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dev/gfdl/2019.08.08

6d6e02b Replaced local mask_tables with links
ecc553c Added JRA55-do version of OM4
d26b3ae Adds file-based rho2 diagnostic to OM4
b7a1dd5 MOM6: Merge pull request #969 from marshallward/dia_diff_saln_fix
a6cfa03 *MOM6/SIS2: Merge branch 'marshallward-hiprec' into dev/gfdl
98fb6a1 Merge branch 'raphaeldussin-bump_mkmf_version' into dev/gfdl
5b8bb33 Merge branch 'bump_mkmf_version' of https://github.com/raphaeldussin/MOM6-examples into raphaeldussin-bump_mkmf_version
81d659d Merge branch 'dev/gfdl' of github.com:NOAA-GFDL/MOM6-examples into dev/gfdl
0a0fa94 bump mkmf version
2394c28 Merge pull request #281 from raphaeldussin/fix_htrans_units
d8a9d8f MOM6: Merge pull request #960 from breichl/user/bgr/Init_from_Z_add_scale_offset
bb7f05a MOM6: Merge branch 'raphaeldussin-fix_transport_units' into dev/gfdl
83938f6 fix units
63e6cb9 Roll forward FMS to f2e2c86f6c0
9738c67 MOM6: Merge branch 'Hallberg-NOAA-code_units_cleanup' into dev/gfdl
1123cdb MOM6: Merge pull request #952 from marshallward/tanh_opacity
c17c2be Merge branch 'marshallward-frictworkmax_param' into dev/gfdl
9925bc0 MOM6: Merge pull request #950 from marshallward/frictworkmax_v3
a797af8 Remove FrictWorkMax from global_ALE params
711d8fa Merge branch 'dev/master' into dev/gfdl
84e8725 Merge branch 'dev-master-candidate-2019-07-08' into dev/master
ae16855 Merge branch 'Hallberg-NOAA-parameterizations_cleanup' into dev/gfdl
5f57477 Updated submodule src/MOM6
0607744 MOM6: Cleaned up vertical parameterization code
3d11154 MOM6: Merge pull request #944 from Hallberg-NOAA/fix_line_lengths
912a1ad Merge pull request #275 from ElizabethYankovsky/newexperiment
bb8049a MOM6: Merge pull request #943 from adcroft/static--mode-fixes-for-pr-935
0b01af1 Merge branch 'dev/master' into dev/gfdl
799219b MOM6: Merge branch 'gustavo-marques-dev-master-candidate-2019-06-11' into dev/master
af2f756 MOM6: Merge pull request #942 from marshallward/meke_kh_diag
fbeb6ae Merge branch 'dev/gfdl' of github.com:NOAA-GFDL/MOM6-examples into dev/gfdl
fa65bff Merge pull request #274 from StephenGriffies/OM4_diag_table_updates
af07b94 Adding .nc files
0cb3b05 Changing gitignore
f6b18b8 Adding the rotating gravity current experiment
38a2aed Merge branch 'dev/gfdl' of https://github.com/NOAA-GFDL/MOM6-examples into dev/gfdl
141cb23 MOM6: Updated MOM6 to version of dev/GFDL with RGC_tracer code
d4616fa min/max zos,tos; heat trans to annual
07126b5 min/max zos,tos; heat trans to annual; remove unused ndiff diagn
310bd73 Update MOM6
01ac90f Disabled coverage job
6e683dc MOM6: Merge branch 'breichl-user/bgr/OSBL_Updates' into dev/gfdl
90da109 Merge branch 'Hallberg-NOAA-Fix_intersperse_ice_test' into dev/gfdl
4d5cb05 Added needed empty CIOD_override file
1f5b03f Merge branch 'Fix_intersperse_ice_test' of https://github.com/Hallberg-NOAA/MOM6-examples into Hallberg-NOAA-Fix_intersperse_ice_test
a7f0436 Updated the version of MOM6 to NOAA-GFDL/MOM6@41cfb68
c73a0de Merge branch 'marshallward-z_diag_param_purge' into dev/gfdl
71abe1c Z diag param purge
ff18d3c Merge branch 'marshallward-no_zdiag_params' into dev/gfdl
a0c6c20 Z diag purge: parameter update
22f1cd9 Z diag purge
8a7f8e2 *Fixed input.nml for Intersperse_ice_1deg test case
3099ac3 Merge branch 'Hallberg-NOAA-remove_newlines' into dev/gfdl
2def9a4 MOM6: Merge branch 'Hallberg-NOAA-remove_newlines' into dev/gfdl
f7f2c4e Added updated SIS2 parameter doc files
5db88e6 MOM6: +Removed hard newlines in get_param calls
65474a8 Merge branch 'dev/gfdl' of https://github.com/NOAA-GFDL/MOM6-examples into dev/gfdl
fcff994 MOM6: Merged MFJansen-GMplusBS_final-alt code
6d30f17 Merge branch 'gustavo-marques-surface_flux_analysis_ocean_only_updates' into dev/gfdl
4e9082f Minor tidy up of jupyter notebook
d491c69 Merge branch 'surface_flux_analysis_ocean_only_updates' of https://github.com/gustavo-marques/MOM6-examples into gustavo-marques-surface_flux_analysis_ocean_only_updates
69dcd9e Merge branch 'Hallberg-NOAA-set_vel_underflow' into dev/gfdl
4478a07 Merge branch 'set_vel_underflow' of https://github.com/Hallberg-NOAA/MOM6-examples into Hallberg-NOAA-set_vel_underflow
ed230a4 Merge branch 'Hallberg-NOAA-double_gyre_depth_list_params' into dev/gfdl
c30cdc2 Merge branch 'double_gyre_depth_list_params' of https://github.com/Hallberg-NOAA/MOM6-examples into Hallberg-NOAA-double_gyre_depth_list_params
9cc4181 Set VEL_UNDERFLOW = 1e-30 in 12 test cases
a928df9 Changed double_gyre DEPTH_LIST parameter settings
8d39a14 Add necessary link to datasets for new expt
949cf34 Fix available_diags
6693b97 Slurm conversion: reduced node count for coverage
86b3ceb Switching from moab to slurm
1275c4e Merge branch 'Hallberg-NOAA-add_interspersed_ice' into dev/gfdl
3a9c367 Updated parameter doc files in Intersperse_ice_1deg
f84e91f Merge branch 'add_interspersed_ice' of https://github.com/Hallberg-NOAA/MOM6-examples into Hallberg-NOAA-add_interspersed_ice
54367eb Merge branch 'Hallberg-NOAA-diabatic_aux_cleanup' into dev/gfdl
a61e347 MOM6: Merge branch 'Hallberg-NOAA-diabatic_aux_cleanup' into dev/gfdl
13d9e0c Added missed MOM_parameter_doc updates
de7b070 Merge branch 'diabatic_aux_cleanup' of https://github.com/Hallberg-NOAA/MOM6-examples into Hallberg-NOAA-diabatic_aux_cleanup
aa70038 Merge branch 'dev/master' into dev/gfdl
485e5a8 Merge branch 'dev-master-candidate-2019-04-26' into dev/master
cbae9fd Use xanadu-fms version of gitlab scripts
5e310e9 MOM6: Merge branch 'dev-master-candidate-2019-04-26' into dev/master
69550e4 MOM6: +Extended MIN_SALINITY and fixed subML_N2
5501702 MOM6: +(*)Added MIN_SALINITY and fixed subML_N2
9d9e35b MOM6: Merge branch 'marshallward-dev/gfdl' into dev/gfdl
1d13a81 MOM6: Merge pull request #915 from adcroft/xanadu-fms
cf73a9a FMS switched to xanadu
2bc3645 Merge branch 'dev-master-candidate-2018-04-22' into dev/master
58fe79c MOM6: Merge branch 'dev-master-candidate-2018-04-22' into dev/master
2eac211 Candidate for dev/master
13f94b7 Update mkmf and specify version of test scripts
ec17a4c Merge branch 'dev/master' into dev/gfdl
4162cfc MOM6: Merge pull request from EMC-MOM6/feature/nuopccapPR to dev/master
d1a6f3c SIS2: Merge branch 'Hallberg-NOAA-remove_Verona_interfaces' into dev/gfdl
3951df3 MOM6: Merge pull request #869 from nikizadehgfdl/nikizadeh_diag_decimation
9439342 Temporary rollback from xanadu
8a3501a Add the new Intersperse_ice_1deg test case
6526357 FMS: Updated to xanadu
8859644 +(*)Updated coupler, SIS2 & MOM6 for interspersed ice
78c1690 Merge pull request #259 from jkrasting/user/jpk/dora-fixes
a285524 Save forcing and surface every 12 hours
7584b48 Update MOM_parameter_doc.layout
63e8d43 Update MOM_parameter_doc.layout
dc97bea Set IO_LAYOUT = 1, 1
42b93fb Update notebooks for layer and z - tendencies are now computed over 12 hours
18ca692 Merge branch 'dev/master' into dev/gfdl
c1f5aa7 MOM6: Merge branch 'gustavo-marques-sync_dev_master_19Dec18' into dev/master
78de7eb Merge branch 'dev/gfdl' into user/jpk/dora-fixes
583cf79 Update logical tests on None type
128b95d Force integer type when slicing array
c890333 Updates available_diags for global_ALE/layer
c764ec7 Revert "Set days = 3"
f82b7bf Merge pull request #255 from gustavo-marques/surface_flux_analysis_ocean_only
68df911 Mentioned that tendencies are over one day.
fe3145c Update Surface flux analysis Notebook
ad0d3b2 available_diags changes because diag_table was updated
2faf484 Set days   = 3
14f0d20 Add fields and increase precision
df55f6c Added random_numbers module to Travis-CI build
b85fe5f MOM6: Merge branch 'hlkong-topoMEKE' into dev/gfdl
e1069e2 Merge branch 'Hallberg-NOAA-document_user_params' into dev/gfdl
08871b5 Merge branch 'document_user_params' of https://github.com/Hallberg-NOAA/MOM6-examples into Hallberg-NOAA-document_user_params
c558371 Document user code parameters
43d933d Merge branch 'Hallberg-NOAA-use_unit_scaling_type' into dev/gfdl
a3881e1 Use unit scaling type
e6f3523 Merge branch 'dev/master' into dev/gfdl
e0b2739 MOM6: Merge branch 'Hallberg-NOAA-test_depth_units' into dev/gfdl
1a42956 MOM6: Merge branch 'gustavo-marques-fix_wd_register' into dev/gfdl
9295738 Merge branch 'breichl-user/bgr/ideal_hurricane' into dev/gfdl
0bb46d5 Updated the version of MOM6 used by MOM6_examples
6467e88 Added updated MOM_parameter_doc files
871ef70 Reverting rename of 'CVmix_SCM_tests' to 'CVMix_SCM_tests'.
11296a5 Updates to input parameters inidealized_hurricane test case
8297256 Updated CVMix_SCM_tests skin_warming_wind case for interior dtdz=0 (as in dev/gfdl). - dtdz was updated in MOM_override to be 0 in dev/gfdl, this commit is fixed to reflect that using the new scm TS init routine.
a022d67 Merge branch 'dev/gfdl' into user/bgr/ideal_hurricane
bf8f9bb MOM6: Merge branch 'Hallberg-NOAA-test_depth_units' into dev/gfdl
df8432a Modifications to run the idealized_hurricane (3d) test case.  - MOM_input changed for a .1 day simulation for the test case.  - MOM_parameter files added  - .nc file added from .cdl file for vertical grid.  - ideal_hurr TS class changed to CVMix TS class for a corresponding PR to MOM6.  - This test-case also relies on a corresponding PR to MOM6
d1f5614 Merge branch 'IdealHurricane' into user/bgr/ideal_hurricane
158d51d Renamed CVmix_SCM_tests folder to CVMix_SCM_tests
e500d54 Update to SCM_idealized_hurricane test case MOM_input file.
f95ad83 Updating input files in CVMix test cases
7da7cf3 Merge branch 'dev/master' into dev/gfdl
585b9ce MOM6: Merge branch 'gustavo-marques-dev-ncar-candidate-2018-09-26' into dev/master
48536b4 Merge branch 'MJHarrison-GFDL-fix_OM4_025_preprocessing' into dev/gfdl
a4918b8 Updated preprocessing of OM4 to use right MIDAS version
34ba40a fixes back checkout instructions for FMS code
046ea9d update MIDAS for shared code
b748b1b Merge pull request #245 from jkrasting/dev/gfdl
e442119 refineDiag updates necessary for OM4_05
e18e50f Merge pull request #4 from StephenGriffies/dev/gfdl
686854d Update diag_table.MOM6
5b675fb Merge pull request #3 from StephenGriffies/dev/gfdl
430b119 Update diag_table.MOM6
8b68682 Merge branch 'jkrasting-user/jpk/OM4_05_updates_for_ESM4' into dev/gfdl
3f29d5c Cleaned up trailing whitespace
4c26fb5 Merge branch 'user/jpk/OM4_05_updates_for_ESM4' of https://github.com/jkrasting/MOM6-examples into jkrasting-user/jpk/OM4_05_updates_for_ESM4
5d88d27 Merge branch 'Hallberg-NOAA-fix_geolonb' into dev/gfdl
12b16f4 MOM6/SIS2: Merge branch 'Hallberg-NOAA-fix_geolonb' into dev/gfdl
128352a Updated missed experiments
3ea8438 Diag table changes for ESM4
1a5e1ac Merge pull request #2 from NOAA-GFDL/dev/gfdl
1584ef2 Update diag_table.MOM6
0334100 Updated examples with code to correct GeoLonB
24106e5 icebergs: Merge pull request #59 from wfcooke/user/wfc/calving_restart_timestamp
2741a88 MOM6: Merge pull request #844 from adcroft/avoid-domain_aux-for-wind-stagger
b864fed MOM6: Merge branch 'Hallberg-NOAA-streamline_restore_state' into dev/gfdl
5dcd7c3 SIS2: +Temporarily avoid new update_ocean_model args
f45003c Use IO_LAYOUT=2,2 in global_ALE
5007183 MOM6: Merge pull request #841 from adcroft/fix-oob-restart-filename
f6ae30c MOM6: Merge pull request #839 from MJHarrison-GFDL/rotation_angle_diagnostic
e795958 Merge branch 'Hallberg-NOAA-use_stress_mag' into dev/gfdl
93be8ff Adding new ideal_hurricane test case
9f11b05 Updated examples with use_stress_mag
d11c6a4 SIS2: Merge branch 'Hallberg-NOAA-add_stress_mag' into dev/gfdl
98b627c Merge branch 'dev/master' into dev/gfdl
78cfb2d MOM6: Merge pull request #820 from adcroft/fix-doxy-1.8.4
7e5d936 MOM6: Merge branch 'ESMG-dev/esmg' into dev/gfdl
fbe2918 MOM6: Merge pull request #820 from adcroft/fix-doxy-1.8.4
ed36e93 MOM6: Merge branch 'ESMG-dev/esmg' into dev/gfdl
054912d Merge branch 'dev/master' into dev/gfdl
9025815 MOM6: Merge branch 'gustavo-marques-update_KPP' into dev/master
aeda3c9 SIS2: Merge branch 'Hallberg-NOAA-dOxyGenize_SIS2' into dev/gfdl
e937dd8 Merge branch 'Hallberg-NOAA-vertex_shearmix' into dev/gfdl
ea2a6be MOM6: Merge pull request #801 from Hallberg-NOAA/vertex_shearmix
ab45a7d Merge branch 'vertex_shearmix' of https://github.com/Hallberg-NOAA/MOM6-examples into Hallberg-NOAA-vertex_shearmix
7632200 MOM6: Merge pull request #799 from adcroft/aniso-hor-visc
4bac59b Update examples with VERTEX_SHEAR
a2162e4 MOM6: Merge branch 'ESMG-cleaning' into dev/gfdl
f894815 MOM6: *Merge branch 'ESMG-dev/esmg' into dev/gfdl
f1e9681 Merge branch 'dev/master' into dev/gfdl
5d17daf MOM6: Merge pull request #787 from NOAA-GFDL/dev-master-candidate-2018-06-03
48d4f8d MOM6: Merge branch 'dev/master' into dev/gfdl
0a13ed9 MOM6: Merge branch 'gustavo-marques-add_old_double_diffusion' into dev/master
f2aa2bd MOM6: Merge branch 'gustavo-marques-legacy_diabatic_driver' into dev/master
20799a1 MOM6: Merge pull request #774 from NOAA-GFDL/dev-master-candidate-2018-05-15
72580e8 MOM6: Merge branch 'ESMG-dev/esmg' into dev/gfdl
bed9677 Merge branch 'adcroft-disable-kpp-in-single-col-bml' into dev/gfdl
f2fd688 Disable KPP in single_column/BML experiment
dc9b61d gitlab: Adds testing of MOM6_parameter_doc and updates coverage
d84538c MOM6: Merge pull request #760 from ESMG/dev/esmg
3bcc768 MOM6: Merge branch 'MJHarrison-GFDL-MOM6_DA_rename' into dev/gfdl
ae71364 Travis: added script to build with OpenMP
c465130 mkmf: Updated to allow -l option
7339de5 MOM6: Merge branch 'Hallberg-NOAA-correct_reset_dtbt' into dev/gfdl
28a4377 Merge branch 'correct_reset_dtbt' of https://github.com/Hallberg-NOAA/MOM6-examples into Hallberg-NOAA-correct_reset_dtbt
b06285a MOM6: Merge branch 'MJHarrison-GFDL-MOM6_DA' into dev/gfdl
c903983 MOM6: Merged dev/ncar & dev/master into dev/gfdl
1091210 MOM6: Merged dev/ncar into dev/master
ef9adaa Merge pull request #1 from NOAA-GFDL/dev/gfdl
fd12185 Revert "mkmf: Updated to latest version on master branch"
2beb300 mkmf: Updated to latest version on master branch
4c080d1 MOM6: (*)Do not recalculate DTBT every coupled timestep
b40aa92 MOM6: Merge branch 'breichl-breichl/user/bgr/waves_update' into dev/gfdl
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 42122e3b
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.
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
5c25451 Added OBC options to DOME's MOM_input
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 #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 #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 #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 #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
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 #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 #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 #203 from jkrasting/user/jpk/section_transport_fix
9a830de Merge pull request #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
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
17d0228 Merge branch 'Hallberg-NOAA-tide_support' into dev/gfdl
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 #181 from jkrasting/user/jpk/webapp_updates_20171010
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

ESM4/v1.0.3

From commit 2778d3566e01c "ESM4 maintenance (#263)":

  * Updates to run OMIP, slab-model configs with Xanadu

    - Updates to calling data_override needed for generic_abiotic.F90
    - Updates to SIS to make compatible with slab-model config
    - New logic to flag old-style restarts that use K[d,v]_turb

OMIP1/v1.0.0

- Version used in OMIP1  experiments.
- dora experiment IDs 980, 985, 986, 987, 1162
- Tag is equivalent to tags dev/gfdl/2018.04.11 and ESM4/v1.0.0

om4/v1.0.5

Fixes to work with xanadu release
- d5cb5443 MOM6:Merge branch 'nikizadehgfdl-xanadu_coupler_compatible' into OM4-maintenance

dev/gfdl/2018.08.25

24106e5 icebergs: Merge pull request #59 from wfcooke/user/wfc/calving_restart_timestamp
2741a88 MOM6: Merge pull request #844 from adcroft/avoid-domain_aux-for-wind-stagger
b864fed MOM6: Merge branch 'Hallberg-NOAA-streamline_restore_state' into dev/gfdl
5dcd7c3 SIS2: +Temporarily avoid new update_ocean_model args
f45003c Use IO_LAYOUT=2,2 in global_ALE
5007183 MOM6: Merge pull request #841 from adcroft/fix-oob-restart-filename
f6ae30c MOM6: Merge pull request #839 from MJHarrison-GFDL/rotation_angle_diagnostic
e795958 Merge branch 'Hallberg-NOAA-use_stress_mag' into dev/gfdl
9f11b05 Updated examples with use_stress_mag
d11c6a4 SIS2: Merge branch 'Hallberg-NOAA-add_stress_mag' into dev/gfdl
98b627c Merge branch 'dev/master' into dev/gfdl
78cfb2d MOM6: Merge pull request #820 from adcroft/fix-doxy-1.8.4
7e5d936 MOM6: Merge branch 'ESMG-dev/esmg' into dev/gfdl
fbe2918 MOM6: Merge pull request #820 from adcroft/fix-doxy-1.8.4
ed36e93 MOM6: Merge branch 'ESMG-dev/esmg' into dev/gfdl
054912d Merge branch 'dev/master' into dev/gfdl
9025815 MOM6: Merge branch 'gustavo-marques-update_KPP' into dev/master
aeda3c9 SIS2: Merge branch 'Hallberg-NOAA-dOxyGenize_SIS2' into dev/gfdl
e937dd8 Merge branch 'Hallberg-NOAA-vertex_shearmix' into dev/gfdl
ea2a6be MOM6: Merge pull request #801 from Hallberg-NOAA/vertex_shearmix
ab45a7d Merge branch 'vertex_shearmix' of https://github.com/Hallberg-NOAA/MOM6-examples into Hallberg-NOAA-vertex_shearmix
7632200 MOM6: Merge pull request #799 from adcroft/aniso-hor-visc
4bac59b Update examples with VERTEX_SHEAR
a2162e4 MOM6: Merge branch 'ESMG-cleaning' into dev/gfdl
f894815 MOM6: *Merge branch 'ESMG-dev/esmg' into dev/gfdl
f1e9681 Merge branch 'dev/master' into dev/gfdl
5d17daf MOM6: Merge pull request #787 from NOAA-GFDL/dev-master-candidate-2018-06-03
48d4f8d MOM6: Merge branch 'dev/master' into dev/gfdl
0a13ed9 MOM6: Merge branch 'gustavo-marques-add_old_double_diffusion' into dev/master
f2aa2bd MOM6: Merge branch 'gustavo-marques-legacy_diabatic_driver' into dev/master
20799a1 MOM6: Merge pull request #774 from NOAA-GFDL/dev-master-candidate-2018-05-15
72580e8 MOM6: Merge branch 'ESMG-dev/esmg' into dev/gfdl
bed9677 Merge branch 'adcroft-disable-kpp-in-single-col-bml' into dev/gfdl
f2fd688 Disable KPP in single_column/BML experiment
dc9b61d gitlab: Adds testing of MOM6_parameter_doc and updates coverage
d84538c MOM6: Merge pull request #760 from ESMG/dev/esmg
3bcc768 MOM6: Merge branch 'MJHarrison-GFDL-MOM6_DA_rename' into dev/gfdl
ae71364 Travis: added script to build with OpenMP
c465130 mkmf: Updated to allow -l option
7339de5 MOM6: Merge branch 'Hallberg-NOAA-correct_reset_dtbt' into dev/gfdl
28a4377 Merge branch 'correct_reset_dtbt' of https://github.com/Hallberg-NOAA/MOM6-examples into Hallberg-NOAA-correct_reset_dtbt
b06285a MOM6: Merge branch 'MJHarrison-GFDL-MOM6_DA' into dev/gfdl
c903983 MOM6: Merged dev/ncar & dev/master into dev/gfdl
1091210 MOM6: Merged dev/ncar into dev/master
fd12185 Revert "mkmf: Updated to latest version on master branch"
2beb300 mkmf: Updated to latest version on master branch
4c080d1 MOM6: (*)Do not recalculate DTBT every coupled timestep
b40aa92 MOM6: Merge branch 'breichl-breichl/user/bgr/waves_update' into dev/gfdl

dev/gfdl/2018.08.24

2741a88 MOM6: Merge pull request #844 from adcroft/avoid-domain_aux-for-wind-stagger
b864fed MOM6: Merge branch 'Hallberg-NOAA-streamline_restore_state' into dev/gfdl
5dcd7c3 SIS2: +Temporarily avoid new update_ocean_model args
f45003c Use IO_LAYOUT=2,2 in global_ALE
5007183 MOM6: Merge pull request #841 from adcroft/fix-oob-restart-filename
f6ae30c MOM6: Merge pull request #839 from MJHarrison-GFDL/rotation_angle_diagnostic
e795958 Merge branch 'Hallberg-NOAA-use_stress_mag' into dev/gfdl
9f11b05 Updated examples with use_stress_mag
d11c6a4 SIS2: Merge branch 'Hallberg-NOAA-add_stress_mag' into dev/gfdl
98b627c Merge branch 'dev/master' into dev/gfdl
78cfb2d MOM6: Merge pull request #820 from adcroft/fix-doxy-1.8.4
7e5d936 MOM6: Merge branch 'ESMG-dev/esmg' into dev/gfdl
fbe2918 MOM6: Merge pull request #820 from adcroft/fix-doxy-1.8.4
ed36e93 MOM6: Merge branch 'ESMG-dev/esmg' into dev/gfdl
054912d Merge branch 'dev/master' into dev/gfdl
9025815 MOM6: Merge branch 'gustavo-marques-update_KPP' into dev/master
aeda3c9 SIS2: Merge branch 'Hallberg-NOAA-dOxyGenize_SIS2' into dev/gfdl
e937dd8 Merge branch 'Hallberg-NOAA-vertex_shearmix' into dev/gfdl
ea2a6be MOM6: Merge pull request #801 from Hallberg-NOAA/vertex_shearmix
ab45a7d Merge branch 'vertex_shearmix' of https://github.com/Hallberg-NOAA/MOM6-examples into Hallberg-NOAA-vertex_shearmix
7632200 MOM6: Merge pull request #799 from adcroft/aniso-hor-visc
4bac59b Update examples with VERTEX_SHEAR
a2162e4 MOM6: Merge branch 'ESMG-cleaning' into dev/gfdl
f894815 MOM6: *Merge branch 'ESMG-dev/esmg' into dev/gfdl
f1e9681 Merge branch 'dev/master' into dev/gfdl
5d17daf MOM6: Merge pull request #787 from NOAA-GFDL/dev-master-candidate-2018-06-03
48d4f8d MOM6: Merge branch 'dev/master' into dev/gfdl
0a13ed9 MOM6: Merge branch 'gustavo-marques-add_old_double_diffusion' into dev/master
f2aa2bd MOM6: Merge branch 'gustavo-marques-legacy_diabatic_driver' into dev/master
20799a1 MOM6: Merge pull request #774 from NOAA-GFDL/dev-master-candidate-2018-05-15
72580e8 MOM6: Merge branch 'ESMG-dev/esmg' into dev/gfdl
bed9677 Merge branch 'adcroft-disable-kpp-in-single-col-bml' into dev/gfdl
f2fd688 Disable KPP in single_column/BML experiment
dc9b61d gitlab: Adds testing of MOM6_parameter_doc and updates coverage
d84538c MOM6: Merge pull request #760 from ESMG/dev/esmg
3bcc768 MOM6: Merge branch 'MJHarrison-GFDL-MOM6_DA_rename' into dev/gfdl
ae71364 Travis: added script to build with OpenMP
c465130 mkmf: Updated to allow -l option
7339de5 MOM6: Merge branch 'Hallberg-NOAA-correct_reset_dtbt' into dev/gfdl
28a4377 Merge branch 'correct_reset_dtbt' of https://github.com/Hallberg-NOAA/MOM6-examples into Hallberg-NOAA-correct_reset_dtbt
b06285a MOM6: Merge branch 'MJHarrison-GFDL-MOM6_DA' into dev/gfdl
c903983 MOM6: Merged dev/ncar & dev/master into dev/gfdl
1091210 MOM6: Merged dev/ncar into dev/master
fd12185 Revert "mkmf: Updated to latest version on master branch"
2beb300 mkmf: Updated to latest version on master branch
4c080d1 MOM6: (*)Do not recalculate DTBT every coupled timestep
b40aa92 MOM6: Merge branch 'breichl-breichl/user/bgr/waves_update' into dev/gfdl

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 42122e3b
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 #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 #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 #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 #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 #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 #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 #203 from jkrasting/user/jpk/section_transport_fix
9a830de Merge pull request #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 #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 #181 from jkrasting/user/jpk/webapp_updates_20171010
f0c6afc Merge pull request #188 from jkrasting/refinediag_fix_20171103
96a8e5f Fixed typo in refineDiag_ocean_month_rho2.py
6a2f1fb Merge pull request #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 #191 from jkrasting/cmip6_analysis_updates
- d6edb4d Transport analysis to work with monthly pp

om4/v1.0.2

f0c6afc Merge pull request #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 #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 #57 from adcroft/berg_diffusion
d779aed Merge pull request #183 from nikizadehgfdl/user/nikizadehgfdl/reset_exec_bit_python_scripts
5e8de3e Merge pull request #185 from jkrasting/ocean_static_script
c36036e Added append_basin_mask.py script
01f14a3 Reset exec permissions of python scripts
96138c6 Merge pull request #182 from ashao/reorder_straits
4cbea5b Reorder indices of straits according to CMIP6/OMIP

dev/gfdl/2017.10.05

- Changes resulting from QC'ing postprocessed data for CMIP6.
- No configuration/code changes from dev/gfdl/2017.09.27, just
  diag_table and script changes.

f15b916 Merge pull request #163 from jkrasting/basin_refinediag
bcd2b90 Tidy-up odds and ends after QC
9647743 Added 'coordinates' attribute to basin/strait vars.
1ebf336 Removed call to calc_varaince.py
9d4536a Updated cell_methods attrs. for refined diags
b1c65de Updated umo in diag_table
8fad2c9 Miscellaneous clean-ups from testing
29c2b13 Flexible mask tiling based on time dimension
e8bd7e2 Merge remote branch 'origin/post_9_27_updates' into basin_refinediag
ab64e2a Various fixes for mfo (straits) diagnostic
f4c5c95 Added thkcello/volcello for rho2 output
839b026 Merge remote branch 'origin/post_9_27_updates' into basin_refinediag
c7c3375 Updated diag table for transport diags
69f35ec Updated calc_variance.py
6ff7aac Modified interface to calc_w_from_convergence()
b235c77 Masked Indo-Pacific heat transport below 34S
350462b Updated coordinates in rho2 refineDiag script
2ab368b Merge pull request #6 from ashao/add_mfo_diagnostic
5d039f6 Adds a script to calculate transport in straits
7f0ab79 Added hfbasin diagnostic to refineDiag script
769eb6b refineDiag script uses basin_codes.nc file
b6a25d3 Merge pull request #5 from NOAA-GFDL/dev/gfdl
b979772 Merge pull request #4 from ashao/add_wmo_to_refine_diag
a38e983 w had the wrong sign because divergence was calculated, not convergence
da8591d Include wmo as part of refine diags
52d52e3 Consolidated refineDiag updates
7173edb MOC reported on interfaces, not levels
47cb72e Initial commit of CMIP6 offline diag script
0814494 Merge pull request #3 from NOAA-GFDL/dev/master