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 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.
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 2778d35 "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

Merge pull request #248 from jkrasting/ESM4-maintenance

Updates to ESM4 maintenance branch

Merge pull request #247 from adcroft/ESM4-maintenance

Updates ESM4 maintenance to dev/gfdl/2018.08.25

om4/v1.0.5

Fixes to work with xanadu release
- d5cb544 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 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

Merge branch 'jkrasting-user/jpk/OM4_05_remap_overrides' into dev/gfdl