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Options for using m6plot in CGI mode #106

Merged
merged 2 commits into from
Aug 29, 2016
Merged

Options for using m6plot in CGI mode #106

merged 2 commits into from
Aug 29, 2016

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jkrasting
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Significant updates to sync the versions of m6plot.py
used on the web server and in the workflow analysis.

  • Added 'cmocean' colormaps as a git submodule.
  • Added Light-Bartlein BrownBlue colormap and
    Parula colormap.
  • Added sigma option to most plot types (currently
    hardcoded at 2.)
  • Added regional sector plots to xycompare using
    Basemap instances; existing plots fully backward
    compatible.
  • Added bbox_inches='tight' to the savefig call
    in xycompare to avoid sector plots being cutoff
    on the edges.
  • Added new functions:
    plotBasemapPanel()
    regionalMasking()
    sectorRanges()
    drawNinoBoxes()

@jkrasting
Options for using m6plot in CGI mode
1ae7c83 
Significant updates to sync the versions of m6plot.py
used on the web server and in the workflow analysis.

  - Added 'cmocean' colormaps as a git submodule.
  - Added Light-Bartlein BrownBlue colormap and
    Parula colormap.
  - Added sigma option to most plot types (currently
    hardcoded at 2.)
  - Added regional sector plots to xycompare using
    Basemap instances; existing plots fully backward
    compatible.
  - Added bbox_inches='tight' to the savefig call
    in xycompare to avoid sector plots being cutoff
    on the edges.
  - Added new functions:
      plotBasemapPanel()
      regionalMasking()
      sectorRanges()
      drawNinoBoxes()
@jkrasting
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@nikizadehgfdl -- could you run the tests you ran for m6toolbox to see if these changes to m6plot break anything in the workflow that I might have missed?

@jkrasting
Fixed error with annotated stats in xycompare
7575ed6 
  - When making a three panel plot with for
    a specific region, the annotate stats
    reflected the global values, not the
    regional values.
@adcroft adcroft merged commit 324e8c7 into dev/master Aug 29, 2016
@adcroft adcroft mentioned this pull request Oct 21, 2016
Open
adcroft added a commit that referenced this pull request Aug 16, 2019
@adcroft
MOM6: Merge branch 'gustavo-marques-dev-master-candidate-ncar-2019-08…
40f9eda 
…-05' into dev/master

- Merge from dev/ncar onto dev/master updates MOM_parameter_doc files.

- NOAA-GFDL/MOM6@1328636 Merge branch 'gustavo-marques-dev-master-candidate-ncar-2019-08-05' into dev/master
- NOAA-GFDL/MOM6@35b5c76 Merge pull request #115 from gustavo-marques/update_meke
- NOAA-GFDL/MOM6@c149c20 Merge pull request #114 from gustavo-marques/update_mom_vert_friction
- NOAA-GFDL/MOM6@815db63 Change default way to computing FrictWork in MEKE
- NOAA-GFDL/MOM6@68ec55e Merge pull request #113 from gustavo-marques/rename_modules
- NOAA-GFDL/MOM6@c56450a Deletes all code related to Jansen15_drag
- NOAA-GFDL/MOM6@21fd427 Make sure that MEKE%GME_snk is only used when the array is allocated
- NOAA-GFDL/MOM6@d292a57 Deletes contribution from kv%slow when computing a_cpl
- NOAA-GFDL/MOM6@a34bdf4 Capitalize MOM inside MCT modules
- NOAA-GFDL/MOM6@fc55c36 Rename modules for NUOPC
- NOAA-GFDL/MOM6@8a04b99 Rename modules for MCT
- NOAA-GFDL/MOM6@3b2ad3f Rename modules in NUOPC
- NOAA-GFDL/MOM6@1305e73 Rename modules in MCT
- NOAA-GFDL/MOM6@06a7c46 Merge pull request #112 from gustavo-marques/mct_nuopc_validation
- NOAA-GFDL/MOM6@562297c more changes to have minimal differences between nuopc and mct
- NOAA-GFDL/MOM6@f72454b changes to have minimal differences between nuopc and mct
- NOAA-GFDL/MOM6@3135f62 removed trailing whitespace
- NOAA-GFDL/MOM6@7c90fa0 changes to get MOM_ocean_model.F90 closer to nuopc_driver
- NOAA-GFDL/MOM6@c4e349d Merge branch 'dev/ncar' into mvertens/validation_fixes2
- NOAA-GFDL/MOM6@3995037 more updates to have caps consistent with dev/ncar
- NOAA-GFDL/MOM6@8da9eb9 changes to the interfaces to bring them more in line with dev/ncar latest
- NOAA-GFDL/MOM6@b9844d7 Merge pull request #108 from gustavo-marques/merge-dev-master-candidate-2019-07-08
- NOAA-GFDL/MOM6@f5899da Merge branch 'dev/master' into merge-dev-master-candidate-2019-07-08
- NOAA-GFDL/MOM6@2a65e65 Merge pull request #107 from NCAR/mvertens/validation_fixes
- NOAA-GFDL/MOM6@05709a1 Merge pull request #104 from gustavo-marques/remove_salt_flux_from_net_FW
- NOAA-GFDL/MOM6@3fcd942 Deletes comments
- NOAA-GFDL/MOM6@87e6f17 removed trailing whitespace
- NOAA-GFDL/MOM6@6ec503f Merge branch 'dev/ncar' into mvertens/validation_fixes
- NOAA-GFDL/MOM6@cac0656 fixes to get taux and tauy roundoff between mct and nuopc
- NOAA-GFDL/MOM6@f8758ec Merge pull request #106 from gustavo-marques/bobs_solution
- NOAA-GFDL/MOM6@3f8c425 Merge pull request #105 from NCAR/mvertens/mom6_validation
- NOAA-GFDL/MOM6@3f7e9f6 changes needed for mom6 validation
- NOAA-GFDL/MOM6@97c2395 Commenting out salt_flux adjustment in net_FW in NUOPC cap
- NOAA-GFDL/MOM6@9d8468a Commenting salt_flux adjustment in net_FW
Hallberg-NOAA added a commit that referenced this pull request Apr 19, 2022
@Hallberg-NOAA
MOM6: Updated version of MOM6 (PRs 99-111) and MOM_parameter_doc files
5cf09ef 
  Updated the version of MOM6 that MOM6-examples points to, and updated the
available_diags files to reflect the changes in MOM6.  Also updated other
MOM_parameter_doc files in infrequently run test cases that previous changes had
altered but which were not updated when the corresponding code changes were
introduced.  All answers are bitwise identical.  The MOM6 commits that are
included in this update are:

- NOAA-GFDL/MOM6@684878ee4 Add a deta_dt diagnostic to the split BT/BC mode (#99)
- NOAA-GFDL/MOM6@b4b7368d5 Merge pull request #111 from marshallward/field_size_fixes
- NOAA-GFDL/MOM6@54b8ff50b Merge branch 'dev/gfdl' into field_size_fixes
- NOAA-GFDL/MOM6@f6fc6ce17 FMS2: get_field_sizes with FMS1 emulation
- NOAA-GFDL/MOM6@f54338ad1 Fix non-standard white space (#109)
- NOAA-GFDL/MOM6@d729c679a +Remove append_substring
- NOAA-GFDL/MOM6@d8bc9639e Removal of non-standard extensions
- NOAA-GFDL/MOM6@7a147ad41 +Document or eliminate undocumented interfaces
- NOAA-GFDL/MOM6@e9fdf5de3 Standardized syntax in mask2d logical tests
- NOAA-GFDL/MOM6@7f6dac283 Merge pull request #105 from marshallward/pedantic
- NOAA-GFDL/MOM6@d3d0c8ecc Merge branch 'dev/gfdl' into pedantic
- NOAA-GFDL/MOM6@c150f37a1 Correct --with-driver args for coupled tests (#106)
- NOAA-GFDL/MOM6@6809ee3a4 Fix tides_CS attribute in unsplit mode (#103)
- NOAA-GFDL/MOM6@d2fb2d0ed MOM_random: Set mask with bits rather than integer
- NOAA-GFDL/MOM6@a5350219b Mixed layer restrat statement function refactor
- NOAA-GFDL/MOM6@936b11fb6 Format string fixes; function index reorder
marshallward added a commit that referenced this pull request Jul 7, 2022
@marshallward
MOM6: Follow MOM6 code style guide
464a34c 
- NOAA-GFDL/MOM6@3b80e443d Follow MOM6 code style guide
- NOAA-GFDL/MOM6@0c1e89a2c Add missing units
- NOAA-GFDL/MOM6@0e8acd90b +(*)Fix a scaling bug in MOM_horizontal_regridding
- NOAA-GFDL/MOM6@005c46066 Impose standard indentation in nuopc_cap code
- NOAA-GFDL/MOM6@3b05cdfdb Impose standard indentation in most driver code
- NOAA-GFDL/MOM6@9b1d382ae Style compliance in external/ODA_hooks code
- NOAA-GFDL/MOM6@1d8fb5091 +Style compliance in external/drifters code
- NOAA-GFDL/MOM6@84d78a661 +Revised stochastics code for style compliance
- NOAA-GFDL/MOM6@8f97b3d2f Corrections to cell-averaged density computation (#213)
- NOAA-GFDL/MOM6@41a278b81 Candidate branch main->dev/gfdl
- NOAA-GFDL/MOM6@e73c231fb +Set thickness_units for use by deta_dt diagnostic
- NOAA-GFDL/MOM6@2cd228fbe Adds conditional for setting fluxes%heat_content_*
- NOAA-GFDL/MOM6@fc3ab450b Avoid rotating arrays that are not associated
- NOAA-GFDL/MOM6@f81414708 Add missing logical to control allocation of fluxes
- NOAA-GFDL/MOM6@b9b67a838 Changes needed for when enthalpy is via coupler
- NOAA-GFDL/MOM6@fc05abe21 Modifications needed for when enthalpy is via CPL
- NOAA-GFDL/MOM6@7924fbaee Modify log/description of ENTHALPY_FROM_COUPLER
- NOAA-GFDL/MOM6@b7665f481 Heat conservation when enthalpy is via coupler
- NOAA-GFDL/MOM6@72daf7b0c Add option to receive enthalpy fluxes via coupler
- NOAA-GFDL/MOM6@861a8f14d Use ODA_2018_ANSWERS to specify ODA remapping
- NOAA-GFDL/MOM6@48ae48ae7 Remove unused variables
- NOAA-GFDL/MOM6@684878ee4 Add a deta_dt diagnostic to the split BT/BC mode (#99)
- NOAA-GFDL/MOM6@f6fc6ce17 FMS2: get_field_sizes with FMS1 emulation
- NOAA-GFDL/MOM6@f54338ad1 Fix non-standard white space (#109)
- NOAA-GFDL/MOM6@d729c679a +Remove append_substring
- NOAA-GFDL/MOM6@d8bc9639e Removal of non-standard extensions
- NOAA-GFDL/MOM6@7a147ad41 +Document or eliminate undocumented interfaces
- NOAA-GFDL/MOM6@e9fdf5de3 Standardized syntax in mask2d logical tests
- NOAA-GFDL/MOM6@c150f37a1 Correct --with-driver args for coupled tests (#106)
- NOAA-GFDL/MOM6@6809ee3a4 Fix tides_CS attribute in unsplit mode (#103)
- NOAA-GFDL/MOM6@28ff86e4e +Convective adjustment outside regridding_main
- NOAA-GFDL/MOM6@fd2060cda +Add Hybgen regridding
- NOAA-GFDL/MOM6@138396107 It would be good to initialize CS%answers_2018.
- NOAA-GFDL/MOM6@8d92579b2 Deleted an unused function, made public OBC funcs.
- NOAA-GFDL/MOM6@9c22ff272 Taking out some unused OBC constants.
- NOAA-GFDL/MOM6@3c7bd19ee More cleaning up for issue #54
- NOAA-GFDL/MOM6@d2fb2d0ed MOM_random: Set mask with bits rather than integer
- NOAA-GFDL/MOM6@a5350219b Mixed layer restrat statement function refactor
- NOAA-GFDL/MOM6@936b11fb6 Format string fixes; function index reorder
- NOAA-GFDL/MOM6@4b218c07a Tweaks in response to Hallberg's comments.
- NOAA-GFDL/MOM6@57a1a8ae2 Rest of fix for issue #54.
- NOAA-GFDL/MOM6@41757c7a5 Fix the rebase
- NOAA-GFDL/MOM6@f50551ce4 Fix to Z_RESCALE bug in ePBL.
- NOAA-GFDL/MOM6@1e6924e03 More fixes for issue #54.
- NOAA-GFDL/MOM6@24f412d77 Part of the fix for issue #54.
- NOAA-GFDL/MOM6@6f48b9d1d Oops, more cleanup.
- NOAA-GFDL/MOM6@1853352a6 correction on type in directory name
- NOAA-GFDL/MOM6@28003a8f7 Adding in that SAL commit again.
- NOAA-GFDL/MOM6@4a9162839 Undoing some patches from others
- NOAA-GFDL/MOM6@11fa11406 Done with EPBL docs?
- NOAA-GFDL/MOM6@918742bbb Working on boundary layer docs.
- NOAA-GFDL/MOM6@a180d3316 return a more accurate error message in MOM_stochasics
- NOAA-GFDL/MOM6@1428a36ac Several little things, one is making sponge less verbose.
- NOAA-GFDL/MOM6@aac6b75dd update to gfdl 20210806 (#74)
- NOAA-GFDL/MOM6@71f7354d9 add comments
- NOAA-GFDL/MOM6@8775c6d41 revert logic wrt increments
- NOAA-GFDL/MOM6@64e83b7aa add logic to remove incrments from restart if outside IAU window
- NOAA-GFDL/MOM6@3e573eb11 add write_stoch_restart_ocn to MOM_stochastics
- NOAA-GFDL/MOM6@8382652d5 doxygen cleanup
- NOAA-GFDL/MOM6@97bbdbf6f move stochastics to external directory
- NOAA-GFDL/MOM6@199126eb7 stochastic physics re-write
- NOAA-GFDL/MOM6@0932b9ec1 remove debug statements
- NOAA-GFDL/MOM6@ebe9d1f6f remove PE_here from mom_ocean_model_nuopc.F90
- NOAA-GFDL/MOM6@077413af9 clean up of mom_ocean_model_nuopc.F90
- NOAA-GFDL/MOM6@b12c09cbb revert MOM_domains.F90
- NOAA-GFDL/MOM6@80fdfb4e8 remove stochastics container
- NOAA-GFDL/MOM6@65e0e71bb clean up of code for MOM6 coding standards
- NOAA-GFDL/MOM6@121ce71b3 correct coupled_driver/ocean_model_MOM.F90 and other cleanup
- NOAA-GFDL/MOM6@045d5c2db make stochastics optional
- NOAA-GFDL/MOM6@f874d1113 clean up MOM_domains
- NOAA-GFDL/MOM6@390fee8d0 re-write of stochastic code to remove CPP directives
- NOAA-GFDL/MOM6@48354da37 fix non stochastic ePBL calculation
- NOAA-GFDL/MOM6@583c6ae1e clean up code
- NOAA-GFDL/MOM6@878543d22 clean up debug statements
- NOAA-GFDL/MOM6@095c36ca4 additions for stochy restarts
- NOAA-GFDL/MOM6@6ff36ec6d add stochy_restart writing to mom_cap
- NOAA-GFDL/MOM6@cefdb81ed Update MOM_diabatic_driver.F90
- NOAA-GFDL/MOM6@2f5d83d3c Update MOM_diabatic_driver.F90
- NOAA-GFDL/MOM6@b6ac287b6 Update MOM_diabatic_driver.F90
- NOAA-GFDL/MOM6@45acf37f1 cleanup of code and enhancement of ePBL perts
- NOAA-GFDL/MOM6@e853f839b additions for stochastic physics and ePBL perts
- NOAA-GFDL/MOM6@78c574be1 Add missing h_neglect (#98)
- NOAA-GFDL/MOM6@edd3f9c68 +Corrected units in dumbbell get_param calls
- NOAA-GFDL/MOM6@db59e142d MOM_neutral_diffusion code cleanup
- NOAA-GFDL/MOM6@063ef75fa Minor get_param call reformatting
- NOAA-GFDL/MOM6@6bfd073b2 +Avoid nonsensical units descriptions
- NOAA-GFDL/MOM6@c626cc464 MOM_internal_tides diagnostic code simplification
- NOAA-GFDL/MOM6@305f74473 Rescale new_depth in apply_topography_edits_from_file
- NOAA-GFDL/MOM6@39206d91b Simplify diagnostics using global_area_integral
- NOAA-GFDL/MOM6@a6992a9d6 Convert global_area_mean diagnostics when writing
- NOAA-GFDL/MOM6@9c4363ed2 +Add optional conversion argument to register_diag_scalar
- NOAA-GFDL/MOM6@356671c20 +Refactor writing the vertical_coordinate file
- NOAA-GFDL/MOM6@08582eead add residual loss term for internal tides (#95)
- NOAA-GFDL/MOM6@4c5e98e1b Error handler support
- NOAA-GFDL/MOM6@2ac64b39c Set INPUT_STR_LENGTH to 1024
- NOAA-GFDL/MOM6@4e94c5d6a Reduce the populate_param_data memory footprint
- NOAA-GFDL/MOM6@3b5d2641a Support arbitrarily long parameter spec lines
- NOAA-GFDL/MOM6@97331e705 +Better multi-line parameter specification handling
- NOAA-GFDL/MOM6@8bf9abbad reworked algebra corner spread, rotation parenthesis (#90)
- NOAA-GFDL/MOM6@ce22d7aea add missing shared variable
- NOAA-GFDL/MOM6@115d71477 Ice dynamics (#80)
- NOAA-GFDL/MOM6@7c3f31bd4 +(*)Write unscaled MOM6 restart files
- NOAA-GFDL/MOM6@11d03b13b +Add unit conversion capability for restarts
- NOAA-GFDL/MOM6@966d50f15 (*)Minor MOM_hor_visc code cleanup
- NOAA-GFDL/MOM6@ab4d226bb +(*)MOM_hor_visc bug fix and loop size cleanup
- NOAA-GFDL/MOM6@8c6ae0eea Corrected the license on RGC_initialization.F90
- NOAA-GFDL/MOM6@a002923ae (*)Fix rescaling in RGC_initialize_sponges
- NOAA-GFDL/MOM6@14a28f477 Avoid copying the tracer registry in advect_tracer
- NOAA-GFDL/MOM6@5a8590b03 +Add Laplacian diffusion of interface heights
- NOAA-GFDL/MOM6@406bc59cd Merge remote-tracking branch 'alexandra/main' into dev/esmg
- NOAA-GFDL/MOM6@9c341f06e Merge remote-tracking branch 'gfdl/dev/gfdl' into dev/esmg
- NOAA-GFDL/MOM6@3675c2169 +Add Hybgen remapping options
- NOAA-GFDL/MOM6@304294260 Fix nolibs build in CI pipeline
- NOAA-GFDL/MOM6@d5601696e +Stop logging NEW_SPONGES
- NOAA-GFDL/MOM6@6963b222d Add KPP nonlocal term to passive tracers (#202)
- NOAA-GFDL/MOM6@efa503bd2 bugfix: static h_new shape remaining_transport_sum
- NOAA-GFDL/MOM6@b4a67c1ad Merge remote-tracking branch 'gfdl/dev/gfdl' into dev/esmg
- NOAA-GFDL/MOM6@464046138 (*)Avoid negative thicknesses in mixed_layer_restrat
- NOAA-GFDL/MOM6@9a01cd501 +Add ALE options mimicking Hycom
- NOAA-GFDL/MOM6@9caa7010f (+) Refactor of MOM_file_parser
- NOAA-GFDL/MOM6@fa2832c11 +(*)Rescale variables with homogenize_forcing
- NOAA-GFDL/MOM6@b3e80f73f +(*)Add tmp_scale arguments to global_area_mean
- NOAA-GFDL/MOM6@a468bee03 Removed trailing white space
- NOAA-GFDL/MOM6@a0d02387e (*)+Use reproducing stocks for all tracer packages
- NOAA-GFDL/MOM6@1bf82205a (*)+Reproducing tracer stocks
- NOAA-GFDL/MOM6@8197cea79 Use global_mass_integral in lateral_bdry_diff
- NOAA-GFDL/MOM6@9c7bf292d +Add global_mass_int_EFP
- NOAA-GFDL/MOM6@d46dbc775 Report mean temperature from MOM_state_stats()
- NOAA-GFDL/MOM6@65b2c8249 Merge remote-tracking branch 'gfdl/dev/gfdl' into dev/esmg
- NOAA-GFDL/MOM6@149073fea Remove hard-wired parameter in adjustEtaToFitBathymetry (#69)
- NOAA-GFDL/MOM6@32e1ecf45 Fixes issues with the GME code and get_param calls for Leith options (#65)
- NOAA-GFDL/MOM6@098f5c9d9 fix u10_sqr dimensional scaling
- NOAA-GFDL/MOM6@b39648adc merge with latest main (2020feb17) and resolve conflicts
- NOAA-GFDL/MOM6@e84160915 remove unnecessary optional flag
- NOAA-GFDL/MOM6@c166358b2 Add optional argument to FMS2 version of get_field_size
- NOAA-GFDL/MOM6@fc5253f73 (*)Correct memory declarations in MOM_regridding
- NOAA-GFDL/MOM6@035ae5c85 Misc dimensional consistency fixes in regridding, remapping, and MEKE routines
- NOAA-GFDL/MOM6@75bf521e2 +Move MOM_scaling_check.F90 to MOM_unique_scales.F90
- NOAA-GFDL/MOM6@56401b637 +Add MOM_check_scaling.F90 and MOM_scaling_check.F90
- NOAA-GFDL/MOM6@c18185422 fix line lenght error in MOM_wave_interface
- NOAA-GFDL/MOM6@ebb643af9 Oops, more cleanup.
- NOAA-GFDL/MOM6@65cccb7a0 correction on type in directory name
- NOAA-GFDL/MOM6@45d615191 Adding in that SAL commit again.
- NOAA-GFDL/MOM6@3dbf2f58d Undoing some patches from others
- NOAA-GFDL/MOM6@71908c8fd Done with EPBL docs?
- NOAA-GFDL/MOM6@b7b4141a6 Working on boundary layer docs.
- NOAA-GFDL/MOM6@c3ff425ce return a more accurate error message in MOM_stochasics
- NOAA-GFDL/MOM6@348a81b63 Several little things, one is making sponge less verbose.
- NOAA-GFDL/MOM6@9221b5d50 update to gfdl 20210806 (#74)
- NOAA-GFDL/MOM6@59e733f3e add comments
- NOAA-GFDL/MOM6@15e402940 revert logic wrt increments
- NOAA-GFDL/MOM6@78b8d7919 add logic to remove incrments from restart if outside IAU window
- NOAA-GFDL/MOM6@a5d90655d add write_stoch_restart_ocn to MOM_stochastics
- NOAA-GFDL/MOM6@e91c96609 doxygen cleanup
- NOAA-GFDL/MOM6@cf1d29628 move stochastics to external directory
- NOAA-GFDL/MOM6@493717a35 stochastic physics re-write
- NOAA-GFDL/MOM6@a67bc78a2 remove debug statements
- NOAA-GFDL/MOM6@e2431bc81 remove PE_here from mom_ocean_model_nuopc.F90
- NOAA-GFDL/MOM6@ea36db238 clean up of mom_ocean_model_nuopc.F90
- NOAA-GFDL/MOM6@4c931094f revert MOM_domains.F90
- NOAA-GFDL/MOM6@c7531a75f remove stochastics container
- NOAA-GFDL/MOM6@08dc1a44b clean up of code for MOM6 coding standards
- NOAA-GFDL/MOM6@e80d5f57e correct coupled_driver/ocean_model_MOM.F90 and other cleanup
- NOAA-GFDL/MOM6@0bf4ff0a1 make stochastics optional
- NOAA-GFDL/MOM6@9e7029ca8 clean up MOM_domains
- NOAA-GFDL/MOM6@58f1fe98f re-write of stochastic code to remove CPP directives
- NOAA-GFDL/MOM6@15dde3622 fix non stochastic ePBL calculation
- NOAA-GFDL/MOM6@49111ff9f clean up code
- NOAA-GFDL/MOM6@0c48bfc6a clean up debug statements
- NOAA-GFDL/MOM6@becb4420e additions for stochy restarts
- NOAA-GFDL/MOM6@36ce2d108 add stochy_restart writing to mom_cap
- NOAA-GFDL/MOM6@5f6973b4d Update MOM_diabatic_driver.F90
- NOAA-GFDL/MOM6@c48a46ae0 Update MOM_diabatic_driver.F90
- NOAA-GFDL/MOM6@a0e5b56af Update MOM_diabatic_driver.F90
- NOAA-GFDL/MOM6@a534541c5 cleanup of code and enhancement of ePBL perts
- NOAA-GFDL/MOM6@0add693a8 additions for stochastic physics and ePBL perts
- NOAA-GFDL/MOM6@a00b7799f Merge remote-tracking branch 'NCAR/surfbands_refactor' into BGR_Stokes_DDT_Fixes
- NOAA-GFDL/MOM6@dc59b117b Fixing restart issue with Stokes time tendency term.
- NOAA-GFDL/MOM6@f89fd1351 Fixing diagnostic mode for vortex force correction term.
- NOAA-GFDL/MOM6@58874a5f3 Updates	to Stokes drift	terms, primarily the pressure gradient routine.
- NOAA-GFDL/MOM6@4f592f298 More changes for surfbands wave coupling: - for ustkb and vstkb, call pass_var, instead of pass_vector because they are on h grd. -remove unused ustk0 and vstk0 arrays. - correct the order of wave-related get param & allocate_forcing calls in nuopc cap. - add lamult flag to allocate_forcing_by_group because lamult should only be allocated if wave_method=="EFACTOR".
- NOAA-GFDL/MOM6@28268d3e6 fixes in MOM_wave_interface array indices
- NOAA-GFDL/MOM6@dc93bdeef Fixes for Stokes time tendency terms
- NOAA-GFDL/MOM6@b619d38eb remove duplicate assignments of dvdx and dudy. These duplicate assignments incorrectly override dvdx and dudy when surfbands wave coupling is on.
- NOAA-GFDL/MOM6@cb671d2c0 merge with latest dev/ncar and resolve conflicts
- NOAA-GFDL/MOM6@d4c36a60a Fix openmp test by adding Stokes_VT to shr clause in MOM_CoriolisAdv. Also remove the Passive_Stokes_VF block since it's never set to true.
- NOAA-GFDL/MOM6@e2ab77e99 initialize wave option flags to false
- NOAA-GFDL/MOM6@c880a156a For the drivers calling MOM_wave_interface_init, add the optional waves_csp arg to initialize_MOM calls so as to ensure that the waves_csp is allocated. This commit also has several misc doxygen fixes.
- NOAA-GFDL/MOM6@e7f628e17 refactoring and changes to write stokes drift profile to restart file when surfbands wave coupling mode is on.
- NOAA-GFDL/MOM6@15c3d53de changes in the nuopc cap to support arbitrary stokes bands With these changes, arbitrary number of of partitioned stokes drift components may be imported from ww3 when coupled within cesm. After the planned unification of ww3 nuopc caps of CESM and EMC, the old (fixed) approach may be removed.
- NOAA-GFDL/MOM6@eacd9d016 fix doxygen errors in surfbands_refactor branch
- NOAA-GFDL/MOM6@a0d1d9982 Do not call get_Langmuir_Number if lamult is already provided via ww3
- NOAA-GFDL/MOM6@b1c341248 enclose stokes vorticity diag computations with Stokes_VF conditional
- NOAA-GFDL/MOM6@824039dac enclose stokes vorticity diag computations with Stokes_VF conditional
- NOAA-GFDL/MOM6@59a31f62c remove unnecessary ampersands from variable declarations
- NOAA-GFDL/MOM6@dcf30ac50 merge pr1507 with dev/ncar and resolve conflicts in MOM_tidal_mixing
- NOAA-GFDL/MOM6@6e94b699b disable the register of tidal mixing coeff diags when they are unavailable
- NOAA-GFDL/MOM6@e3d190db3 In NUOPC cap, add ability to import fields with ungridded dimensions
- NOAA-GFDL/MOM6@380a04090 Merge remote-tracking branch 'breichl/Stokes_Forces' into pstokes_wave_cpl_mehtod
- NOAA-GFDL/MOM6@c5f1d442e Updating name of Stokes PGF routine to be more descriptive.
- NOAA-GFDL/MOM6@a6de11c92 Remote application of Stokes tendency on thermodynamic step
- NOAA-GFDL/MOM6@9fbdf11ec Finish incomplete merge in MOM_wave_interface.
- NOAA-GFDL/MOM6@77084ecc9 Adding Stokes forces implementation and diags.

SIS2: Replace MOM_memory.h with SIS2_memory.h

- NOAA-GFDL/SIS2@55dbb3a Replace MOM_memory.h with SIS2_memory.h
- NOAA-GFDL/SIS2@33589c6 Fixed the syntax of new comments in PR #173
- NOAA-GFDL/SIS2@164e404 Getting OBCs with MERGED_CONTINUITY to work
- NOAA-GFDL/SIS2@d62188d OBC's for C-grid stress.
- NOAA-GFDL/SIS2@c84a83b Start of ice OBCs - it compiles.
- NOAA-GFDL/SIS2@2ac240a Merge remote-tracking branch 'gfdl/dev/gfdl' into dev/esmg
- NOAA-GFDL/SIS2@a9884b8 Merge remote-tracking branch 'gfdl/dev/gfdl' into dev/esmg
- NOAA-GFDL/SIS2@3399a73 Merge remote-tracking branch 'gfdl/dev/gfdl' into dev/esmg
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@jkrasting @adcroft