dev/master/2016.05.13

Major answer changes:
- Transition from c1 to c3 (onGaea)
  - 5a0939c *Updated answers to gaea c3
- Bugfix for double counting of viscosity
  - 3e4cae4 MOM6: *Answer changes due to bug fixed by B. Reichl
  - 41faa65 MOM6: *Answer changes due to bug fixed by B. Reichl

f9ee9bb MOM6: Updated to head of dev/master
4b7a999 icebergs: Updated to head of dev/master
95e3394 Added missed MOM_parameter_doc
d6e3b3b MOM6: +Added parameter to thicken viscous boundary layers
d2f1489 Use python/2.7.3_workstation on PAN nodes for analysis
bdfa235 MOM6: Added ISOMIP source code
d6b945f MOM6: Added run-time options for new remapping algorithms
96bfefd MOM6: Updated to latest commit
acfa2cf mkmf: now supports -l option for link flags
f4a95c0 MOM6: *Added halo updates with ALE_remap_init_conds
ab703cf *MOM6: Reverting 2f529dc8c7ao due to PGI problem
2f529dc *MOM6: Corrected remapping for zero-thickness source grid
156fbf5 MOM6: *Rewrote find_root for set_grid_metrics_mercator
f617960 Corrected typo in Windward passage diagn thetao
75c60a9 Merge branch 'dev/master' of github.com:NOAA-GFDL/MOM6-examples into dev/master
49affaf Mods to PEUC section to correspond to literature.
872833f *MKMF: Update intel template with -msse2
8c75f34 Repalced PNG in flow_downslope with jupyter notebook
cebb896 Merge pull request NOAA-GFDL#91 from NOAA-GFDL/user/mjh/OM_360x320_C180
5ead4b7 Merge branch 'dev/master' into user/mjh/OM_360x320_C180
d130360 Diagnostics modification for neutral diffusion
bbcd9c2 MOM6: Added comment about how G%max_depth is set
5a0939c *Updated answers to gaea c3
0cc12f9 Added submodule src/mkmf
83ddbce SIS2: Updated src/SIS2
ac7fa88 MOM6: Updated src/MOM6
3512a7b Fix version of fre_nctools for OM4_025 preprocessing
1b4acd1 Merge pull request NOAA-GFDL#85 from NOAA-GFDL/user/nnz/calc_variance_5daily_fix
db1a4a1 Merge pull request NOAA-GFDL#86 from NOAA-GFDL/user/mjh/gfdl_python_module_fix
6f41566  Fix GFDL python module problem
e98f26e include an extra data point in August
6c7a177 Fix script calc_variance.py to use ocean_5daily
17a07e8 Updated MOM_example_docs for mothballed examples
2e655c1 SIS2: *Corrected Celsius to Kelvin conversion
ae16691 SIS2: +Set LATENT_HEAT_FUSION at run time
a526063 SIS2 & coupler: +Eliminated cell_area and Ice%ice_mask
34ddb30 SIS2: *+G_EARTH and OMEGA are SIS2 runtime parameters
3e4cae4 MOM6: *Answer changes due to bug fixed by B. Reichl
41faa65 MOM6: *Answer changes due to bug fixed by B. Reichl
d81aa9a Updating MOM6 code
10ce4d6 SIS2: +Added CHANNEL_CONFIG and related code to SIS2
b43d6e0 Merge branch 'dev/master' of github.com:NOAA-GFDL/MOM6-examples into dev/master
8fa008a Diagnostics for SSS_sq and ndiff tracer transport
0914d9d SIS2: +Ported MOM6 code into SIS_fixed_initialization
caa8085 Refactored flow_downslope (DOME2d) initialization
8008b1f Undid SYMMETRIC_MEMORY_ in ice_ocean_SIS2 parameter docs
bdb9dd5 Updated MOM_parameter_doc for seamount/rho
7adf792 SIS2: Made GLOBAL_INDEXING a layoutParam & log G_EARTH
7cb786f Merge remote-tracking branch 'refs/remotes/origin/dev/master' into dev/master
a93ef3d MOM6: Made GLOBAL_INDEXING a layoutParam.
570b74f SIS2: +Added required GRID_CONFIG parameter to SIS2
51b0d76 Merge pull request NOAA-GFDL#83 from NOAA-GFDL/user/mjh/fix_ts_depth_integrals
72af50b Fix TS_depth_integrals.py to work with CMOR output
b14d5c3 MOM6: *Changed default KV_BBL_MIN to KV
792e227 MOM6: +Split MOM_coord_initialization from MOM_fixed_init
9349db3 SIS2: Changed to use MOM6-like code in setting masks
9f6157a MOM6: +Added MOM_initialize_coord
f5eea84 MOM6: +Moved WRITE_GEOM into initialize_MOM
c547a34 SIS2: +Added NIBLOCK and NJBLOCK
93f2c74 MOM6: +Added GLOBAL_INDEXING run-time parameter
06ec2c9 Added Davis strait and remove Canadian Archipelago
f994c3c MOM6: Fixed "rhoinsitu" diagnostic
5523e8e Corrected latitudes in Pacific EUC diagnostic
0a19709 MOM6: +Revised ocean_grid_type to harmonize with SIS2
909ff11 MOM6: Added diagnostics of potential and in-situ density
e8c8148 MOM6: *Separated initial profile from coordinate in sea mount test
371e828 Updated seamount example to use "ts_range" coordinate mode
c970ffd Merge pull request NOAA-GFDL#80 from NOAA-GFDL/user/jpk/smg_section_flow_plots
4a6bf80 Typo with Taiwan-Luzon Strait
56c7800 Added obs values and color coding
f00b5ae Merge pull request NOAA-GFDL#78 from NOAA-GFDL/user/jpk/smg_section_flow_plots
5d96bc3 Updated comment for argparse description
6295d96 Minor update to dora label
ce5baf7 Analysis script for plotting section flows
74081e2 MOM6: Changed the default for DEPTH_LIST_MIN_INC
fbcfd5b Added rsdo = penetrative SW diagnostic for CMIP6
663a870 Change diagnostic rsdo to rsdoabsorb as per CMIP6
da09ccc Shortened land_.../OM_360x320_C180 to 1 day
ecaccd0 Added static_input.nml for land.../OM_360x320_C180
bd75815 MOM6: *Replaced Area*GV%Angstrom*0.1 by Area*h_min
dcbeae8 *Updated seamount example to use GFS = 9.8
c1854b6 Merge pull request NOAA-GFDL#76 from NOAA-GFDL/user/jpk/minor_dora_updates
e7c5a3e 'centered' vs. 'autocenter' fix to TS_drift.py
3a511b5 Merge branch 'gustavo-marques-seamount_rho' into dev/master
a045362 *Added ocean.stats for seamount/rho
bdf1fdc Corrected MOM_parameter_doc for seamount/rho
9525f6c Merge branch 'seamount_rho' of https://github.com/gustavo-marques/MOM6-examples into gustavo-marques-seamount_rho
f498510 Merge pull request NOAA-GFDL#74 from NOAA-GFDL/user/jpk/dora_analysis_mods
4e7ae2b New coordinate, rho, for the seamount test.

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