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Candidate for dev/master 2017-08-17#579

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adcroft merged 183 commits intodev/mastermom-ocean/MOM6:dev/masterfrom candidate-dev-master-2017-08-17mom-ocean/MOM6:candidate-dev-master-2017-08-17Copy head branch name to clipboardAug 22, 2017

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Commits

Commits on Jul 19, 2016

• Add to generate Neverland using the benchmark source. We change thickness, topography and ts.. stuffs.

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• Add Neverland topography to the Neverland initialization

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Commits on Jul 20, 2016

• Added a blank template Neverland_surface_forcing

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• Merge pull request #1 from adcroft/user/adcroft/add_neverland_winds_template

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• Add the forcing structure to Neverland.

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• Removed T/S initialization from Neverland

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• Refactored Neverland initial thicknesses

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• Added run-time parameters for bottom roughness

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Commits on Jul 21, 2016

• Fixed a typo on surface forcing in Neverland

  sinakhani

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• Update the surface forcing to include the ``off'' parameter

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Commits on Aug 22, 2016

• Adjust the Neverland wind stress near the Antarctica to fix some undesirable behavior.

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Commits on May 17, 2017

• Neutral positions by discontinuous PPM

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Commits on May 18, 2017

• Additional changes to make sure that code compiles. Development of the

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Commits on Jun 20, 2017

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

  

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Commits on Jun 22, 2017

• Bracketing fix for transform test. Changes answers. Closes #531

  

  Nicholas Hannah

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• Some initial changes for the neutral surface positions found using a discontinuous reconstruction

  

  Andrew Shao

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Commits on Jun 23, 2017

• Discontinuous T/S reconstruction still does not work correctly because

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Commits on Jun 26, 2017

• Code fix to remove 2nd call to extractfluxes1d when using ePBL.

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• Adding code changes that are part of previous commit.

  

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Commits on Jun 28, 2017

• Make changes based on python prototyping of the discontinuous version of

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• Fixed which pressure array is supposed to be used

  

  Andrew Shao

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Commits on Jun 29, 2017

• Discontinuous reconstruction of neutral diffusion is working better, but

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Commits on Jul 3, 2017

• Remove apostrophe from comments in MOM_forcing_type.F90

  

  Brandon Reichl

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• Merge branch 'user/bgr/BuoyFluxFix' into user/bgr/Fix_BuoyFlux_merged

  

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Commits on Jul 6, 2017

• Corrected the chksum scaling for pbce

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• Added chksum calls for h_u and h_v in btcalc

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• (*)Convert GV%Angstrom to units of H

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• Added Doxygen Comments

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

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• Add missing comment to MOM_forcing_type.F90

  

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Commits on Jul 7, 2017

• Merge pull request #546 from Hallberg-NOAA/dev/gfdl

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• Merge pull request #547 from CarolineCardinale/dev/gfdl

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• (*)close_param_file always closes the input files

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• Merge pull request #548 from breichl/user/bgr/Fix_BuoyFlux_merged

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

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• Merge pull request #549 from Hallberg-NOAA/dev/gfdl

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• Merge branch '531-transform-bracketing-fix' of https://github.com/nicjhan/MOM6 into nicjhan-531-transform-bracketing-fix

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• Merge branch 'nicjhan-531-transform-bracketing-fix' into dev/gfdl

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• OpenMP fixes for MOM_diabatic_aus.F90

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• Merge pull request #551 from adcroft/fix-openmp-diabatic-aux

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Commits on Jul 11, 2017

• Updated the discontinuous reconstruction, but not working as expected, so

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Commits on Jul 12, 2017

• Added Doxygen Comments

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  Caroline Cardinale

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Commits on Jul 13, 2017

• Try to reduce RTD memory usage

  adcroft

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• Turned off gen-HTML and listings

  adcroft

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• Return to orig w/o HTML

  adcroft

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• Removed program listing

  adcroft

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• Newer algorithm works away from top and bottom boundaries

  

  Andrew Shao

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• Fixed conflict with upstream

  

  Andrew Shao

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• Neutral surface discontinuous reconstuction with no boundary extrap

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  Andrew Shao

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

  

  Andrew Shao

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• Change module name variable from mod to mdl

  

  Andrew Shao

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Commits on Jul 14, 2017

• Avoid allocation/execution in horizontal_viscosity()

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• Restricts scaling/initialization of h to computational domain

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• Avoids building grids on land points

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Commits on Jul 16, 2017

• Avoid inviscid warning in single column mode

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• White-space.

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• Merge branch 'dev/master' into neverland-rebuild

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• Merge branch 'dev/gfdl' into neverland-rebuild

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• Fix white space in Neverland mods

  adcroft

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Commits on Jul 17, 2017

• Replace column reconstruction with functions from PPM_routines.F90

  

  Andrew Shao

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• Merge pull request #555 from adcroft/avoid-oob-hor-visc

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• Merge pull request #556 from adcroft/avoid-grid-building-on-land

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• Merge pull request #557 from adcroft/remove-blanket-h-initialization

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• Revert to ROMSish version of Raymond and Kuo OBC.

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• Merge remote-tracking branch 'remotes/gfdl/dev/gfdl' into user/ksh/open_bc

  kshedstrom

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• Replace more routines with those from MOM_remapping.F90

  

  Andrew Shao

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• Modification of OBLIQUE OBC.

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Commits on Jul 18, 2017

• Continue to replace discontinuous reconstruction with MOM_remapping

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  Andrew Shao

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

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Commits on Jul 19, 2017

• Merge pull request #558 from CarolineCardinale/dev/gfdl

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• Fixes to avoid errors when running doxygen on source

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• Merge branch 'fix-doxy-errors' into readthedocs

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• Updated pip requirements.txt

  adcroft

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• Need to figure out why some kind of spurious perfectly horizontal diffusion

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  Andrew Shao

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• Merge pull request #559 from adcroft/fix-doxy-errors

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• +Still more silly value fixes to OBCs.

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Commits on Jul 20, 2017

• Working as expected in z* (not rho) coordinate mode. However, do need to

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  Andrew Shao

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• (*) Rescale Regridding

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  CarolineCardinale

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• Fix trailing spaces

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  CarolineCardinale

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• Replace the linear interpolation used to calculate temperature gradients

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  Andrew Shao

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• Merge pull request #560 from CarolineCardinale/dev/gfdl

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Commits on Jul 22, 2017

• Included new functions to calculate the second derivatives of density from

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  Andrew Shao

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• Begin to add a rootfinder to solve for the position of a nuetral surface

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  Andrew Shao

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• Add scalar version of routines for higher order density derivatives

  

  Andrew Shao

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• Finished at least the original code for the refinement of neutral position.

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  Andrew Shao

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Commits on Jul 23, 2017

• Add an extractor routine for the remapping control structure

  

  Andrew Shao

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• Refinement of neutral surface position routine is ready to be tested

  

  Andrew Shao

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Commits on Jul 24, 2017

• Merge remote-tracking branch 'gfdl/dev/gfdl' into user/ksh/open_bc

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Commits on Jul 25, 2017

• Undoing last commit to MOM_open_boundary.

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• Avoids a SEGV when OBC are not in use with bi-harmonic friction

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• Merge pull request #561 from adcroft/avoid-segv-obc-hor-visc

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• +Updating OBC ORLANSKI and OBLIQUE algorithms.

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Commits on Jul 26, 2017

• *Merge branch 'user/ksh/open_bc' of https://github.com/ESMG/MOM6 into ESMG-user/ksh/open_bc

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• *Merge branch 'ESMG-user/ksh/open_bc' into dev/gfdl

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• Fix OpenMP in continuity_PPM

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• Root-finding algorithm works as expected. Need to replace the current

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Commits on Jul 27, 2017

• Added options to choose (exclusively) between bisection, Newton's, or

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• +More fixes for the silly value OBC stuff.

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• Fix to indices in OBC code.

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Commits on Jul 28, 2017

• (*)Fixes gprime(1) when no layer coordinates are set

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• +Cleaning out more dependence on outside h.

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• Further insulation from exterior values

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• Fixes openMP directives for recent OBC changes

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• Silly value stuff.

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• Merge branch 'fix-obc-vert-visc' of git://github.com/adcroft/MOM6 into adcroft-fix-obc-vert-visc

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• Merge branch 'adcroft-fix-no-layer-file-in-ALE-mode' into dev/gfdl

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• (*) Rescale apply_sponge

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• *Corrected parentheses in APE calculation

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Commits on Jul 31, 2017

• +More OBC stuff.

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

  

  Caroline Cardinale

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• Merge remote-tracking branch 'gfdl/dev/gfdl' into user/ksh/open_bc

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• (*)Merge branch 'Hallberg-NOAA-dev/gfdl' into dev/gfdl

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• Update MOM_EOS and MOM_EOS_Wright to include calculation of second

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• Update neutral diffusion with the following:

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

  

  Caroline Cardinale

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• Fixed some bugs in refine_nondim_position

  

  Andrew Shao

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Commits on Aug 1, 2017

• Merge pull request #565 from CarolineCardinale/dev/gfdl

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Commits on Aug 2, 2017

• Merge branch 'neverland-rebuild' into import-neverland

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Commits on Aug 3, 2017

• Realized that same_direction should be false if reached_bottom is true.

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• Write unit tests for refine_nondim_position. Next up is the discontinuous

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Commits on Aug 4, 2017

• Avoid FATAL for allowed combination of options

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• Fixes GMwork for buoyancy mode

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Commits on Aug 7, 2017

• Merge pull request #568 from adcroft/fix-meke-false-fatal

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• Merge remote-tracking branch 'gfdl/dev/gfdl' into user/ksh/open_bc

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• Removed commented code in MOM_continuity_PPM.

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• -Adds unit tests for discontinuous routines

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• Make convergence criteria runtime parameters as opposed to hardcoded

  

  Andrew Shao

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

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• Undo an unnecessary change in MOM_remapping.F90

  

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• Merge pull request #570 from adcroft/import-neverland

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Commits on Aug 8, 2017

• Allow runtime option for verbose output in neutral diffusion

  

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Commits on Aug 9, 2017

• Copied new coupler_types.F90 into solo_driver

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• Added a verbosity argument to aof_set_coupler_flux

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• +Added flux_init_OCMIP2_CFC

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• +Added call_tracer_flux_init

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• +Added verbosity argument to MOM_generic_flux_init

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• Set tracer surface values via coupler_type_set_data

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• +Call call_tracer_flux_init in ocean_model_flux_init

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• +Make extensive use of new coupler_type routines

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• +Added gas_fields_ocn argument to ocean_model_init

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• Rewrite logic. Only unit test failing now is two unstable mixed layers

  

  Andrew Shao

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• Removed trailing white space

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• Rearranged spawning of coupler_bc_types

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• Merge branch 'user/ksh/open_bc' of https://github.com/ESMG/MOM6 into ESMG-user/ksh/open_bc

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• Merge branch 'ESMG-user/ksh/open_bc' into dev/gfdl

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• Whew, finally figured out logic that passes all unit tests.

  

  Andrew Shao

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• +Allocate zero-sized values arrays in CT_spawn

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• (*)Added a missing line setting an OBC index

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

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• Merge branch 'dev/gfdl' into fix-gmwork-stacked-swe-mode

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• Doxygen updates for interface/isopycnal slope functions

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• *Fix dimension conversion for GMwork term

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Commits on Aug 11, 2017

• Merge pull request #569 from adcroft/fix-gmwork-stacked-swe-mode

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

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

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• Merge pull request #573 from Hallberg-NOAA/OBC_fix_index

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• Logic has been updated to be more consistent with the original code and

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  Andrew Shao

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• Cleanup some of the code and prepare for pull request

  

  Andrew Shao

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• Add option to use a different reference pressure other than the current

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  Andrew Shao

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• Accidentally had changed the bounds of a do-loop in the continuous case

  

  Andrew Shao

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• Turned off caching of objects for Travis

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• Option to use a globally constant reference pressure has been implemented.

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• Don't register diagnostics conSST absSSS, abssalt, contemp unless

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  Nicholas Hannah

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• Don't register h_pre_dyn, it is never posted. #574

  

  Nicholas Hannah

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• +Added name prefix argument to CT_register_restarts

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• +Created allocate_surface_state

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• (*)Made ustar_min have units of m/s, not H/s.

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• (*)Corrected the default for TOLERENCE_ENT

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Commits on Aug 15, 2017

• Create procedures for array and scalar inputs to EOS functions

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  Andrew Shao

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• Make logic explicit to avoid out-of-bounds error

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  Andrew Shao

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• Merge pull request #575 from nicjhan/574-diags-reg-no-post

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• Undo changes to continuous code that lead to answer-changes

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• Merge branch 'ndiff_update_neutral_position' of https://github.com/ashao/MOM6 into ashao-ndiff_update_neutral_position

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• Merge branch 'ashao-ndiff_update_neutral_position' into dev/gfdl

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Commits on Aug 16, 2017

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

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  Andrew Shao

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• Fix conflict due to changed MOM_EOS.F90 interfaces

  

  Andrew Shao

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Commits on Aug 17, 2017

• Pipeline: major refactor

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• Pipeline: fix cleanup stage

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• Merge pull request #576 from Hallberg-NOAA/dev/gfdl

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

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• Merge pull request #577 from ashao/ndiff_referenced_density

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

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• Patch for candidate-dev-master-2017-08-17

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