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Added local variables to reduce the use of multiply dereferenced grid variables. All answers and interfaces are bitwise identical.
Added code that will allow set_viscosity to operate properly when there are massless layers. Some of these changes are commented out because they changes answers, while others involve adding H_neglect to Angstrom, which does not change answers unless Angstrom is set to 0. All answers and interfaces are bitwise identical in the standard test cases.
- add first draft of ALE_sponge - add two new tests cases: TVWS and ISOMIP
- Kd_ePBL has intent(out) from the PBL routine but was being
initialized by the calling routine and conditionally on whether
a diagnostic is active:
- Kd_ePBL is a mandatory output, no-longer conditional on the
diagnostic;
- initializing values by the caller is not guaranteed to work when the
callee has intent(out);
- ePBL was only setting values for non-land points.
- The conditional initialization has been removed entirely.
- ePBL now sets values on all computational points.
- Addresses issue discussed in mom-ocean#257 where DEBUG=True was detecting
NaN's in Kd_ePBL.
- The 0.5 degree model runs with THERMO_SPANS_COUPLING=True which also requires DIABATIC_FIRST=False (we prefer True). Restart regression tests were failing because the MLD from the PBL was missing a halo update after being restored from restart. This did not manifest as a problem with DIABATIC_FIRST=True which calls the PBL and sets MLD before the mixedlayer_restrat call. - Added a pass_var of CS%visc%MLD in MOM.F90. - Added some more debugging checksums in mixedlayer_restrat. - Closes mom-ocean#257.
- We had accumulated quite a few out-of-date openMP directives. - No answer changes.
Replaced all indirect references to the ocean's vertical grid in the directory parameterizations/vertical with verticalGrid_type arguments. All answers are bitwise identical, but many subroutines have new arguments.
Corrected the OpenMP directives in a number of files that had recently been checked in. All answers are bitwise identical, but the model would not compile correctly if OpenMP is enabled.
Replaced all indirect references to the ocean's vertical grid in the directory parameterizations/lateral with verticalGrid_type arguments. All answers are bitwise identical, but many subroutines have new arguments.
- A numeric conversion not representable netcdf error was reported for the 0.5 degree model which turns out to be due to the use of DIABATIC_FIRST=False for which the diagnostic is called after and interval of 0. - The fix is to test the interval length and zero out the result if the interval is zero. - Closes mom-ocean#249. - No answer changes.
- The gnu compiler seems to fail to read 1.0 to an integer
variable.
- A user provided WRITE_GEOM = 1.0 in a test case that triggered
this only for problem only for the gnu compiler.
- I've added err= in the read() statements to catch these errors are
report the variable and string value that failed to parse.
- No answer changes.
…rtical/MOM_ALE_sponge.F90), that applies sponge when using ALE mode. - The following files use this module and therefore had to be modified: - src/core/MOM.F90 - src/initialization/MOM_state_initialization.F90 - src/parameterizations/vertical/MOM_diabatic_driver.F90 - src/tracer/MOM_tracer_flow_control.F90
Several variables in thickness_diffuse had been given "save" attributes, in contravention to MOM6 coding standards, and in a way that could preclude the use of ensembles. These save attributes have now been removed. All answers in test cases are bitwise identical.
…now, but still not good!
Replaced many indirect references to the ocean's vertical grid in the core directory with verticalGrid_type arguments. All answers are bitwise identical, but many subroutines have new arguments.
The SZI_(G), etc., macros are the ones that are supposed to be used to specify array sizes for arguments, but NIMEM_, etc., were being used instead, which would cause errors if the model were ever run without G%isd=1. The proper argument array size macros are now used in the code in the param...s/lateral diretory. This change also required that G and GV be defined as arguments before they are used, so the order of a few lines had to be changed in many places. All answers are bitwise identical.
Changed a variable name in an OMP directive. This is needed due to the recent diagnostic code changes with commit NOAA-GFDL/MOM6@4c801e6
The SZI_(G), etc., macros are the ones that are supposed to be used to specify array sizes for arguments, but NIMEM_, etc., were being used instead, which would cause errors if the model were ever run without G%isd=1. The proper argument array size macros are now used in the code in the user directory. This change also required that G and GV be defined as arguments before they are used, so the order of a few lines had to be changed in many places. All answers are bitwise identical.
The SZI_(G), etc., macros are the ones that are supposed to be used to specify array sizes for arguments, but NIMEM_, etc., were being used instead, which would cause errors if the model were ever run without G%isd=1. The proper argument array size macros are now used in the code in the tracer directory. This change also required that G and GV be defined as arguments before they are used, so the order of a few lines had to be changed in many places. It also required the addition of an ocean_grid_type argument to register_tracer. All answers are bitwise identical.
The ALE module had a 3-d work array, dzRegrid, that was allocated at initialization and deallocated at the model's end. This has been replaced by an automatic work array in ALE_main, and as a result ALE_memory_allocation and ALE_memory_deallocation could be eliminated as well. All answers are bitwise identical.
The SZI_(G), etc., macros are the ones that are supposed to be used to specify array sizes for arguments, but NIMEM_, etc., were being used instead, which would cause errors if the model were ever run without G%isd=1. The proper argument array size macros are now used in the code in the diagnostics directory. This change also required that G and GV be defined as arguments before they are used, so the order of a few lines had to be changed in many places. All answers are bitwise identical.
The SZI_(G), etc., macros are the ones that are supposed to be used to specify array sizes for arguments, but NIMEM_, etc., were being used instead, which would cause errors if the model were ever run without G%isd=1. The proper argument array size macros are now used in the code in the ALE directory. This change also required that G and GV be defined as arguments before they are used, so the order of a few lines had to be changed in many places. All answers are bitwise identical.
The SZI_(G), etc., macros are the ones that are supposed to be used to specify array sizes for arguments, but NIMEM_, etc., were being used instead, which would cause errors if the model were ever run without G%isd=1. The proper argument array size macros are now used in the code in the framework directory. This change also required that G and GV be defined as arguments before they are used, so the order of a few lines had to be changed in many places. All answers are bitwise identical.
Modified ISOMIP files so they are compatible with those changes. In particular, dev/master had changes to the vertical grid structures. The code now compiles.
Remerged it in and removed the conflicts.
Merged
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Jul 26, 2016
…dary_module Move ocean_OBC_type into MOM_open_boundary.F90
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Oct 28, 2016
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
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Jan 5, 2017
User/aja/diag interp and extrinsic
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Jul 5, 2017
Removes frazil's contribution to evaporation
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Aug 23, 2017
…emplate Added a blank template Neverland_surface_forcing
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May 21, 2018
removed copy_profiles, using linked profiles in ensemble_filter
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Oct 23, 2018
Pull latest MOM6 changes into dev/gfdl fork
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Apr 15, 2019
Fixes code-style issues and adds doxygen comments
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Dec 9, 2019
merge dev/emc into fork
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Dec 31, 2019
T scaling and OpenMP fixes
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Apr 21, 2021
Bugfix: sign error on fprec for nuopc and mct caps
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May 17, 2022
update with NOAA-EMC fork
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May 20, 2022
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 #9 from pjpegion/dev/emc_merge - 0a62737 Merge branch 'ocn_stoch' into dev/emc_merge - 3cad1ba Merge pull request #8 from NOAA-EMC/dev/emc - c2aa2a8 updates from dev/emc - 182ef34 additions for stochastic physics and ePBL perts - 671c714 Merge pull request #1 from NOAA-EMC/dev/emc
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* 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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Merged in dev/master. There were a lot of differences. The largest one was that the vertical grid structure was changed. The routines in ISOMIP were edited to be compatible with these changes.