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Group update for the barotropic solver #1

Merged
merged 2 commits into from
Feb 18, 2014
Merged

Group update for the barotropic solver #1

merged 2 commits into from
Feb 18, 2014

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Zhi-Liang
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Replaces step-by-step halo updates with grouped updates

@adcroft adcroft merged commit b408789 into dev/master Feb 18, 2014
@Zhi-Liang Zhi-Liang deleted the user/z1l/original_z1l branch July 9, 2014 20:19
adcroft pushed a commit that referenced this pull request Oct 24, 2016
@ashao
Merge pull request #1 from adcroft/ashao-origin/offline_tracers
fe2e8f3 
Proposed update to ashao:origin/offline tracers. I agree that renaming the flag from DO_ONLINE to OFFLINE_TRACER_MODE is more descriptive. I checked that this still works as intended with the Baltic_ALE_z_offline_tracers and updated the MOM_override for that test case in NOAA-GFDL/MOM6-examples#110
adcroft pushed a commit that referenced this pull request Nov 25, 2016
Merge pull request #1 from adcroft/user/aja/diag_interp_and_extrinsic
73207b5 
User/aja/diag interp and extrinsic
Hallberg-NOAA pushed a commit that referenced this pull request Aug 7, 2017
@sinakhani
Merge pull request #1 from adcroft/user/adcroft/add_neverland_winds_t…
b72c3be 
…emplate

Added a blank template Neverland_surface_forcing
adcroft pushed a commit that referenced this pull request Aug 17, 2017
@alperaltuntas
Merge pull request #1 from gustavo-marques/ice_shelf
405fecb 
Removes frazil's contribution to evaporation
nikizadehgfdl referenced this pull request in nikizadehgfdl/MOM6 Oct 9, 2017
@adcroft
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!
nikizadehgfdl referenced this pull request in nikizadehgfdl/MOM6 Oct 9, 2017
@adcroft
Updated icebergs, SIS2 and MOM6
231c5d1 
- 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.
nikizadehgfdl referenced this pull request in nikizadehgfdl/MOM6 Oct 9, 2017
@adcroft
MOM6: Merge branch 'ESMG-user/ksh/open_bc' into dev/master
e00cc6f 
- 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 mom-ocean#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
nikizadehgfdl referenced this pull request in nikizadehgfdl/MOM6 Oct 9, 2017
@adcroft
MOM6: Merge branch 'ashao-origin/offline_tracers' into dev/master
2036991 
- 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
nikizadehgfdl referenced this pull request in nikizadehgfdl/MOM6 Oct 9, 2017
@jkrasting
Merge pull request #1 from NOAA-GFDL/dev/master
503b8a3 
Updated fork with commits from NOAA-GFDL/MOM6-examples
nikizadehgfdl referenced this pull request in nikizadehgfdl/MOM6 Oct 9, 2017
@adcroft
MOM6: Merge pull request mom-ocean#578 from NCAR/dev/ncar
8b801de 
- NOAA-GFDL/MOM6@ae22a0f Merge pull request mom-ocean#578 from NCAR/dev/ncar
- NOAA-GFDL/MOM6@f4f882f Merge pull request mom-ocean#23 from gustavo-marques/combine_mct_modules
- NOAA-GFDL/MOM6@a85b728 Merge MCT modules
- NOAA-GFDL/MOM6@ba5b5ba Merge pull request mom-ocean#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 mom-ocean#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 mom-ocean#20 from gustavo-marques/fix_merge
- NOAA-GFDL/MOM6@fb89b08 Adds code that got lost during merge
- NOAA-GFDL/MOM6@7480492 Merge pull request mom-ocean#19 from gustavo-marques/new_merge
- NOAA-GFDL/MOM6@be1e6cf Merge branch 'dev/master' into dev/ncar
- NOAA-GFDL/MOM6@76565cb Merge pull request mom-ocean#17 from gustavo-marques/fix_ssh_slopes
- NOAA-GFDL/MOM6@c04f081 Fix ssh slope calculation
- NOAA-GFDL/MOM6@17d4586 Merge pull request mom-ocean#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 mom-ocean#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 mom-ocean#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 mom-ocean#13 from alperaltuntas/dev/ncar
- NOAA-GFDL/MOM6@37a53bc reorganize file structure
- NOAA-GFDL/MOM6@e6c5ddd Merge pull request mom-ocean#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 mom-ocean#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 mom-ocean#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
nikizadehgfdl referenced this pull request in nikizadehgfdl/MOM6 Oct 9, 2017
@adcroft
MOM6: Merge branch 'dev/master' into dev/gfdl
3f17d14 
- Updates MOM_parameter_doc files.

- NOAA-GFDL/MOM6@cde6d3f Merge branch 'dev/master' into dev/gfdl
- NOAA-GFDL/MOM6@ae22a0f Merge pull request mom-ocean#578 from NCAR/dev/ncar
- NOAA-GFDL/MOM6@f4f882f Merge pull request mom-ocean#23 from gustavo-marques/combine_mct_modules
- NOAA-GFDL/MOM6@a85b728 Merge MCT modules
- NOAA-GFDL/MOM6@ba5b5ba Merge pull request mom-ocean#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 mom-ocean#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 mom-ocean#20 from gustavo-marques/fix_merge
- NOAA-GFDL/MOM6@fb89b08 Adds code that got lost during merge
- NOAA-GFDL/MOM6@7480492 Merge pull request mom-ocean#19 from gustavo-marques/new_merge
- NOAA-GFDL/MOM6@be1e6cf Merge branch 'dev/master' into dev/ncar
- NOAA-GFDL/MOM6@76565cb Merge pull request mom-ocean#17 from gustavo-marques/fix_ssh_slopes
- NOAA-GFDL/MOM6@c04f081 Fix ssh slope calculation
- NOAA-GFDL/MOM6@17d4586 Merge pull request mom-ocean#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 mom-ocean#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 mom-ocean#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 mom-ocean#13 from alperaltuntas/dev/ncar
- NOAA-GFDL/MOM6@37a53bc reorganize file structure
- NOAA-GFDL/MOM6@e6c5ddd Merge pull request mom-ocean#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 mom-ocean#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 mom-ocean#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
nikizadehgfdl referenced this pull request in nikizadehgfdl/MOM6 Oct 9, 2017
@adcroft
SIS2: Merge branch 'Hallberg-NOAA-dev/gfdl' into dev/gfdl
06ae1dd 
- 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
feiyulu referenced this pull request in feiyulu/MOM6 Apr 4, 2018
@MJHarrison-GFDL
Merge pull request #1 from feiyulu/MOM6_DA
59625bd 
removed copy_profiles, using linked profiles in ensemble_filter
Hallberg-NOAA pushed a commit that referenced this pull request Aug 15, 2018
@wrongkindofdoctor
Merge pull request #1 from NOAA-GFDL/dev/gfdl
171e0c8 
Pull latest MOM6 changes into dev/gfdl fork
@jiandewang jiandewang mentioned this pull request Oct 23, 2018
Merged
adcroft pushed a commit that referenced this pull request Apr 12, 2019
@JessicaMeixner-NOAA
Merge pull request #1 from gustavo-marques/nuopccapPR_fixes
d3d7ce9 
Fixes code-style issues and adds doxygen comments
marshallward pushed a commit that referenced this pull request Nov 13, 2019
@Hallberg-NOAA
Merge pull request #1 from marshallward/pr_1019_fix
b3e4b3c 
T scaling and OpenMP fixes
adcroft pushed a commit that referenced this pull request Nov 27, 2019
@marshallward
Merge pull request #1 from MJHarrison-GFDL/gcc_7_4_0_patch
1b96028 
Gcc 7 4 0 patch
adcroft pushed a commit that referenced this pull request Apr 1, 2020
@DeniseWorthen
Merge pull request #1 from NOAA-EMC/dev/emc
ba6140c 
merge dev/emc into fork
adcroft pushed a commit that referenced this pull request Mar 25, 2021
@jiandewang
Merge pull request #1 from DeniseWorthen/bugfix/li2016fix
faeb139 
Bugfix: sign error on fprec for nuopc and mct caps
Hallberg-NOAA pushed a commit that referenced this pull request May 14, 2021
@OlgaSergienko
Merge pull request #1 from NOAA-GFDL/dev/gfdl
f4ba5a3 
dev/gfdl updates
marshallward pushed a commit that referenced this pull request Aug 6, 2021
@pjpegion
Merge pull request #1 from NOAA-EMC/dev/emc
4b8f940 
Update to EMC fork
marshallward pushed a commit that referenced this pull request May 3, 2022
@pjpegion
Merge pull request #1 from NOAA-EMC/dev/emc
671c714 
update with NOAA-EMC fork
angus-g pushed a commit to angus-g/MOM6 that referenced this pull request May 16, 2022
@marshallward
Candidate branch main->dev/gfdl
41a278b 
Note that most of these commits are from previously squashed pull
requests, and this PR is restoring them.

- 6360dbb Merge branch 'main' into main_to_dev
- bac8031 Merge pull request mom-ocean#1566 from jiandewang/EMC-FMS-mixed-mode-20220411
- e532d86 Merge pull request mom-ocean#88 from marshallward/missing_attrib_with_class_bugfix
- d380f1d An alternate fix to class(*) issues with FMS 2022-01
- 8ecf333 Merge pull request mom-ocean#87 from jiandewang/feature/update-to-main-20220317
- ba37f94 Merge remote-tracking branch 'FSU/main' into feature/update-to-main-20220317 this is corresponding to MOM6 main 20220317 commit (hash # 399a7db)
- 44313d9 Merge pull request mom-ocean#85 from jiandewang/feature/update-to-main-20220217
- 966707f Merge remote-tracking branch 'GFDL/main' into feature/update-to-main-20220217 this is corresponding to MOM6 main branch 20220217 commit (hash # 6f6d4d6), which originally based on GFDL-candidate-20220129
- 32c0e1e Merge pull request mom-ocean#81 from jiandewang/feature/update-to-main-20211220
- 9642b1d delete external/OCEAN_stochastic_phyiscs directory as Phil re-coded in external/stochastic_physics directory
- e7c9ada solve minor conflict in mom_cap.F90 mom_ocean_model_nuopc.F90 and MOM_energetic_PBL.F90, add two new files: src/parameterizations/stochastic/MOM_stochastics.F90 and config_src/external/stochastic_physics/stochastic_physics.F90
- 90d5961 Merge pull request mom-ocean#78 from jiandewang/feature/update-to-GFDL-20211019
- fd02017 Merge remote-tracking branch 'GFDL/main' into feature/update-to-GFDL-20211019
- 36f17eb Merge pull request mom-ocean#72 from pjpegion/ocn_stoch_july2021
- a9a957e return a more accurate error message in MOM_stochasics
- 56bb41e Merge branch 'ocn_stoch_july2021' of https://github.com/pjpegion/MOM6 into ocn_stoch_july2021
- ca2ae1c update to dev/emc
- 14ca4a1 Merge pull request mom-ocean#76 from jiandewang/feature/update-to-GFDL-20210914
- 29016c2 Merge remote-tracking branch 'GFDL/main' into feature/update-to-GFDL-20210914 merge GFDL main 20210914 commit (hash # c09e199)
- a8577df Merge branch 'NOAA-EMC:dev/emc' into ocn_stoch_july2021
- f8a8e4c update to gfdl 20210806 (mom-ocean#74)
- 16e6af0 update to dev/emc
- 237a510 add comments
- 1b4273d revert logic wrt increments
- 5b2040e add logic to remove incrments from restart if outside IAU window
- c5f2b72 add write_stoch_restart_ocn to MOM_stochastics
- bdf2dc7 doxygen cleanup
- 8bc4acc move stochastics to external directory
- a3fa3a1 Merge remote-tracking branch 'upstream/dev/emc' into ocn_stoch_july2021
- e4bc007 stochastic physics re-write
- 202cbd4 update to dev/emc
- 61717ee Merge remote-tracking branch 'origin/dev/emc' into ocn_stoch
- 565e0bb remove debug statements
- a4c0411 Merge remote-tracking branch 'upstream/dev/emc' into ocn_stoch
- 689a73f remove PE_here from mom_ocean_model_nuopc.F90
- 8afe969 clean up of mom_ocean_model_nuopc.F90
- 25ed4fc revert MOM_domains.F90
- b8d9888 place stochastic array in fluxes container and make SPPT specific arrays allocatable
- d984a7e remove stochastics container
- eb88219 clean up of code for MOM6 coding standards
- 6e3ea1b correct coupled_driver/ocean_model_MOM.F90 and other cleanup
- 0b99c1f make stochastics optional
- 85023f8 Merge remote-tracking branch 'upstream/dev/emc' into ocn_stoch
- 80f9f44 clean up MOM_domains
- 5443f8e remove blank link in MOM_diagnostics
- 1727d9a re-write of stochastic code to remove CPP directives
- 600ebf9 Merge remote-tracking branch 'upstream/dev/emc' into ocn_stoch
- 6bb9d0b fix non stochastic ePBL calculation
- 1d7ffa3 clean up code
- 040e1f1 Merge pull request mom-ocean#13 from NOAA-EMC/dev/emc
- 2cba995 Merge branch 'dev/emc' into ocn_stoch
- 1dc0f4f Merge remote-tracking branch 'upstream/dev/emc' into dev/emc
- 4bd9b9e clean up debug statements
- 25ed5ef additions for stochy restarts
- a2a374b add stochy_restart writing to mom_cap
- 0c15f4c Update MOM_diabatic_driver.F90
- 167a62e Merge pull request mom-ocean#12 from pjpegion/dev/emc
- bd477a9 Update MOM_diabatic_driver.F90
- 7212400 Update MOM_diabatic_driver.F90
- 7de295c cleanup of code and enhancement of ePBL perts
- cd06356 Merge pull request mom-ocean#11 from NOAA-EMC/dev/emc
- 9896d61 Merge pull request mom-ocean#9 from pjpegion/dev/emc_merge
- 0a62737 Merge branch 'ocn_stoch' into dev/emc_merge
- 3cad1ba Merge pull request mom-ocean#8 from NOAA-EMC/dev/emc
- c2aa2a8 updates from dev/emc
- 182ef34 additions for stochastic physics and ePBL perts
- 671c714 Merge pull request mom-ocean#1 from NOAA-EMC/dev/emc
raphaeldussin pushed a commit to raphaeldussin/MOM6 that referenced this pull request Jun 21, 2022
@marshallward
Makedep (mom-ocean#1)
4bcc849 
* Autoconf: Fix makedep path

The current path of makedep in the autoconf build assumes a directory tree as in .testing.  This patch uses the 
generalized @SrcDir@ to support more general autoconf builds.

Other minor changes:
* The `depend` rule was split into an explicit Makefile.dep rule and a phony rule to support `make depend`

* SRC_DIRS shell assignment is replaced with an Autoconf macro.

* A "self-generate" rule was added to `Makefile.in`, so that changes to `Makefile.in` do not trigger a full `./configure` run and regeneration of `.config.status`.

  This could possibly be extended to support `make depend` but let's first see how this one goes.

* Autoconf: makedep uses autoconf var conventions

This patch changes the makedep script to use autoconf environment variable conventions rather than mkmf ones:

* FCFLAGS in place of FFLAGS

* DEFS in place of CPPDEFS

* LDFLAGS and LIBS rather than just LDFLAGS
  (NOTE: This differs from Makefile's LDLFLAGS/LDLIBS)

This also allowed us to remove the custom build rule in the FMS build. Note that we now use an autoconf-friendly rule, rather than the default Makefile rule (which was arguably for fixed-format Fortran anyway).

The description of autoconf->mkmf translation from the Makefile templates has also been removed, since they're no longer relevant.

Some other minor changes in this build:

* The `make depend` rule was added to the FMS Makefile template.

* @SrcDir@ is directly passed to FMS makedep, rather than identically re-defining it in a variable.

* Testing: Resolve makedep paths

This patch resolves some issues relating to finding the path to makedep in both .testing and more generalized autoconf builds.

An explicit autoconf test for makedep has been added, with a default path which includes the `ac` directory relative to `deps`.

The .testing directory, which does not lie within `ac`, instead modifies the PATH to allow autoconf to find makedep.

The absolute path is determined and substituted into the appropriate Makefile.in template.

Some redundant operations in .testing/Makefile have been removed, but I suspect there are even more.  Much of the structure required to support mkmf and list_paths is probably no longer needed.
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2 participants
@Zhi-Liang @adcroft