Merge main candidate from 09/18/2020#160
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alperaltuntas merged 426 commits intoOct 23, 2020
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Modified doc_module so that new lines are added only when modules are documented, and are added in all parameter_doc files in which modules are documented. All answers and output are identical, but there are white space changes in MOM_parameter_doc and SIS_parameter_doc files.
Added the new optional argument like_default to the log_param and doc_param routines to help control where the documentation appears. This new argument is used for logging EPBL_USTAR_MIN, the diagnosed output value of MAXIMUM_DEPTH when the input value is negative, and the diagnosed number of columns where sponges occur with MOM_ALE_sponge. An '!' was also added to the logging of EPBL_USTAR_MIN. All answers are bitwise identical but there are minor changes in the contents of some MOM_parameter_doc.short files.
…nto add_dens_deriv_diag
Added diagnostics for partial derivatives of density
Removed #ifdef debugging blocks
Added code to determine whether all parameters in the MOM_grid, MOM_restart, MOM_write_cputime and MOM_tracer_registry modules are being used with their default settings, and added all_default arguments to the log_version calls for these modules. All answers and output are identical, but there are white space changes in MOM_parameter_doc.short and SIS_parameter_doc.short files.
Testing: Explicit OpenMP CPU affinity
- Members of a type cannot be individually labelled as shared/private - One variable was converted to shared since it was defiend in a non-OMP section and then labelled as private which meant it was uninitialized.
…A/MOM6 into Hallberg-NOAA-module_doc_newlines
…hub.com/nikizadehgfdl/MOM6 into nikizadehgfdl-fix_openmp_affinity_issues_with_FMS2020
- Stanley et al., 2020, adds the Brankart modification to volume mean density via linear corrections involving SGS sample variances and covariances of T and S. This commit adds the new interfaces that allow a call to calculate_density to include the variances and covariance as arguments. This correction sits above the particular EOS and thus can use any EOS so long as second derivatives are available within the EOS module.
- The routines pressure_gradient_plm() and pressure_gradient_ppm() were poorly named and had comments referring to the pressure gradient calculation even though the only calculate edge values in the vertical for T/S using ALE functions. The routines are actually more general and can be used outside of the PGF. The comments have been shortened and no longer refer to the PGF.
- The integrals of density routines used (mostly) by the PGF calculation were part of MOM_EOS. Originally, when writing the analytic FV PGF paper, this was the right place to put the integrals. The additional variants using the ALE reconstruction functions mean that it is cleaner to have these routines sit in a layer above EOS and ALE.
- ppoly_E meant something to someone a while ago but we felt it would be better to clean up the ALE APIs. This is a pre-cursor to switching to a more precise description of reconstructions.
Added several documentation READMEs to using the autoconf build. Also added some changes to the Makefile template so that `make ac-clean` wiped out the autoconf output (configure, aclocal.m4, autom4te.cache).
Pointed out by @raphaeldussin
Typo fix
Autoconf-based build framework
Fix typo in README link
Markdown formatting fixes.
GM-Brankart update from NCAR
The COVERAGE variable was incorrectly quoted, and was causing incorrect quotes in the compile flag arguments. This patch removes the redundant quotes.
Testing: Remove quotes in COVERAGE
Member
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@gustavo-marques we are getting answer changes in all our tests except BMOM. |
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Thanks, @alperaltuntas. This is likely due to changes in the default parameters. I will look into it this afternoon. |
Member
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@gustavo-marques , two differences between our GMOM and BMOM are the following flags: At least one of these must be causing forced cases to have answer changes. |
This was referenced Oct 16, 2020
gustavo-marques
commented
Oct 16, 2020
| CS%use_net_FW_adjustment_sign_bug, & | ||
| "If true, use the wrong sign for the adjustment to "//& | ||
| "the net fresh-water.", default=.false.) | ||
| "the net fresh-water.", default=.true.) |
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The default for this parameter did not have to be changed. We (NCAR) had already set this to False and, unintentionally, @Hallberg-NOAA set it back to True in https://github.com/NOAA-GFDL/MOM6/pull/1127
gustavo-marques
commented
Oct 16, 2020
| CS%use_net_FW_adjustment_sign_bug, & | ||
| "If true, use the wrong sign for the adjustment to "//& | ||
| "the net fresh-water.", default=.false.) | ||
| "the net fresh-water.", default=.true.) |
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Author
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Same here. The default should be False.
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After manually setting I also noticed that changes in MOM_hor_visc.F90 introduced in #158 lead to changes in answers since we have LEITH_AH = True (@alperaltuntas mentioned that when merging #158). |
- The default for USE_NET_FW_ADJUSTMENT_SIGN_BUG had been changed to False but during the merge of main onto dev/gfdl the default was inadvertently flipped. @gustavo-marques pointed this out when reviewing NOAA-GFDL/MOM6#1211. - This affects EMC and NCAR versions of drivers and is not tested at GFDL.
Change default for USE_NET_FW_ADJUSTMENT_SIGN_BUG in drivers
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@alperaltuntas, this PR is ready to be merged. |
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Oct 23, 2020
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* Change dumbbell initialization * Change in Dumbbell Layer Mode
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Merging the main candidate from GFDL:
https://github.com/NOAA-GFDL/MOM6/pull/1211
There has been some reorganization of the source code and, therefore, changes in MOM_interface are needed to compile CESM/MOM6 from now on. In addition, the default value for many parameters has been changed. Although we foresaw these changes and already modified the default parameters used in CESM/MOM6 accordingly (ESCOMP/MOM_interface#65), care must be taken before this PR is merged to make sure answers in aux_mom are not changed.
I have confirmed that this PR does not change the answers in MOM6-examples using intel. It remains to be tested whether we get b4b for the aux_mom tests.