dev/master/2016.12.13

- Fixed vmo diagnostics (inside 9b5691f)
- Changed OM4 answers in fcc4e6c, dca4e7c, 930c9cb.

66a5f99 Updated SIS2 available diags
930c9cb SIS2: *Set EULERIAN_TSURF=True
dca4e7c SIS2: *Set RECATEGORIZE_ICE=True
22c077f SIS2: Explicitly set EULERIAN_TSURF & RECATEGORIZE_ICE
7fac3dc SIS2: +Added the runtime parameter EULERIAN_TSURF
525d0e8 SIS2: +Added the runtime parameter RECATEGORIZE_ICE
fcc4e6c *OM4: Set VSTAR_SCALE_FACTOR=1
9b5691f MOM6: Changed default IO_LAYOUT from 0,0 to 1,1

dev/master/2016.12.11

- Updated baseline OM4 configuration:
  - use ePBL "n" settings
  - OM4_025 uses same hybrid coordinate bounds as OM4_05
  - SIS2 fixes change OM4 answers
- Primary diagnostics use the new general-coordinate diagnostics

7d01ed5 MOM6: Stop boundary extrapolation in wave_speed remapping
f0693b3 Merge branch 'nicjhan-328-diagnostic-testing' into dev/master
6ded29f Merge branch '328-diagnostic-testing' of https://github.com/nicjhan/MOM6-examples into nicjhan-328-diagnostic-testing
a9dc32e Corrected DIAG_COORD_DEF_Z in Baltic test
9039c8f Updated SIS2 and icebergs sub-modules
0d7b368 OM4: Added transport and MLE diagnostics
871d438 MOM6: Updated cell_methods for vhml and vhGM
6b54d72 *OM4 updated to use ePBLn settings
a46e5e5 Merge branch 'dev/master' of github.com:NOAA-GFDL/MOM6-examples into dev/master
061932c Merge branch 'dev/master' of github.com:NOAA-GFDL/MOM6-examples into dev/master
12eb835 Merge pull request NOAA-GFDL#115 from NOAA-GFDL/user/jpk/aja_dora_underscore_z
fa59484 SIS2: *Reset t_surf to T_freeze ocean when part_size==0
1965c9e "webversion" option argument added back in
4cdf013 *OM4_025 updated coordinate bounds to match OM4_05
d67a48d Merge branch 'dev/master' into diagnostic-regridding
570c16f SIS2: Updated layout files for SIS2
f892f94 Merge branch 'dev/master' into diagnostic-regridding
6dcf7cf MOM6: Finalizing merge of nicjhan-334-rho-sigma-diagnostic-regridding
19aa406 Update MOM6 with @aja additions. NOAA-GFDL#328
94d8205 Python3 fixes. NOAA-GFDL#328
4972110 SIS2: Made VERONA_COUPLER a layout param
70aed9d SIS2: +Call data_override_unset_domain in get_sea_surface
af6cb4d MOM6: Moved umo,vmo to MOM.F90 and based on uhtr,vhtr
1b79978 Merge branch 'dev/master' into diagnostic-regridding
f4b9657 Merge branch 'dev/master' of github.com:NOAA-GFDL/MOM6-examples into dev/master
6d3bab8 SIS2: *Added halo updates for IST%t_surf
3dbb68c MOC plotting scripts uses vmo first before vh
0ae02de Updated Baltic_ALE_z_offline_tracers/SIS_input to recover answers
0c29727 FMS: +Updated FMS to origin/user/z1l/data_override
0cbd055 SIS2: *+Set the default for ADVECT_TSURF to True
255106b SIS2: *Set ADVECT_TSURF in SIS_input files
8744d3c +Added ADVECT_TSURF run time option
7006c85 Add get_z() to m6toolbox.py to handle new _z diagnostics
5e2d6ca Merge branch 'dev/master' into diagnostic-regridding
2fe5535 Synced submodules MOM6, SIS2 and icebergs
94aca6e MOM6: Handled multiple pull requests
4b5c906 MOM6: Merge branch 'ESMG-user/ksh/open_bc' into dev/master
83415bc MOM6: Moved to flat (no subdirs) mode for doxygen
e4a54da SIS2: +Added slow_Domain_NH to ice_data_type
b838b7f Merge branch 'dev/master' into diagnostic-regridding
f260f57 Use new format to specify Z coordinate locations for diagnostic regridding. NOAA-GFDL#328
f4edf7b Update test scripts to support Python3, update MOM. NOAA-GFDL#328
9a7c873 MOM6: Added _xyave to all remapped diagnostics
e10184a MOM6: Fix conflict with dimension names in diag_manager
66d6aeb MOM6: Changed default DIAG_COORD_Z grid to be WOA09 for deep configurations
2bf75a8 MOM6: Moved reading of regridding parameters into MOM_regridding.F90
f44755c MOM6: Hide interp_scheme when not needed, pt 2
379fb48 MOM6: Added arbitrary number of diagnostic coordinates, NUM_DIAG_COORDS
30e2680 Adding a few mask tables for 1/4 degree grid
16b4635 SIS2: +Merge branch 'MichaelWinton-user/mw/cmip6_diagnostics' into dev/master
d488a94 MOM6: Using the new remapped diagnostics branch
7460103 SIS2: *Corrected the visible albedo transpose bug
94910d2 The dump diags tool should delete any diags that will be recreated. NOAA-GFDL#328
c7cecd9 Merge and fix conflict. NOAA-GFDL#328
64e809c Don't delete old diags when testing, these may be needed for manual inspection. NOAA-GFDL#328
4ac2a56 Increase max number of diag files. NOAA-GFDL#328
800027b Extend testing to handle dumping rho and sigma remapped diagnostics as well as z. NOAA-GFDL#328
6110b55 Update MOM6 with new vertical remapping changes. NOAA-GFDL#328
1032171 Add link to diagnostic testing from the README. NOAA-GFDL#328
a035f79 Diag testing: ensure that experiment has run before processing available diags. NOAA-GFDL#328
90a8357 Update MOM6 version. NOAA-GFDL#328
62e9e88 Clean up diagnostic tests so they require fewer models runs to finish. NOAA-GFDL#328
68a3657 Update MOM6 submodule with vertical remapping changes. NOAA-GFDL#328
65ac3b1 Update tests for diags vertically remapped to z star coordinates. NOAA-GFDL#328
665a43f Correct specification of z grid used for vertical remapping. NOAA-GFDL#328
c1bf67d Update diagnostic testing to handle multiple platforms. NOAA-GFDL#328
7361b91 Missing define from build script used for testing. NOAA-GFDL#328
b5f1655 Keep build output on failed build during testing. NOAA-GFDL#328
87ccc87 Test diagnostic data, rather than entire file. NOAA-GFDL#328
8f0a259 Make experiment.py work with Python 3. NOAA-GFDL#328
bc917d7 Default to GNU DEBUG builds for diagnostics testing. NOAA-GFDL#328
0852ad2 Missing define from build script used for testing. NOAA-GFDL#328
f96bd92 Keep build output on failed build during testing. NOAA-GFDL#328
f654337 Be able to build models before testing begins. NOAA-GFDL#328
4bb826c By default use mpirun for runs when doing diagnostics tests. NOAA-GFDL#328
87fdccd Added missed file, SIS_parameter_doc.layout
67e4ee0 SIS2: +Modified SIS2 fast ice MOM_domains_init call
b434543 Added missed SIS_parameter_doc.all

dev/master/2016.11.10

- Adds vertical structure to KHTH
- Fixes iceberg "pole problem"
- Includes prototype Langmuir driven mixing
- No configurations changes.

ccb2e99 MOM6: Added equivalent barotropic vertical structure to KHTH
a1a2fa8 MOM6: Added diagnostic of equiv. barotropic wave speed/structure
a42dc92 SIS2: +Added Verona_coupler argument to ice_model_init
aef4b18 MOM6: Removed MOM_wave_speed dependence on file-parser
2d6f00b icebergs: Obsoleted parameter read_old_restarts
f5e9782 *icebergs: Revert previous logic update for polar cells
13dae1b Added missed SIS_parameter_doc file
0d4f2ab SIS2: +Added VERONA_COUPLER runtime argument
f4ffce7 *Corrected bad commit with icebergs
2fa5a51 *Modified ice_ocean_SIS2/SIS2_bergs_cgrid to better test icebergs
96e676c Last commits missed SIS_parameter_doc in one experiment
1e833d2 SIS2: +Grouped fast and slow module initializations
e4b1314 SIS2: +Grouped fast and slow restart registrations
a49fecf Added SIS_fast.available_diags to .gitignore
d44e9a8 Merge branch 'dev/master' of github.com:NOAA-GFDL/MOM6-examples into dev/master
7efe2af MOM6: Merge branch 'ashao-add_bir_tracer' into dev/master
89de111 Merge branch 'dev/master' of github.com:CommerceGov/NOAA-GFDL-MOM6-examples into dev/master
c08859f MOM6: Merge branch 'nicjhan-381-forcing-diag-registration-sequence' into dev/master
7f3ce0f SIS2: +Revised the albedo and shortwave diagnostics
809b0f9 Merge branch 'dev/master' of github.com:NOAA-GFDL/MOM6-examples into dev/master
e85ffc1 MOM6: Merge branch 'gustavo-marques-ale/ice_shelf' into dev/master
b268ac7 *Set ICEBERG_WINDSTRESS_BUG=True in 2 SIS_input files
edfa7ca icebergs: 497382717f0e6c6da5ccfa127debf0fa45f7dcc5
902b52c Added missed SIS_parameter_doc.all files
9e10225 SIS2: *Changed to ICEBERG_WINDSTRESS_BUG=False by default
a33c615 SIS2: +Added the runtime option ICEBERG_WINDSTRESS_BUG
47966ed SIS2: *Correctly rescale wind-stresses for changing ice
59bbf21 SIS2: +Moved SIS_hor_grid_type to Ice%fCS and Ice%sCS
d55362a Merge branch 'dev/master' of github.com:CommerceGov/NOAA-GFDL-MOM6-examples into dev/master
9296d1a MOM6: Merge branch 'breichl-user/bgr/EPBL_LT_function' into dev/master

dev/master/2016.10.25

- Fixes analysis workflow (hopefully because untested!)
- Provides new options in ePBL
- Fixes restart issues with ePBL MLD_USE_ITERATION
- Fix for iceberg v_ice interpolation

32d8fe3 MOM6: Merge branch 'breichl-user/bgr/EPBL_dissipation' into dev/master
361fef2 Merge pull request NOAA-GFDL#112 from NOAA-GFDL/user/jpk/dora-web-updates
2235ec7 Merge branch 'ashao-Baltic_ALE_z' into dev/master
34ee0f2 Updated parameter_doc/added stats for Baltic_ALE_z_offline_tracers
86db383 Replaced binary files with symbolic links to existing files
8daf84a Merge branch 'Baltic_ALE_z' of https://github.com/ashao/MOM6-examples into ashao-Baltic_ALE_z
711fec7 MOM6: Merge branch 'breichl-user/bgr/EPBL_MLD_GUESS' into dev/master
2036991 MOM6: Merge branch 'ashao-origin/offline_tracers' into dev/master
bd8bcf6 Updated MOM_override with OFFLINE_TRACER_MODE replacing DO_ONLINE as per @adcroft PR and suggestions. Also, added data_table which was not added in previous commit and updated which offline diagnostics are written out"
fddd5fb Fix for cmocean module import
163962f SIS2: +Added run time parameter SINGLE_ICE_STATE_TYPE
1603144 Merge branch 'dev/master' of github.com:CommerceGov/NOAA-GFDL-MOM6-examples into dev/master
bb981f9 FMS: Updated submodule to placeholder for verona patch
a418a73 SIS2: +Added FAST_ICE_RESTARTFILE and split restart files
8eb1ebb Merge branch 'dev/master' of github.com:NOAA-GFDL/MOM6-examples into dev/master
babd1fb SIS2: +Added ice_diags_fast_init
51d13a7 *icebergs: Bug fix: Interpolated ice velocity used ocean velocity

dev/master/2016.10.14

- Potentially more stable ePBL iteration of boundary layer depth

d584dce SIS2: +Moved registration of SIS2 state diagnostics
04f9c14 SIS2: +Removed ice_thm_CSp from the ice_state_type
58ef4e7 SIS2: +Created ice_thermo_init and ice_thermo_end
3d953f6 SIS2: +Created SIS_optics.F90
cdd0252 Fix for Jenkins "fast run"
d64263b SIS2: +Only save iceberg diagnostics if icebergs are used
297cbd8 SIS2: Merge branch 'sternalon-iceberg_run_call_only' into dev/master
4c13468 SIS2: +Renamed SIS_slow.F90 to SIS_dyn_trans.F90
b216c3d MOM6: Merge branch 'sternalon-passing_ustar_through_coupler_from_dev_master' into dev/master
46051fe +Added the prototype melt pond code into SIS2
6697885 MOM6: +Added run-time parameters for MOM_energetic_PBL

dev/master/2016.09.23

- Possibly significant bugfix for MEKE in eada7c0

eada7c0 *MOM6: Merge branch 'sinakhani-user/skhani/meke_work_bugfix' into dev/master
f5b43b0 Switched submodule URLs to use https

dev/master/2016.09.22

- 1da6fc5 includes NOAA-GFDL/MOM6@c3b810c which fixes the _z diagnostics
  that were briefly broken in dev/master/2016.09.18
- No answer changes.

Commits for MOM6-examples:
57a4a4c MOM6: Fixed openMP directives
479dfc5 MOM6: Merge branch 'ESMG-user/ksh/open_bc' into dev/master
b17cd34 eOM6: Merge branch 'breichl-user/bgr/SCM_updt' into dev/master
1da6fc5 MOM6: Merge branch 'ashao-vertical_tracer_fix' into dev/master
83270d0 Changed to PEN_SW_NBANDS=1 in CVmix_SCM_tests

dev/master/2016.09.22a

- e83a409 MOM6: Added back in abiotic mods
  - Fixes compilation compatibility with ocean_shared.

dev/master/2016.09.18

- 40d1fba Includes "USE_MLD_ITERATION" for ePBL.
- Answer changes for OBCs only.

3dcdc6b *MOM6: Set u-point areas for specified boundary conditions
048d74a Merge branch 'dev/master' of github.com:NOAA-GFDL/MOM6-examples into dev/master
4640266 *MOM6: Set normal gradient of KE to zero on open boundaries
c233c8a Revert "Custom tag of dev/master for generic_abiotic testing"
b6965d9 Custom tag of dev/master for generic_abiotic testing
0d9b27e MOM6: Simplified OBC%apply_OBC_*_Flather flags
14553ce MOM6: Moved obsoletion of APPLY_OBC_* flags to MOM_obsolete_params.F90
0ec325c MOM6: Merge branch 'ESMG-user/ksh/open_bc' into dev/master
15d7971 *MOM6: Altered initial conditions for circle_obcs
03d877f Corrected URL for MOM6 repository policies
40d1fba MOM6: Merge branch 'breichl-user/bgr/EPBL_MLD_iteration' into dev/master
2a77170 Merge pull request NOAA-GFDL#109 from NOAA-GFDL/user/jpk/dora-web-updates
a15f833 Removed print statement used in testing
5366943 Added clim options for TS_drift.py
aaf7ab1 Merge pull request NOAA-GFDL#108 from nicjhan/97-jenkins-build-status
45cca09 Add Jenkins 'fast run' tests to README testing status.
2bb2f84 MOM6: Merge branch 'breichl-user/bgr/LMD94' into dev/master
b1fda6d SIS2: Merge branch 'user/nnz/fix_restart_issue42' into dev/master
00b9226 MOM6: Merge branch 'gustavo-marques-MOM_F90_FIX' into dev/master
0ec2697 MOM6: Moved call to write_static_fields()
324e8c7 Merge pull request NOAA-GFDL#106 from NOAA-GFDL/user/jpk/dora-web-updates

Custom tag of dev/master for generic_abiotic testing