dev/master/2016.03.22

- 35a0204 MOM6: Updated OpenMP directives
  - NOAA-GFDL/MOM6@69d9e15 Updated OpenMP directives
  - NOAA-GFDL/MOM6@15cc139 Corrected NOAA-GFDL/MOM6@aba072c
  - NOAA-GFDL/MOM6@aba072c Fixed restarts with the new mixedlayer_restrat + DIABATIC_FIRST=False
  - NOAA-GFDL/MOM6@b4f8cdb Bug fix: Uninitialized data in Kd_ePBL
- 63167ac SIS2: OpenMP updates
- d2e3037 MOM6: Added link between CMOR/native names in available_diags
- 1503160 Log spatial cell_methods in available_diags
- 60355e6 MOM6: Added CMOR versions of _z_new diagnostics
  - NOAA-GFDL/MOM6@bd04faa updates available_diags.
  - NOAA-GFDL/MOM6@bd04faa Added CMOR versions of _z_new diagnostics
  - NOAA-GFDL/MOM6@73637b4 Added CF-convention "cell_methods" attribute to output
  - NOAA-GFDL/MOM6@fcf70eb Refactored MOM_diag_mediator to use remapping_core_h
  - NOAA-GFDL/MOM6@e82522b Symmetrized PLM and PPM pointwise evaluation
  - NOAA-GFDL/MOM6@c0dc2c2 Arguments to remap_all_state_vars() include h_new
  - NOAA-GFDL/MOM6@e28e854 Moved more parameters into set_regrid_params()
  - NOAA-GFDL/MOM6@3077ecb Added remapping_set_param(), rewrote initialize_remapping()
  - NOAA-GFDL/MOM6@653775f Deleted unused s/r in remapping
  - NOAA-GFDL/MOM6@685b1e7 Use remapping_core_h() in remap_all_state_vars()
  - NOAA-GFDL/MOM6@6b33a01 Grouped debugging call to measure_input_bounds() in MOM_remapping.F90
  - NOAA-GFDL/MOM6@e3027af Removed debugging line MOM_remapping.F90
  - NOAA-GFDL/MOM6@b1567da +Removed thickness unit conversions from ocean_grid_type
  - NOAA-GFDL/MOM6@89bfbbc +Removed Angstrom and H_subroundoff from ocean_grid_type
  - NOAA-GFDL/MOM6@d12b5f1 +Removed Boussinesq and Rho0 from ocean_grid_type
- 5b845b9 Updated SIS parameter docs in land_ice_ocean_LM3_SIS2
- 151dfe1 Updated parameter docs in land_ice_ocean_LM3_SIS2
- b20f2ef MOM6: +Moved get_flux_units to MOM_verticalGrid
- 276938f SIS2: +Separated set_hor_grid from set_ice_grid

dev/master/2016.03.02

- Fixed restart problem with new PBL depth used in mixed-layer restratification (4d54998).
- Added work-around for ice-ocean coupled instability triggered by strong ice-ocean
  stresses (90ac4f6).

- 0a3197c SIS2: Updated OMP directives
- 7699d43 Merge branch 'user/jpk/OM4_05_analysis_mods' into dev/master
- 4d54998 MOM6: (*)Bugfix: update halo after restarts for mixed_layer_restrat
- 90ac4f6 SIS2: Added parameter for the minimal inertial thickness of ocean
- 08499ae Added error messages for some common failures
- 0b71b84 Set-up modules environment for GFDL systems
- bd77926 Simple CSH script to repair automated frepp analysis
- f9b8b0c Updates for dora web analysis
- 2c9c497 Updated land_ice_ocean_LM3_SIS2 MOM_parameter_doc missed in previous commit
- ea37d37 Generic tracer update from JGJ
- ffe9724 Bring ESM4 SIS2 up-to-date
- 12cabc9 Updated .frepp files
- c344903 Analysis mods for use with multiple grids
- 0816e7d Analysis script to compute y-direction heat transport
- 33acab5 MOM6: *Changed fluxes%p_surf_SSH to fluxes%p_surf_full
- eca2acd MOM6: Added fluxes%p_surf_SSH
- 43b83c3 MOM6: Fixed halo in MLD passed to MLE from PBL
- 64738c8 (*)OM4_025: Correctly damp gravity waves due to sea-ice rigidity
- a970b85 OM4_025: Added monthly t,s,u,v to ocean_month_z
- 1a17c37 Removed 8 test cases from routine testing.
- 5c667a5 SIS2: Updated SIS_parameter_doc.all for land_ice_ocean_LM3_SIS2
- 4979616 SIS2: *Enabled SIS2_FILLING_FRAZIL for Baltic test case
- c47e7e5 Removed unused parameters from Baltic SIS_input
- 4d2f30a +Added the SIS2_FILLING_FRAZIL option
- e42d419 Updated answers in land_ice_ocean_LM3_SIS2/OM_360x320_C180
- 80b4fc7 *Changed OCEAN_SURFACE_STAGGER to "C" for OM4_025

Generic tracer update from JGJ

  - See MOM6 commit ae530a2e

dev/master/2016.02.03

- SIS2: Reordered flux accumulation in SIS2_thermo
- OM4: Enabled river heat content in ALE mode
- Major re-factor of vertical remapping (cf 86c37fe, 9368f46, caae885, 6628d63, 86c37fe)

- 98950b6 MOM6: *Changed default for OCEAN_SURFACE_STAGGER to "C"
- bfa9db3 MOM6: *Corrected arguments in 3 calls to set_time
- 21b878b Reduced stats file lengths for single_column cases
- 86c37fe *MOM6: Bounds edges after limiting
- 6628d63 *MOM6: Ensure bound_edge_values() is bounded!
- ae26132 MOM6: Added option REMAP_BOUND_INTERMEDIATE_VALUES
- 8b6f862 *Updated land_ice_ocean_LM3_SIS2/OM_360x320_C180 missed in last commit
- 5b780b1 SIS2: *Reordered flux accumulation in SIS2_thermo
- eb9bb7e Edits to OMIP diagnostic long names.
- 7d667b9 Merge branch 'dev/master' of github.com:NOAA-GFDL/MOM6-examples into dev/master
- c6dac00 Edits to the comments in this table for clarity.
- caae885 *MOM6: Switched to remap_via_sub_cells() method
- 8ec068f Merge pull request NOAA-GFDL#71 from NOAA-GFDL/user/nnz/fix_EddyKineticEnergyScript
- 6470d1b Use full grid ocean_static.nc
- f24b9a1 MOM6: Added ability to check result of remapping
- 9368f46 *MOM6: Re-factored PPM_functions.F90
- 2147c23 *MOM6: Rewrote PLM to completely satisfy bounds
- a9e3d6c MOM6: Added ability to check reconstructions
- 6619c78 (*)MOM6: Enabled river heat content in ALE mode
- cb6cb4f MOM6: Merge branch 'bmater-ray_tracing' into dev/master
- 0166793 Added "protected" comment to OM4_025 diag_table
- 0c51a85 Fix the analysis script to use ocean_5daily.nc
- d00206c Added missed MOM_parameter_dco in last commit
- 6b67b20 MOM6: MOM_parameter_doc.all changes from merge
- 94133e5 Merge pull request NOAA-GFDL#66 from tahvildarzadeh/patch-2

dev/master/2016.01.16

OM4_025 configuration changes:
- Added sea-ice rigidity that damps gravity waves
- Also added back weak AH_VEL_SCALE for biharmonic viscosity
- Changed C_P to more sensible value
- Activated topography edits including for Caribbean and Red Sea.

- 3396c8f MOM6: Fix a memory leak for diagnostic Kd_user
- e29c4a9 OM4_025: Damp gravity waves due to sea-ice rigidity
- b835145 OM4_025: Changed heat capacity C_P
- d2d224e Added topo edits to baseline OM4_025
- ccb7caa Updated MOM_params missed in last commit
- 48c71a2 MOM6: Check if regrid target densities are set
- 2801b5d MOM6: *Use implicit temporal weights for ALE regridding
- b0c5796 Analysis: Create SSH variance from 5 daily fields
- f457411 OM4_025: Added Caribbean and Red Sea topography edits
- 01ec404 Added annual diagnostics and salte_restore diagn.
- 7af8687 Merged with diag_table.CMIP6 and reorganized.
- 17097ff Table is obsolete: merged into diag_table.MOM6
- 5b23e4d File now placed in OM4_025 test directory.
- ae3df83 Updated notebook analysis for straights transport
- 80400df MOM6: Added call to set_filter_depths() from MOM_ALE.F90
- d1d232a SIS2: Allow SIS2 to compile with -openmp
- ac4f991 Updated parameter_doc files missed in last commt
- 0a09f4e MOM6: +Added module MOM_hor_index and hor_index_type.
- ec01382 Added CPU_stats.* after labels added to ENERGYFILE
- 1887444 MOM6: Changed the default for ENERGYFILE to ocean.stats

dev/master/2015.12.17

- cb6db21 needed for OM4_025 stability with MEKE.
- New features for SLight coordinate.

cb6db21 OM4_025: Changed KHTH_MAX_CFL to stabilize model with KHTH>0
e6ce2a2 Updated missing MOM_parameter_doc.all
0408d02 MOM6: +Set thickness diffusivity max CFL at run-time
1c42712 MOM6: *Adjust effective depth of forcing for strong mass loss
228aa4b Added missed MOM_parameter_doc.all
bcdb0c2 MOM6: +Added maximum layer thicknesses
fc10e08 MOM6: *Corrected limited fraction of forcing when losing mass
0490e6a MOM6: Added run-time parameters for bounding surface forcing
3eb7007 Updated MOM_parameter_doc for land_ice_ocean example
6045de1 Added SLight MOM_override file for OM4_025
13344ce +Made global_ALE/hycom use maximum interface depths
290f838 Analysis: Fixing MLD monthly analysis
c08ab93 Merge branch 'dev/master' of github.com:CommerceGov/NOAA-GFDL-MOM6-examples into dev/master
b8c265c Added halocline corrections to global_ALE/SLight
5ad40ae MOM6: +Improve resolution in haloclines and light water
a534fef Added preprocessing scripts for OM4_05
432a900 OM4_033: Added md5sums.txt
2195e01 New sample data for more thorough testing.
58f6586 Merge branch 'dev/master' of github.com:CommerceGov/NOAA-GFDL-MOM6-examples into dev/master
6353528 Updated diagnostics using longer time series example.
846dc30 Added preprocessing scripts for OM4_033
f583750 Merge branch 'angus-g-tracer-vardec' into dev/master
d5d76ef Merge branch 'user/mjh/land_ice_ocean_LM3_SIS2' into dev/master

MOM6: *Corrected limited fraction of forcing when losing mass

From commit NOAA-GFDL/MOM6@f8a2aea:
- When losing mass and the mass loss would consume most of that available
  in the layer we limit the fraction of forcing to use. However, we were
  basing the test on the full forcing rather than on the scaled forcing.
  This commit fixes that so we limit based on what we were about to use.
- Should only matter for configurations with thin surface resolution.
  Actually only changed answers in:
  - ocean_only/global_ALE/hycom
  - ocean_only/global_ALE/SLight

dev/master/2015.11.30

- Optimization of remapping code (ALE) changed roundoff (e6537af).
- New coordinate options.

- ff9662a MOM6: Added CMOR diagnostic "vo" back to _z output
- 202a313 Correct Barents opening: vm,vmo --> um,umo
- 171c3ed iPython sections mass transport time series
- b49187d Fixes for OM_360x320_C180
- 5a1445e Redirected links to .datasets in OM_360x320_C180
- c6eefe6 Delete README
- f4aa66e Delete README~
- 75ac608 Delete LM3.0_MOM6z_C180_pi_spinup_SP1.xml
- 2ef4192 Delete LM3.0_FLOR2_C180_pi_spinup_SP1
- 471ec0e Update diag_table
- 1520655 New land_ocean_seaice experiment.
- 55d03fb Merge branch 'dev/master' of github.com:NOAA-GFDL/MOM6-examples into dev/master
- 4796a6c New CMOR diagnostic for neutral diffusivity.
- 5fca06e New CMOR diag diftrelo and Khtr_h
- 9c65565 MOM6: *Changed build_grid_SLight to use min_thickness
- 9bf2ecc OM4_025: Increased max_files in diag_manager_nml
- 429656c OM4_025: Fixed mismatched filenames in diag_table
- 59be3db Using FNC1 to specificy dz in OM4_025
- 8ee03b0 Commented out unregistered diagnostics
- 488930a New Sections; reduce month file size; increase ann
- 0cc63ce Added the ocean_only/global_ALE/SLight test case
- 2f3f29e Updated atmos_null submodule
- 6de925f LM3: Updates to work with gnu/pgi and new land-ice-ocean model
- e6537af *MOM6: Refactored evaluation of polynomials in remapping
- 3bad3a8 Merge pull request NOAA-GFDL#64 from NOAA-GFDL/user/jpk/web_analysis_refactor
- 164ffc7 Added line to call main() function
- 3fefa94 Refactoring of analysis scripts for web use
- 7ded54b New grid diags; static diagns in available.diagn
- c95027e MOM6: Added SLIGHT regridding string and coordinate mode
- 929ab54 Testing grid time-filer in global_ALE/hycom
- 9f9a1d4 Updates to tracer budget diagnostics

dev/master/2015.11.12

Minor revs

- 8f374e1 Analysis: Updated MOC script to work on z-output file
- 5ea8e3f Diagn fix for remap tendency: missing dimensions
- 057ca9f MOM6: Merge branch 'bmater-ray_tracing' into dev/master

dev/master/2015.11.09

- Bugfix in MEKE advection
- Added various tweaks for hybrid coordinates
- New diagnostics
- Fixes for analysis

b6ac91c MOM6: Uninitialized variable in MEKE advection
c402677 Added REGRID_COMPRESSIBILITY_FRACTION hybrid coordinates
e891afd MOM6: Added time-filter for regridding
da126e5 Added some more folders to .gitignore
40dbba1 Merge pull request NOAA-GFDL#63 from NOAA-GFDL/user/jpk/xyave_diagtable_entries
a67586f Added xyave diagnostic diag_table entries
d65ce31 Merge pull request NOAA-GFDL#59 from NOAA-GFDL/user/jpk/sea-ice-analysis-fix
221defe Merge pull request NOAA-GFDL#61 from NOAA-GFDL/nikizadehgfdl-patch-2
0f930f8 Merge pull request NOAA-GFDL#62 from NOAA-GFDL/nikizadehgfdl-patch-3
9f0d57e Added Kd_interface to OM4_025 diag_table
dd460f1 MOM6: Merge branch 'user/jpk/z-layer_average_diags' into dev/master
9e5cdc8 Diagn tracer tendencies from vert remapping
f430696 Update EddyKineticEnergy.py
72431a8 Update MOM6_refineDiag.csh
b7cc806 Added if-test for multiple area variable names
645dd19 Diagn (umo_2d,vmo_2d) = vertical sum (umo,vmo)
415e962 Added diagnostics (x,y) advective heat transport
6c079d3 New diagn for mass transports
8992627 Diagnostics: net T/S tendency & lateral advection
4baf7be Diagnostics: net T/S tendency & lateral advection
1435805 MOM6: Corrected documentation for MIXEDLAYER_RESTRAT
1f36497 Updated coupled components to ulm_201510
6dd2356 Tendency diagn for ALE version of diabatic diffuse
9397c14 Fix for Hosoda analysis in post-processing