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Added an optional reference density argument to subtract from the densities returned by the various calculate density routines. Also eliminated the unused routine int_density_dz_generic_cell. This new capability has been tested, but it is not yet being used in the pressure gradient calculations to avoid changing answers in any test cases.
Reformulated Wright-EOS expression for rho with rho_ref. All answers are bitwise identical.
Use the new rho_ref argument in all of the calls to density in the finite volume pressure gradient integrals. This makes the solutions more accurate, but it does change the solutions in numerous test cases. New reference solutions have been checked in for the MOM6_examples test cases at GFDL.
Fix conflicts due to restructuring of coupler types.
… into breichl/user/bgr/waves_update
There's never a modification of the grid structure parameter G, and having it as intent(inout) can prevent compilation, depending on whether G can be modified at the call site. This shouldn't affect the compilation or answers of any existing configurations.
…o ashao-post_diag_chksums
- normal_trans needs to include appropriate dx or dy. - Remove the masking on specified OBC segments (required when reading in array values from files). - Remove unused dx_Cv_obc and dy_CU_obc variables. - Clean up continuity for cases with more than one kind of OBC. - Changes answers on "simple" OBC cases.
- still looks like crap
Lower-level code provides interfaces alone. Used for implementing
interfaces for ensemble aggregation and for offline MOM6 ensemble driver.
Added dOxyGen comments for many arguments in the tracer utility codes, including MOM_neutral_diffusion.F90, MOM_neutral_diffusion_aux.F90, MOM_tracer_advect.F90, MOM_tracer_hor_diff.F90, and MOM_tracer_diabatic.F90. All answers are bitwise identical.
Added dOxyGen comments for many arguments in the tracer packages in src/tracer. All answers are bitwise identical.
- A test for division by zero is made but the parameters being tested are uninitialized. - I moved the loop to within the overall `if (OBC%number_of_segments > 0)` so that I could rely on the setting of the parameters to zero. - However, this problem occurred because the parameters are only read if Flather BCs are being used. If they are not it seems the tracer reservoir parameters are not read - it might work by chance but this does requirement for Flather does not seem correct to me. @khedstrom ? - Detected by NCI tests, thanks @nicjhan: https://accessdev.nci.org.au/jenkins/job/mom-ocean.org/job/MOM6_run/build=DEBUG,compiler=intel,experiment=ocean_only-DOME,label=nah599,memory_type=dynamic/139/console
Code standardization and dOxyGenization of framework code
- A test for division by zero is made but the parameters being tested are uninitialized. - I moved the loop to within the overall `if (OBC%number_of_segments > 0)` so that I could rely on the setting of the parameters to zero. - However, this problem occurred because the parameters are only read if Flather BCs are being used. If they are not it seems the tracer reservoir parameters are not read - it might work by chance but this does requirement for Flather does not seem correct to me. @khedstrom ? - Detected by NCI tests, thanks @nicjhan: https://accessdev.nci.org.au/jenkins/job/mom-ocean.org/job/MOM6_run/build=DEBUG,compiler=intel,experiment=ocean_only-DOME,label=nah599,memory_type=dynamic/139/console
Also try to fix the hanging while killing the job from mask_outside_OBCs if the OBC segments are inconsistent.
- that dying test in MOM_open_boundary hung again...
Fix to rad-nud OBC on normal velocities
- Also adding more possible OBC type strings (FLATHER, etc), upping from 5 to 8. - Other random small stuff.
Fixed uninitialized data in OBC config code
Added 'implicit none ; private' to MOM_unit_tests.F90, MOM_oda_driver.F90, MOM_diag_manager_wrapper.F90, MOM_OCMIP2_CO2calc.F90 and MOM_offline_aux.F90. All answers are bitwise identical.
Split post_surface_diagnostics into post_surface_dyn_diags and post_surface_thermo_diags, and call each of them only if appropriate. This corrects the NaNs described in NOAA-GFDL#767. All solutions are bitwise identical, but this can increase the frequencey with which the dynamics surface diagnostics are sent for output.
- Stretch column height in remapping to ensure consistency between source and target total column height. - Also change string length in MOM_file_parser.F90.
Fix divide by zero in surface diagnostics
alperaltuntas
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Feb 18, 2022
* additions for stochastic physics and ePBL perts * cleanup of code and enhancement of ePBL perts * Update MOM_diabatic_driver.F90 remove conflict with dev/emc * Update MOM_diabatic_driver.F90 further resolve conflict * Update MOM_diabatic_driver.F90 put id_sppt_wts, etc back. * add stochy_restart writing to mom_cap * additions for stochy restarts * clean up debug statements * clean up code * fix non stochastic ePBL calculation * re-write of stochastic code to remove CPP directives * remove blank link in MOM_diagnostics * clean up MOM_domains * make stochastics optional * correct coupled_driver/ocean_model_MOM.F90 and other cleanup * clean up of code for MOM6 coding standards * remove stochastics container * revert MOM_domains.F90 * clean up of mom_ocean_model_nuopc.F90 * remove PE_here from mom_ocean_model_nuopc.F90 * remove debug statements * stochastic physics re-write * move stochastics to external directory * doxygen cleanup * add write_stoch_restart_ocn to MOM_stochastics * add logic to remove incrments from restart if outside IAU window * revert logic wrt increments * add comments * update to gfdl 20210806 (#74) * remove white space and fix comment * Update MOM_oda_incupd.F90 remove unused index bounds, and fix sum_h2 loop. Co-authored-by: pjpegion <Philip.Pegion@noaa.gov> Co-authored-by: Marshall Ward <marshall.ward@noaa.gov> * Fussing with zotero.bib. Getting a warning about a repeated bibliography entry for adcroft2004. Rob thinks this is a hash failure. * Still fussing with zotero.bib - it was complaining about the (unused) Kasahara reference. * Several little things, one is making sponge less verbose. - Pointing to OBC wiki file from the lateral parameterizations doc. - Using the MOM6 verbosity to control the time_interp verbosity. - Making the check for negative water depths more informative. * return a more accurate error message in MOM_stochasics * Working on boundary layer docs. * Done with EPBL docs? * Undoing some patches from others * Cleaning up too-new commits * Adding in that SAL commit again. * correction on type in directory name * Added some to vertical viscisity doc. * Cleaned up whitespace leftover from porous topomerge. - Spacing within expressions was uneven and made multiplation look like POW functions. Leftover from merging NOAA-GFDL#3. - No answer changes. * Fix out-of-bounds k index in PPM flux - An errant use of the porous face area led to an out-of-bounds k-index reported in NOAA-GFDL#19. - Closes #19 * Adding Channel drag figure * Take cite out of figure caption. * Copyright year 2022
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Resolved the conflicts in MOM_KPP and MOM_tidal_mixing modules.