM_MEKE.F90

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• modified: src/parameterizations/lateral/MOM_MEKE.F90

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Commits on Nov 14, 2018

• modified: src/parameterizations/lateral/MOM_MEKE.F90

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• Corrected 8 comments

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• +Add US arg to set_up_ALE_sponge_vel_field_varying

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• +Rescaled variables in MOM_internal_tides

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• +Rescaled variables in MOM_tidal_mixing

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• +Add unit_scale_type argument to tracer_Z_init

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• Added perturbations to initial layer thicknesses in Neverland

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• +Add unit_scale_type argument to diag_remap_update

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Commits on Nov 15, 2018

• +Add unit_scale_type arg to MOM_initialize_fixed

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• +Add unit_scale_type arg to MOM_sum_output_init

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• +Add optional unit_scale_type arg to initialize_masks

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• +Eliminated Zd_to_m from grid types

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• Recast internal MOM_barotropic variables into Z

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• Merge pull request #880 from Hallberg-NOAA/rescale_ustar

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• Merge pull request #881 from Hallberg-NOAA/correct_comments

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• Merge branch 'topoMEKE' of https://github.com/hlkong/MOM6 into hlkong-topoMEKE

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• Corrected soma comment/doxygen syntax

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• Merge branch 'dev/gfdl' into eliminate_Zd_to_m

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• Fixed line wrap in new parameter documentation

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• +Rescale depth in DOME_initialize_topography

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• +Rescale depth in ISOMIP_initialize_topography

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• +Rescale depth in Kelvin_initialize_topography

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• +Rescale depth in Phillips_initialize_topography

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• +Rescale depth in benchmark_initialize_topography

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• +Rescale depth in shelfwave_initialize_topography

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• +Rescale depth in USER_initialize_topography

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• Better comments in initialize_topography routines

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• +Rescale topography in MOM_shared_initialization

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• Rescale topography during initialization

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• Merge branch 'dev/gfdl' of https://github.com/MFJansen/MOM6 into MFJansen-dev/gfdl

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• Added run-time parameter for Neverland perturbation

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• Adds random noise option for Neverland IC

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• Merge branch 'MFJansen-dev/gfdl' into dev/gfdl

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• Merge branch 'eliminate_Zd_to_m' of https://github.com/Hallberg-NOAA/MOM6 into Hallberg-NOAA-eliminate_Zd_to_m

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• Merge branch 'rescale_topography' of https://github.com/Hallberg-NOAA/MOM6 into Hallberg-NOAA-rescale_topography

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• Merge branch 'Hallberg-NOAA-rescale_topography' into dev/gfdl

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• This update fixes compilation issues of ESM

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• Extended comments to clarify Z units

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• Added comments explaining the '~>' notation

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• Renamed internal variables in EF4

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• Extended comments to clarify H units

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• Reduced use of square brackets in comments

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• Further reduced use of square brackets in comments

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• Use square-bracket syntax in unit documentation

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• Updated comments explaining the '~>' notation

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• Use square-brackets in height documentation

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• Use square-brackets in thickness documentation

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• Document additional thickness variable units

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• Document more variable units with square brackets

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• Document velocity units with square brackets

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• Document frequency units with square brackets

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• dOxyGenize ice_solo_driver/MOM_surface_forcing.F90

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• Documented miscellaneous variable units

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• Documented density variable units

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• Documented temperature variable units

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• Documented units of 280 more variables

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• Documented units of 110 core variables

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• Documented units of 50 grid variables

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• Documented 300 miscellaneous variable units

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• Documented 288 parameterization variable units

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• Documented 116 tracer variable units

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• Documented 170 variable units

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• Documented 93 thermodynamic variable units

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• Merge pull request #886 from Hallberg-NOAA/unit_rescale_comments

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• Merge branch 'dev/gfdl' into nikizadeh_diag_decimation

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• Diagnostics downsampling, shorten line more than 120 chars long

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• Merge branch 'dev/master' into dev/gfdl

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• +New variants of safe_alloc_ptr & safe_alloc_alloc

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• Trap or deal with instances when dt=0 in diabatic

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• +Opt args to step_MOM can override DIABATIC_FIRST

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• Fix bug causing openmp answers change

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• Correct thermo clock with update_ocean_model calls

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Commits on Mar 12, 2019

• changes vector notation and fixes typos

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• fixes typo and adds Angus link

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• some more typos and a few nablas that were left unbolded

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• adds parentheses in general-coordinate versions of temp and sal

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• adds parentheses in general-coordinate versions of temp and sal

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• fixes notation in mom_hor_visc module documentation

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• Merge pull request #897 from nikizadehgfdl/nikizadehgfdl/fix_openmp_answers

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• Merge pull request #896 from Hallberg-NOAA/coupling_options

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• fixes geopotential gradient term in governing eqs.

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• fixes geopotential gradient term in eqs and typo in \nabla def in notation.

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• undo changes in MOM_hor_visc.F90 doc

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• Merge pull request #869 from nikizadehgfdl/nikizadeh_diag_decimation

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• Merge pull request #901 from navidcy/UpdatesDocEquations

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• +Added dimensional rescaling of Coriolis parameter

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• Travis: switch to mpich2

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• Merge pull request #906 from adcroft/travis-switch-to-mpich2

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• Merge branch 'dev/gfdl' into rescale_Coriolis

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• Fix doxygen typos

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• Doxygenized down sampling routine in diag_mediator

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• Merge pull request #5 from NOAA-GFDL/dev/gfdl

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• Merge pull request #905 from Hallberg-NOAA/rescale_Coriolis

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• Logic to flag obsolete restart fields

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• Registering Kd_turb and Kv_turb as obsolete restart fields

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• Merge pull request #907 from adcroft/doxy-down-sampling

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• dOxygenize for obsolete restarts, tweak to FATAL message

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• Merge pull request #908 from jkrasting/user/jpk/trap-kd-turb

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Commits on Apr 16, 2019

• Re-factor of Travis-CI usage

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• Set ca13csed to zero at k>1

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• Merge pull request #910 from jkrasting/zero_out_13C_cased

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• Merge pull request #909 from adcroft/travis-stages

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Commits on Apr 23, 2019

• +Added missing US arguments to nuopc_cap code

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