dev/gfdl/2018.04.11

192fb89 Merge branch 'jkrasting-user/jpk/OM4_05_remap_overrides' into dev/gfdl
ba3a9a8 *OM4: Updated doc files after configuration change
d58aa84 Merge branch 'user/jpk/OM4_05_remap_overrides' of https://github.com/jkrasting/MOM6-examples into jkrasting-user/jpk/OM4_05_remap_overrides
46b529c Merge branch 'Hallberg-NOAA-debug_params' into dev/gfdl
b41a6f9 MOM6+SIS2: Merge branch 'Hallberg-NOAA-debug_params' into dev/gfdl
b4874a7 Added missed doc updates from 42122e3
42122e3 Merge branch 'debug_params' of https://github.com/Hallberg-NOAA/MOM6-examples into Hallberg-NOAA-debug_params
f42b1f4 Merge branch 'Hallberg-NOAA-diffusion_CFL' into dev/gfdl
fe0320f MOM6: Merge branch 'Hallberg-NOAA-diffusion_CFL' into dev/gfdl
e32f79b Updated missed MOM_parameter_doc files
e472ac6 *Set MAX_TR_DIFFUSION_CFL = 2.0 in OM4_05
88f0662 MOM6: +Added run time parameter MAX_TR_DIFFUSION_CFL
e1ebe6f Set USE_NET_FW_ADJUSTMENT_SIGN_BUG to False
4ddf555 MOM6 & SIS2: +Log debugging params to MOM_param_doc.debugging
de69617 Removed Z_INIT_REMAP* overrides from OM4_05
eca64d3 MOM6-examples: *Added new OBC options to DOME test case
6be2e41 Merge branch 'dev/gfdl' of https://github.com/ESMG/MOM6-examples into dev/gfdl
b7e190f MOM6: *Fixing more SIMPLE OBC problems.
5c25451 Added OBC options to DOME's MOM_input

dev/gfdl/2018.04.06

a4ee1a2 *OM4_025: Switch initial conditions from WOA05 to WOA13
1dd6f07 *OM4: Corrected salt restore file
422c229 OM4: DT_THERM = 7200
9e3fb8c *OM4_05: Switch initial conditions from WOA05 to WOA13
fcc2d7a OM4_05: Use more PEs during testing

dev/gfdl/2018.03.30

144bcb7 *OM4: Use newer SeaWIFS and runoff datasets
5bdb986 *OM4: Updated dt_cpld to be consistent with production
1dc7975 MOM6: Merge branch 'nikizadehgfdl-user/nikizadehgfdl/fix_MEKE_Ku_loop' into dev/gfdl
a5c3ba5 *MOM6: Merge branch 'ESMG-dev/esmg' into dev/gfdl
a25c232 Merge pull request NOAA-GFDL#219 from Hallberg-NOAA/add_SIS2_diagnostics
2391b0d MOM6: Merge pull request #742 from adcroft/add-chl-varname-parameter
37baa83 SIS2: Merge branch 'Hallberg-NOAA-dev/gfdl' into dev/gfdl
2d3e816 SIS2: +Added ice_melt and fsitherm diagnostics
545294f Merge pull request NOAA-GFDL#220 from jkrasting/OM4_05_diag_table
aa03a5c Added separate diag_table.MOM6 for OM4_05 config
aba6acc Removed heat_content_vprec from CM4 diag_table
07a28c1 SIS2: +Added ice_melt and fsitherm diagnostics
6886957 *MOM6: Merge branch 'enhance_PGF' of https://github.com/Hallberg-NOAA/MOM6 into dev/gfdl
f7a76ee MOM6: Merge branch 'ashao-post_diag_chksums' into dev/gfdl
5ef68d0 MOM6: Merge branch 'ESMG-link_tracers' into dev/gfdl
1e88d50 OM4_025: Added preprocessing for PHC2 salt restoring file
eb8a5ea OM4_05: Changed pathway for creating salt_restore.nc
b8d8ad6 Merge pull request NOAA-GFDL#217 from jkrasting/user/jpk/iaf_data_tables
a800145 Merge branch 'Hallberg-NOAA-enhance_PGF' into dev/gfdl
4253ea4 MOM6: Merge branch 'Hallberg-NOAA-enhance_PGF' into dev/gfdl
09df91f Update MOM_docs for missed experiments in NOAA-GFDL#218
70c69f0 Corrected MOM_override for global_ALE/layer
9810b34 Separate data table for IAF configuration
f216a85 MOM6: +Moved pressure gradient parameters out of MOM_ALE

dev/gfdl/2018.03.06

0a806d4 OM4: Added links for WOA2013 initial conditions
291c122 Merge branch 'jkrasting-update_OM4_05_datasets' into dev/gfdl
05c5a9b MOM6: Merge pull request #730 from adcroft/fix-z-init-many-layers
8422d3e OM4_05: Updated generated parameter docs
b77ea8e Merge branch 'update_OM4_05_datasets' of https://github.com/jkrasting/MOM6-examples into jkrasting-update_OM4_05_datasets
1a7cd2f Added missing .gitignore files
153f554 MOM6: Merge branch 'ESMG-dev/esmg' into dev/gfdl
e62d3f3 Merge branch 'dev-master-candidate-2018-02-28' into dev/master
2afd337 Updated runoff filename in OM4_05 data_table
1040824 Added symlink to static file
3ad53b4 Merge branch 'jkrasting-OM4_05_for_ESM4_dev' into dev/gfdl
e60fec2 MOM6: Merge pull request #723 from adcroft/fix-geometric-savedays
954b690 (*)OM4_05: Replaced file-based background viscosity with function
0779f3b *OM4_05: Tidied up MOM_input
5bcd58b Updated grid_spec files for OM4_05
c133ce2 Edit input filenames in MOM_input and MOM_restore
b277e81 Updated links to OM4_05 config INPUT files
9b10d87 Merge branch 'OM4_05_for_ESM4_dev' of https://github.com/jkrasting/MOM6-examples into jkrasting-OM4_05_for_ESM4_dev
6a9de59 Update parameters for OM4_05 configuration
37a36cf MOM6: Merge branch 'nikizadehgfdl-user/nikizadehgfdl/add_param_to_avoid_checksum_compare' into dev/gfdl
76ed67e MOM6: Merge branch 'ashao-remapped_tendency_diagnostics' into dev/gfdl
d0d0288 MOM6: Merge branch 'angus-g-flux-const' into dev/gfdl
5363923 SIS2: Merge branch 'wfcooke-user/wfc/iceberg_restart_timestamp' into dev/gfdl
05e27fe MOM6:  Merge branch 'Hallberg-NOAA-restructure_step_MOM' into dev/gfdl
dbe9f18 MOM6: +Restructured step_MOM(2)
172ce80 OM4_05 preproc: fixes meta-data
cdb4936 OM4_05 preproc: cleaned up Makefile
fed549a MOM6: Merge branch 'ESMG-fixdome' into dev/gfdl
6087290 Merge pull request NOAA-GFDL#210 from MJHarrison-GFDL/user/mjh/OM4_05_preprocessing
6056316 Merge branch 'Hallberg-NOAA-restructure_step_MOM' into dev/gfdl
f27f972 MOM6: Merge branch 'Hallberg-NOAA-restructure_step_MOM' into dev/gfdl
ae734ca Added missed MOM_parameter_doc.all
7ec313f Fix lingering issues with COREv2 input datasets
3634224 MOM6: Removed trailing blanks from two lines
599e8f4 MOM6: +Restructured step_MOM
ca3659b Merge branch 'dev/gfdl' into restructure_step_MOM
b6ec3b7 Merge branch 'dev/gfdl' into restructure_step_MOM
24922b0 Includes SGS topograpy variance in ocean_topog.nc 	 - this was inadvertantly removed in a previous commit
1491a53 No longer need to modify time axis info when processing PHC data
83391f6 Merge branch 'dev/gfdl' of https://github.com/NOAA-GFDL/MOM6-examples into user/mjh/OM4_05_preprocessing
7a465df Updates for the COREv2 protocol experiments 	- Jenkins is copying PHC salinity restoring 	data from /archive/gold/datasets file which has 	header adjustments needed by FMS. 	- new answers for salt_restore.nc
0119c49 OM4_05: Replaceed user paths with centralized source for data
73447e4 Merge branch 'MJHarrison-GFDL-user/mjh/OM4_05_preprocessing' into dev/gfdl
5428b4e Merge branch 'dev/gfdl' of https://github.com/NOAA-GFDL/MOM6-examples into user/mjh/OM4_05_preprocessing
c4909da fix bad path for PHC data and dependency for tidal_amplitude.nc
2dff48e Merge branch 'Hallberg-NOAA-correct_diabatic_clock' into dev/gfdl
c9fd7cb MOM6: Merge branch 'Hallberg-NOAA-correct_diabatic_clock' into dev/gfdl
f905634 Merge branch 'correct_diabatic_clock' of https://github.com/Hallberg-NOAA/MOM6-examples into Hallberg-NOAA-correct_diabatic_clock
e18bedd icebergs: Merge pull request NOAA-GFDL#58 from wfcooke/user/wfc/iceberg_restart_timestamp
b0b5547 Merge branch 'dev-master-candidate-2018-02-06' into dev/master
b8e6d95 MOM6: Merge branch 'dev-master-candidate-2018-02-06' into dev/master
6bfe277 MOM6: *Corrected the clock as seen by diabatic processes
0a8a1f8 Corrected ENERGYSAVEDAYS in DOME/MOM_input
22952c8 Added static_input.nml for Baltic_OM4_025
dbbbb12 remove JRA salt restoring file from checksums
9bb7fca Merge branch 'dev/gfdl' of https://github.com/NOAA-GFDL/MOM6-examples into user/mjh/OM4_05_preprocessing
0b355f8 new answers for salt_restore
b115dad Switch to COREv2 PHC file for salt restoring.
6c37e76 New answers for OM4_05 preprocessing
085f03c Fix previous commit gave the wrong topography.   - The topo_edits file was derived by differencing     a previously constructed bathy file with the first guess.
a7b2723 MOM6: Merge pull request #707 from adcroft/fix-nan-in-radiation-obc
87da7fb icebergs: Merge branch 'nikizadehgfdl-user/nikizadehgfdl/fix_ensemble_restart_filenames' into dev/gfdl
50e93ea Corrected names of OM4_05 pp files to reflect resolution
c8c4aba Added missing .datasets link in Baltic_OM4_025
d32dab3 Merge branch 'ashao-add_OM4_025' into dev/gfdl
4afb0a3 Baltic_OM4_025: Cleaned up paths and symbolic links
7b526b0 Baltic_OM4_05: Corrected some symbolic links
7f29a58 OM4_025: Undo changes from bad commit
8dea726 Merge branch 'add_OM4_025' of https://github.com/ashao/MOM6-examples into ashao-add_OM4_025
ba33c6f Merge branch 'MJHarrison-GFDL-user/mjh/OM4_05_preprocessing' into dev/gfdl
a7d8ebb OM4 preproc: Remove unnecessary copies from archive
6a0c009 Merge branch 'dev/gfdl', remote branch 'origin' into user/mjh/OM4_05_preprocessing
070e872 new answers for mosaic_ocean.1080x768/atmos_mosaic_tile1Xland_mosaic_tile1.cdl
c0052ad Merge branch 'ashao-add_Baltic_OM4_05' into dev/gfdl
bbffa81 Baltic_OM4_05: Cleaned up paths in symbolic links
09b6904 Merge branch 'add_Baltic_OM4_05' of https://github.com/ashao/MOM6-examples into ashao-add_Baltic_OM4_05
7d7e199 Merge branch 'Hallberg-NOAA-restructure_MOM_CS' into dev/gfdl
d44a5fa Merge branch 'restructure_MOM_CS' of https://github.com/Hallberg-NOAA/MOM6-examples into Hallberg-NOAA-restructure_MOM_CS
dd0d3e1 Merge branch 'Hallberg-NOAA-restructure_MOM_CS' into dev/gfdl
aa386eb Corrected MOM_parameter_doc
f3c30c4 MOM6: +Moved u, v, and h diagnostics & other changes
cb9bca3 MOM6: Merge branch 'ashao-collapse_vertmap_ndiff_diags' into dev/gfdl
16df984 Include runoff in checksums file
1b2b5b4 updates for Jenkins and md5sum updates for landxatm mosaic
d67e280 MOM6: +Made MOM_control_struct opaque
2d1a063 Merge pull request NOAA-GFDL#203 from jkrasting/user/jpk/section_transport_fix
9a830de Merge pull request NOAA-GFDL#204 from jkrasting/user/jpk/change_scalar_precision
1223fb4 MOM6: Merge branch 'travissluka-bug-netfw-zero' into dev/gfdl
addcc92 *MOM6: Merge branch 'ashao-ndiff_filter_unstable_stratified' into dev/gfdl
8bff5ee MOM6: Merge branch 'restructure_step_MOM' of https://github.com/Hallberg-NOAA/MOM6 into dev/gfdl
8a400d0 Fill SSS restore field land values with 0 and get rid of soft links
aac8b54 MOM6: Merge branch 'wfcooke-user/wfc/grid_initialization' into dev/gfdl
5adac64 Merge branch 'dev/gfdl', remote branch 'origin' into user/mjh/OM4_05_preprocessing
421795d Regridding of JRA55-do-suppl data to OM4_05 grid
a091b5c Updates to OM4_05 preprocessing
29ecd96 Merge branch 'user/mjh/OM4_05_preprocessing' of https://github.com/MJHarrison-GFDL/MOM6-examples into dev/gfdl
4f792a2 MOM6: +Merged in PR with documentation corrections
e37d28c Changed precision for ocean_scalar* output
67b88a0 Corrected diag_table for salt restoring diagnostic
ad0dbd7 Add pp/ts/daily/5yr option for section trans. plots
f819a2e Merge branch 'underflow_external_gwave' of https://github.com/Hallberg-NOAA/MOM6-examples into dev/gfdl
da2c832 MOM6: +Merged in ESMG-dumbbell
f43150e *Set VEL_UNDERFLOW in external_gwave
55c4028 MOM6: Merge branch 'Hallberg-NOAA-restructure_step_MOM' into dev/gfdl
0e557d4 MOM6: Merge pull request #680 from Hallberg-NOAA/restructure_step_MOM
da9141a MOM6: Merge pull request #679 from Hallberg-NOAA/reform_convert_thickness
11a19b0 MOM6: Option for boundary extrapolation in main remapping
027c518 fix topo mismatch from current prod runs. Added IAF runoff
81b6765 Fix for environment change at GFDL
e96509c Merge branch 'OM4-maintenance' into dev/gfdl
12f7ee2 More instances where ordering of axes limits should change
852cc39 Fixed bug in yzcompare
bc70366 Changed ppfreq to monthly for MLD analysis
10357d5 Added 'ppfreq' key to manifest.json
800d000 Fixed issue with multiple files
25a99a2 Fixes poleward heat trans analysis
62473ce Updated cmocean module import
c5d4c49 Add a Baltic_OM4_025 for development purposes
8c03e4e Uncomment out lines in the make_from_OM4_05 script
540c554 Adds Baltic OM4_05 test case
1f82805 MOM6: Merge pull request #674 from Hallberg-NOAA/reform_convert_thickness
c6eb8be Merge branch 'Hallberg-NOAA-reform_convert_thickness' into dev/gfdl
0fb4dc3 Merge branch 'reform_convert_thickness' of https://github.com/Hallberg-NOAA/MOM6-examples into Hallberg-NOAA-reform_convert_thickness
650daf8 Merge branch 'Hallberg-NOAA-reform_convert_thickness' into dev/gfdl
149825e Merge branch 'dev/gfdl' into reform_convert_thickness
2011774 Merge branch 'dev/gfdl' into reform_convert_thickness
b793b3f MOM6: *Refactored convert_thickness
104627e (*)MOM6: Merge pull request #666 from Hallberg-NOAA/restructure_step_MOM
55838d6 mkmf: Fixes for symbolically linked files
16b4b4f Merge branch 'dev/master' into dev/gfdl
c1cb38c MOM6: Bringing up to date for purpose of dev/master PR
12ff1c5 Merge branch 'Hallberg-NOAA-restructure_step_MOM' into dev/gfdl
bbe3c65 Merge branch 'restructure_step_MOM' of https://github.com/Hallberg-NOAA/MOM6-examples into Hallberg-NOAA-restructure_step_MOM
edb0529 FMS: Updated to warsaw_201710
9452ed2 Added ocean_only/tides_025 test case
2bc46af MOM6: Changes related to restructuring MOM.F90
539a74d MOM6: Converted outside land masker to use tiles.
96b99d3 Merge branch 'OM4-maintenance' into dev/gfdl
36ee8e5 Merge pull request NOAA-GFDL#191 from jkrasting/cmip6_analysis_updates
17d0228 Merge branch 'Hallberg-NOAA-tide_support' into dev/gfdl
d6edb4d Transport analysis to work with monthly pp
8c037c5 Merge branch 'tide_support' of https://github.com/Hallberg-NOAA/MOM6-examples into Hallberg-NOAA-tide_support
6b18621 Merge branch 'OM4-maintenance' into dev/gfdl
ac58394 MOM6: Made 4 commits to support barotropic tides
22eb9a9 MOM6: +Made 4 commits to support barotropic tides
20b0aeb +Added mean density and heat capacity diagnostics
1f1d57c +Geometric progression for ENERGYSAVEDAYS
fad8ff2 MOM6: +Corrected available_diags file frazil entries
051a0ad Merge pull request NOAA-GFDL#181 from jkrasting/user/jpk/webapp_updates_20171010
f0c6afc Merge pull request NOAA-GFDL#188 from jkrasting/refinediag_fix_20171103
96a8e5f Fixed typo in refineDiag_ocean_month_rho2.py
6a2f1fb Merge pull request NOAA-GFDL#187 from jkrasting/refinediag_fix_20171103
5a724dc More robust refineDiag scripts
49795eb MOM6: Two PRs for MOM6 to resolve diagnostics issues
e57d90d OM4: Turned off empty diagnostics in OM4_025
21b3db3 Removed LT_Enhancement from diag_table
60a055c MOM6: Removed masking of areas in ocean_static.nc
c95392e Use only 2 cores for multi-core Travis-CI tests
660b42c MOM6: Merge branch 'NCAR-dev/ncar' into dev/master
d9dd61d MOM6: Merge branch 'MJHarrison-GFDL-HVisc_masking' into dev/gfdl
5d867c1 MOM6: Merge branch 'MJHarrison-GFDL-SfcRestoringMask' into dev/gfdl
78fadfa Updated cmocean module import

om4/v1.0.4

Fixes for dora, analysis and post-processing

- 12f7ee2 More instances where ordering of axes limits should change
- 852cc39 Fixed bug in yzcompare
- bc70366 Changed ppfreq to monthly for MLD analysis
- 10357d5 Added 'ppfreq' key to manifest.json
- 800d000 Fixed issue with multiple files
- 25a99a2 Fixes poleward heat trans analysis
- 62473ce Updated cmocean module import

om4/v1.0.3

- 36ee8e5 Merge pull request NOAA-GFDL#191 from jkrasting/cmip6_analysis_updates
- d6edb4d Transport analysis to work with monthly pp

om4/v1.0.2

f0c6afc Merge pull request NOAA-GFDL#188 from jkrasting/refinediag_fix_20171103
96a8e5f Fixed typo in refineDiag_ocean_month_rho2.py

om4/v1.0.1

- Fixes for fails in the refine-diag step of post-processing

6a2f1fb Merge pull request NOAA-GFDL#187 from jkrasting/refinediag_fix_20171103

om4/v1.0

This tags the final version of OM4 0.25-degree configuration.

This tag is the first tag on branch OM4-maintenance which
diverges from dev/gfdl at tag dev/gfdl/2017.10.19.

Changes since dev/gfdl/2017.10.19:

49795eb MOM6: Two PRs for MOM6 to resolve diagnostics issues
e57d90d OM4: Turned off empty diagnostics in OM4_025
21b3db3 Removed LT_Enhancement from diag_table
60a055c MOM6: Removed masking of areas in ocean_static.nc

dev/gfdl/2017.10.19

- Fixes for CMIP workflow and post-processing.
- New feature in icebergs (6f87aeb) to help with apparent mass loss due to stuck icebergs.

6f87aeb icebergs: Merge pull request NOAA-GFDL#57 from adcroft/berg_diffusion
d779aed Merge pull request NOAA-GFDL#183 from nikizadehgfdl/user/nikizadehgfdl/reset_exec_bit_python_scripts
5e8de3e Merge pull request NOAA-GFDL#185 from jkrasting/ocean_static_script
c36036e Added append_basin_mask.py script
01f14a3 Reset exec permissions of python scripts
96138c6 Merge pull request NOAA-GFDL#182 from ashao/reorder_straits
4cbea5b Reorder indices of straits according to CMIP6/OMIP