add .frepp analysis template for CM2G63L example #1

nikizadehgfdl · 2014-10-23T20:27:26Z

No description provided.

- Took .frepp files from OM4_025 and replace paths to CM2G63L WOA05 data and mosaic directories. - Hopefully helps address issue #1. - Completely untested!

adcroft · 2014-11-19T22:31:25Z

@jkrasting Can you confirm the .frepp's for CM2G63L are working for you and close this ticket?

jkrasting · 2014-11-20T12:44:36Z

Yes, everything appears to be working!

See: /nbhome/jpk/mdt/20141117/tikal_201409_drag_updates_mom6_2014.11.17/CM4i_c96L48_1deg_2000_A01/ocean_0001-0005/

- NOAA-GFDL/MOM6@7f5be9a Revised stdout "MOM Day format" - NOAA-GFDL/MOM6@2a09234 Fix internal formatting error from set_grid_metrics() - NOAA-GFDL/SIS2@5a49e30 Fixes for divide by zero in ice_dyn_cgrid.F90 - NOAA-GFDL/SIS2@b32a1cc Fix internal formatting error from set_grid_derived_metrics() - NOAA-GFDL/icebergs@788d956 Fixed uninitialized variable in write_restart() - NOAA-GFDL/icebergs@255fb34 Fix order of trajectory segments for local PE - NOAA-GFDL/icebergs@314713b Reverted the reverse_list changes - NOAA-GFDL/icebergs@8368e69 Merge branch 'user/nnz/fix_trajectory_append_hang' into dev/master - NOAA-GFDL/icebergs@074a75c Merge branch 'sternalon-Calving_flux_input' into dev/master - NOAA-GFDL/icebergs@1558d14 Merge branch 'Calving_flux_input' of https://github.com/sternalon/icebergs into sternalon-Calving_flux_input - NOAA-GFDL/icebergs@a3913a7 Added ability to frequently write trajectories - NOAA-GFDL/icebergs@6af1a80 Corrected terminal message for creating trajectory file - NOAA-GFDL/icebergs@cea2074 Nullify pointers on repeated calls to write_trajectory() - NOAA-GFDL/icebergs@150ae95 Ensure that trajectory memory is deallocated - NOAA-GFDL/icebergs@19107e7 Updated write_trajectory() to not clobber existing file - NOAA-GFDL/icebergs@6854f3a Add capabality to write one traj file per core - NOAA-GFDL/icebergs@1711492 Fix issue #1 the apparent hang in writing the trajectories - NOAA-GFDL/icebergs@6031716 Changed 0.25 back to 0.24 on the smallest category of the iceberg distribution since I was getting the error messaged "Calving is Over distributed". - NOAA-GFDL/icebergs@15f3388 Flag for using mass vs freq distribution has been included. - NOAA-GFDL/icebergs@9dff46b Flag added which allows the user to input a calving freq distribution rather than a mass flux distribution. If this flag is on, the code converts the input freq distribution into a mass flux distribution. - No answer changes.

- Brings in a major refactor of open boundary code from branch user/ksh/open_bc on the ESMG fork. - Updates MOM_parameter_doc files. - No answer changes. - NOAA-GFDL/MOM6@c2799bc Merge branch 'ESMG-user/ksh/open_bc' into dev/master - NOAA-GFDL/MOM6@be8080a Added description for log_version in MOM_open_boundary - NOAA-GFDL/MOM6@cff9f0e Fixed uninitialized logical in MOM_continuity_PPM - NOAA-GFDL/MOM6@d4fe7f7 Merge branch 'user/ksh/open_bc' of https://github.com/ESMG/MOM6 into ESMG-user/ksh/open_bc - NOAA-GFDL/MOM6@fd8cf8a Merge branch 'gustavo-marques-ICE_SHELF' into dev/master - NOAA-GFDL/MOM6@299bdab Merge branch 'user/mjh/dye_tracers_restart_fix' into dev/master - NOAA-GFDL/MOM6@30bc60b Chaged allocation of water/heat fluxes - NOAA-GFDL/MOM6@da43065 Merge branch 'dev/master' into ICE_SHELF - NOAA-GFDL/MOM6@12b8cc5 Put back OBC_SIMPLE tests. - NOAA-GFDL/MOM6@ca7313e Merge branch 'dev/master' into user/ksh/open_bc - NOAA-GFDL/MOM6@ad3219b Merge branch 'dev/master' of github.com:NOAA-GFDL/MOM6 into dev/master - NOAA-GFDL/MOM6@8cb5593 Changed do_i test for Flather OBC - NOAA-GFDL/MOM6@1bd381b Allocated fluxes%buoy in MOM_ice_shelf - NOAA-GFDL/MOM6@6ee04ef Backing out unstable change to OBC - NOAA-GFDL/MOM6@fbc1297 Merge branch 'dev/master' into user/ksh/open_bc - NOAA-GFDL/MOM6@7ee3e4d Merge branch 'dev/master' of github.com:NOAA-GFDL/MOM6 into dev/master - NOAA-GFDL/MOM6@0c103bb Merge branch 'user/ksh/open_bc' into user/ksh/open_bc_uv - NOAA-GFDL/MOM6@3fa6245 Fix for cases without OBC - NOAA-GFDL/MOM6@5edb9c9 Merge of dev/master - NOAA-GFDL/MOM6@080e159 Merge branch 'dev/master' into user/ksh/open_bc - NOAA-GFDL/MOM6@c4ff34d Merge branch 'dev/master' of github.com:NOAA-GFDL/MOM6 into dev/master - NOAA-GFDL/MOM6@0cf8497 CCS1 runs with six cores. - NOAA-GFDL/MOM6@bd59a04 Don't deallocate OBC on pes without boundary - NOAA-GFDL/MOM6@ffb4aea Fix OBC after merge. - NOAA-GFDL/MOM6@9862707 Update to ISOMIP_tracer for OBC - NOAA-GFDL/MOM6@2861388 Merge branch 'dev/master' into user/ksh/open_bc - NOAA-GFDL/MOM6@f9613a8 Merge branch 'dev/master' of github.com:NOAA-GFDL/MOM6 into dev/master - NOAA-GFDL/MOM6@5f222f0 Added OBC for flow parallel to boundary. - NOAA-GFDL/MOM6@8e10ec5 Merge pull request #8 from adcroft/user/aja/obc_split_kind_and_direction - NOAA-GFDL/MOM6@f182829 Unified deallocation of OBC on PE without OBs - NOAA-GFDL/MOM6@c3c1106 Split OBC_kind_u into OBC_kind_u and OBC_direction_u - NOAA-GFDL/MOM6@983ce84 Adjust OBC mask to be consistent with land mask. - NOAA-GFDL/MOM6@c421b4b ISOMIP_tracer fix for OBC reorg. - NOAA-GFDL/MOM6@ada7e63 Merge branch 'dev/master' into user/ksh/open_bc - NOAA-GFDL/MOM6@75a8557 Merge branch 'dev/master' of github.com:NOAA-GFDL/MOM6 into dev/master - NOAA-GFDL/MOM6@f1795fc Merge branch 'dev/master' into user/ksh/open_bc - NOAA-GFDL/MOM6@97f0ecc Merge branch 'dev/master' of github.com:ESMG/MOM6 into dev/master - NOAA-GFDL/MOM6@3119c76 Merge branch 'dev/master' of github.com:NOAA-GFDL/MOM6 into dev/master - NOAA-GFDL/MOM6@be8e34d Merge branch 'dev/master' of https://github.com/NOAA-GFDL/MOM6 into dev/master - NOAA-GFDL/MOM6@ae0a293 Merge branch 'dev/master' of github.com:ESMG/MOM6 into dev/master - NOAA-GFDL/MOM6@4f4952d Merge pull request #2 from adcroft/user/aja/obc_refactor - NOAA-GFDL/MOM6@5e86623 Merge from aja/obc_refactor - NOAA-GFDL/MOM6@ee365bd Loop bound fix in set_Flather_Bdry_data() - NOAA-GFDL/MOM6@4f5a51f Merge branch 'ESMG-user/ksh/open_bc' into user/aja/obc_refactor - NOAA-GFDL/MOM6@2558954 Moved call to open_boundary_init from MOM to MOM_state_initialize - NOAA-GFDL/MOM6@2074943 License line and loop bounds fix. - NOAA-GFDL/MOM6@643063c Added license line to MOM_open_boundary.F90 - NOAA-GFDL/MOM6@0b8dc7b New function open_boundary_impose_normal_slope() - NOAA-GFDL/MOM6@c6d6b76 Merge branch 'user/ksh/open_bc' of github.com:ESMG/MOM6 into dev/master - NOAA-GFDL/MOM6@ead182e Merge pull request #1 from adcroft/user/aja/move_obctype_to_open_boundary_module - NOAA-GFDL/MOM6@0248eb2 Separated set_Flather_... into fixed and state parts - NOAA-GFDL/MOM6@59c5676 Moved set_Flather_Bdry_Conds() into MOM_open_boundary - NOAA-GFDL/MOM6@c90bec4 Moved allocation of OBC type to MOM_open_boundary - NOAA-GFDL/MOM6@d5efae2 Moved calls that set OBC masks into MOM_fixed_initialization - NOAA-GFDL/MOM6@2d3856f Split out OBC positions in USER_initialization - NOAA-GFDL/MOM6@83e50eb Split out DOME OBC positions - NOAA-GFDL/MOM6@89b858f Re-ordered s/r in MOM_open_boundary.F90 - NOAA-GFDL/MOM6@98c4918 Moved calls to open_boundary_init() from MOM_dynamics_* to MOM.F90 - NOAA-GFDL/MOM6@ec8ba6f Moved open_boundary_CS parameters into ocean_OBC_type - NOAA-GFDL/MOM6@2db5e11 Doxygenized MOM_open_boundary.F90 - NOAA-GFDL/MOM6@0a42b83 Moved ocean_OBC_type from MOM_variables to MOM_open_boundary - NOAA-GFDL/MOM6@5baded0 Fix dye tracer restarts - NOAA-GFDL/MOM6@b0dfd01 Merge branch 'dev/master' of github.com:ESMG/MOM6 into dev/master - NOAA-GFDL/MOM6@6a61e89 Merge branch 'dev/master' of github.com:ESMG/MOM6 into dev/master - NOAA-GFDL/MOM6@8cc50a1 Merge branch 'dev/master' of github.com:ESMG/MOM6 into dev/master - NOAA-GFDL/MOM6@4d5d490 Merge branch 'dev/master' of github.com:ESMG/MOM6 into dev/master - NOAA-GFDL/MOM6@f6ca193 Merge remote-tracking branch 'gfdl/dev/master' into dev/master

@adcroft

- Updates MOM_parameter_doc.all for ocean_only experiments (adds OFFLINE_TRACER_MODE). - Also modifies list of availables_diags. - NOAA-GFDL/MOM6@f34360f Merge branch 'ashao-origin/offline_tracers' into dev/master - NOAA-GFDL/MOM6@fe2e8f3 Merge pull request #1 from adcroft/ashao-origin/offline_tracers - NOAA-GFDL/MOM6@4a728ca Make sure that logical flag 'converged' is initialized to .false. every call of step_tracers - NOAA-GFDL/MOM6@cd1f4db Merge branch 'origin/offline_tracers' of https://github.com/ashao/MOM6 into ashao-origin/offline_tracers - NOAA-GFDL/MOM6@7319c0f Merged in commits from dev/offline_tracers which introduce two different ways of dealing with residual mass fluxes if advection fails to converge - NOAA-GFDL/MOM6@8fc1698 Tested both barotropic and upwards options for redistributing residual mass fluxes with OM4_05 - NOAA-GFDL/MOM6@0190b7b Ready to test the two vertical redistribution methods on OM4_05 - NOAA-GFDL/MOM6@50b145a Reverse logic so that (online) dynamics is the normal mode - NOAA-GFDL/MOM6@2dc1be6 Corrected cell_method for h_preale diagnostic - NOAA-GFDL/MOM6@8fd4475 Merge branch 'origin/offline_tracers' of https://github.com/ashao/MOM6 into ashao-origin/offline_tracers - NOAA-GFDL/MOM6@bfee951 Merge branch 'gustavo-marques-dev/isomip_tmp' into dev/master - NOAA-GFDL/MOM6@67f7c22 Restored default value of S_REF to 35.0 - NOAA-GFDL/MOM6@46ce1b0 Restored local work array needed for ISOMIP_tracers - NOAA-GFDL/MOM6@87e47d9 Merge branch 'dev/isomip_tmp' of https://github.com/gustavo-marques/MOM6 into gustavo-marques-dev/isomip_tmp - NOAA-GFDL/MOM6@a5ea1d0 Merge branch 'ESMG-user/ksh/open_bc' into dev/master - NOAA-GFDL/MOM6@f2617db Merge branch 'user/ksh/open_bc' of https://github.com/ESMG/MOM6 into ESMG-user/ksh/open_bc - NOAA-GFDL/MOM6@69c643d Workaround for PGI 16.5.0 - NOAA-GFDL/MOM6@54eea3b Added redistrubtion of fluxes up the column for u-direction, need to make one for v-direction then test in OM4_05 - NOAA-GFDL/MOM6@af2c6b8 Beginning work on second option of redistributing fluxes more locally - NOAA-GFDL/MOM6@73c5b15 Redistribution of residual fluxes works in Baltic_ALE_z, now test in OM4 - NOAA-GFDL/MOM6@56a7685 Merge branch 'origin/offline_tracers' of github.com:ashao/MOM6 into dev/offline_tracers - NOAA-GFDL/MOM6@6e6ab58 Test routine to redistribute the remaining horizontal fluxes - NOAA-GFDL/MOM6@ecd412e Test routine to redistribute the remaining horizontal fluxes - NOAA-GFDL/MOM6@f837dc5 Answer changes were due to aggressive compiler optimizations on workstation... - NOAA-GFDL/MOM6@cb796e0 Need to figure otu why answers are changing - NOAA-GFDL/MOM6@ecdde94 Fixed conflict - NOAA-GFDL/MOM6@44d71c9 Need to figure out why answers changed - NOAA-GFDL/MOM6@c211584 Removed the option to use usehmix when doing the surface averaged. - NOAA-GFDL/MOM6@43a738c Add a scheme to redistribute remaining flux into water column - NOAA-GFDL/MOM6@ef5d3e1 Merge branch 'dev/master' into dev/isomip_tmp - NOAA-GFDL/MOM6@7808bfd Reorganized readin of offline mode runtime parameters to ensure that the offline_transport_init .. - NOAA-GFDL/MOM6@3010d0f Added in checks to ensure that contained within non-associated control structures are not copied from .. - NOAA-GFDL/MOM6@4513996 Removed references to MOM_CSp%do_online from step_tracers routine. The previous commit removed it from .. - NOAA-GFDL/MOM6@e84577a Removed unused declaration of do_online from step_MOM in core/MOM.F90. - NOAA-GFDL/MOM6@039baf5 Revert changes to .DoxygenLayout.xml - NOAA-GFDL/MOM6@e175527 Doxygenized comments in MOM_offline_control.F90 and responded to requests by @adcroft - NOAA-GFDL/MOM6@966814f Removed one unnecessary temporary file - NOAA-GFDL/MOM6@d9f8b85 Added some brief instructions of use to the end of MOM_offline_control.F90 - NOAA-GFDL/MOM6@c441686 Converting more OBC stuff to segments. - NOAA-GFDL/MOM6@fd3f1dd Fixed a conflict in .DoxygenLayout.xml - NOAA-GFDL/MOM6@e298f41 Tested with OM4. Ready for merge - NOAA-GFDL/MOM6@1209161 Cleaned up and commented in the code. Answers do not change across PE count. Ready for testing in OM4 - NOAA-GFDL/MOM6@724dc3e Answers do not change across PE counts

Updated fork with commits from NOAA-GFDL/MOM6-examples

- NOAA-GFDL/MOM6@ae22a0f Merge pull request #578 from NCAR/dev/ncar - NOAA-GFDL/MOM6@f4f882f Merge pull request #23 from gustavo-marques/combine_mct_modules - NOAA-GFDL/MOM6@a85b728 Merge MCT modules - NOAA-GFDL/MOM6@ba5b5ba Merge pull request #22 from gustavo-marques/check_fluxes - NOAA-GFDL/MOM6@f5a8483 Adds option to write restart files - NOAA-GFDL/MOM6@8745b4b Fills additional IOB fluxes - NOAA-GFDL/MOM6@f6b22ff Merge branch 'dev/ncar' into check_fluxes - NOAA-GFDL/MOM6@369d5d6 Merge pull request #21 from alperaltuntas/dev/ncar - NOAA-GFDL/MOM6@2582e0a Adds run paramaters to control SW decomposition - NOAA-GFDL/MOM6@58f78b9 Fill IOB, some fluxes still need to be checked - NOAA-GFDL/MOM6@06a30ab Fixed clock and timing - NOAA-GFDL/MOM6@1bca79b Merge pull request #20 from gustavo-marques/fix_merge - NOAA-GFDL/MOM6@fb89b08 Adds code that got lost during merge - NOAA-GFDL/MOM6@7480492 Merge pull request #19 from gustavo-marques/new_merge - NOAA-GFDL/MOM6@be1e6cf Merge branch 'dev/master' into dev/ncar - NOAA-GFDL/MOM6@76565cb Merge pull request #17 from gustavo-marques/fix_ssh_slopes - NOAA-GFDL/MOM6@c04f081 Fix ssh slope calculation - NOAA-GFDL/MOM6@17d4586 Merge pull request #16 from adcroft/ncar-cherry-picked-fixes - NOAA-GFDL/MOM6@be46fee (*)Fixes gprime(1) when no layer coordinates are set - NOAA-GFDL/MOM6@fccb7ae Avoids a SEGV when OBC are not in use with bi-harmonic friction - NOAA-GFDL/MOM6@f42c970 Merge pull request #15 from gustavo-marques/small_fixes - NOAA-GFDL/MOM6@31787c2 Adds reference to set_time that was lost during a conflict handling - NOAA-GFDL/MOM6@d77936e Fix intent(inout) in ice_ocean_boundary - NOAA-GFDL/MOM6@b403edd Merge pull request #14 from gustavo-marques/docs - NOAA-GFDL/MOM6@4d346ca Merge branch 'dev/ncar' into docs - NOAA-GFDL/MOM6@f7c26a5 Clean the module and start doxygenizing it - NOAA-GFDL/MOM6@cd58e2a Merge pull request #13 from alperaltuntas/dev/ncar - NOAA-GFDL/MOM6@37a53bc reorganize file structure - NOAA-GFDL/MOM6@e6c5ddd Merge pull request #12 from gustavo-marques/fill_ice_ocean_bnd - NOAA-GFDL/MOM6@6b6289a Remove trailing whitespace - NOAA-GFDL/MOM6@7ce40e5 Fix undefined reference to fill_ice_ocean_bnd - NOAA-GFDL/MOM6@d517719 Merge branch 'dev/ncar' into fill_ice_ocean_bnd - NOAA-GFDL/MOM6@b69ab33 Filling ice_ocean_bnd - Draft - NOAA-GFDL/MOM6@a306c90 Merge pull request #11 from adcroft/use-ocn-public-for-surface - NOAA-GFDL/MOM6@c83e238 Correct indexing when using ocean_public_type - NOAA-GFDL/MOM6@1f39c84 Replaces use of "surface" with "ocean_public_type" - NOAA-GFDL/MOM6@5cd8d7a Filling ice_ocean_bnd, still needs work - NOAA-GFDL/MOM6@3ceef26 Merge pull request #10 from adcroft/sketch-out-mct-run - NOAA-GFDL/MOM6@714e8d6 Adds placeholders for stepping foward MOM - NOAA-GFDL/MOM6@7f2207c Merge pull request #7 from adcroft/fix-mct-whitespace - NOAA-GFDL/MOM6@a1db77f Cleans up white space - NOAA-GFDL/MOM6@5700d67 Merge pull request #6 from adcroft/add-use-only-for-imports - NOAA-GFDL/MOM6@beac3ed Adds "only" for all use statements - NOAA-GFDL/MOM6@231d19e Merge pull request #5 from alperaltuntas/dev/ncar - NOAA-GFDL/MOM6@3a923a2 Got initialization working - NOAA-GFDL/MOM6@8b38141 Wrapped global data - NOAA-GFDL/MOM6@970f848 added debugging - NOAA-GFDL/MOM6@2540ed8 Filled empty subroutines in ocn_comp_mct.F90 - NOAA-GFDL/MOM6@ed3ed30 Added ocn_import_export module - NOAA-GFDL/MOM6@aba7dc2 Completed ocn_init_mct - NOAA-GFDL/MOM6@5df3bc3 Added method to point ponters to members of ocean_state_type - NOAA-GFDL/MOM6@57e6086 Added methods to return domain/grid shape - NOAA-GFDL/MOM6@37e7356 Added ocn_import_export.F90 - NOAA-GFDL/MOM6@2b794da Merge pull request #4 from alperaltuntas/dev/ncar - NOAA-GFDL/MOM6@fbd405b Added coupler indices module - NOAA-GFDL/MOM6@fa86163 Merge pull request #3 from NCAR/dev/gfdl - NOAA-GFDL/MOM6@e8f2999 Merge pull request #2 from gustavo-marques/temp_salt_z_init_file - NOAA-GFDL/MOM6@86936ba Adds option to read initial temp and salt from separate files - NOAA-GFDL/MOM6@54f7976 Most initialization working - NOAA-GFDL/MOM6@426357c Time and calendar initialization in ocn_comp_mct.F90 - NOAA-GFDL/MOM6@346097d Moved blank ocn_comp_mct.F90 - NOAA-GFDL/MOM6@405fecb Merge pull request #1 from gustavo-marques/ice_shelf - NOAA-GFDL/MOM6@711a613 Removes frazil's contribution to evaporation

- Updates MOM_parameter_doc files. - NOAA-GFDL/MOM6@cde6d3f Merge branch 'dev/master' into dev/gfdl - NOAA-GFDL/MOM6@ae22a0f Merge pull request #578 from NCAR/dev/ncar - NOAA-GFDL/MOM6@f4f882f Merge pull request #23 from gustavo-marques/combine_mct_modules - NOAA-GFDL/MOM6@a85b728 Merge MCT modules - NOAA-GFDL/MOM6@ba5b5ba Merge pull request #22 from gustavo-marques/check_fluxes - NOAA-GFDL/MOM6@f5a8483 Adds option to write restart files - NOAA-GFDL/MOM6@8745b4b Fills additional IOB fluxes - NOAA-GFDL/MOM6@f6b22ff Merge branch 'dev/ncar' into check_fluxes - NOAA-GFDL/MOM6@369d5d6 Merge pull request #21 from alperaltuntas/dev/ncar - NOAA-GFDL/MOM6@2582e0a Adds run paramaters to control SW decomposition - NOAA-GFDL/MOM6@58f78b9 Fill IOB, some fluxes still need to be checked - NOAA-GFDL/MOM6@06a30ab Fixed clock and timing - NOAA-GFDL/MOM6@1bca79b Merge pull request #20 from gustavo-marques/fix_merge - NOAA-GFDL/MOM6@fb89b08 Adds code that got lost during merge - NOAA-GFDL/MOM6@7480492 Merge pull request #19 from gustavo-marques/new_merge - NOAA-GFDL/MOM6@be1e6cf Merge branch 'dev/master' into dev/ncar - NOAA-GFDL/MOM6@76565cb Merge pull request #17 from gustavo-marques/fix_ssh_slopes - NOAA-GFDL/MOM6@c04f081 Fix ssh slope calculation - NOAA-GFDL/MOM6@17d4586 Merge pull request #16 from adcroft/ncar-cherry-picked-fixes - NOAA-GFDL/MOM6@be46fee (*)Fixes gprime(1) when no layer coordinates are set - NOAA-GFDL/MOM6@fccb7ae Avoids a SEGV when OBC are not in use with bi-harmonic friction - NOAA-GFDL/MOM6@f42c970 Merge pull request #15 from gustavo-marques/small_fixes - NOAA-GFDL/MOM6@31787c2 Adds reference to set_time that was lost during a conflict handling - NOAA-GFDL/MOM6@d77936e Fix intent(inout) in ice_ocean_boundary - NOAA-GFDL/MOM6@b403edd Merge pull request #14 from gustavo-marques/docs - NOAA-GFDL/MOM6@4d346ca Merge branch 'dev/ncar' into docs - NOAA-GFDL/MOM6@f7c26a5 Clean the module and start doxygenizing it - NOAA-GFDL/MOM6@cd58e2a Merge pull request #13 from alperaltuntas/dev/ncar - NOAA-GFDL/MOM6@37a53bc reorganize file structure - NOAA-GFDL/MOM6@e6c5ddd Merge pull request #12 from gustavo-marques/fill_ice_ocean_bnd - NOAA-GFDL/MOM6@6b6289a Remove trailing whitespace - NOAA-GFDL/MOM6@7ce40e5 Fix undefined reference to fill_ice_ocean_bnd - NOAA-GFDL/MOM6@d517719 Merge branch 'dev/ncar' into fill_ice_ocean_bnd - NOAA-GFDL/MOM6@b69ab33 Filling ice_ocean_bnd - Draft - NOAA-GFDL/MOM6@a306c90 Merge pull request #11 from adcroft/use-ocn-public-for-surface - NOAA-GFDL/MOM6@c83e238 Correct indexing when using ocean_public_type - NOAA-GFDL/MOM6@1f39c84 Replaces use of "surface" with "ocean_public_type" - NOAA-GFDL/MOM6@5cd8d7a Filling ice_ocean_bnd, still needs work - NOAA-GFDL/MOM6@3ceef26 Merge pull request #10 from adcroft/sketch-out-mct-run - NOAA-GFDL/MOM6@714e8d6 Adds placeholders for stepping foward MOM - NOAA-GFDL/MOM6@7f2207c Merge pull request #7 from adcroft/fix-mct-whitespace - NOAA-GFDL/MOM6@a1db77f Cleans up white space - NOAA-GFDL/MOM6@5700d67 Merge pull request #6 from adcroft/add-use-only-for-imports - NOAA-GFDL/MOM6@beac3ed Adds "only" for all use statements - NOAA-GFDL/MOM6@231d19e Merge pull request #5 from alperaltuntas/dev/ncar - NOAA-GFDL/MOM6@3a923a2 Got initialization working - NOAA-GFDL/MOM6@8b38141 Wrapped global data - NOAA-GFDL/MOM6@970f848 added debugging - NOAA-GFDL/MOM6@2540ed8 Filled empty subroutines in ocn_comp_mct.F90 - NOAA-GFDL/MOM6@ed3ed30 Added ocn_import_export module - NOAA-GFDL/MOM6@aba7dc2 Completed ocn_init_mct - NOAA-GFDL/MOM6@5df3bc3 Added method to point ponters to members of ocean_state_type - NOAA-GFDL/MOM6@57e6086 Added methods to return domain/grid shape - NOAA-GFDL/MOM6@37e7356 Added ocn_import_export.F90 - NOAA-GFDL/MOM6@2b794da Merge pull request #4 from alperaltuntas/dev/ncar - NOAA-GFDL/MOM6@fbd405b Added coupler indices module - NOAA-GFDL/MOM6@fa86163 Merge pull request #3 from NCAR/dev/gfdl - NOAA-GFDL/MOM6@e8f2999 Merge pull request #2 from gustavo-marques/temp_salt_z_init_file - NOAA-GFDL/MOM6@86936ba Adds option to read initial temp and salt from separate files - NOAA-GFDL/MOM6@54f7976 Most initialization working - NOAA-GFDL/MOM6@426357c Time and calendar initialization in ocn_comp_mct.F90 - NOAA-GFDL/MOM6@346097d Moved blank ocn_comp_mct.F90 - NOAA-GFDL/MOM6@405fecb Merge pull request #1 from gustavo-marques/ice_shelf - NOAA-GFDL/MOM6@711a613 Removes frazil's contribution to evaporation

- NOAA-GFDL/SIS2@d57d276 Merge branch 'Hallberg-NOAA-dev/gfdl' into dev/gfdl - NOAA-GFDL/SIS2@6995ce7 Merge pull request #1 from Hallberg-NOAA/coupler_type_reform_rwh - NOAA-GFDL/SIS2@725d709 (*)Save gas fluxes to restarts with concurrent ice - NOAA-GFDL/SIS2@9020bf1 +Added optional gas_flux args to ice_model_init - NOAA-GFDL/SIS2@e2497e6 +Complete reformulation of SIS2 tracer fluxes - NOAA-GFDL/SIS2@3209acc +Use new coupler_type routines in the SIS2 code

- NOAA-GFDL/MOM6@11f1cb6 Merge branch 'MJHarrison-GFDL-MOM6_DA' into dev/gfdl - NOAA-GFDL/MOM6@aa5a910 Merge branch 'MOM6_DA' of https://github.com/MJHarrison-GFDL/MOM6 into MJHarrison-GFDL-MOM6_DA - NOAA-GFDL/MOM6@70e9e25 typo error - NOAA-GFDL/MOM6@a45a176 new interface apply_oda_tracer_increments - NOAA-GFDL/MOM6@6a4c369 Updated version of pkg/MOM6_DA_hooks - NOAA-GFDL/MOM6@066d9ae Merge branch 'dev/gfdl' of https://github.com/NOAA-GFDL/MOM6 into MOM6_DA - NOAA-GFDL/MOM6@fb8fbef restructuring of DA repositories - NOAA-GFDL/MOM6@5d446d3 Moved MOM_oda_driver to src/ocean_data_assim - NOAA-GFDL/MOM6@1c8922a Merge pull request #2 from feiyulu/MOM6_DA - NOAA-GFDL/MOM6@19209ef Less output from MOM_oda_driver - NOAA-GFDL/MOM6@3592d9c commentted out eakf_oda_mod - NOAA-GFDL/MOM6@83e9f79 use ocean instead of global pes in MOM_oda_driver - NOAA-GFDL/MOM6@59625bd Merge pull request #1 from feiyulu/MOM6_DA - NOAA-GFDL/MOM6@857d5ff removed copy_profiles, using linked profiles in ensemble_filter - NOAA-GFDL/MOM6@57102da updated MOM6_DA_hooks driver - NOAA-GFDL/MOM6@25cc168 spelling correction - NOAA-GFDL/MOM6@3586910 switching PElist in oda routines - NOAA-GFDL/MOM6@98e6b3e newer version of DA hooks - NOAA-GFDL/MOM6@5e1d0bb update MOM6_DA_hooks submodule - NOAA-GFDL/MOM6@ccf225c Updates for DA interfaces - Add time argument to set_prior and get_posterior - NOAA-GFDL/MOM6@c711500 Optional argument to get_MOM_input to append ensemble number suffix - NOAA-GFDL/MOM6@0260598 updates for DA interfaces - NOAA-GFDL/MOM6@706b433 Fix stale submodule - NOAA-GFDL/MOM6@acb8bec DA_hooks - NOAA-GFDL/MOM6@3ff22ec Fix DA_hooks submodule - NOAA-GFDL/MOM6@a681809 New flag "ENSEMBLE_OCEAN" enables ensemble DA interfaces - NOAA-GFDL/MOM6@a3e5395 Locate DA_hooks in pkg directory - NOAA-GFDL/MOM6@a4d52ca Added MOM_oda_driver module. - NOAA-GFDL/MOM6@c0640fa Added MOM6_DA submodule. Lower-level code provides interfaces alone. Used for implementing interfaces for ensemble aggregation and for offline MOM6 ensemble driver.

Re-sync with NOAA-GFDL repository

Dimensional scaling update to MOM6, including the introduction of a new density scaling parameter, R_RESCALE_POWER. NOAA-GFDL/MOM6@840881d Merge pull request #1019 from Hallberg-NOAA/density_rescale NOAA-GFDL/MOM6@ef462a8 Removed the accidental 2 in a comment NOAA-GFDL/MOM6@186beda +Pass timesteps to diagnostic routines in [T] NOAA-GFDL/MOM6@e2815d2 Merge branch 'dev/gfdl' into density_rescale NOAA-GFDL/MOM6@a919f23 +Fixed unit conversion factors for 7 diagnostics NOAA-GFDL/MOM6@0c390a3 Merge pull request #1026 from marshallward/nan_merge NOAA-GFDL/MOM6@02bb5d7 Merge branch 'dev/gfdl' into nan_merge NOAA-GFDL/MOM6@81f3a58 RK2 split pass_init clock timer initialization NOAA-GFDL/MOM6@148fcf2 Rescaled timesteps in MOM.F90 NOAA-GFDL/MOM6@0fab529 Merge branch 'dev/gfdl' into density_rescale NOAA-GFDL/MOM6@8000b1c Merge pull request #1023 from marshallward/visc_max_chksums NOAA-GFDL/MOM6@2da48dc Use enable_averages in MOM_dynamics modules NOAA-GFDL/MOM6@1b5d722 +Added enable_averages NOAA-GFDL/MOM6@1a4903e Corrected the dimensional rescaling in MOM_MEKE.F90 NOAA-GFDL/MOM6@0949df6 Merge branch 'dev/gfdl' into nan_merge NOAA-GFDL/MOM6@5af42c6 Merge branch 'dev/gfdl' into density_rescale NOAA-GFDL/MOM6@b541527 Merge branch 'dev/gfdl' into visc_max_chksums NOAA-GFDL/MOM6@58e84e8 Merge branch 'dev/gfdl' into visc_max_chksums NOAA-GFDL/MOM6@76425c9 Merge branch 'dev/gfdl' into visc_max_chksums NOAA-GFDL/MOM6@eca876e Merge branch 'dev/gfdl' into nan_fixes NOAA-GFDL/MOM6@2980893 Merge branch 'dev/gfdl' into nan_fixes NOAA-GFDL/MOM6@54fc734 Mixedlayer_restrat density update NOAA-GFDL/MOM6@f607a45 MOM_set_viscosity logic split NOAA-GFDL/MOM6@fa97128 MOM_entrain_diffusive logical nesting NOAA-GFDL/MOM6@2518c36 Initialize surface forcing adjustments to zero NOAA-GFDL/MOM6@b2e2511 advect_x logical test split NOAA-GFDL/MOM6@a016e3b Neutral diffusion unit testing tolerance set NOAA-GFDL/MOM6@aec5eb4 opacity: netPen explicit summation NOAA-GFDL/MOM6@0eaeb81 Wave speed diag: explicit argument calcs NOAA-GFDL/MOM6@ec851ed Extend z_top and z_btm density calculation in diag NOAA-GFDL/MOM6@ce4ed7d Kh_max_x[xy], Ah_max_xy chksum and alloc fixes NOAA-GFDL/MOM6@34e612f Pass dt in [T] to tracer_vertdiff for temperature NOAA-GFDL/MOM6@3c71c13 +Corrected restart registration for US%m_to_L NOAA-GFDL/MOM6@88fcb8a +Rescaled timestep arguments to several routines NOAA-GFDL/MOM6@2cd8276 Clarified comments in MOM_tracer_diabatic NOAA-GFDL/MOM6@41c860a +Rescaled advective and diffusive tracer diags NOAA-GFDL/MOM6@7e0e505 Renamed internal variables dt_in_T to dt NOAA-GFDL/MOM6@0be3f0e +Pass timesteps to sponge code in [T] NOAA-GFDL/MOM6@241f3ba Renamed internal vars dt to dt_in_s in MOM_dynamics NOAA-GFDL/MOM6@3367d0e Merge branch 'density_rescale' of https://github.com/Hallberg-NOAA/MOM6 into denisty_rescale NOAA-GFDL/MOM6@b3e4b3c Merge pull request #1 from marshallward/pr_1019_fix NOAA-GFDL/MOM6@12d3aac T scaling and OpenMP fixes NOAA-GFDL/MOM6@629416b +Rescaled the units of tv%salt_deficit NOAA-GFDL/MOM6@d518449 Corrected units in MOM_hor_visc code comments NOAA-GFDL/MOM6@0d43bc3 Corrected units in parameterization code comments NOAA-GFDL/MOM6@8ade6de +Pass MLDdensityDifference in units of [R] NOAA-GFDL/MOM6@f1b9c66 +Pass timestep to btstep in units of [T] NOAA-GFDL/MOM6@59b18f0 +Pass timestep to btstep in units of [T] NOAA-GFDL/MOM6@55a0484 Fixed a rescaling factor in entrainment_diffusive NOAA-GFDL/MOM6@e55ad23 +Pass timestep to step_forward_MEKE in units of [T] NOAA-GFDL/MOM6@5312d99 Cleaned up code in insert_brine NOAA-GFDL/MOM6@a4da592 +Rescaled the units of fluxes%heat_content_... vars NOAA-GFDL/MOM6@d5ee19a Store timestep in [T} in sum_output_CS NOAA-GFDL/MOM6@ecf5813 +Pass timestep to thickness_diffuse in units of [T] NOAA-GFDL/MOM6@3f69350 +Pass timestep to extractFluxes1d in units of [T] NOAA-GFDL/MOM6@5484ab0 +Pass timestep to insert_brine in units of [T] NOAA-GFDL/MOM6@35b884d Fixed a recently added bug in insert_brine NOAA-GFDL/MOM6@1d3e21e Merge branch 'dev/gfdl' into density_rescale NOAA-GFDL/MOM6@838bc41 Removed unused code in MOM_barotropic.F90 NOAA-GFDL/MOM6@3b6ccd8 Rescaled RHO0 to [R] in four modules NOAA-GFDL/MOM6@8f3c126 Rescaled FLUXCONST to [Z T-1] in eight modules NOAA-GFDL/MOM6@cbe3996 Refactored solo_driver/MOM_surface_forcing.F90 NOAA-GFDL/MOM6@be8e18c +Rescaled the units of surface salt fluxes NOAA-GFDL/MOM6@37d5405 Combined scaling factors in MOM_forcing_type NOAA-GFDL/MOM6@965c2c2 +Rescaled _rate variables from extractFluxes1d NOAA-GFDL/MOM6@76172d4 Simplified scaling factors in MOM_forcing_type NOAA-GFDL/MOM6@dbad998 +Rescaled the units of surface mass fluxes NOAA-GFDL/MOM6@34193e9 +Added scale arguments in MOM_spatial_means NOAA-GFDL/MOM6@fa35255 +Rescaled the units of taux_shelf and tauy_shelf NOAA-GFDL/MOM6@3b4ea9c +Turned heat budget pointers into arrays NOAA-GFDL/MOM6@1175786 Rescaled density units in MOM_regridding.F90 NOAA-GFDL/MOM6@e9b36cc +Rescaled density units in coord_slight.F90 NOAA-GFDL/MOM6@d7f08f5 +Rescaled density units in coord_hycom.F90 NOAA-GFDL/MOM6@dfd5278 +Changed units of fluxes%TKE_tidal to [R Z3 T-3] NOAA-GFDL/MOM6@fb47d7b +Changed set_derived_forcing_fields Rho0 arg units NOAA-GFDL/MOM6@79d004b Rescaled gustiness in MOM_surface_forcing files NOAA-GFDL/MOM6@1cbf498 +Rescaled units of forces%taux to [R Z L T-2] NOAA-GFDL/MOM6@a669294 +Rescaled density units in coord_rho.F90 NOAA-GFDL/MOM6@e2e4bcb +Rescaled taux_bot and tauy_bot NOAA-GFDL/MOM6@08980a7 Merge branch 'dev/gfdl' into density_rescale NOAA-GFDL/MOM6@15a5cb5 Rescaled density units in adjustment_init.F90 NOAA-GFDL/MOM6@0a8e67f Rescaled density units in benchmark_init.F90 NOAA-GFDL/MOM6@fbed637 Rescaled density units in Rossby_front_2d_init.F90 NOAA-GFDL/MOM6@a14bca0 Rescaled density units in ISOMIP_initialization.F90 NOAA-GFDL/MOM6@e137451 Rescaled density units in DOME_initialization.F90 NOAA-GFDL/MOM6@45de704 Rescaled density units in MOM_tracer_hor_diff.F90 NOAA-GFDL/MOM6@d072db2 Rescaled density units in wave_structure NOAA-GFDL/MOM6@8efd5ae Rescaled density units in MOM_wave_speed.F90 NOAA-GFDL/MOM6@594300e Rescaled density units in calc_diagnostic_fields NOAA-GFDL/MOM6@27a9edd Rescaled density units in adjust_ssh_for_p_atm NOAA-GFDL/MOM6@fa02d85 Rescaled density units in MOM_PressureForce_AFV NOAA-GFDL/MOM6@7a65682 +Rescaled density units in MOM_PressureForce_Mont NOAA-GFDL/MOM6@34f2c39 Rescaled density units in find_eta NOAA-GFDL/MOM6@e4fea0a (*)Simplified convert_thickness with no eqn of state NOAA-GFDL/MOM6@235d3b6 Rescaled density units in calc_isoneutral_slopes NOAA-GFDL/MOM6@f03495f +Rescaled density units in MOM_T_S_init_from_Z NOAA-GFDL/MOM6@36fef34 Rescaled density units in initialize_temp_salt_fit NOAA-GFDL/MOM6@58cb2d4 Removed a commented out statement NOAA-GFDL/MOM6@401ea2b Rescaled density units in MOM_MEKE.F90 NOAA-GFDL/MOM6@1865f4f (*)+Rescaled MEKE source element units in MEKE_type NOAA-GFDL/MOM6@ef1080b +Rescaled energy units in MOM_internal_tides NOAA-GFDL/MOM6@3567989 +Rescaled units of set_int_tide_input variables NOAA-GFDL/MOM6@04901cd Rescaled density units in MOM_mixed_layer_restrat NOAA-GFDL/MOM6@3fb51fd Rescaled units of FrictWork in MOM_hor_visc.F90 NOAA-GFDL/MOM6@2e3f9c4 Rescaled density units in MOM_thickness_diffuse NOAA-GFDL/MOM6@e5ca06e Rescaled units of dRhodT in applyBoundaryFluxesInOut NOAA-GFDL/MOM6@8e231df +Pass mixed layer densities to sponges in [R] NOAA-GFDL/MOM6@08231ca Used GV%H_to_RZ to simplify rescalings NOAA-GFDL/MOM6@2d1f647 +Rescaled specific volume units of dSV_dT args NOAA-GFDL/MOM6@5122e33 +Rescaled density units of cTKE arguments NOAA-GFDL/MOM6@68e322b Rescaled density units in MOM_energetic_PBL NOAA-GFDL/MOM6@80b2d99 +Partially rescaled the units of TKE_itidal_input NOAA-GFDL/MOM6@727199a Corrected dimensions in comments NOAA-GFDL/MOM6@4808e3a +Rescaled density units in MOM_geothermal NOAA-GFDL/MOM6@87a2c4d Rescaled density units in MOM_tidal_mixing NOAA-GFDL/MOM6@3fe1c7b Rescaled density units in diagnoseMLDbyDensityDiff NOAA-GFDL/MOM6@af57dab Rescaled density units in MOM_internal_tide_input NOAA-GFDL/MOM6@7f8b55b Rescaled density units in MOM_kappa_shear NOAA-GFDL/MOM6@ac329db Rescaled density units in MOM_set_diffusivity NOAA-GFDL/MOM6@297ffe5 Rescaled density units in MOM_set_viscosity NOAA-GFDL/MOM6@f7b4b77 Rescaled density units in MOM_regularize_layers NOAA-GFDL/MOM6@ee6baaa +Changed units of GV%Rho0 to [R] NOAA-GFDL/MOM6@bc378e3 +Move rescaling of Rlay into set_coord routines NOAA-GFDL/MOM6@57794ad +Changed units of GV%Rlay to [R] NOAA-GFDL/MOM6@4156851 Rescaled density units in MOM_entrain_diffusive NOAA-GFDL/MOM6@535950c Merge branch 'dev/gfdl' into density_rescale NOAA-GFDL/MOM6@d4c2dfb +Rescale BML densities via calculate_density calls NOAA-GFDL/MOM6@74cc9bb +Add optional scale argument to calculate_density NOAA-GFDL/MOM6@8eaa01c Rescaled density units in MOM_bulk_mixedlayer NOAA-GFDL/MOM6@5274403 +Add H_to_RZ and RZ_to_H to the verticalGrid_type NOAA-GFDL/MOM6@3704a66 +Add density rescaling factors in unit_scale_type NOAA-GFDL/MOM6@1016be3 +Pass timestep arguments to vertvisc in [T]

- Last merge updates MOM_parameter_doc files - NOAA-GFDL/MOM6@c9a7f98 Merge branch 'Hallberg-NOAA-ALE_remap_fix' into dev/gfdl - NOAA-GFDL/MOM6@4158a7e Merge branch 'dev/gfdl' into ALE_remap_fix - NOAA-GFDL/MOM6@bfa303d Merge pull request #1039 from adcroft/fix-units-for-meke-advection - NOAA-GFDL/MOM6@7a404fe Added more converted MKS units in comments - NOAA-GFDL/MOM6@285273a Corrected/added converted MKS units in comments - NOAA-GFDL/MOM6@7dca672 Corrected the formatting of a doxygen comment - NOAA-GFDL/MOM6@9c4d22d Updated/added comments for units of variables in MOM_MEKE.F90 - NOAA-GFDL/MOM6@b7b7fbc Removed out-of-date commented code - NOAA-GFDL/MOM6@aac71f5 Fix units for terms used in advection of MEKE - NOAA-GFDL/MOM6@e9ee86a +Added REMAPPING_2018 runtime option - NOAA-GFDL/MOM6@4edc165 (*)Fixed dimensional inconsistency in P3M_functions - NOAA-GFDL/MOM6@0e0f6e9 Merge pull request #1037 from Hallberg-NOAA/revise_OBCs - NOAA-GFDL/MOM6@1c17bc4 Merge branch 'dev/gfdl' into revise_OBCs - NOAA-GFDL/MOM6@3ea8609 Merge pull request #1031 from marshallward/tc4_fix - NOAA-GFDL/MOM6@279fd7b Merge branch 'dev/gfdl' into tc4_fix - NOAA-GFDL/MOM6@98e1450 (*)Fixed invariance bugs in MOM_open_boundary.F90 - NOAA-GFDL/MOM6@aaa58ca Dimensional rescaling in MOM_open_boundary.F90 - NOAA-GFDL/MOM6@ba45244 Merge pull request #1034 from marshallward/adiabatic_clock_id_fix - NOAA-GFDL/MOM6@686302e Update MOM.F90 - NOAA-GFDL/MOM6@4b241f6 Merge branch 'dev/gfdl' into adiabatic_clock_id_fix - NOAA-GFDL/MOM6@be50409 Merge pull request #1032 from Hallberg-NOAA/rescale_cleanup - NOAA-GFDL/MOM6@2ae0a68 Corrected an OMP declaration - NOAA-GFDL/MOM6@f8f106a Adiabatic clock ID bugfix - NOAA-GFDL/MOM6@8b7a692 Merge branch 'dev/gfdl' into rescale_cleanup - NOAA-GFDL/MOM6@c741390 Correction of documented units in comments - NOAA-GFDL/MOM6@6e115b7 +Changed the units of minimum_forcing_depth to [H] - NOAA-GFDL/MOM6@05b136b Rescaled internal variables in wave_speed - NOAA-GFDL/MOM6@4053e7d Merge branch 'dev/gfdl' into tc4_fix - NOAA-GFDL/MOM6@8791de3 Merge pull request #1030 from marshallward/travis_regression_fix - NOAA-GFDL/MOM6@558b5e0 Testing: Makefile typo - NOAA-GFDL/MOM6@f8b7564 Travis: Move regression tests to separate build - NOAA-GFDL/MOM6@44cfd27 Revised wave_speed to return speed in [L T-1] - NOAA-GFDL/MOM6@b48b594 Simplified expressions in MOM_offline_aux - NOAA-GFDL/MOM6@2b0fea2 Corrected dimensional epsilons in downscaling - NOAA-GFDL/MOM6@a3b7adc Simplified expressions in MOM_PointAccel - NOAA-GFDL/MOM6@b80d82e +Pass timesteps to applyTracerBoundaryFluxesInOut in [T] - NOAA-GFDL/MOM6@0281e21 +Pass timesteps to tracer column_physics in [T] - NOAA-GFDL/MOM6@00da24e +Pass timesteps to ALE_main in [T] - NOAA-GFDL/MOM6@08dbb59 +Rescaled tracer advective flux diagnostics - NOAA-GFDL/MOM6@605d1bc +Pass timeesteps to tracer diagnostics in [T] - NOAA-GFDL/MOM6@18e5894 Enable tc4.restart test - NOAA-GFDL/MOM6@096761e Merge branch 'dev/gfdl' into tc4_fix - NOAA-GFDL/MOM6@77e7342 Merge pull request #2 from MJHarrison-GFDL/gcc_7_4_0_patch - NOAA-GFDL/MOM6@251b0d9 remove trailiny ws - NOAA-GFDL/MOM6@8a52f40 Merge branch 'gcc_7_4_0_patch' of github.com:MJHarrison-GFDL/MOM6 into gcc_7_4_0_patch - NOAA-GFDL/MOM6@c4606e1 fix restart fail for tc4 and some cleanup - NOAA-GFDL/MOM6@231f120 add unit scaling - NOAA-GFDL/MOM6@1b96028 Merge pull request #1 from MJHarrison-GFDL/gcc_7_4_0_patch - NOAA-GFDL/MOM6@817bdde remove trailing whitespace - NOAA-GFDL/MOM6@3c0d52a Make tc4 faster - NOAA-GFDL/MOM6@9fdbe98 Merge branch 'tc4_fix' of github.com:marshallward/MOM6 into gcc_7_4_0_patch - NOAA-GFDL/MOM6@defb0c5 Verify ENABLE_THERMODYNAMICS is True before posting C_p diagnostic - NOAA-GFDL/MOM6@a5082d5 Travis python support; tc4 Makefile - NOAA-GFDL/MOM6@1f9144f TC4 integration into test suite

…-27' into dev/master - Update of MOM6 from NCAR/MOM6 - NOAA-GFDL/MOM6@010492e Merge branch 'gustavo-marques-dev-master-candidate-ncar-2020-03-27' into dev/master - NOAA-GFDL/MOM6@e73db38 Merge branch 'dev-master-candidate-ncar-2020-03-27' of https://github.com/gustavo-marques/MOM6 into gustavo-marques-dev-master-candidate-ncar-2020-03-27 - NOAA-GFDL/MOM6@6ce3dd9 Change CDRAG_MEKE to MEKE_CDRAG - NOAA-GFDL/MOM6@0cddf1f Merge pull request #146 from NCAR/fix_tracer_advect_omp - NOAA-GFDL/MOM6@8025fd4 refactor advect_x and advect_y calls - NOAA-GFDL/MOM6@3768a11 make advect_y thread-safe - NOAA-GFDL/MOM6@3d05d85 make T_adx_2d diagnostics thread-safe - NOAA-GFDL/MOM6@6636e0f fix OMP directive variable list - NOAA-GFDL/MOM6@afe0335 Merge pull request #144 from gustavo-marques/merge_GME_outside_MEKE - NOAA-GFDL/MOM6@1f308a0 Extend loop indices and add calls to pass_vector - NOAA-GFDL/MOM6@1ecade5 Updates GME by removing dependency on MEKE - NOAA-GFDL/MOM6@c012019 Merge pull request #143 from gustavo-marques/fix_vhGM_GEOMETRIC - NOAA-GFDL/MOM6@c429824 Fix a bug in the vmGM field when using GEOMETRIC - NOAA-GFDL/MOM6@0eb0615 Merge pull request #142 from NCAR/omp_fixes - NOAA-GFDL/MOM6@f832925 initialize fluid entrainment arrays - NOAA-GFDL/MOM6@276c6b4 call chksum for drag_vel if its allocated - NOAA-GFDL/MOM6@4478066 uncomment omp do block in advect_tracer - NOAA-GFDL/MOM6@7533454 fix omp in calculate_diagnostic_fields - NOAA-GFDL/MOM6@21918b4 comment out OMP directives in KPP_compute_BLD temporarily - NOAA-GFDL/MOM6@049abb0 fix omp directives in set_viscous_BBL - NOAA-GFDL/MOM6@67e5481 fix omp directive for melt_potential - NOAA-GFDL/MOM6@46b1f34 correct namespace name for doxygen - NOAA-GFDL/MOM6@83da090 Merge pull request #141 from alperaltuntas/fix_gnu_bugs - NOAA-GFDL/MOM6@ba5a442 if not allocated, do not assign R_rho - NOAA-GFDL/MOM6@435a741 Close param file before it gets opened by ocean_model_init again. - NOAA-GFDL/MOM6@ab54b96 Merge pull request #140 from alperaltuntas/fix_omp2 - NOAA-GFDL/MOM6@a9c896e set CS%MEKE_equilibrium_restoring, to false by default - NOAA-GFDL/MOM6@3540446 fix unitialized logical var in MOM_MEKE - NOAA-GFDL/MOM6@63cf741 fix kpp omp directives - NOAA-GFDL/MOM6@22f0242 Merge branch 'dev/ncar' of https://github.com/NCAR/MOM6 into dev/ncar - NOAA-GFDL/MOM6@1ed6b94 Merge pull request #139 from gustavo-marques/update_LBD - NOAA-GFDL/MOM6@9db5ba1 Improve documentation and unit tests - NOAA-GFDL/MOM6@0525a4c Change flux limiting calculation - NOAA-GFDL/MOM6@248a87c Fix units description and delete placeholder for the pressure reconstruction - NOAA-GFDL/MOM6@c8361e7 Add a note saying khtr_avg should be computed once khtr is 3D - NOAA-GFDL/MOM6@dce59f4 Fix a bug in the LBD method 2 - NOAA-GFDL/MOM6@5c8b32f Fix a bug when checking if hbl > htot - NOAA-GFDL/MOM6@408bd2f Merge branch 'near_surface_fluxes' of github.com:ashao/MOM6 into near_surface_fluxes - NOAA-GFDL/MOM6@31d2941 Fix bug in boundary_k_range if hbl > htot - NOAA-GFDL/MOM6@4fe0191 Compute tracer tendency due to lateral diffusion - NOAA-GFDL/MOM6@e2bafc5 fix omp directives in MOM_thickness_diffuse - NOAA-GFDL/MOM6@1ae069b Merge branch 'dev/ncar' into near_surface_fluxes - NOAA-GFDL/MOM6@44d36c4 Merge pull request #138 from gustavo-marques/fix_ocean_model_data_get - NOAA-GFDL/MOM6@1d1914f Merge pull request #136 from gustavo-marques/merge-dev-master-candidate-2019-12-17 - NOAA-GFDL/MOM6@0188f35 Merge branch 'dev-master-candidate-2019-12-17' into merge-dev-master-candidate-2019-12-17 - NOAA-GFDL/MOM6@f7debed Delete ocean_model_data_get from MCT and NUOPC caps - NOAA-GFDL/MOM6@a12abd6 Revert "Merge pull request #133 from gustavo-marques/clean_caps" - NOAA-GFDL/MOM6@c7c7bf1 Merge branch 'dev-master-candidate-2019-12-17' into merge-dev-master-candidate-2019-12-17 - NOAA-GFDL/MOM6@c358114 Merge pull request #135 from gustavo-marques/LBD_merge - NOAA-GFDL/MOM6@d276f3f Merge branch 'dev/ncar' into near_surface_fluxes - NOAA-GFDL/MOM6@8a3e3e7 Merge branch 'near_surface_fluxes' into LBD_merge - NOAA-GFDL/MOM6@2cccc83 Merge pull request #134 from gustavo-marques/fix_leith - NOAA-GFDL/MOM6@3d17e03 Merge pull request #133 from gustavo-marques/clean_caps - NOAA-GFDL/MOM6@e538144 remove duplicate fld_list_add calls - NOAA-GFDL/MOM6@2c7de66 Merge pull request #132 from NOAA-EMC/dev/emc - NOAA-GFDL/MOM6@78bb4c1 Delete quotes from doxygen comment - NOAA-GFDL/MOM6@8c95cc0 Fix bugs in Leith add new input parameter - NOAA-GFDL/MOM6@c50a978 Toggle continuous neutral diffusion in interior only - NOAA-GFDL/MOM6@89eaede Delete ocean_model_data_get* from all the caps - NOAA-GFDL/MOM6@20d076b Modify continuous neutral diffusion to account for boundary layer - NOAA-GFDL/MOM6@a2d9636 Merge pull request #131 from gustavo-marques/meke_khtr - NOAA-GFDL/MOM6@cb79e97 add changes from old MOM6 repo in cmeps_integration branch that were (#10) - NOAA-GFDL/MOM6@97d07bc Set the default for CDRAG_MEKE to CDRAG - NOAA-GFDL/MOM6@02c986a Set default value to 0.003 - NOAA-GFDL/MOM6@e71a573 Fix doxygen references - NOAA-GFDL/MOM6@9303e99 Fix typos and bugs - NOAA-GFDL/MOM6@f3dba16 Add new option to avoid negative thicknesses - NOAA-GFDL/MOM6@7135281 Merge pull request #8 from DeniseWorthen/feature/runoff_optional - NOAA-GFDL/MOM6@147f7a3 Merge pull request #130 from DeniseWorthen/feature/runoff_optional - NOAA-GFDL/MOM6@2c6bdf9 Create a separate param for MEKE bottom drag (CDRAG_MEKE) - NOAA-GFDL/MOM6@b66eafe backs out change in standard name for liquid and frozen heat flux since this will require a change in the nuopc field_dictionary. The fields are not currently used. - NOAA-GFDL/MOM6@b1ce184 Documentation and minor improvements - NOAA-GFDL/MOM6@0a89aac Fix registry of lbd diagnostics - NOAA-GFDL/MOM6@6bce8ab Clean the code and fix line length exceeding 120 - NOAA-GFDL/MOM6@7f2b93e Replace lbm to lbd (lateral boundary diffusion) - NOAA-GFDL/MOM6@64be85f minor text changes; uncomment runoff heat flux terms; required change made in feature/runoff_names branch of NEMS - NOAA-GFDL/MOM6@419a021 removes data_override and associated calls from mom_cap renames: iob%rofl_flux => iob%lrunoff iob%rofi_flux => iob%frunoff iob%runoff_hflx = > iob%lrunoff_hflx iob%calving_hflx => iob%frunoff_hflx makes changes in mom_cap_methods and mom_surface_forcing_nuopc consistent w/ new iob names temporarily comments out _hflx terms in mom_cap,mom_cap_methods adds flag in mom_surface_forcing_nuopc for adding liquid river runoff via data_override - NOAA-GFDL/MOM6@ba6140c Merge pull request #1 from NOAA-EMC/dev/emc - NOAA-GFDL/MOM6@9a6f7f6 Merge NOAA-GFDL dev/master from 20191107 - NOAA-GFDL/MOM6@07481e4 updating mom_cap to add data override which was deleted in merge - NOAA-GFDL/MOM6@100e92d Merge remote-tracking branch 'GFDL/dev/master' into testnewdevmaster20191107 - NOAA-GFDL/MOM6@80743e6 Adding river runoff (from Jiande) Squashed commit of the following: - NOAA-GFDL/MOM6@462768b Merge pull request #128 from gustavo-marques/fix_MEKE_GM_src - NOAA-GFDL/MOM6@050aa31 Moves allocation of CS%equilibrium_value inside subroutine MEKE_equilibrium_restoring - NOAA-GFDL/MOM6@3f041d9 MEKE diagnostic array fixes - NOAA-GFDL/MOM6@2bb321e Merge pull request #127 from gustavo-marques/depth_scaled_khth - NOAA-GFDL/MOM6@ebf5ee0 Adds MEKE_equilibrium_restoring - NOAA-GFDL/MOM6@1522ad0 Minor changes in the doxygen comments - NOAA-GFDL/MOM6@223037c Deletes unneeded variables from calc_depth_function - NOAA-GFDL/MOM6@67016eb Reverts description in DO_DYNAMICS to older version as this was changed by mistake. - NOAA-GFDL/MOM6@bb785a8 Adds option to scale KHTH with depth - NOAA-GFDL/MOM6@839217d Rearranged MEKE_EQUILIBRIUM subroutine - NOAA-GFDL/MOM6@486da1d Replaces trunit to conc in the documentation - NOAA-GFDL/MOM6@15c9f06 Hard-code min of SN to be 1.0e-7 - NOAA-GFDL/MOM6@8f3cf96 Add placeholders for adding method3 and applying filter on method1 - NOAA-GFDL/MOM6@5583f84 Renames lateral_boundary_mixing to lateral_boundary_diffusion - NOAA-GFDL/MOM6@69ec18c Removes redundant statement in netrual diffusion - NOAA-GFDL/MOM6@af41095 Fix uninitialized variables in find_surface when NDIFF_INTERIOR_ONLY = False - NOAA-GFDL/MOM6@e806fba Fixes a bug in the bulk_method - NOAA-GFDL/MOM6@d7da982 Improves the calculation of F_bulk to minimize roundoff errors - NOAA-GFDL/MOM6@82c1bca First set of commits to limit neutral diffusion to the interior - NOAA-GFDL/MOM6@3c5c7d1 Merge branch 'rewrite_discontinuous_sort' into near_surface_fluxes - NOAA-GFDL/MOM6@91ca2d1 Fix flux limiter in LBM when < 0 - NOAA-GFDL/MOM6@ca23e66 Make fluxes_bulk_method more roundoff safe - NOAA-GFDL/MOM6@5aaf34b Add flux limiter for bulk layer fluxes - NOAA-GFDL/MOM6@9f15e4f Adds new unit test and fixes diagnostics - NOAA-GFDL/MOM6@c880539 Update LBM flux names and fix posting of 2d diags - NOAA-GFDL/MOM6@bcec94c Merge branch 'dev/ncar' into fix_MEKE_GM_src - NOAA-GFDL/MOM6@bb46c38 Calculates bottomFac2 IF CS%MEKE_GEOMETRIC=True - NOAA-GFDL/MOM6@66a8f0a Fix bug in LBM diagnostics and add diags - NOAA-GFDL/MOM6@a4f9550 Added new equilibrium formula for MEKE - NOAA-GFDL/MOM6@73d0d78 Fixes a bug in method2 of LBM, where diffusivities were not used - NOAA-GFDL/MOM6@4d5c786 Fixes undoxygenized LBM module variables - NOAA-GFDL/MOM6@e5645b1 Fixes line length exceeding 120 - NOAA-GFDL/MOM6@f38a369 Fixes unit test for layer by layer and removes the hbl_min = MIN(hbl_L, hbl_R) - NOAA-GFDL/MOM6@c41b8b0 Adds two unit tests for layer by layer method - NOAA-GFDL/MOM6@6d6d3b8 Adds two unit tests for layer by layer method - NOAA-GFDL/MOM6@3cb68d3 Adds missing arguments after merge - NOAA-GFDL/MOM6@62e3227 Adding layer by layer method for bottom boundary - NOAA-GFDL/MOM6@8d9c6a4 Merge branch 'dev/ncar' into near_surface_fluxes - NOAA-GFDL/MOM6@3bb1f55 Adding first version of LBM method=2 - NOAA-GFDL/MOM6@4d0aed6 Fixes units and moves bulk diags inside if statement - NOAA-GFDL/MOM6@f6800c2 Update halos for hbl in LBM - NOAA-GFDL/MOM6@915bcb1 Diagnostics for lateral boundary mixing scheme - NOAA-GFDL/MOM6@223a815 Merge branch 'near_surface_fluxes' of github.com:ashao/MOM6 into HEAD - NOAA-GFDL/MOM6@322aa77 Rename MOM_boundary_lateral_mixing.F90 for consistency - NOAA-GFDL/MOM6@332a264 Try to restore commits from accidental move of file - NOAA-GFDL/MOM6@e5f96f4 Fix minor bugs in lateral boundary mixing - NOAA-GFDL/MOM6@9b4d2c2 Only allocate KPP_CS if requested - NOAA-GFDL/MOM6@8ab7aa8 Convert diffusive flux convergence to a change in tracer - NOAA-GFDL/MOM6@8a4ed84 Guard against case where the boundary layer is 0 on one column - NOAA-GFDL/MOM6@df938a1 Add masking in lateral_boundary_fluxes - NOAA-GFDL/MOM6@ae6529e Hook lateral boundary mixing into tracer_hor_diff - NOAA-GFDL/MOM6@a4dbeb1 Hook in lateral boundary mixing initialization - NOAA-GFDL/MOM6@2b10a8b Skeleton for boundary layer mixing interfaces - NOAA-GFDL/MOM6@4e63c75 Update API for boundary_layer_fluxes unit tests - NOAA-GFDL/MOM6@79bea68 New unit tests for surface boundary fluxes - NOAA-GFDL/MOM6@f87aaa2 Fixes bulk_average calculation and takes into account partial cells when computing fluxes - NOAA-GFDL/MOM6@a36f5d6 Removes more trailing space - NOAA-GFDL/MOM6@17385cc Removes trailing space and fixes line length exceeded - NOAA-GFDL/MOM6@6677820 Updates layer_fluxes_bulk_method and bulk_average - NOAA-GFDL/MOM6@8385231 Add function and unit tests for boundary layer mixing - NOAA-GFDL/MOM6@654a12c Add additional unit tests for bulk method - NOAA-GFDL/MOM6@576fafb Initial commit for implementing near-surface mixing

…ssure - NOAA-GFDL/MOM6@c745c5b14 Merge pull request #1089 from Hallberg-NOAA/rescale_pressure - NOAA-GFDL/MOM6@8cddc685a Merge branch 'dev/gfdl' into rescale_pressure - NOAA-GFDL/MOM6@59d2537ac Merge pull request #1070 from ashao/remap_v_extensive - NOAA-GFDL/MOM6@f5eb17194 Eliminated some US args in MOM_neutral_diffusion - NOAA-GFDL/MOM6@18b21938b Fixed compile time bugs in mom_surface_forcing_mct - NOAA-GFDL/MOM6@37d30b596 Eliminated the use of GV%mks_g_Earth - NOAA-GFDL/MOM6@3a817efe9 Fixed a diagnostic halo extent - NOAA-GFDL/MOM6@e3c434e57 Store return values from EOS_domain - NOAA-GFDL/MOM6@718c3ab1f Removed US argument to find_depth_of_pressure_in_cell - NOAA-GFDL/MOM6@9c5239eaf Corrected MOM_EOS dimensional rescaling problem - NOAA-GFDL/MOM6@f0f894c57 Merge branch 'Adcroft_rescale_pressure' into rescale_pressure - NOAA-GFDL/MOM6@7282956a8 Merge branch 'rescale_pressure' of git://github.com/adcroft/MOM6 into Adcroft_rescale_pressure - NOAA-GFDL/MOM6@cdeda16d3 Switched versions of calculate_density in 22 calls - NOAA-GFDL/MOM6@760dc3960 +Rescaled variables in coord_adapt - NOAA-GFDL/MOM6@9b53927c1 Rescaled internal MOM_CVMix variables - NOAA-GFDL/MOM6@371ed85ca Initialize scaling params without EOS_init() - NOAA-GFDL/MOM6@0caf9ccab Missed a conflict resolution - NOAA-GFDL/MOM6@353f441f9 Merge branch 'dev/gfdl' of https://github.com/NOAA-GFDL/MOM6 into remap_v_extensive - NOAA-GFDL/MOM6@abecf021e Merge branch 'Hallberg-NOAA-rescale_pressure' into rescale_pressure - NOAA-GFDL/MOM6@4f42d7278 Fixed the spelling in an openMP directive - NOAA-GFDL/MOM6@18d520e3c Remove optional US from most MOM_EOS functions - NOAA-GFDL/MOM6@acf23a413 Use the 'dom=' interface to calculate_density - NOAA-GFDL/MOM6@c309289b6 Add doxygen comments for h_begin in diag_ctrl - NOAA-GFDL/MOM6@415a6bce2 Adds unit conversions to EOS type - NOAA-GFDL/MOM6@ab9d8e95f +Added dom interface to calculate_density - NOAA-GFDL/MOM6@620a97c4d Merge branch 'dev/gfdl' into rescale_pressure - NOAA-GFDL/MOM6@6c0e58b7d Merge pull request #1090 from adcroft/rm-gearth-from-obcs - NOAA-GFDL/MOM6@b4c4f28aa Resolve conflict with NOAA-GFDL/MOM6#1088 - NOAA-GFDL/MOM6@71d1c733e Merge branch 'dev/gfdl' into rm-gearth-from-obcs - NOAA-GFDL/MOM6@e8dba197b Merge branch 'index_rotation' into dev/gfdl - NOAA-GFDL/MOM6@c325f9c1b Removes G_EARTH from OBCs - NOAA-GFDL/MOM6@f632ffc87 Explicit array rotation index; modulo chksum turns - NOAA-GFDL/MOM6@a00c3277f (*)Reordered setting calculate_density loop bounds - NOAA-GFDL/MOM6@77b6b7471 (*)Set loop bounds in calculate_density calls - NOAA-GFDL/MOM6@87054b464 Added an omitted dOxygen comment - NOAA-GFDL/MOM6@ae944c212 Merge branch 'dev/gfdl' into rescale_pressure - NOAA-GFDL/MOM6@da120120c Minor cleanup related to pressure rescaling - NOAA-GFDL/MOM6@b84b2d35f Rescaled variables in convert_thickness - NOAA-GFDL/MOM6@4182ad23c +Add optional US arg to calculate_compress - NOAA-GFDL/MOM6@bb73bb8f3 +(*)Rescaled pressures used to build coordinates - NOAA-GFDL/MOM6@a01dae523 Corrected 3 openMP declarations - NOAA-GFDL/MOM6@608d210a6 Rescaled pressures in wave speed calculations - NOAA-GFDL/MOM6@ad0c70e2a Rescaled three diagnosed densities - NOAA-GFDL/MOM6@030a63681 Nullify a pointer in neutral diffusion unit tests - NOAA-GFDL/MOM6@7643bce4e Simpler calculate_density in ISOMIP_initialization - NOAA-GFDL/MOM6@a7836f0a7 +Rescaled variables in MOM_neutral_diffusion.F90 - NOAA-GFDL/MOM6@b72afce2b +Made arguments to unit_scaling_init optional - NOAA-GFDL/MOM6@22215cb0b Internal field index rotation - NOAA-GFDL/MOM6@04fcfd456 +Rescaled args to find_depth_of_pressure_in_cell - NOAA-GFDL/MOM6@2a951e7b7 Redirected various EOS interfaces to common code - NOAA-GFDL/MOM6@00db8d5fb Corrected a bug in calculate_spec_vol_derivs_H1_1d - NOAA-GFDL/MOM6@500c9e313 Rescaled pressures in 17 calculate_density calls - NOAA-GFDL/MOM6@8df34f4e2 Rescaled internal MOM_diapyc_energy_req variables - NOAA-GFDL/MOM6@1e8c50166 Corrected pressure units in comments - NOAA-GFDL/MOM6@6948cb743 +Replaced optional pres_scale args with US args - NOAA-GFDL/MOM6@fb820c1e7 +Rescaled pressure arguments to multiple routines - NOAA-GFDL/MOM6@3223eb6bd +Rescaled the units of tv%P_Ref to [R L2 T-2] - NOAA-GFDL/MOM6@2fc1c2e5a Use new HI_1d forms of calculate_density calls - NOAA-GFDL/MOM6@ce0905e17 +Add hor_index_type variants of EOS routines - NOAA-GFDL/MOM6@1252e3b82 Pass rescaled pressures to calculate_TFreeze - NOAA-GFDL/MOM6@5e1645878 +Add optional pres_scale arg to calculate_TFreeze - NOAA-GFDL/MOM6@3e9c645d1 Merge pull request #1087 from adcroft/vkernal-tests-to-stdout - NOAA-GFDL/MOM6@3767883f3 Replaced 0,6 with stderr,stdout - NOAA-GFDL/MOM6@916be3c56 Rescaled ice_shelf_CS%g_Earth like GV%g_Earth - NOAA-GFDL/MOM6@30063376c Write test fails to both stderr and stdout - NOAA-GFDL/MOM6@978d772be Moved vkernel unit tests to stdout - NOAA-GFDL/MOM6@20ae74d65 Merge branch 'dev/gfdl' into rescale_pressure - NOAA-GFDL/MOM6@6af725f2b +Rescaled the units of fluxes%p_surf - NOAA-GFDL/MOM6@fc9dfd071 Merge branch 'ESMG-dev/esmg' into dev/gfdl - NOAA-GFDL/MOM6@27e7a1f2d Merge branch 'dev/esmg' of https://github.com/ESMG/MOM6 into ESMG-dev/esmg - NOAA-GFDL/MOM6@7e6443238 Merge branch 'Hallberg-NOAA-fix_iceshelf_problems' into dev/gfdl - NOAA-GFDL/MOM6@6d7dde480 Use combined scaling factors - NOAA-GFDL/MOM6@f9b63f304 +Added RL2_T2_to_Pa element to unit_scale_type - NOAA-GFDL/MOM6@efbbd317b Rescaled pressures in calculate_vertical_integrals - NOAA-GFDL/MOM6@f29e32a44 Rescaled pressure in calc_isoneutral_slopes - NOAA-GFDL/MOM6@94f94ede6 Rescaled pressure in find_eta routines - NOAA-GFDL/MOM6@3b3c34ab9 +Rescaled non-Boussinesq pressure force calcs - NOAA-GFDL/MOM6@7632abe2d +Add optional SV_scale arg to int_specific_vol_dp - NOAA-GFDL/MOM6@63c451005 +Rescaled Boussinesq pressure force calculations - NOAA-GFDL/MOM6@5a56df7d7 +Add optional pres_scale arguments to EOS routines - NOAA-GFDL/MOM6@f75edd93a Added a ramp option for SSH OBCs. - NOAA-GFDL/MOM6@43ebd34bb Removed spaces from a blank line - NOAA-GFDL/MOM6@4693962ce Merge branch 'dev/gfdl' into fix_iceshelf_problems - NOAA-GFDL/MOM6@5ec169e95 Merge branch 'dev/master' into dev/gfdl - NOAA-GFDL/MOM6@bcc3f5ed8 Merge branch 'dev/gfdl' into fix_iceshelf_problems - NOAA-GFDL/MOM6@7cdffb103 (*)Use state%taux_shelf to set state%ustar_shelf - NOAA-GFDL/MOM6@684681b2b +Ice shelf code cleanup - NOAA-GFDL/MOM6@010492e2c Merge branch 'gustavo-marques-dev-master-candidate-ncar-2020-03-27' into dev/master - NOAA-GFDL/MOM6@04d5a83dc (*)Use a blend of ice-shelf and open water fluxes - NOAA-GFDL/MOM6@fcb1e92a1 +Add optional arg to ice_shelf_min_thickness_calve - NOAA-GFDL/MOM6@e87c66427 (*)Removed rescaling from mean_melt_flux to vprec - NOAA-GFDL/MOM6@e88732c3e (*)Do not use Hml>0 as an ice shelf melt filter - NOAA-GFDL/MOM6@1a8c75aa6 (*+)Set ice shelf latent heat consistently - NOAA-GFDL/MOM6@880da8024 (*+)Corrected a bug in setting ustar_shelf - NOAA-GFDL/MOM6@3c3f72167 (*+)Corrected bugs in 3-eqn ice shelf skin salinity - NOAA-GFDL/MOM6@7121619b2 (*)Use global_area_integral in add_shelf_flux - NOAA-GFDL/MOM6@63fd8e1e8 +Added optional arg area to global_area_integral - NOAA-GFDL/MOM6@7fb8f5555 Flipped the sign convention for wT_flux - NOAA-GFDL/MOM6@e73db3840 Merge branch 'dev-master-candidate-ncar-2020-03-27' of https://github.com/gustavo-marques/MOM6 into gustavo-marques-dev-master-candidate-ncar-2020-03-27 - NOAA-GFDL/MOM6@6ce3dd9b7 Change CDRAG_MEKE to MEKE_CDRAG - NOAA-GFDL/MOM6@0cddf1f28 Merge pull request #146 from NCAR/fix_tracer_advect_omp - NOAA-GFDL/MOM6@8025fd4d7 refactor advect_x and advect_y calls - NOAA-GFDL/MOM6@3768a118d make advect_y thread-safe - NOAA-GFDL/MOM6@3d05d8537 make T_adx_2d diagnostics thread-safe - NOAA-GFDL/MOM6@6636e0f43 fix OMP directive variable list - NOAA-GFDL/MOM6@afe033517 Merge pull request #144 from gustavo-marques/merge_GME_outside_MEKE - NOAA-GFDL/MOM6@1f308a02f Extend loop indices and add calls to pass_vector - NOAA-GFDL/MOM6@24782fa85 Move allocation of diagnostic arrays - NOAA-GFDL/MOM6@9a330fab8 Loop over recreation of diagnostic grid explicitly - NOAA-GFDL/MOM6@e23f03c81 Fix compilation errors - NOAA-GFDL/MOM6@3a3a10217 Merge branch 'remap_v_extensive' of github.com:ashao/MOM6 into remap_v_extensive - NOAA-GFDL/MOM6@1ecade5e0 Updates GME by removing dependency on MEKE - NOAA-GFDL/MOM6@46ce21ec7 Store h_extensive for both native and remapped coordinates - NOAA-GFDL/MOM6@c01201978 Merge pull request #143 from gustavo-marques/fix_vhGM_GEOMETRIC - NOAA-GFDL/MOM6@3477bbe45 Revert "Set target diagnostic grid based on boolean" - NOAA-GFDL/MOM6@9abcb1036 Set target diagnostic grid based on boolean - NOAA-GFDL/MOM6@c42982419 Fix a bug in the vmGM field when using GEOMETRIC - NOAA-GFDL/MOM6@0eb06153a Merge pull request #142 from NCAR/omp_fixes - NOAA-GFDL/MOM6@f83292592 initialize fluid entrainment arrays - NOAA-GFDL/MOM6@276c6b4d2 call chksum for drag_vel if its allocated - NOAA-GFDL/MOM6@447806678 uncomment omp do block in advect_tracer - NOAA-GFDL/MOM6@75334543b fix omp in calculate_diagnostic_fields - NOAA-GFDL/MOM6@988f8f2b0 Merge branch 'dev/gfdl' into remap_v_extensive - NOAA-GFDL/MOM6@ed51bcd66 Modify remapping of vertically extensive diagnostics - NOAA-GFDL/MOM6@21918b451 comment out OMP directives in KPP_compute_BLD temporarily - NOAA-GFDL/MOM6@049abb032 fix omp directives in set_viscous_BBL - NOAA-GFDL/MOM6@67e5481df fix omp directive for melt_potential - NOAA-GFDL/MOM6@46b1f34a0 correct namespace name for doxygen - NOAA-GFDL/MOM6@83da0906a Merge pull request #141 from alperaltuntas/fix_gnu_bugs - NOAA-GFDL/MOM6@ba5a44271 if not allocated, do not assign R_rho - NOAA-GFDL/MOM6@435a7412c Close param file before it gets opened by ocean_model_init again. - NOAA-GFDL/MOM6@ab54b961c Merge pull request #140 from alperaltuntas/fix_omp2 - NOAA-GFDL/MOM6@a9c896e65 set CS%MEKE_equilibrium_restoring, to false by default - NOAA-GFDL/MOM6@3540446d5 fix unitialized logical var in MOM_MEKE - NOAA-GFDL/MOM6@63cf741f4 fix kpp omp directives - NOAA-GFDL/MOM6@22f0242e7 Merge branch 'dev/ncar' of https://github.com/NCAR/MOM6 into dev/ncar - NOAA-GFDL/MOM6@1ed6b9462 Merge pull request #139 from gustavo-marques/update_LBD - NOAA-GFDL/MOM6@9db5ba14a Improve documentation and unit tests - NOAA-GFDL/MOM6@0525a4c10 Change flux limiting calculation - NOAA-GFDL/MOM6@248a87ca4 Fix units description and delete placeholder for the pressure reconstruction - NOAA-GFDL/MOM6@c8361e799 Add a note saying khtr_avg should be computed once khtr is 3D - NOAA-GFDL/MOM6@dce59f430 Fix a bug in the LBD method 2 - NOAA-GFDL/MOM6@5c8b32fb1 Fix a bug when checking if hbl > htot - NOAA-GFDL/MOM6@408bd2f63 Merge branch 'near_surface_fluxes' of github.com:ashao/MOM6 into near_surface_fluxes - NOAA-GFDL/MOM6@31d2941d0 Fix bug in boundary_k_range if hbl > htot - NOAA-GFDL/MOM6@4fe019156 Compute tracer tendency due to lateral diffusion - NOAA-GFDL/MOM6@e2bafc51c fix omp directives in MOM_thickness_diffuse - NOAA-GFDL/MOM6@1ae069b37 Merge branch 'dev/ncar' into near_surface_fluxes - NOAA-GFDL/MOM6@44d36c4a2 Merge pull request #138 from gustavo-marques/fix_ocean_model_data_get - NOAA-GFDL/MOM6@1d1914ff9 Merge pull request #136 from gustavo-marques/merge-dev-master-candidate-2019-12-17 - NOAA-GFDL/MOM6@0188f3507 Merge branch 'dev-master-candidate-2019-12-17' into merge-dev-master-candidate-2019-12-17 - NOAA-GFDL/MOM6@f7debedda Delete ocean_model_data_get from MCT and NUOPC caps - NOAA-GFDL/MOM6@a12abd6db Revert "Merge pull request #133 from gustavo-marques/clean_caps" - NOAA-GFDL/MOM6@c7c7bf184 Merge branch 'dev-master-candidate-2019-12-17' into merge-dev-master-candidate-2019-12-17 - NOAA-GFDL/MOM6@c3581144d Merge pull request #135 from gustavo-marques/LBD_merge - NOAA-GFDL/MOM6@d276f3f84 Merge branch 'dev/ncar' into near_surface_fluxes - NOAA-GFDL/MOM6@8a3e3e7e4 Merge branch 'near_surface_fluxes' into LBD_merge - NOAA-GFDL/MOM6@2cccc837a Merge pull request #134 from gustavo-marques/fix_leith - NOAA-GFDL/MOM6@3d17e0390 Merge pull request #133 from gustavo-marques/clean_caps - NOAA-GFDL/MOM6@e53814498 remove duplicate fld_list_add calls - NOAA-GFDL/MOM6@2c7de6631 Merge pull request #132 from NOAA-EMC/dev/emc - NOAA-GFDL/MOM6@78bb4c14c Delete quotes from doxygen comment - NOAA-GFDL/MOM6@8c95cc061 Fix bugs in Leith add new input parameter - NOAA-GFDL/MOM6@c50a97891 Toggle continuous neutral diffusion in interior only - NOAA-GFDL/MOM6@89eaede6c Delete ocean_model_data_get* from all the caps - NOAA-GFDL/MOM6@20d076b4d Modify continuous neutral diffusion to account for boundary layer - NOAA-GFDL/MOM6@a2d9636e2 Merge pull request #131 from gustavo-marques/meke_khtr - NOAA-GFDL/MOM6@cb79e977f add changes from old MOM6 repo in cmeps_integration branch that were (#10) - NOAA-GFDL/MOM6@97d07bcb4 Set the default for CDRAG_MEKE to CDRAG - NOAA-GFDL/MOM6@02c986a77 Set default value to 0.003 - NOAA-GFDL/MOM6@e71a5736a Fix doxygen references - NOAA-GFDL/MOM6@9303e9946 Fix typos and bugs - NOAA-GFDL/MOM6@f3dba1609 Add new option to avoid negative thicknesses - NOAA-GFDL/MOM6@7135281fb Merge pull request #8 from DeniseWorthen/feature/runoff_optional - NOAA-GFDL/MOM6@147f7a382 Merge pull request #130 from DeniseWorthen/feature/runoff_optional - NOAA-GFDL/MOM6@2c6bdf925 Create a separate param for MEKE bottom drag (CDRAG_MEKE) - NOAA-GFDL/MOM6@b66eafe4e backs out change in standard name for liquid and frozen heat flux since this will require a change in the nuopc field_dictionary. The fields are not currently used. - NOAA-GFDL/MOM6@b1ce184a3 Documentation and minor improvements - NOAA-GFDL/MOM6@0a89aaca9 Fix registry of lbd diagnostics - NOAA-GFDL/MOM6@6bce8ab9e Clean the code and fix line length exceeding 120 - NOAA-GFDL/MOM6@7f2b93e4c Replace lbm to lbd (lateral boundary diffusion) - NOAA-GFDL/MOM6@64be85f76 minor text changes; uncomment runoff heat flux terms; required change made in feature/runoff_names branch of NEMS - NOAA-GFDL/MOM6@419a021d9 removes data_override and associated calls from mom_cap renames: iob%rofl_flux => iob%lrunoff iob%rofi_flux => iob%frunoff iob%runoff_hflx = > iob%lrunoff_hflx iob%calving_hflx => iob%frunoff_hflx makes changes in mom_cap_methods and mom_surface_forcing_nuopc consistent w/ new iob names temporarily comments out _hflx terms in mom_cap,mom_cap_methods adds flag in mom_surface_forcing_nuopc for adding liquid river runoff via data_override - NOAA-GFDL/MOM6@ba6140c33 Merge pull request #1 from NOAA-EMC/dev/emc - NOAA-GFDL/MOM6@9a6f7f65e Merge NOAA-GFDL dev/master from 20191107 - NOAA-GFDL/MOM6@07481e41d updating mom_cap to add data override which was deleted in merge - NOAA-GFDL/MOM6@100e92db5 Merge remote-tracking branch 'GFDL/dev/master' into testnewdevmaster20191107 - NOAA-GFDL/MOM6@80743e6cb Adding river runoff (from Jiande) Squashed commit of the following: - NOAA-GFDL/MOM6@462768be6 Merge pull request #128 from gustavo-marques/fix_MEKE_GM_src - NOAA-GFDL/MOM6@050aa31b3 Moves allocation of CS%equilibrium_value inside subroutine MEKE_equilibrium_restoring - NOAA-GFDL/MOM6@3f041d93f MEKE diagnostic array fixes - NOAA-GFDL/MOM6@2bb321efb Merge pull request #127 from gustavo-marques/depth_scaled_khth - NOAA-GFDL/MOM6@ebf5ee0d3 Adds MEKE_equilibrium_restoring - NOAA-GFDL/MOM6@1522ad0d7 Minor changes in the doxygen comments - NOAA-GFDL/MOM6@223037c76 Deletes unneeded variables from calc_depth_function - NOAA-GFDL/MOM6@67016eba9 Reverts description in DO_DYNAMICS to older version as this was changed by mistake. - NOAA-GFDL/MOM6@bb785a8e0 Adds option to scale KHTH with depth - NOAA-GFDL/MOM6@839217d9d Rearranged MEKE_EQUILIBRIUM subroutine - NOAA-GFDL/MOM6@486da1dfc Replaces trunit to conc in the documentation - NOAA-GFDL/MOM6@15c9f0646 Hard-code min of SN to be 1.0e-7 - NOAA-GFDL/MOM6@8f3cf968d Add placeholders for adding method3 and applying filter on method1 - NOAA-GFDL/MOM6@5583f84db Renames lateral_boundary_mixing to lateral_boundary_diffusion - NOAA-GFDL/MOM6@69ec18c3a Removes redundant statement in netrual diffusion - NOAA-GFDL/MOM6@af410950e Fix uninitialized variables in find_surface when NDIFF_INTERIOR_ONLY = False - NOAA-GFDL/MOM6@e806fbabd Fixes a bug in the bulk_method - NOAA-GFDL/MOM6@d7da98270 Improves the calculation of F_bulk to minimize roundoff errors - NOAA-GFDL/MOM6@82c1bca13 First set of commits to limit neutral diffusion to the interior - NOAA-GFDL/MOM6@3c5c7d181 Merge branch 'rewrite_discontinuous_sort' into near_surface_fluxes - NOAA-GFDL/MOM6@91ca2d13e Fix flux limiter in LBM when < 0 - NOAA-GFDL/MOM6@ca23e661b Make fluxes_bulk_method more roundoff safe - NOAA-GFDL/MOM6@5aaf34b7f Add flux limiter for bulk layer fluxes - NOAA-GFDL/MOM6@9f15e4f7a Adds new unit test and fixes diagnostics - NOAA-GFDL/MOM6@c8805391f Update LBM flux names and fix posting of 2d diags - NOAA-GFDL/MOM6@bcec94ce2 Merge branch 'dev/ncar' into fix_MEKE_GM_src - NOAA-GFDL/MOM6@bb46c38d8 Calculates bottomFac2 IF CS%MEKE_GEOMETRIC=True - NOAA-GFDL/MOM6@66a8f0afb Fix bug in LBM diagnostics and add diags - NOAA-GFDL/MOM6@a4f9550f9 Added new equilibrium formula for MEKE - NOAA-GFDL/MOM6@73d0d7895 Fixes a bug in method2 of LBM, where diffusivities were not used - NOAA-GFDL/MOM6@4d5c7862f Fixes undoxygenized LBM module variables - NOAA-GFDL/MOM6@e5645b14c Fixes line length exceeding 120 - NOAA-GFDL/MOM6@f38a36972 Fixes unit test for layer by layer and removes the hbl_min = MIN(hbl_L, hbl_R) - NOAA-GFDL/MOM6@c41b8b0c7 Adds two unit tests for layer by layer method - NOAA-GFDL/MOM6@6d6d3b8a4 Adds two unit tests for layer by layer method - NOAA-GFDL/MOM6@3cb68d348 Adds missing arguments after merge - NOAA-GFDL/MOM6@62e322735 Adding layer by layer method for bottom boundary - NOAA-GFDL/MOM6@8d9c6a430 Merge branch 'dev/ncar' into near_surface_fluxes - NOAA-GFDL/MOM6@3bb1f5561 Adding first version of LBM method=2 - NOAA-GFDL/MOM6@4d0aed6b2 Fixes units and moves bulk diags inside if statement - NOAA-GFDL/MOM6@f6800c2bc Update halos for hbl in LBM - NOAA-GFDL/MOM6@915bcb19f Diagnostics for lateral boundary mixing scheme - NOAA-GFDL/MOM6@223a815a2 Merge branch 'near_surface_fluxes' of github.com:ashao/MOM6 into HEAD - NOAA-GFDL/MOM6@322aa77b8 Rename MOM_boundary_lateral_mixing.F90 for consistency - NOAA-GFDL/MOM6@332a2648d Try to restore commits from accidental move of file - NOAA-GFDL/MOM6@e5f96f424 Fix minor bugs in lateral boundary mixing - NOAA-GFDL/MOM6@9b4d2c2bb Only allocate KPP_CS if requested - NOAA-GFDL/MOM6@8ab7aa8ef Convert diffusive flux convergence to a change in tracer - NOAA-GFDL/MOM6@8a4ed840d Guard against case where the boundary layer is 0 on one column - NOAA-GFDL/MOM6@df938a1bb Add masking in lateral_boundary_fluxes - NOAA-GFDL/MOM6@ae6529ea8 Hook lateral boundary mixing into tracer_hor_diff - NOAA-GFDL/MOM6@a4dbeb158 Hook in lateral boundary mixing initialization - NOAA-GFDL/MOM6@2b10a8bbc Skeleton for boundary layer mixing interfaces - NOAA-GFDL/MOM6@4e63c751c Update API for boundary_layer_fluxes unit tests - NOAA-GFDL/MOM6@79bea6876 New unit tests for surface boundary fluxes - NOAA-GFDL/MOM6@f87aaa22b Fixes bulk_average calculation and takes into account partial cells when computing fluxes - NOAA-GFDL/MOM6@a36f5d64c Removes more trailing space - NOAA-GFDL/MOM6@17385cc86 Removes trailing space and fixes line length exceeded - NOAA-GFDL/MOM6@667782043 Updates layer_fluxes_bulk_method and bulk_average - NOAA-GFDL/MOM6@838523136 Add function and unit tests for boundary layer mixing - NOAA-GFDL/MOM6@654a12c60 Add additional unit tests for bulk method - NOAA-GFDL/MOM6@576fafbf2 Initial commit for implementing near-surface mixing

- NOAA-GFDL/MOM6@b92d763ec Merge pull request #1357 from marshallward/emc_update_20210322 - NOAA-GFDL/MOM6@8cc501820 Style: Line length fix in MCT_cap - NOAA-GFDL/MOM6@a1206ede8 Merge branch 'dev/gfdl' into emc_update_20210322 - NOAA-GFDL/MOM6@4fd897da2 Merge pull request #1355 from marshallward/test_submod_update - NOAA-GFDL/MOM6@b33b3af7f Testing: Recurse target submodules, LDFLAGS hook - NOAA-GFDL/MOM6@3193ab081 Merge pull request #1338 from OlgaSergienko/ice_dynamics - NOAA-GFDL/MOM6@edc15f61c Merge branch 'dev/gfdl' into ice_dynamics - NOAA-GFDL/MOM6@b89152c41 Merge branch 'dev/emc' into feature/allowmaskchanges - NOAA-GFDL/MOM6@e5a40353f Merge pull request #61 from jiandewang/feature/update-to-GFDL-20210308 - NOAA-GFDL/MOM6@8dd907275 Merge pull request #1346 from marshallward/fgnv_bound_fix - NOAA-GFDL/MOM6@33d28f138 Merge branch 'dev/gfdl' into fgnv_bound_fix - NOAA-GFDL/MOM6@a6f680cc2 Merge pull request #1351 from adcroft/units-for-slope - NOAA-GFDL/MOM6@ab241b642 Merge branch 'dev/gfdl' into units-for-slope - NOAA-GFDL/MOM6@4255adad0 Merge pull request #1344 from adcroft/cvmix-update - NOAA-GFDL/MOM6@5839494ce Merge branch 'dev/gfdl' into ice_dynamics - NOAA-GFDL/MOM6@b911a3928 Merge branch 'dev/gfdl' into cvmix-update - NOAA-GFDL/MOM6@0d60fd026 Change units of slope returned from calc_isoneutral_slopes() to "Z L-1" - NOAA-GFDL/MOM6@250f00700 Merge pull request #1350 from Hallberg-NOAA/set_io_domain - NOAA-GFDL/MOM6@abc8fe463 Removed blocks of commented text and multiplications by 0 - NOAA-GFDL/MOM6@8494ba8d6 change logical from "topog_..." to "topo_..." - NOAA-GFDL/MOM6@5b686c838 add parameter for allowing land mask changes - NOAA-GFDL/MOM6@bb5eb2527 Explicitly set (1x1) io_domain as a default - NOAA-GFDL/MOM6@b47e493d3 Removed blocks of commented code. Added parentheses in calc_shelf_visc - NOAA-GFDL/MOM6@3703ca7dd Merge remote-tracking branch 'GFDL/main' into feature/update-to-GFDL-20210308 this is corresponding to GFDL 20210308 main branch commit (hash # a4049e7) - NOAA-GFDL/MOM6@a4049e784 Merge branch 'dev/gfdl' into main - NOAA-GFDL/MOM6@651b4673f Bugfix: FGNV streamfunction vertical bounds - NOAA-GFDL/MOM6@00cb11ce5 Merge pull request #56 from jiandewang/feature/update-to-GFDL-20210224 - NOAA-GFDL/MOM6@43dadc16a Defined variables in ice_shelf_solve_outer - NOAA-GFDL/MOM6@aed4f0ee7 More style errors - NOAA-GFDL/MOM6@2232fa288 corrected style errors in MOM_ice_shelf.F90; MOM_ice_shelf_dynamics.F90; MOM_ice_shelf_initialize.F90 - NOAA-GFDL/MOM6@9aa75c869 Modified MOM_ice_shelf_initialize.F90 - NOAA-GFDL/MOM6@5483bfed1 Cleaned initialize_ice_shelf_boundary_channel - NOAA-GFDL/MOM6@e56d45335 Update CVMix to v0.98-beta - NOAA-GFDL/MOM6@34dc0c848 Update CVMix to v0.94b-beta with API change - NOAA-GFDL/MOM6@28b1ac922 Update CVMix to v0.93-beta (no API change) - NOAA-GFDL/MOM6@a729a7fb4 Merge commit '00c2819457ab6d2497c871ce9a02d5e67e7f741c' into feature/update-to-GFDL-20210224 this is corresponding to GFDL 20210224 main branch commit (hash # 00c2819) - NOAA-GFDL/MOM6@32cfe35a4 modified MOM_ice_shelf_initialize for testing with viscosity from a file - NOAA-GFDL/MOM6@fdd83e658 dynamic ice shelf with non-linear viscosity and evolving ice thickness due to sub-ice-shelf melting - NOAA-GFDL/MOM6@271bfce94 corrected boundary mask in init_boundary_channel and updated u_ and v_bdry_val through halo - NOAA-GFDL/MOM6@89f4386eb corrected initialize_boundary_channel call - NOAA-GFDL/MOM6@f0ae41c0c modified viscosity computations - NOAA-GFDL/MOM6@cdc7690f4 Merge pull request #54 from DeniseWorthen/feature/optmesh - NOAA-GFDL/MOM6@775205208 fixed ice-shelf advection - NOAA-GFDL/MOM6@f30f636b2 corrected indecises in computation of driving stresses - NOAA-GFDL/MOM6@a34ebb141 remove tempory bypass of mesh abort code - NOAA-GFDL/MOM6@12b389520 Merge branch 'dev/emc' into feature/optmesh - NOAA-GFDL/MOM6@13a5a2e0f comment out mask check which fails for mx100 - NOAA-GFDL/MOM6@7db2cc7a4 make mom mesh optional - NOAA-GFDL/MOM6@d531a324a Merge pull request #51 from jiandewang/feature/update-to-GFDL-20210120 - NOAA-GFDL/MOM6@faeb13972 Merge pull request #1 from DeniseWorthen/bugfix/li2016fix - NOAA-GFDL/MOM6@e7d0976de Fixes latent heat from fprec and frunoff - NOAA-GFDL/MOM6@66ec49b2e Merge remote-tracking branch 'JiandeWang/feature/update-to-GFDL-20210120' into bugfix/li2016fix - NOAA-GFDL/MOM6@e928fe22a Merge branch 'dev/emc' into bugfix/li2016fix - NOAA-GFDL/MOM6@b544dad71 Merge remote-tracking branch 'upstream/dev/emc' into dev/emc - NOAA-GFDL/MOM6@d63c2de85 Merge remote-tracking branch 'GFDL/main' into feature/update-to-GFDL-20210120 This is corresponding GFDL 20210120 main branch commit (hash # fe5e605) - NOAA-GFDL/MOM6@cec1ad3b2 Merge pull request #49 from breichl/user/bgr/Tau_halo_updates_in_nupoc - NOAA-GFDL/MOM6@91282c106 add brandon's halo update fix for LI_2016 - NOAA-GFDL/MOM6@29d768065 Add two halo updates for taux and tauy in mom_surface_forcing_nupoc - In A and B grid configuration halos were never updated after taux/tauy were populated. - This propogated through to the ustar_gustless field, hence caused a restart issue when using ustar_gustless in parameterizations. - This appears to correct the restart issue by updating the halos at the end of the A and B grid taux/tauy loops. - NOAA-GFDL/MOM6@69b2a2354 Merge remote-tracking branch 'upstream/dev/emc' into dev/emc - NOAA-GFDL/MOM6@ebac0adb8 Modifications to register_diag_field in MOM_ice_shelf_dynamics to make ice-shelf_fields consistent with diag_table Modifications to MOM_ice_shelf.F90 to apply melting to the case of a dynamic ice shelf. - NOAA-GFDL/MOM6@d27bcbdba Matt's changes to drivers Merge branch 'revert_drivers' of https://github.com/MJHarrison-GFDL/MOM6 into matts-revert-drivers - NOAA-GFDL/MOM6@39dd3e322 Modified MOM_ice_shelf_dynamics.F90 - NOAA-GFDL/MOM6@f1041d1f9 Fixed bugs in CG_action, matrix_diagonal and calc_shelf_visc in MOM_ice_shelf_dynamics.F90 modified initialize_ice_shelf_boundary_channel in MOM_ice_shelf_initialze.F90 - NOAA-GFDL/MOM6@a98f7db5e Merge remote-tracking branch 'upstream/dev/emc' into dev/emc - NOAA-GFDL/MOM6@f3bb72834 Merge remote-tracking branch 'upstream/dev/emc' into dev/emc - NOAA-GFDL/MOM6@16ade2fe8 Merge remote-tracking branch 'upstream/dev/emc' into dev/emc - NOAA-GFDL/MOM6@bfbd95aac white space changes - NOAA-GFDL/MOM6@6164f63a9 manual add of dev/emc changes (statediagnose) - NOAA-GFDL/MOM6@4e51baea1 Revert "Merge remote-tracking branch 'upstream/dev/emc' into dev/emc" - NOAA-GFDL/MOM6@e4ca1dcb0 Merge remote-tracking branch 'upstream/dev/emc' into dev/emc - NOAA-GFDL/MOM6@40bfb4bfe Merge remote-tracking branch 'upstream/dev/emc' into dev/emc - NOAA-GFDL/MOM6@6371e4892 Merge remote-tracking branch 'upstream/dev/emc' into dev/emc - NOAA-GFDL/MOM6@58a69fcb6 Merge pull request #10 from NOAA-EMC/dev/emc - NOAA-GFDL/MOM6@d53791175 Merge pull request #9 from NOAA-EMC/dev/emc - NOAA-GFDL/MOM6@1be1217b2 Merge pull request #7 from NOAA-EMC/dev/emc - NOAA-GFDL/MOM6@59270484c Merge pull request #6 from NOAA-EMC/dev/emc - NOAA-GFDL/MOM6@fb02b3a4b Merge pull request #5 from NOAA-EMC/dev/emc - NOAA-GFDL/MOM6@74f8d112c Merge pull request #4 from NOAA-EMC/dev/emc - NOAA-GFDL/MOM6@2b7abecdc Merge pull request #2 from NOAA-EMC/dev/emc

Updated the MOM_parameter_doc files to reflect the fact that VISBECK_MAX_SLOPE is not being recorded in some cases where its value is not used as a result of MOM6 PR #1413. Also updated the parameter doc files for several of the test cases that are not routinely run in the pipeline testing. Updated the versions of MOM6 and SIS2 that are pointed to the versions right after MOM6 PR #1413 was merged into dev/gfdl and SIS2 PR #147 was merged into its dev/gfdl. No solutions change as the result of the updated versions of MOM6 and SIS2. The non-merge MOM6 commits in this update include: - NOAA-GFDL/MOM6@da287e1a7 Merge pull request #1413 from marshallward/valgrind_fixes - NOAA-GFDL/MOM6@a6a799928 Merge pull request #1412 from ESMG/ESMG_sponge_masking - NOAA-GFDL/MOM6@d9edec107 Update MOM_internal_tide_input.F90 - NOAA-GFDL/MOM6@121ec5c47 Merge pull request #1411 from Hallberg-NOAA/rescale_user_OBC_code - NOAA-GFDL/MOM6@616413a58 Memory management cleanup and initialization fixes - NOAA-GFDL/MOM6@b583c00d8 Change to masking of u,v sponges. - NOAA-GFDL/MOM6@627ae3f5d Tiny cleaning up edits. - NOAA-GFDL/MOM6@29061de6a +Dimensional rescaling of user OBC test cases The SIS2 commits in this update include: - NOAA-GFDL/SIS2@11934c6 Merge pull request #147 from ESMG/dev/esmg - ESMG/SIS2@a4cdaf0 Take guts back out of a routine. - ESMG/SIS2@2acd393 Merge branch 'n_aero' into dev/esmg - ESMG/SIS2@16e1b4b Don't need the guts of icepack_query_tracer_sizes - ESMG/SIS2@87bca6f Guts of things copied over from Icepack. - ESMG/SIS2@4ea2d75 Working version of icepack_tracers.F90 - ESMG/SIS2@e525f5b Integer n_aero, n_iso. - ESMG/SIS2@27c6f8a Merge pull request #5 from MJHarrison-GFDL/n_iso_to_int - ESMG/SIS2@f4c1aa3 Changes parameter n_iso and n_aero type to integer - ESMG/SIS2@079c7b1 Merge pull request #4 from MJHarrison-GFDL/ice_ridging_interfaces - ESMG/SIS2@54f9039 additional Icepack interfaces - ESMG/SIS2@77b49be Merge remote-tracking branch 'gfdl/dev/gfdl' into dev/esmg - ESMG/SIS2@9aa2b52 Clean out some trailing whitespace. - ESMG/SIS2@12432e3 Merge remote-tracking branch 'matt/Icepack' into dev/esmg - ESMG/SIS2@184036d Call compress ice after ice_ridging to clean up any residual part size excess - ESMG/SIS2@b662f69 Merge pull request #1 from MJHarrison-GFDL/Icepack - ESMG/SIS2@b528a23 Re-normalized ice coverage after call to ridge_ice - ESMG/SIS2@4d0d910 Modifications to enable Icepack APIs for ridging.

- NOAA-GFDL/MOM6@835b1661c (*)Use visc%Kv_shear in calculate_CVMix_conv call - NOAA-GFDL/MOM6@371c8bb26 +Eliminated 3 unused elements of the surface type - NOAA-GFDL/MOM6@79eb80794 In the case that nonzero_count <=1, a (dummy) value is set for non_unique_scales before returning - NOAA-GFDL/MOM6@8c605fef3 (*)Internal thickness variable unit correction - NOAA-GFDL/MOM6@4bcc8490b Makedep (#1) - NOAA-GFDL/MOM6@546312aed Adds "makedep" script to replace mkmf - NOAA-GFDL/MOM6@e5580e3b9 Re-factored GFDL gitlab pipeline - NOAA-GFDL/MOM6@3b80e443d Follow MOM6 code style guide - NOAA-GFDL/MOM6@0c1e89a2c Add missing units - NOAA-GFDL/MOM6@466ca80f7 Remove Travis CI config - NOAA-GFDL/MOM6@328c44000 +Clean up dimensional rescaling in OBC code - NOAA-GFDL/MOM6@aa86abaa0 Put CVMix convective viscosity into shear term - NOAA-GFDL/MOM6@8f97b3d2f Corrections to cell-averaged density computation (#213) - 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@6963b222d Add KPP nonlocal term to passive tracers (#202) - NOAA-GFDL/MOM6@098f5c9d9 fix u10_sqr dimensional scaling - NOAA-GFDL/MOM6@b39648adc merge with latest main (2020feb17) and resolve conflicts - NOAA-GFDL/MOM6@035ae5c85 Misc dimensional consistency fixes in regridding, remapping, and MEKE routines - NOAA-GFDL/MOM6@c18185422 fix line lenght error in MOM_wave_interface - 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. New parameters - STOCH_EOS - STANLEY_COEFF - STANLEY_A - USE_STANLEY_GM - USE_STANLEY_PGF - USE_STANLEY_ML - USE_STANLEY_ISO Removed parameters: - STANLEY_PRM_DET_COEFF

- NOAA-GFDL/MOM6@c61978184 (*)Fix set_up_ALE_sponge_field call T & S scaling - NOAA-GFDL/MOM6@8ddd0c1a2 (*)Corrected OBC allocated tests in advect_y - NOAA-GFDL/MOM6@c8a62692c Added tracer debugging checksum calls - NOAA-GFDL/MOM6@58db99ba2 +Overload MOM_tracer_chksum to use tracer registry - NOAA-GFDL/MOM6@2217e6319 +Restored public interface to post_data_1d_k - NOAA-GFDL/MOM6@64fe4fc67 Fix to dumbbell initialization in layer mode (#160) - NOAA-GFDL/MOM6@05e705da9 +*Use runtime parameters in DOME initialization - NOAA-GFDL/MOM6@c2e8465cf *Fix DOME2d_initialize_temperature_salinity bug - NOAA-GFDL/MOM6@4f039a880 +Fix diagnostic conversions in code from dev/ncar - NOAA-GFDL/MOM6@48875ea0d Fix to reading of partial OBCs from file. - NOAA-GFDL/MOM6@43771d85c (*)Correct salinity rescaling in OBCs from files - NOAA-GFDL/MOM6@58d704bc1 fix call to tridiagonal solver - NOAA-GFDL/MOM6@c9dd80404 MacOS support - NOAA-GFDL/MOM6@1f64bf1ab +Tiny fix to SIMPLE Northern OBC - NOAA-GFDL/MOM6@9ecf1a6c7 makedep: Allow two versions of same file - NOAA-GFDL/MOM6@258111803 makedep: replaced includes_in_path() with list comprehension - NOAA-GFDL/MOM6@5121534cf makedep: fix for F90 includes - NOAA-GFDL/MOM6@cde444a85 Re-developed makedep in python - NOAA-GFDL/MOM6@1c0e1f873 +Add set_initialized - NOAA-GFDL/MOM6@12f2e55f5 gitlab-ci: add concurrent jobs in run stage - NOAA-GFDL/MOM6@1e9febecf Fix PGI warnings about intent for restart_CS - NOAA-GFDL/MOM6@835b1661c (*)Use visc%Kv_shear in calculate_CVMix_conv call - NOAA-GFDL/MOM6@371c8bb26 +Eliminated 3 unused elements of the surface type - NOAA-GFDL/MOM6@48adab788 +Add option to apply bottom drag as a body force - NOAA-GFDL/MOM6@a824f802f +Convert 16 vertvisc_type pointers to allocatables - NOAA-GFDL/MOM6@0a8210adc +Add DEBUG_FULL_COLUMN for debugging accelerations - NOAA-GFDL/MOM6@79eb80794 In the case that nonzero_count <=1, a (dummy) value is set for non_unique_scales before returning - NOAA-GFDL/MOM6@8c605fef3 (*)Internal thickness variable unit correction - NOAA-GFDL/MOM6@4bcc8490b Makedep (#1) - NOAA-GFDL/MOM6@546312aed Adds "makedep" script to replace mkmf - NOAA-GFDL/MOM6@e5580e3b9 Re-factored GFDL gitlab pipeline - NOAA-GFDL/MOM6@466ca80f7 Remove Travis CI config - NOAA-GFDL/MOM6@328c44000 +Clean up dimensional rescaling in OBC code - NOAA-GFDL/MOM6@aa86abaa0 Put CVMix convective viscosity into shear term - NOAA-GFDL/MOM6@4288d418c Move underflow code into separate loops - NOAA-GFDL/MOM6@c35da375a +Add user-controlled underflow of tracers - NOAA-GFDL/MOM6@ec8892383 Rescale ice shelf temperatures - NOAA-GFDL/MOM6@95119a251 (*)Fix ice shelf dimensional rescaling bugs - NOAA-GFDL/MOM6@4a6a175ca Bugfix: find_index in FMS2 infra - NOAA-GFDL/MOM6@1ad842cdb Replace findloc() with user-defined find_index - NOAA-GFDL/MOM6@37782ebbc Fixes badge for doc build status - NOAA-GFDL/MOM6@203a19f48 Fix a rescaling bug with MEKE_EQUILIBRIUM_ALT - NOAA-GFDL/MOM6@27bb8b833 (*)Corrected OBC restart scaling bugs - NOAA-GFDL/MOM6@9a604d467 (*)Fix occasional bug with PFv_visc_rem diagnostic - NOAA-GFDL/MOM6@8b513055b Simplify set_grid_metrics_from_mosaic - NOAA-GFDL/MOM6@2b5b4388a +Add optional scale argument to time_interp_external - NOAA-GFDL/MOM6@0b056864e Fix bugs in output files with rescaled heights - NOAA-GFDL/MOM6@cf448a1ec MOM_file_parser unit test implementation - NOAA-GFDL/MOM6@1c6696427 Rescaled dumbbell_initialize_thickness salinities - NOAA-GFDL/MOM6@079fd3e44 +Add cons_temp_to_pot_temp & abs_saln_to_prac_saln - NOAA-GFDL/MOM6@d4ccf5663 Fix data read for on-grid interpolation - NOAA-GFDL/MOM6@b3c41b105 +Rescale vars in MOM_temp_salt_initialize_from_Z - NOAA-GFDL/MOM6@31d411776 Correct a few more temperature and salin units - NOAA-GFDL/MOM6@6d78d2b0a +Add rescaling for temperature and salinity (2) - NOAA-GFDL/MOM6@5a89a9d0c +Add rescaling for temperature and salinity (1) - NOAA-GFDL/MOM6@44a786178 +Add scale argument to set_up_ALE_sponge - NOAA-GFDL/MOM6@47f13924c Modify more units in temperature and saln comments - NOAA-GFDL/MOM6@14a222ea3 Use simpler calculate_TFreeze interfaces - NOAA-GFDL/MOM6@b8e599034 +Temperature and salinity rescaling in MOM_EOS.F90 - NOAA-GFDL/MOM6@5d88f2e47 Modify units in temperature and salinity comments - NOAA-GFDL/MOM6@f52c40aec Fix a bug in the rescaling of drho_dT_dP - NOAA-GFDL/MOM6@0903609a6 +Make equation of state interfaces more consistent - NOAA-GFDL/MOM6@f51355476 Clarify argument units for int_density_dz_wright - NOAA-GFDL/MOM6@75ebb4090 +Refactored MOM_density_integrals - NOAA-GFDL/MOM6@3a9d51163 Revise how the drho_dT diagnostic is calculated - NOAA-GFDL/MOM6@07df0bfd7 Clarify units for equation of state arguments - NOAA-GFDL/MOM6@9c2e57310 Document variables in diagnoseMLDbyEnergy - NOAA-GFDL/MOM6@548be25b5 Remove unused module use for calculate_density - NOAA-GFDL/SIS2@6e0eda1 +(*)Write unscaled SIS2 restart files - NOAA-GFDL/SIS2@547cda8 Standardize syntax in mask2d logical tests (#172) - NOAA-GFDL/SIS2@f77d1f1 Fix indents per review - NOAA-GFDL/SIS2@8b5ad57 Bug Fix for specified ice - NOAA-GFDL/SIS2@acf0d89 Pass flux,fluv to compute_ocean_albedo for white cap parametrization - NOAA-GFDL/SIS2@0a0dce6 Fix specified_ice restart issue. - NOAA-GFDL/SIS2@5bf4d4a Pass flux_u,flux_v to compute_ocean_albedo for white caps parametrization

nikizadehgfdl self-assigned this Oct 23, 2014

adcroft added a commit that referenced this issue Nov 10, 2014

Draft of frepp files for CM2G63L

4a9eb0e

- Took .frepp files from OM4_025 and replace paths to CM2G63L WOA05 data and mosaic directories. - Hopefully helps address issue #1. - Completely untested!

adcroft mentioned this issue Nov 10, 2014

Draft of frepp files for CM2G63L #6

Merged

jkrasting closed this as completed Nov 20, 2014

adcroft pushed a commit that referenced this issue Mar 21, 2017

Merge pull request #1 from NOAA-GFDL/dev/master

503b8a3

Updated fork with commits from NOAA-GFDL/MOM6-examples

adcroft pushed a commit that referenced this issue Oct 1, 2018

Merge pull request #1 from NOAA-GFDL/dev/gfdl

ef9adaa

Re-sync with NOAA-GFDL repository

andreasschmittner mentioned this issue Oct 3, 2019

Configuration on CENTOS linux cluster with intel compiler and openmpi #289

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add .frepp analysis template for CM2G63L example #1

add .frepp analysis template for CM2G63L example #1

nikizadehgfdl commented Oct 23, 2014

adcroft commented Nov 19, 2014

jkrasting commented Nov 20, 2014

add .frepp analysis template for CM2G63L example #1

add .frepp analysis template for CM2G63L example #1

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nikizadehgfdl commented Oct 23, 2014

adcroft commented Nov 19, 2014

jkrasting commented Nov 20, 2014