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Add initialization tests using CS%initialized
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Added the new optional argument OBC_N2 to calc_isoneutral_slopes that can be use to specify that only interior points are used to calculate the buoyancy frequencies at velocity points when open boundary conditions are in use. When the new OBC_N2 argument is absent or false, the solutions are identical to what they had been previously, but this gives a dependence on the arbitrary outer thicknesses when open boundary conditions are used. By default, all answers are bitwise identical, but there is a new optional argument to a publicly visible interface.
Added the new runtime option MIXING_COEFS_OBC_BUG that can be set to false to specify that only interior data should be used for thickness weighting in the lateral mixing coefficient calculations when open boundary conditions are in use, and that only interior temperatures, salinities, pressures and thicknesses should be used when calculating the buoyancy frequency at open boundary velocity faces. These changes are implemented by introducing two new 3-d arrays that set the thicknesses at velocity points and there are a few new logical tests inside of some loops, which may slow down the code slightly in routines that had never previously been notable for the amount of time spent there. They also make use of the recently added OBC_N2 argument to calc_isoneutral_slopes(). There are new ocean_OBC_type arguments to calc_resoln_function() and calc_sqg_struct() as a part of these changes. The default setting for MIXING_COEFS_OBC_BUG retains the previous (incorrect) answers, and all answers are bitwise identical in cases without open boundary conditions regardless of how it is set. There is a new entry in some MOM_parameter_doc files for some cases with active open boundary conditions and new arguments to publicly visible interfaces.
This commit revises setup_OBC_tracer_reservoirs and other OBC routines to allow some cases using open boundary conditions and tracer reservoirs to reproduce across restarts and added the new runtime parameter OBC_RESERVOIR_INIT_BUG that can be set to true to recover the previous answers in cases that are not initialized from a restart file. There is a new optional MOM_restart_CS argument to setup_OBC_tracer_reservoirs that can be used to query whether the reservoirs have been read from a restart file before resetting them to values that may have been set during initialization. If the reservoirs have not been set from a restart file, there is now a preference to set them from the tracer reservoir (tres) element in the OBC tracer registry on the segments (if it has been initialized) rather than the interior tracer values that have been recorded on the segment. Fill_temp_salt_segments and fill_obgc_segments have been modified to only set the tres segment data if it has not been initialized already, as indicated by the is_initialized field. This commit adds the new public routine set_initialized_OBC_tracer_reservoirs that can be used to record in the restart control structure that the OBC%tres_x and OBC%tres_y fields have been initialized and should not be reset to new values during initialization. The calls to setup_OBC_tracer_reservoirs and open_boundary_halo update have been moved after the call to tracer_flow_control_init so that the full arrays of tracer reservoirs do not need to be initialized in fill_obgc_segments. Fill_obgc_segments was refactored to separate out the steps that should occur there from those that should not and are wrapped in a bug flag. A debugging checksum call to chksum_OBC_segments was added to the top of radiation_open_bdry_conds to assist in any future debugging of the OBC code. Added doxygen comments describing several routines that were previously missing such a description. By default, all answers are bitwise identical, but there is a new publicly visible routine, a new optional argument to a public interface and a new runtime parameter that can be used to correct the previous behavior that broke the reproducibility across restarts of some cases using open boundary conditions with tracer reservoirs.
Copy segment tracer registry data from the input segment to the target segment in rotate_OBC_segment_data, including the tracer reservoirs on segments. With this change, configurations using tracers with open boundary conditions are now passing the rotational consistency tests. This will change answers with some rotated cases with active OBCs, but all answers in non-rotated cases or cases without tracers in OBCs are bitwise identical.
When there are specified open boundary conditions, dyed_channel_update_flow() was setting the normal transport with the wrong units of [L2 T-1 ~> m2 s-1] instead of [H L2 T-1 ~> m3 s-1 or kg s-1], effectively omitting the layer thickness in the transports. This has been corrected by adding the new runtime parameter CHANNEL_FLOW_OBC_TRANSPORT_BUG that either uses a fixed thickness if true (of 1 m or 1 kg m-2) or the actual interior thickness. In either case, the model is now passing the dimensional consistency testing. This change requires a new layer thickness argument to dyed_channel_update_flow(). In addition, code was added to dyed_channel_update_flow so that it also satisfies rotational consistency. By default, answers are bitwise identical when no dimensional rescaling or grid rotation is applied, but there is a new runtime parameter and a new argument to dyed_channel_update_flow.
Modified shelfwave_set_OBC_data to work properly with grid rotation of 90, 180 or 270 degrees. With these changes the ESMG shelfwave test case is now giving bitwise identical answers under grid rotation. This commit also corrects a recently added problem with potentially unallocated arrays being used to test whether a pointer is set to the unrotated tracer reservoirs in cases where there are no tracers. This commit does change (and fix) answers when grid rotation is used, but answers are bitwise identical when there is no grid rotation, and there are no changes to any public interfaces.
Modified tidal_bay_set_OBC_data to work properly with grid rotation of 90, 180 or 270 degrees. With these changes the ESMG Tidal_bay test case is now giving bitwise identical answers under grid rotation. This commit does change (and fix) answers when grid rotation is used, but answers are bitwise identical when there is no grid rotation, and there are no changes to any public interfaces.
* *Implement subcycing for internal tides refraction/propagation This PR allows to bring back the thermodynamics timestep higher while keeping the raytracing under CFL by doing multiple steps within the thermo step. The only variable that needs to be accumulated in the subcycling is the slope loss (residual of transmission and reflection on slopes) Since it is already accumulated within the 2 directions of propagation, it only needs to be initialized outside of the subcycling. * unindent loop for easier git diff (will indent back later) * fix bad placement of complete_group_pass and sync En * rewrite subcycle in terms of a timestep and group_pass * fix indexing bug, remove useless init/passing * fixes from review --------- Co-authored-by: Raphael Dussin <Raphael.Dussin@noaa.gov>
This commit adds the new runtime parameter ENABLE_BUGS_BY_DEFAULT and use it to set the defaults for a number of bug-fix parameters that have been added within about the past year and have not yet had their defaults set to correct the bugs. The default value (True) allows us to move the version of the code forward without changing any existing answers by default. Conversely, setting this to false means that no bugs are used unless they are actively selected, which is probably the right choice for new runs. The defaults for groups of bug-fix flags are periodically changed to correct the bug, at which point this new parameter will no longer be used to set their default. This commit also uses ENABLE_BUGS_BY_DEFAULT to set the defaults for 16 existing runtime parameters, including DETERMINE_TEMP_CONVERGENCE_BUG, RHO_PGF_REF_BUG, VISC_REM_BUG, OBC_RESERVOIR_INIT_BUG, OBC_HOR_INDEXING_BUG, EXTERIOR_OBC_BUG, VERTEX_SHEAR_VISCOSITY_BUG, VERTEX_SHEAR_OBC_BUG, EPBL_MLD_ITER_BUG, MEKE_GM_SRC_ALT_SLOPE_BUG, HOR_DIFF_LIMIT_BUG, MIXING_COEFS_OBC_BUG, FRICTWORK_BUG, LA_MISALIGNMENT_BUG, IDL_HURR_SCM_EDGE_TAPER_BUG and CHANNEL_FLOW_OBC_TRANSPORT_BUG, which are scattered across 16 modules. For 7 of these parameters, the default will be reset to false soon. By default all solutions are bitwise identical, but there is a new runtime parameter that will occur in all of the MOM_parameter_doc.all files.
Corrected the previous PE-count and layout dependency of answers for cases with open boundaries are not at the natural edges of the domain by storing the previous barotropic velocities in ubt_prev and vbt_prev over a wider range of loop indices, and by increasing the stencil size used in btstep_timeloop in such cases. Because the required loop range no longer matches the range over which the new velocities are set in bt_loop_update_u() and bt_loop_update_v(), the code setting these arrays has been moved out of these routines and into the main body of btstep_timeloop(). This commit will change answers (and make them invariant to the PE count and layout) in some cases, such as the ESMG-configs Kelvin_wave/rotate45_BT and Kelvin_wave/rotate_BT test cases, where there are southern open boundaries appearing in the northern halo regions on any PEs, for example. In all the Kelvin_wave test cases, the answers now agree with the previous single-PE answers. Most regional configurations with OBCs only apply them at the edges of the domain and hence will not be impacted, and no answers are changed in cases without open boundary conditions.
This commit adds the new runtime parameters BT_WIDE_HALO_MIN_STENCIL and DEBUG_BT_WIDE_HALOS to control the stencil width used with wide halos and to specify whether the checksums for the entire active halo of values are written when DEBUG_BT is enabled, or just the symmetric computational domain. Setting `BT_WIDE_HALO_MIN_STENCIL = 2` and `DEBUG_BT_WIDE_HALOS = False` provides for cleaner checksums in some cases because they are invariant to the use of wide halos, the width of those wide halos, or the relative positions of interior- domain OBCs relative to PE boundaries. This commit also changes a number of velocity point checksums in btstep_timeloop to do symmetric output. All model solutions are bitwise identical regardless of how these new parameters are set, but they can alter some debugging output.
Inconsistencies in jobs within a workflow were leading to differences in
compiler versions across jobs. This was breaking GitHub Actions
workflows. We want to continue using `*-latest` runners, so we have
merged the FMS stage into each of the MOM6 builds.
There are additional changes which improve the overall workflow/job
decomposition.
* FMS builds included in MOM6 stage
* Artifacts are now packed into tarballs, which preserve most of the
file state (mtime, file mode, etc).
* No longer any need to chmod the executables.
* `*.gnco` timestamp warnings are removed.
* Overall simplification of generated executable lists; we now
assume that build/* only contains executables.
* build.timing and build.unit are now correctly tagged as .NOTPARALLEL
* Macros for defining the target URL are now environment variables,
stored in the workspace `env`.
Fixed spatial indexing bugs with Kelvin_set_OBC_data when the new runtime parameter KELVIN_SET_OBC_INDEXING_BUGS is set to false. All answers are mathematically equivalent even when KELVIN_SET_OBC_INDEXING_BUGS is true, but only because in the existing cases using Kelvin_set_OBC_data use an f-plane with a uniform depth, but there are changes at roundoff with some compilers for some of the ESMG/Kelvin_wave test cases. Also added comments noting where there are missing temporal variability factors. By default, all answers are bitwise identical but there is a new runtime parameter.
Modified Kelvin_set_OBC_data to work properly with grid rotation of 90, 180 or 270 degrees. With these changes the ESMG Kelvin_wave test cases are now giving (mostly) bitwise identical answers under grid rotation. This commit does change (and fix) answers when grid rotation is used. There are no changes to any public interfaces.
update MOM6 to its main repo. 20250527 commit.
Do not set non-segment 3d OBC arrays in the unrotated OBC type when grid rotation is in use, and added a fatal error if there is an attempt to use grid rotation with tracer reservoirs when OBC_RESERVOIR_INIT_BUG is true. Also eliminated duplicative statements nullifying these pointers after they have been deallocated. Also converted the non-segment 3d OBC arrays from pointers to allocatables, as there is no longer any reason for them to be pointers. All answers are bitwise identical unless undergoing a grid rotation test, and the grid rotation tests work properly for all cases with the relevant bugs disabled.
Added the new on_face element to the OBC_segment_data_type to indicate where a field is staggered, and the used this to simplify the code and the logical tests in initialize_segment_data and update_OBC_segment_data. The new function field_is_on_face() is used to set the on_face elements. Also, duplicated code that determines whether data requirements have been satisfied has been moved into a single block of code that used regardless of whether the data is specified or provided from a file. There is also the new routine field_is_tidal that can be used to determine the appropriate vertical extent of a field within the model. With these changes, there has been a substantial consolidation of the blocks of code that allocates and initializes the various input buffers. In addition, some of the duplicated code setting the tracer reservoir values for temperatures, salinities and other "obgc" tracers has been consolidated into a single block of code. The code setting the SSH at boundaries was also consolidated rather than having duplicate blocks with and without the ramping enabled. Several redundant logical tests or unneeded arrays were also eliminated. With these changes, MOM_open_boundary.F90 is shorter by about 190 lines and should be easier to read and maintain. There are no changes to publicly visible interfaces, and all answers are bitwise identical.
Fix a bug in determining where to apply OBC-related masking when interpolating v-velocities to u-points to calculate the surface friction velocity under ice shelves. It would usually only arise at eastward OBCs under ice-shelves, but it could also occur for westward OBCs that are within a few points of the western side of the domain. This bug breaks rotational symmetry and reproducibility across processor counts and layout when there are any open boundary conditions under ice shelves. However, there are no reports of the detection of any such problems, and I am unaware of any cases using open boundary conditions under ice shelves, so it seems very likely that there are no existing MOM6 configurations that would trigger this specific bug. Given all these considerations and the resulting expectation that it is exceptionally unlikely that fixing this bug would impact any existing work, rather than introducing a bug-fix runtime parameter to retain this bug, this commit simply fixes it with the obvious single-character correction.
Set the sign of OBC%segnum_u and OBC%segnum_v to indicate the direction of open boundary currents at the u- and v- velocity faces, with positive values at logically eastern and northern boundary condition faces and negative values at western and souther boundary condition faces. This new information is used to set open boundary condition properties in 10 files, while in 5 of these files the absolute value is used to recover the previous answers. Also added the new elements u_OBCs_on_PE and v_OBCs_on_PE to the ocean_OBC_type. All answers are bitwise identical, but there are two new elements and an important change to two elements of the publicly visible transparent ocean_OBC_type.
Add 16 integer elements to the ocean_OBC_type to indicate the ranges of indices over which various directions of open boundary conditions are found in the data and computational domain of the local PE. Also added 4 logical elements that indicate whether each of the 4 orientations of OBCs are fond on the local PE.All answers are bitwise identical, but there are 16 new integer elements and 4 new logical elements in a transparent public type.
Refactored the OBC-related code in 5 routines (set_viscous_BBL(), vertvisc_coef(), find_coupling_coef(), calc_isoneutral_slopes() and ALE_remap_set_h_vel_OBC()) in 4 modules to use the restricted OBC loop ranges for the various orientations of OBCs for greater efficiency, and in some cases to avoid the use of multiple levels of nested types and looping over segments that seem to be causing problems with our efforts to port MOM6 to GPUs. The cases where the loop over the OBC segments continue to be used are those where the details of the segments matter (and not just their orientation) or where they are being applied in ways where the order of the segments might matter. All answers are bitwise identical, and there are no changes to any publicly visible interfaces.
Added the new parameter INTERPOLATED_SQG_STRUCTURE that can be set to false to avoid interpolating properties to velocity points and then interpolating the buoyancy frequencies and layer thicknesses back to tracer points when calculating the SQG vertical structure. This involves extensive additions to calc_sqg_struct() to calculate the SQG vertical structure on an individual column without interpolation. The new code also cancels out common thicknesses in the numerator and denominator and uses thickness_to_dz() to find the vertical extents of the layers rather than using find_eta() and taking a difference between the heights of pairs of interfaces, making it far less susceptible to roundoff errors and able to work properly with vanishing layers. The one change when this new option is not set to false is that the diagnostics of N2_u and N2_v are no longer posted when SQG_EXPO is not positive, although it is not clear to me that these diagnostics should ever be posted from this routine. The default for INTERPOLATED_SQG_STRUCTURE is true, but I suspect that all of this interpolation of N2 may be undesirable, especially as it might lead to problematic behavior near coastlines or seamounts, and I will recommend that the default be changed to false once this can be done gracefully without disrupting any applications that are already using calc_sqg_struct(). As a part of these changes, SQG_EXPO will only be logged when it would actually be used, and the logic governing a number of deallocate calls in VarMix_end() was simplified. The Laplac3_const_u, Laplac3_const_v, KH_u_QG and KH_v_QG elements of the VarMix_CS were converted from potentially static arrays to allocatable arrays to reduce the MOM6 memory footprint when they are not in use. These should always have been allocatable, and there is no change when MOM6 is not in static memory mode. By default all solutions are bitwise identical, but there is a new runtime parameter that will appear in some MOM_parameter_doc files, while another unused runtime parameter will disappear from others.
Converted 28 arrays from potentially static using the ALLOCABLE_ and ALLOC_ macros into dynamic arrays in three modules. This change reduces the static memory footprint of MOM6. These arrays are only ever used conditionally based on parameter settings, so they should never have been declared using these static memory macros. All answers are bitwise identical and there are no changes to any public interfaces.
* Add conditional halo pass for frazil inside make_frazil Frazil may need an extra halo pass, but only when all of the following are true: (1) frazil is calculated and applied in the halo (e.g., vertex_shear is true) (2) the thermodynamic loop is called more than once before passing frazil to the sea-ice (dt_therm<dt_cpld) (3) reclaim_frazil is true (4) a previous make_frazil was called after the diabatic loop and before T&S were updated in halos. This commit adds the halo pass inside make_frazil since it is where we can know all of these conditions at once. We needed to add a flag to know if frazil was reset (which happens if dt_therm>=dt_cpld), in which case the halo pass would be unnecessary. We needed an optional argument for make_frazil so we could flag to only do this update on the first call to make_frazil (which is needed because the previous call to make_frazil was after the diabatic loop, condition 4) * Shorten line in MOM_diabatic_driver * Move halo update on frazil out of make_frazil and into post_diabatic_halo_updates --------- Co-authored-by: brandon.reichl <brandon.reichl@noaa.gov>
Refactored 34 calls to real_to_time() to use the new unscale argument and replaced 16 calls to time_type_to_real() with calls to the new routine time_to_real(), of which 15 use a scale argument. Also use the new scale argument in 5 calls to time_minus_signed(). In four instances, extensive expressions for the end of a diagnostic interval are being stored in new temporary time-type variables. Although these changes lead to some lines that are longer than before, the use of the scale and unscale arguments makes it much easier to detect incorrect rescaling factors. All answers are bitwise identical.
This commit reworks segment%field array. Previously, the array is dynamically decided by available input fields, i.e. segment%num_fields = number of input fields + number of BGC tracers. Problems: 1) indexing of the field is not fixed. 2) There is no direct one-on-one mapping between field array and a dozen of xxx_needed flags in segment. The new approach always creates a field array with its first 13 members being the 13 physical fields, which predetermines the indexing. It also merges the xxx_needed flags to their corresponding fields. Note that only used/available fields have their buffer_src and buffer_dst arrays allocated, so there is no additional memory cost. With the new structure, initialize_segment_data is refactored to have four steps, 1) Initialize 13 physical fields, including toggling required fields using subroutine segment_determine_required_fields. 2) Create a list of available inputs from parameter file and map their indices with the 13 physical fields. 3) Allocate available physical fields. (allocated() = is_available) 4) Determine and allocate BGC fields. Misc * Two new subroutine/function * subroutine segment_determine_required_fields * function find_phys_field_index * The model stops if a variable not in the 13 physical field is given. * The model stops if there is a required input missing and informs which segment and field. * A warning is now issued if a field is provided but not needed. * MAX_OBC_FIELDS (=100) is replaced by NUM_PHYS_FIELDS (=13)
* Remove all x_values_needed flag and 6 indices to locate tidal fields * Remove subroutine rotate_OBC_segment_values_needed * Apply fixed indices to tidal fields in update_OBC_segment_data
- MOM_ice_shelf_dynamics.F90: split loop_bounds_type members (ish, ieh, - MOM_ice_shelf.F90: add missing = -1 initializer to id_dhdt_shelf A disclosure: Copilot has been used to make these changes.
t17d and t20d are the depth of the 17 and 20 degC isotherms respectively, measured from the surface. Interpolation is done via Recon1d reconstruction and then a new function in the class that solves that inverts the reconstruction. This solver was not in the original class because I had originally only thought it would be used in the new grid generator which interpolates density and not for the reconstructed field. Since some other diagnostics for CMIP will make use of remapping or T, I figured we might as well use the reconstructions to do the interpolation. - adds to new registrations and posts in MOM_diagnostics - adds function `%x(self, k, val)` to the Recon1d class.
Revised the MOM_ice_shelf_diag_mediator code that creates the MOM_IceShelf.available_diags file to follow the same pattern of logging as the rest of MOM6. The specific changes include moving the module name(s) to their own line, adding static diagnostics to the variables that are logged in the available_diags file (however, the ice shelf code does not have any static diagnostics yet), logging the axes of the diagnostic, and adding cell metrics to describe how a diagnostic might be reduced and logging these as well. All solutions are bitwise identical, but there are new entries and added information in the MOM_IceShelf.available_diags files.
Modified set_IS_axes_info() to follow the pattern from the rest of MOM6 and take the units for the horizontal axes from the grid type. In most cases, this has the effect of changing the units from "degrees_E" and "degrees_N" to "degrees_east" and "degrees_north" to follow CMIP protocols, and to mirror changes that were made to the standard MOM6 framework code in 2017. The names of the gridspace axes were changed from `xB`, `yB`, `xT` and `yT` to `Iq`, `Jq`, `ih` and `jh` to mirror the names in MOM6. The long descriptions of these array axis variables were also updated for clarity when `USE_INDEX_DIAGNOSTIC_AXES` is true. All solutions are bitwise identical, but there are changes to the metadata and axis variable names in some output files, and some runtime parameters that had been read from both `set_IS_axes_info()` and `set_grid_metrics()` in MOM_grid_initialize.F90 are now only read in the latter routine. As a result of these changes, `set_IS_axes_info()` no longer takes a `param_file_type` argument and the grid argument is now `intent(in)`.
Added a missing dimensional scaling argument in the test for when to write harmonic analysis diagnostics in HA_accum. Also used the new unscale argument in 2 calls to real_to_time in HA_init and used the new scale argument in one call to time_to_real in HA_accum. Answers and diagnostics are bitwise identical when scaling is not applied, but this does correct a problem where some diagnostics may have been written at the wrong time previously when dimensional rescaling of time is being used.
Edited the conversion factors for the 'ale_u2' and 'ale_v2' diagnostics to use an equivalent form that makes it a little more obvious that the conversion factors correspond to the declared units. All answers are bitwise identical.
This commit clarifies a number of comments in the MOM_diag_mediator. It also corrects multiple instances of spelling errors or non-standard use of white space in comments. There was also some rearrangement of module use statements and the elimination of other unneeded module use calls. Only comments or spacing are changed, and all answers are bitwise identical.
A locally allocated array was uninitialized which is harmless for most configurations that use time-filtering in the vertical grid generation. The time-filter uses land masks and sets things to zero on land. Without the time-filter, we encountered non- reproducible behavior on the root PE. I also de-allocated a local variable (Rb) used on another if-branch in the same routine.
This commit refactors update_OBC_segment_data using the previously
introduced new structure segment%field component. Specifically, the code
that calculates normal_vel, normal_trans, normal_trans_bt,
tangential_vel gradient and external values of tracer / thickness
reservoir, is updated. The changes include,
* The previous loop + if structure is replaced by direct indexing of the
physical fields.
* Tidal velocity and SSH code is refactored to cji structure (c for
constituent), rather than an embedded if-branch within [ji] loop of a
[ij]c structure.
* As a result, segment has three new 2D arrays, tidal_v[nt] and
tidal_elev.
* Introduce orientation-agnostic looping indices [ij][se]_seg, currently
only used for tracer cell fields.
* Add tr_index in OBC_segment_data_type (segment%field) to facilitate
reservoir update.
* Add Newton iterations for the ice-shelf velocity solution The previous Shallow Shelf Approximation solution used an iteration-on-viscosity scheme with Picard iterations only. This commit adds the capability to change to Newton iterations once a certain tolerance is met, which should reduce the number of iterations needed to reach convergence. This tolerance to change to Newton is set by the new parameter NEWTON_AFTER_TOLERANCE. This parameter defaults to the same value of ICE_NONLINEAR_TOLERANCE so that Newton is not called by default. The Newton scheme is paired with the Eisenstat & Walker 1994 approach for adapting the CG tolerance to help the Newton scheme achieve quadratic convergence without over-tightening at later Newton steps. To use the adaptive CG tolerance, set NEWTON_ADAPT_CG_TOLERANCE=True (default is True). * Newton iteration PR fix Style changes, parentheses, removed string comparison from loops * Pass_var optimization and FMAs Made some changes to pass_var 'complete' arguments for Newton-related variables. Also removed some Newton-related pass_vars and a CS%doing_newton=.false. that were made before entering the the SSA solution loop (at this point, Newton is already false, and there is no need to update Newton-related halos yet). Added parentheses for rotational symmetry with FMAs.
Replaced "end if" with "endif" in 35 places in 10 files and "end do" with "enddo" in 12 places in 4 files to comply with the MOM6 style guide. In addition, in 23 places in 7 files, code like `if(test)` were replaced with `if (test)`, also to align with the MOM6 style guide. All answers are bitwise identical.
Removed 41 trailing semicolons (MOM6 is in Fortran, not C). In 406 other lines of code the white space around semicolons was standardized to ' ; ' to match the other ~14000 lines of code with semicolons joining Fortran statements on the same line. In a few cases there were also some improvements to indents related to these changes. With these changes, all semicolons that could be replaced with a newline and still have correct Fortran follow the ' ; ' pattern. These changes are scattered across 86 files. Most of these changes involve only white space, and all answers are bitwise identical.
Create a new subroutine read_OBC_segment_data out of a very chunky update_OBC_segment_data. The new subroutine enables better control on whether the update is associated with new external data through IO or just recalculation (with evolved model internal state, i.e thickness, tides). Misc * Use orientation-agnostic loop indices for segment%h and segment%htot * Add [ij]_offset_in to loop over interior cells * Field segment%Cg, which is never used, is now removed.
Create a new subroutine initialize_OBC_segment_reservoirs to initialize thickness and tracer reservoir of OBC segments. This part of code was original part of update_OBC_segment_data, but it is only called during initialization.
This commit fixes a bug in particle advection of particles that are advected by uh and vh. When the tracer timestep doesn't match the dynamics timestep, these particles need to be advected using the tracer timestep. The previous version of the code sometimes leads to unphysical particle movement, and this commit fixes the issue.
Added the new interfaces `symmetric_sum()` and `symmetric_sum_unit_tests()` to the MOM_array_transform module, and added a call to `symmetric_sum_unit_tests()` to `unit_tests()`. The two functions wrapped by the `symmetric_sum()` interface are intended to be a general template for rotationally symmetric sums, but they demonstrably work as intended (as demonstrated by the passing unit tests) for any rectangular arrays. The new driver in test_MOM_array_transform.F90 tests these new arrays. Although `symmetric_sum()` is not used yet in the MOM6 code apart from the tests, it was developed to address problems with failures of rotational symmetry in the diagnostic downscaling routines, and will be used there soon. All answers are bitwise identical, but there are two new publicly visible interfaces.
Resolves merge conflict due to new PLM_WLS test.
This commit refactors normal velocity/transport calculation in update_OBC_segment_data, using the orientation-agnostic loop ranges. Note that there is still an orientation-branch because the grid spacing G%dyCu and G%dxCv are different. * The field segment%h is removed, as we can just use h directly. * Comments are added to better illustrate the subroutine structure
Remove inaccurate warning message in logs when OBC_TEMP_SALT_NEEDED_BUG is false but temperature and salinity are needed and provided.
This commit fixes the bug that OBC segment data does not update if only value mode is used for all segments. Previously, there were two issues, 1. Subroutine update_OBC_data, which is a wrapper over subroutine update_OBC_segment_data is only called if global flag OBC%update_OBC is True. This flag, however, is only turned on if there OBC is specified by files. 2. Inside of update_OBC_data, subroutine update_OBC_segment_data is only called if global flags OBC%any_needs_IO_for_data or OBC%add_tide_constituents is True, which again prohibits OBC update with "value". Example: if normal velocity is specified by value, the transport is calculate once during initialization using initial thickness. And the transport is never updated through the run. And the model will restart with a different transport. A new runtime parameter OBC_VALUE_UPDATE_BUG is added to fix/recover this bug. In addition, OBC%update_OBC is set to True if initialize_segment_data is called. a separate procedure is added to set any_needs_IO_for_data, for clarity.
Added diag_mediator capabilities that had been developed and used in the SIS2 and MOM_ice_shelf versions of the diag mediator, in preparation for some of these separate versions to be combined into a single version. This includes adding an overload to the register_scalar_field() interface so that scalars can be registered with or without providing a null axis, retaining the existing interface while adding the one that is widely used with the ice shelf code. The previous routine register_scalar_field() is now register_scalar_field_CS(), but it has the same public interface. This commit also adds the new public interface MOM_diag_send_complete() that calls the FMS routine that flushes the IO buffers. Although this call can be too expensive for production runs, it can be very useful for debugging. Internally, register_diag_field() now checks for standard axes for 2-d fields, analogously to what was previously done for 3-d fields, thereby avoiding the allocation of a separate axis group for each 2-d diagnostic. This has been the case for ice-shelf code for some time, and it will save memory will giving identical results. The testing for incompatible mask and array sizes was consolidated into a single call each in post_data_2d_low() and post_data_3d_low(), paving the way for adding the option of masking static fields. All solutions are bitwise identical and diagnostic output (including metadata) is identical to what was previously output, but there are two new public interfaces.
Renamed the q-point index space axis names to be uniformly Iq and Jq, rather than having names that change depending on whether or not symmetric memory is being used. This commit also changes the long names of the grid space axes to be consistent between the x and y axes and to mirror those that have been adopted in the ice shelf code. The order of the logical tests for index space axes and symmetric memory around the calls to diag_axis_init were swapped to that corresponding cases are next to each other, perhaps making any inconsistencies more obvious. There were also minor changes to the code setting the axis label variables to follow the MOM6 case convention for indices and the spacing conventions for assignments, as described in the MOM6 style guide. All solutions are bitwise identical, but there are changes to the names of the axis label variables and their long descriptions when USE_INDEX_DIAGNOSTIC_AXES is true.
Corrected the cell_methods for 8 families of tracer content tendency diagnostics. Without this change, the 2-fold downscaled tendencies are 4 times too large, and the 3-fold downscaled tendencies 9 times too large. The misleading comment describing the local `conv_units` string variable in register_tracer_diagnostics() was also fixed. All solutions and standard diagnostics are bitwise identical, but there are changes in the values of downscaled diagnostics and changes in metadata.
Makedep preprocessor parsing assumed define macros of the form `#define macro(X) some-macro` but did not support empty macros of the form `#define macro(X)`. Preprocessor flag macros were assumed to be of the form `-DMACRO=VALUE`, and did not support empty macros `-DMACRO`. This patch addresses both issues.
…_vars - To reproduce across restart files requires an additional halo update on diffu and diffv in MOM_dynamics_split_RK2.F90 - To reproduce across layouts with vertex shear option requires a halo update on thickness before remapping the viscosities on the vertex points.
- Setting BBL_USE_TIDAL_BG = True causes the model to fail dimensional consistency test. If you set the spatial scale as m_to_L instead of m_to_Z in MOM_set_viscosity it fixes the issue. - Fixing documentation fo L/T scaling of tideamp - Change suggested Hallberg
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