new loss term for internal waves: scattering to higher modes #33
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This patch fixes an error in the `sync` flag of the cpu clocks. Previously, we would set the sync bit of a flag based on the presence of sync, rather than testing if the value was true. This would cause potential hangs in any clock that set `sync`, including `.false.`. This patch correctly replaces the single `ibset` call with an if-block to either `ibset` or `ibclr`.
Added the public interface unit_no_scaling_init() to the MOM_unit_scaling module to initialize a non-scaling unit_scale_type without requiring a param_file_type argument. This should be useful for certain trivial unit tests, and it makes it more plausible to make the unit_scale_type arguments mandatory. As a part of this change, the new internal subroutine set_unit_scaling_combos() was carved out of unit_scaling_init to avoid code duplication. Also added comments describing the effective units of the various scaling factors with the standard MOM6 notation. All answers and output are bitwise identical.
Provide optional US arguments to 4 existing calls to set_grid_metrics() and MOM_initialize_topography(), enabling these arguments to become mandatory in the next commit. In some cases this requires a call to unit_no_scaling_init() or the removal of a call to rescale_dyn_horgrid_bathymetry(). In addition, a mis-scaled value was corrected in the initialization of the ODA control structures private thickness array; this latter issue is not a problem for Boussinesq models without dimensional rescaling (i.e. the tested cases), but could change answers in other cases with data assimilation. All answers in the MOM6-examples or TC test cases are bitwise identical.
Made the unit_scale_type arguments non-optional for 28 routines. These arguments had been optional in the first place to manage the coordination between the MOM6 and SIS2 repositories, but SIS2 has been using these optional arguments for several years now, and they can be made mandatory without imposing any disruptions. This change simplifies and clarifies the code. All answers and output are bitwise identical.
This patch updates the PNG file of the consortiums in the docs to include the NASA-GMAO group.
Codecov Report
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## dev/gfdl #33 +/- ##
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- Coverage 29.06% 29.03% -0.04%
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Files 240 244 +4
Lines 71319 71949 +630
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+ Hits 20731 20892 +161
- Misses 50588 51057 +469
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Removed clocks that were being called from inside of j-loops in two modules. These are inefficient and can cause the model to hang in some cases if used, and there are better ways to get timing information at this level. If there is interest in the timing breakdown at this level, the code should be restructured to move the key blocks outside of the j-loops. The run-time parameter ALLOW_CLOCKS_IN_OMP_LOOPS is no longer being used so it is now obsoleted. All answers are bitwise identical, but there are changes to some MOM_parameter_doc files.
Added a deallocate call for eta_PF_start in step_MOM_dyn_split_RK2() to avoid a possible memory leak. All answers are bitwise identical.
Set find_salt_root even if SHELF_THREE_EQN = .False. to avoid using an uninitialized logical to determine which parameters are logged. Without this the contents of some MOM_parameter_doc.all files could depend on the state of uninitialized memory and was compiler dependent in some cases. All answers are bitwise identical, but in some cases the contents of MOM_parameter_doc files could be corrected.
The runtime parameter ETA_TOLERANCE_AUX was being read but was never used, so it is being obsoleted. However, because some experiments were using this and there are effectively no changes in behavior, a warning will be issued instead of a fatal error if this parameter is set. All answers are bitwise identical, but there are changes to some MOM_parameter_doc files.
Return the diabatic_aux_CSp from extract_diabatic_member it is present as an optional argument. Somehow this was omitted when this routine was created, but without this correction the offline tracer mode returns a segmentation fault. Also, added the proper conversion factor in the register_diag_field call for e_predia, and internally calculate the interface heights in units of [Z ~> m] for dimensional consistency testing. All answers are bitwise identical in cases that ran before.
Issue a warning with a helpful message if opacity_from_chl is called with no shortwave fluxes, and added logical tests to avoid a segmentation fault later in this routine. This should not happen, as it makes no sense, but it was occurring with the offline tracer code, and can be avoided by setting PEN_SW_NBANDS=0 if there are no shortwave fluxes to penetrate. Also turned the real dimensional parameter op_diag_len into a variable and set it immediately before where it is used. Many spelling errors were also corrected in MOM_opacity.F90. All answers are identical in cases that ran before.
Corrected the comments describing the optional arguments to advect_tracer and fixed a few spelling errors in comments. All answers are bitwise identical.
The arrays passed to data_overrride need to be sized as the compute domain. Added indices to pass to data_override.
Corrected the expressionfs for the por_face_areaU arguments being passed to zonal_face_thickness to avoid the array out-of-bounds index errors highlighted in MOM6 issue mom-ocean#24. Also added comments noting where the por_face_area arrays should probably be included in the effective (relative) face thickness calculations that are later used for finding the vertically averaged accelerations by the barotropic solver. All answers and output are bitwise identical in cases that work, but this should avoid some run-time or compile-time errors with some compiler settings.
Corrected bugs in the offline tracer code that were preventing it from reproducing across processor counts (and perhaps working sensibly at all). All answers and output in the MOM6-examples regression suite are bitwise identical. Although answers with the offline tracer code will change because of the bug fix, because of some bugs that were fixed in another recent commit, it was previously impossible to have run the offline tracer cases at all.
Substantially refactored the offline tracer code. This refactoring includes adding grid and unit_scale_type arguments to several routines related to the offline tracer code. An offline tracer advection test case is now consistent across processor layouts and pass the dimensional rescaling tests (including the chksums in debug mode), and there are comments describing all the real variables and their dimensions in the offline tracer routines. All answers and output are bitwise identical.
Minorly revised the algorithms used for offline tracer advection for rotational consistency, and for exact reproducibility across PE layouts by using reproducing sums to detect convergence. This also includes some changes to use roundoff to detect convergence instead of fixed values. Also replaced some divisions with multiplication by a reciprocal. In addition, some of the optional arguments to advect_tracer that are only used for offline tracer advection were renamed or revised for clarity and reordered for the convenience of the non-offline-tracer code. Although answers with the offline tracer code will change slightly because of this refactoring, because of some bugs that were fixed in another recent commit, it was previously impossible to have run the offline tracer cases at all. All answers and output in the MOM6-examples regression suite are bitwise identical.
+(*)Make unit_scale_type arguments non-optional
Bugfix: cpu clock sync error
Docs: Add NASA-GMAO to consortium figure
Added two new modules, the MOM6-specific MOM_check_scaling.F90 and the generic framework module MOM_scaling_check.F90, to assess the uniqueness of the unit scaling factors for all of the variables used by MOM6. If there are overlaps in scaling factors for different units, this also identifies and suggests alternate scaling factors with less overlaps. This commit includes the introduction of the new publicly visible routines check_scaling_factors(), scales_to_powers() and check_MOM6_scaling_factors. This new capability does not do anything for sufficiently low levels of model verbosity, and it is silent if the scaling factors are unique, or if less than 2 dimensions are being rescaled. All answers and output files are bitwise identical, but there can be additional messages to stdout.
Renamed the framework module MOM_scaling_check.F90 to MOM_unique_scales.F90 to help differentiate it from MOM_check_scaling.F90, and renamed the subroutine check_scaling_factors() as check_scaling_uniqueness(). Also added _Dimensional_consistency.dox to describe the dimensional consistency testing. This commit should address the issues raised in the review of MOM6 PR mom-ocean#49. All answers and output are bitwise identical.
Pointers to the diabatic driver's energetic PBL field are now only associated when `use_energetic_PBL` is true. The `energetic_PBL` field was also renamed to `ePBL` to avoid potential conflict with the `energetic_PBL` subroutine. Thanks to Alper Altuntas for detecting this issue and the proposed fix. Co-Authored-By: Alper Altuntas <alperaltuntas@gmail.com>
Corrected memory declarations in MOM_regridding.F90 in cases where the vertical size of the input and output grids are not the same. Although this is not know to have caused any particular problems, these inconsistencies could lead to segmentation faults in cases where the target grid (e.g., diagnostic output) is larger than the input grid (e.g., the model's native grid). In some cases, certain grid generation options were only written to work with the same size of input and output grids, and error handling has been added to these cases to gracefully bring down the model if they are used with different grid sizes. All answers are bitwise identical in the MOM6-examples test suite, but it is conceivable that this could correct subtle (memory-related) issues in some configurations.
- default behavior returns field size using fms1 format.
…ate-2022-01-29 GFDL to main (Jan 2022)
…om-ocean#65) * Eliminate GET_ALL_PARAMS in hor_visc_init Added do_not_log arguments to get_param calls in MOM_hor_visc.F90 that are only used conditionally, and eliminated the unlogged GET_ALL_PARAMS runtime parameter and get_all variable in hor_visc_init(). By design, all logging of parameters after this commit is identical to before, even for variables that are inactive and therefore should not be logged. In several places, there were some problems, mostly with the GME code, that have been noted in comments marked with '###'. Also cleaned up the code alignment and eliminated unneeded temporary variables in a few places in hor_visc(). All solutions are bitwise identical, and no output is changed. * Move call to get get_KH outside k-loop The call to get the 3-d GME diffusivity arrays and the subsequent blocking halo update was moved outside of the k-loop. * Increase loop range for calculation of GME fluxes * Makes GME filter rotationally invariant * Makes the GME filter rotationally invariant * Adds a runtime param to allow the user to control how many smoothing passes should be done. * Rearranges the get_param calls related to Leith The get_param calls for Leith were not in the correct location. This commit fixes that. * Adding halo updates * Fixes do loops indices and adds diagnostics * Adds option to save barotropic tension and strain; * Fixes many i and j loops indices associated with GME to avoid halo problems and unnecessary halo updates. With these changes, the model is now conserving mass and tracers when USE_GME = True. * Fixes issues related to the merging with dev/gfdl * Fixes calculation of FrictWork_GME The calculation now mimics the calculation of FrictWork and it includes the energy diffusion term. * Removes dependency of FrictWork_GME calculation on MEKE * Adding sh_xy_sq and sh_xx_sq in the OMP directives Co-authored-by: Robert Hallberg <Robert.Hallberg@noaa.gov>
Subroutine adjustEtaToFitBathymetry had a hard-wired parameter (hTolerance = 0.1) controlling the tolerance when adjusting the thickness to fit the bathymetry. This patch adds an user-controlled parameter (THICKNESS_TOLERANCE), which replaces hTolerance. THICKNESS_TOLERANCE is only activated when ADJUST_THICKNESS=True.
Actually calculate the mean temperature and salinity reported by MOM_state_stats(). Due to an oversight, these means were always being reported as 0. This changes the output when the debugging flag DEBUG_CONSERVATION=True. All answers are bitwise identical.
Added the new function global_mass_int_EFP(), which is analogous to global_mass_integral but returns its result in extended fixed point (EFP_type) format and always uses reproducing sums, to facilitate layout-invariant global integrals but with the potential for deferred global reductions so that this last step can be combined for various global reductions for efficiency. All answers are bitwise identical, but there is a new public interface.
Use global_mass_integral for the debugging diagnostics of the tracer amounts before and after diffusion in lateral_boundary_diffusion, and replaced a call to write(*,*) with a call to MOM_mesg to actually write the message. The global_mass_integral uses reproducing sums, and is invariant to layout, while MOM_mesg is preferable for output because it will allow us to more cleanly control how output is handled and which processors do the writing. All solutions are bitwise identical, although some debugging output will change.
Use reproducing sums for tabulating tracer stocks, and move the global sum for the tracer stocks form write_energy into call_tracer_stocks. This involves changes to the type of an argument (from real to EFP_type) for two arguments to the internal routine store_stocks. Existing tracer stock packages will still work, but to benefit from the reproducing sums, they will also have to change their reported values from real to EFP_type. This is demonstrated for two packages (advection_test_tracer and ideal_age_example), where the stocks are now found with calls to global_mass_int_EFP(), replacing the previous explicit sums. With this change, the reported stock values from these packages are identical for different PE layouts and can be much more accurate than before, but they are different from the previously reported values at roundoff (for positive-definite tracers), but it could be larger for tracers with a near-zero mean value. All solutions are bitwise identical, but output changes.
Modified the remaining tracer packages to use the reproducing stocks. The reported stock values from these packages will have changed slightly, but they now reproduce across PE layouts. All solutions are bitwise identical, but output changes.
Removed trailing white space on two lines. All answers are bitwise identical.
This patch includes several minor changes to the MOM_file_parser and supporting modules in order to accommodate stronger unit testing. It includes the following API changes: - Removal of `static_value` from `get_param` - Redefined `link_parameter` and `parameter_block` as private - New functions: `all_across_PEs()`, `any_across_PEs()` `static_value` was not used in any known experiments (outside of internal GFDL testing), and the two derived types describe internal operations within `MOM_file_parser`, so we do not expect any disruptions from these changes. A detailed summary of the changes are listed below. - `assert()` is now used to detect same files with different IO units. Detection of reopenend files of the same name but different IO unit has been changed from `MOM_error(FATAL, ...)` to `assert()`, to reflect that this should be a logically impossible result. - Bugfix: Reopened files are now reported to all PEs. If an open file is re-opened, then only the root PE will detect this and will `return` immediately. However, the others will proceed into `populate_param_data` and will get stuck in a broadcast waiting for root. We fix this by communicating the reopened state to all PEs and allow all ranks to return before re-processing the data. Note that this could also be resolved by allowing all ranks to track IO unit numbers, but for now we do not attempt to change this behavior. - `newunit=` used to generate parameter file IO unit The parameter IO unit is now generated by `newunit=` rather than an explicit search for an unused IO unit. Note that this is a Fortran 2008 feature. Testing around available IO units has also been removed. - Removal of generic IO error handling Generic "IO error" tests, and corresponding `err=` arguments, have been removed in most cases. We now rely on the Fortran runtime to provide diagnostics on these errors, which should typically exceed any information that MOM6 could provide. - Removal of purported `namelist` support There were several blocks of code provided to support namelist syntax, but did not appear to be working, nor was there any known instance of it being used by anyone, so it has been removed. - `#define/undef/=` syntax testing across ranks Previously, only the root PE would test for consistency of the #define-like syntax, even though all ranks have this information. This required a second, awkwardly placed syntax test later in the subroutine. This test is redefined to run over all ranks, and the subsequent test has been removed. - `define/override` test reordering The `found_override` test when coupled to a `#define`-like declaration was unreachable due to the presence of an even stronger test related to valid syntax. This test has been moved to provide more detailed information about the nature of the error. - `link_parameter`, `parameter_block` defined as private Internal derived types of `MOM_file_parser` are redefined as private. This preserves the integrity of instances of these types, and also prevents creation of implicit object code required to access them externally. - Removal of `static_value` from `get_param` interface The `static_value` argument of `get_param` has been removed, since it is functionally equivalent to `default`. While this is an API change, there is no known case of anyone using this argument. - The `param_type%doc` fields are now properly deallocated after closed. - Quotes have been added around some filename error warnings, to help detect issues related to whitespace. - `any_across_PEs` and `all_across_PEs` New functions for calling `any()` and `all()` across PE ranks have been added. Behavior is in line with other functions, such as `min_across_PEs`.
(+) Refactor of MOM_file_parser
Added a number of options to MOM_ALE to mimic options that are found in Hycom. By default, all answers are bitwise identical, but there are several new runtime parameters. The code changes include: . Added the ability to use a different remapping scheme for velocities than for tracers, using the new runtime parameter VELOCITY_REMAPPING_SCHEME . Added the new runtime option PARTIAL_CELL_VELOCITY_REMAP to use partial cell thicknesses for remapping at velocity points, which triggers a call to the new internal routine apply_partial_cell_mask. . Added the new internal routine mask_near_bottom_vel to allow MOM6 to mimic Hycom in zeroing out the velocities in thin layers in a bottom boundary layer with a thickness given by the new runtime parameter REMAP_VEL_MASK_BBL_THICK, while the definition of thin is specified by REMAP_VEL_MASK_H_THIN. Setting these to be negative (as is the default) avoids this. . Modified the interface to remap_all_state_vars to take just the ALE_CS, which then provides the remapping control structure that is appropriate for the tracers or velocities, rather than also passing this in as an argument. . Eliminated some unnecessary internal variables, and added others to be more explicit avoid array syntax copies in arguments.
Enforce a minimum thickness of 0.5*Angstrom in the mixed_layer_restrat routines. The streamfunctions in these routines attempt to limit the thicknesses to exceed Angstrom, but they can be less than this due to roundoff. The new limit prevents thicknesses from becoming negative when Angstrom is set to 0, but should not change any answers for test cases with positive values of Angstrom. Also added some comments describing variables and their units and simplified the OMP directives. Also corrected error messages in MOM_diabatic_aux.F90 to identify the file or module where these messages come from, and modified an error message in applyTracerBoundaryFluxesInOut so that it is written if the localized fault does not happen to occur on the root PE. All answers in the existing MOM6-examples regression suite are bitwise identical.
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this term uses the residual from the reflection/transmission coefficients to compute the energy loss due to scattering to higher modes on the slopes.