Coaps fsu into dev/emc #3
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Latest MOM6 updates
merge in latest MOM updates * GFDL_MOM6/dev/gfdl: (220 commits) Update cache dir for /lustre/f2 Update cache dir for /lustre/f2 Calculate height-related diagnostics in Z Set coord_adapt and coord_slight parameters in H Corrected comments in build_zlike_column +Pass max_depth to initialize_regridding in Z Corrected comments in build_sigma_column Combined scaling factors in build_adapt_column Clarified comments in Idealized_Hurricane +Recast MOM_diag_to_Z to work in units of Z +Recast MOM_ALE_sponge to work in units of Z +Added m_to_Z arg to horiz_interp_and_extrap_tracer Find energetic_PBL column height changes in Z +Find diapyc_energy_req column height changes in Z Use local variables to rescale in MOM_Point_Accel Recast MOM_sum_output to work in units of Z Simplify MOM_diagnostics code +Rescale depth inside of MEKE_lengthScales_0d +Add conversion argument to register_static_field Rescale values reported by PointAccel ...
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Merge in latest dev/gfdl updates
Merge in latest dev/gfdl updates
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Merge in latest dev/gfdl updates
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merge in latest dev/gfdl updates
Merge in latest MOM6 updates
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merge in latest dev/gfdl updates
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Merge in updates to remap_all_state_vars
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* TC4 integration into test suite This patch renames the tc4 test to activate it in the test suite. It also modifies the Makefile to build the input field test scripts. It also modifies the Python build scripts to be PEP8-conformant. We temporarily disable tc4 in the restart tests, since they currently fail. This needs to be addressed before we can merge this into the main branch. The patch does not enable the necessary Python modules for running on Travis, that will also be addressed later. * Travis python support; tc4 Makefile The custom TC4 Makefile has been added (oops), and the presumed Python Ubuntu packages have been added for Travis. * Verify ENABLE_THERMODYNAMICS is True before posting C_p diagnostic * Make tc4 faster * remove trailing whitespace * add unit scaling * fix restart fail for tc4 and some cleanup * remove trailiny ws * Enable tc4.restart test * +Pass timeesteps to tracer diagnostics in [T] Pass timeesteps to the tracer diagnistics routines post_tracer_diagnostics and postALE_tracer_diagnostics and to adiabatic in units of [T}. All answers are bitwise identical. * +Rescaled tracer advective flux diagnostics Rescaled the internal units of the tracer advective flux diagnostics to units of [conc H L2 T-1] for code simplicity and dimensional consistency testing. Also corrected the units of some tracer fluxes as documented in comments and commented out unused elements of the tracer_type. All answers are bitwise identical. * +Pass timesteps to ALE_main in [T] Pass the timesteps to ALE_main, ALE_main_offline, and ALE_main_accelerated in units of [T] for code simplicity and dimensional consistency testing. This also includes the rescaling of remapping-driven tracer tendencies. All answers and diagnostics are bitwise identical. * +Pass timesteps to tracer column_physics in [T] Pass timesteps to the various tracer column_physics routines in [T] for dimensional consistency testing. Also added a new unit_scale_type argument to these routines. All answers are bitwise identical, but there are minor interface changes to 13 subroutines. * +Pass timesteps to applyTracerBoundaryFluxesInOut in [T] Pass timesteps to applyTracerBoundaryFluxesInOut in [T], and use units of [T-1] for internal source and decay rates for the oil tracer and in fluxes of CFCs. Also modified extract_offline_main to return timesteps as real values with units of [T]. Also there is a new unit_scale_type argument to register_oil_tracer. All answers in the MOM6_examples test cases and regression tests are bitwise identical. * Simplified expressions in MOM_PointAccel Simplified expressions inside of MOM_PointAccel, taking into account that all velocities use the same units of [L T-1]. All answers are bitwise identical. * Corrected dimensional epsilons in downscaling Added distinct negligible volumes, face areas, horizonal areas and lengths with proper dimensional rescaling in the downsample field routines. With these changes, downscaled diagnostics should now pass the dimensional rescaling tests, whereas previously there would have been a problem when the numbers used to represent lengths are smaller than about 1e-8 times their MKS values. All answers are bitwise identical without dimensional rescaling. * Simplified expressions in MOM_offline_aux Simplified expressions in distribute_residual_uh_barotropic. All answers are bitwise identical. * Revised wave_speed to return speed in [L T-1] Revised wave_speed to return the internal wave speed in units of [L T-1] and to use mono_N2_depth in units of [Z] for code simplification and expanded dimensional consistency testing. Also revised the internal units of some related diagnostics in calculate_diagnostic_fields. All answers and diagnostics are bitwise identical. * Rescaled internal variables in wave_speed Rescale internal calculations in wave_speed and wave_speeds for greater robustness and dimensional consistency testing. All answers are bitwise identical and pass dimensional scaling tests. * +Changed the units of minimum_forcing_depth to [H] Changed the units of minimum_forcing_depth passed to applyBoundaryFluxesInOut and applyTracerBoundaryFluxesInOut to [H]. All answers are bitwise identical. * Correction of documented units in comments Corrected some units in comments and eliminated some unused variables. All answers are bitwise identical. * Adiabatic clock ID bugfix This patch fixes an initialization bug of the diabatic timer, which was being used to measure adiabatic time but was never initialized if the experiment was configured as adiabatic. We fix this by introducing a separate timer for the adiabatic solver. Although we could have reused the diabatic timer, the addition of a new variable should not add any overhead on modern compilers. * Corrected an OMP declaration Added a variable to an OMP declaration. All answers are bitwise identical, and a recently added compile-time error with openMP was fixed. * Update MOM.F90 Fixed Alistair's embarrassing error. * Dimensional rescaling in MOM_open_boundary.F90 Added rescaling for dimensional consistency testing in MOM_open_boundary.F90, including splitting variables with different units that had previously shared the same variable and adding more extensive documentation of variables. Also changed the dimensions of the timesteps passed to radiation_open_bdry_conds and update_segment_tracer_reservoirs to [T] and added vertical_grid_type and unit_scale_type arguments to open_boundary_init and open_boundary_test_extern_h. All answers are bitwise identical, although some probably bugs have been noted in comments and there are new or altered arguments to several routines. * (*)Fixed invariance bugs in MOM_open_boundary.F90 Corrected dimensional consistency bugs in update_segment_tracer_reservoirs and horizontal indexing and related bugs in gradient_at_q_points with oblique_grad OBCs. These will both change answers in test cases that use some open boundary condition options, but not in any of the MOM6-examples test cases.
+Add dimensional rescaling of wave variables
3D thickness x momentum diagnostics
…rder Collocate units and conversion for register_diag_field calls
Added variable_att_exists calls before two calls to get_variable_attribute in the FMS2 version of get_file_fields so that runs do not crash if there are variables being read that do not have a long_name or units attribute. All answers are bitwise identical in cases that did not crash.
Corrected typos in comments, and removed unnecessary commented out code as noted by Brandon Reichl in his review of MOM6 dev/gfdl PR# 1404. All answers are bitwise identical.
- Better, but doesn't quite pass RESCALE tests.
In the removal of regrid_edge_slopes, a couple of the solvers became duplicated between regrid_edge_values and regrid_solvers. Here, they're simply made consistent by removing the solvers from regrid_edge_values, and bringing over the zero-pivot check for the linear solver that was in one variation but not the other.
Call variable_att_exists before get_variable_att
The autoconf build was updated to verify that calls to diag_axis_init support the domain_position argument. This was introduced in FMS 2019.01.02, so this acts as an implicit minimum FMS version test. This test is done indirectly by confirming that the valid domain_position values (NORTH, EAST, CENTER) are in diag_axis_mod. A `--with-framework=` flag was also added to select either the FMS1 or FMS2 backend.
+Move wave module variables into control structure
Trying to fix Kelvin wave boundary condition.
Autoconf: FMS 2020.x compatibility testing (diag_axis_mod, data_override_mod)
…rection and general clean up - Add option to use or not uv increment - The calculation of the increment when using full field has been moved at initialization - A SSH correction has been applied to h_obs to account for the different SSH between the background and target state - The incremental update is now done over nstep-1 - a general clean up has been done with variable name change to make the code easier to follow
Remove duplicated solvers between regrid modules
…art_fix Ice shelf restart fix
…ility - remove the u,v,tv pointers from the set_up_oda_incupd subroutines - explicitly put tv,u,v in arguments of apply_oda_incupd - change name get_oda_increments to calc_oda_increments - explicitly put tv,u,v in arguments of calc_oda_increments - use loops to calculate sum of h’s - remove the 2018_answers options - added option to output increments when using full fields - added subroutine output_oda_incupd_inc to write a separate double-precision file for the increments. - add if (mask==1 ) condition to apply/calculate the increments -add pass_var,pass_vector on increments and u,v,tv at the end of calc_oda_increments and apply_oda_incupd respectively - added CS%ncount to restart file to have reproducibility on restart. - Added option ODA_INCUPD_RESET_NCOUNT (! default= True, If True, reinitialize number of updates already done.)
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