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Feature to flag and trap cases where obsolete restart fields are attempted to be used
…d by shear production (excluding the energy diffusion term which can be positive).
Conflicts: config_src/mct_driver/ocn_cap_methods.F90 src/core/MOM_forcing_type.F90
…hich calculates the GM coefficient using the Visbeck et al. (1997) formulation. Previously this was being done whenever VarMix was enabled, but I wanted to separate VarMix from this diffusivity call.
- Uses stages to parallelize testing process - Adds a doxygen job that tests for doxygen errors - Reduces dependency on other repositories - No longer uses scripst from MOM6-examples/tools/tests/Travis-MOM6/ - Still uses configurations from MOM6-examples/ocean_only/ - Adds test building/using a debug executable - Adds a .testing/ directory - Uses the latest xenial image on Travis (with openmpi) Todo: - Add code coverage (needs more experiments) - Break dependence on MOM6-examples (long term project) - Add other portable tests (e.g. parameter scaling, rotation, etc)
- Like the original cased tracer, the ca13csed tracer used in generic_BLING.F90 needs to be initialized to zero at all subsurface layers (when do_13c = .true.)
Set ca13csed to zero at k>1
Re-factor of Travis-CI usage
… More specifically, I moved the calculation of dudx and dvdy outside of the Leith loop so now it is being calculated with sh_xx.
Adding the NUOPC cap
With the xanadu release of FMS, the coupler_types module within FMS has finally been properly scoped without adding unnecssary dependencies. The coupler_types.F90 files in the MOM6 config_src/solo_driver directories are no longer needed. In addition, the routines inside coupler_util.F90 files have not been used anywhere in MOM6 for some time, their functionality being provided via interfaces inside the coupler_types_mod. These 5 files have now been removed. All answers are bitwise identical.
…candidate-2018-04-22 Conflicts: config_src/mct_driver/MOM_surface_forcing.F90
…-candidate-2018-04-22 Merge dev master candidate 2018 04 22
Added unit_scale_type arguments to several subroutines in the nuopc_driver directory, added a unit_scale_type element to the nuopc_driver versoin of ocean_state_type, and use this argument to appropriately rescale forces%ustar for dimensional consistency testing. These changes are required to go with the dev-master-candidate-2018-04-22 updates to MOM6. With these changes, the code in origin/dev-master-candidate-2018-04-22 compiles up through the nuopc_driver version of MOM_ocean_model.o.
This patch appends a checksum for the dependencies of the depth and area
lists stored in the Depth_list.nc file, which are used to compute
diagnostics based on APE.
The data in Depth_list.nc depends on the grid fields, and may not be
reproducible when such grids are constructed internally using compiled
code within the executable. This issue was observed in the
'double_gyre' experiment when a PGI-compiled executable was tested using
a Depth_list.nc file generated by a GNU-compiled executable.
By appending a checksum for the grid fields used to compute
Depth_list.nc, we can ensure that the data is consistent with the
experiment grid data. Grid data which is read from external files, such
as mosaic or topography fields, are unaffected by this issue.
This patch improves the reproducibilty of standard diagnostics, such as
total energy, but has no impact on the reproducibility of the internal
model dynamics, which does not depend on Depth_list.nc.
Checksums are computed for the G%bathyT and masked G%areaT grid fields
using the FMS mpp_checksum subroutine, which require collective
operations, and are stored as hex strings in global attributes of the
netCDF file. Strings are used to remain consistent with FMS restart
checksums, and to avoid an observed re-casting of 8-byte integers to
4-bytes by the netCDF library. Attribute names are based on the grid
variable names.
Two flags have been introduced to control this behavior:
REQUIRE_DEPTH_LIST_CHECKSUMS (default: True)
This flag will abort the run if the Depth_list.nc file is present
and checksums are absent from the file. Although this could impose
greater restrictions on existing runs, few runs are configured to
save the depth list file (READ_DEPTH_LIST) and the default behavior
is to reconstruct these lists on every run.
UPDATE_DEPTH_LIST_CHECKSUMS (default: False)
When REQUIRE_DEPTH_LIST_CHECKSUMS is set to false, this flag will
automatically update the checksums of the Depth_list.nc file. While
this can affect the reproducibility of APE diagnostics, it will
ensure the reproducibility of such diagnostics in subsequent runs.
Additional documentation of the parameters used to store Depth_list.nc attribute names was added.
Fixes for debug mode
…guments_nuopc_cap
The depth checksum is now replaced with masked depth, mask2dT * bathyT, and the calculation of the depth list has also been updated to use the masked depth. Various style conformance changes, such as contraction of do and if terminations (enddo, endif) and reduction of whitespace in various multiline function call, has also been applied. Finally, the attribute name docstrings were updated for clarity.
…rguments_nuopc_cap Add missing us arguments nuopc cap
use ESMF operators
…ation Refactor MCT driver to make modules consistent with those in the NUOPC driver
Rename modules in NUOPC and MCT
In the calculation of MEKE%mom_src, made the old method (using FrictWork) the default and made the new calculation of FrictWork only available when using GME.
…_friction Deletes contribution from kv%slow when computing a_cpl
Updates in MEKE and hor_visc
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Sync dev/gfdl with NOAA-GFDL version of repository
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Explicit domain decomposition of horizontal axes
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Update MOM_oda_incupd.F90
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Added a new variable, initialized, to the control structures of modules that had been testing for an allocated control structure to verify that it had been initialized before it was going to be used, and then duplicated the tests using this new variable. This was done to enable us to go ahead with MOM6 PR JCSDA-internal#5, which eliminated many of these checks when converting the control structures from pointers in the parent modules to elements that are always there, and then passing them as simple types instead of as pointers. If we decide that we do not need these tests after all, we can easily delete them, but until this is discussed, this commit avoids losing the messages, as it was easier to do it this way instead of trying to recreate them after they had been removed. All answers and output are bitwise identical.
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Redefine ~500 pointers as local or stack variables
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* initial hooks for stochastic EOS modifications * remove debug statements * add documentation * Change ampltiude from 0.39 to sqrt(.39) * remove global_indexing logic from stoch_eos_init * switch to using MOM_random and add restart capability * update random sequence to update each each time-step * remove tseed0 from MOM_random (leftover from debugging) * Added necessary submodules and S^2, T^2 diagnostics to MOM_diagnostics * Added diagnostics for outputting variables related to the stochastic parameterization. * Diagnostics in MOM_PressureForce_FV updated for stochastic (rather than deterministic) Stanley SGS T variance parameterization. * Added parentheses for reproducibility. * Changed diagnostics to account for possible absence of stoch_eos_pattern in MOM_PressureForce_FV, when deterministic parameterization is on. * remove mom6_da_hooks and geoKdTree from pkg * add stochastic compoment to MOM_thickness_diffuse * fix array size declaration and post_data * Corrected indexing of loops in MOM_calc_varT * Changed how parameterization of SGS T variance (deterministic and stochastic) is switched on in PGF and thickness diffusion codes * Corrected a few typos * Cleaned up indices, redundant diagnostic, printing * Fixed diagnostic IDs * Fixed diagnostics typo * Corrected indices in calculation of tv%varT * Minor index fix * Corrected bug in pressure in Stanley diagnostics * Fixed whitespace error * Stoch eos clock (JCSDA-internal#5) *Added a clock for the Stanley parameterization Co-authored-by: jkenigson <jkenigso@gmail.com> * add halo update to random pattern * Update MOM_stoch_eos.F90 Fix bug for looping over compute domain (is -> isc etc.) * Avoid unnessary computations on halo (MOM_stoch_eos) and code clean-up (MOM_thickness_diffuse) * Removed halo updates before determ param calc * Update MOM_stoch_eos.F90 Removed unnecessary code * Bug - indices are transposed * Changed Stanley stochastic coefficient from exp(X) to exp(aX) (JCSDA-internal#9) * Changed Stanley stochastic coefficient from exp(X) to exp(aX) * Extra spaces removed * Stoch eos init fix (JCSDA-internal#10) * Don't bother calculating tv%varT if stanley_coeff<0 * Missing then added * Merge Ian Grooms Tvar Discretization (JCSDA-internal#11) * Update MOM_stoch_eos.F90 In progress updating stencil for$ | dx \times \nabla T|^2$ calculation * New discretization of |dx\circ\nablaT|^2 Co-authored-by: Ian Grooms <ian.grooms@colorado.edu> * Multiplied tvar%SGS by grid cell thickness ratio * Added limiter for tv%varT * Stoch eos ncar linear disc (JCSDA-internal#12) * Update MOM_stoch_eos.F90 In progress updating stencil for$ | dx \times \nabla T|^2$ calculation * New discretization of |dx\circ\nablaT|^2 * AR1 timescale land mask Adds land mask to the computation of the AR1 decorrelation time * Update dt in call to MOM_stoch_eos_run The call to `MOM_stoch_eos_run` (which time steps the noise) is from within `step_MOM_dynamics`. `step_MOM_dynamics` advances on time step `dt` (per line 957), but the noise is updated using `dt_thermo`. It seems more appropriate to update the noise using `dt`, since it gets called from within `step_MOM_dynamics`. * Fixed the units for r_sm_H * Remove vestigial declarations The variables `hl`, `Tl`, `mn_T`, `mn_T2`, and `r_sm_H` are no longer used, so I removed their declarations and an OMP private clause Co-authored-by: Ian Grooms <ian.grooms@colorado.edu> * Update MOM_thickness_diffuse.F90 Changed index for soft convention * Update CVMix-src * Ensure use_varT, etc., initialized * Don't register stanley diagnostics if scheme is off * Stanley density second derivs at h pts (JCSDA-internal#15) * Change discretization of Stanley correction (drho_dT_dT at h points) * Limit Stanley noise, shrink limiting value * Revert t variance discretization * Reverted variable declarations * Stanley scheme in mixed_layer_restrat, vert_fill in stoch_eos, code cleanup (JCSDA-internal#19) * Test Stanley EOS param in mixed_layer_restrat * Fix size of TS cov, S var in Stanley calculate_density calls * Test move stanley scheme initialization * Added missing openMP directives * Revert Stanley tvar discretization (JCSDA-internal#18) * Perform vertical filling in calculation of T variance * Variable declaration syntax error, remove scaling from get_param * Fix call to vert_fill_TS * Code cleanup, whitespace cleanup Co-authored-by: Jessica Kenigson <jessicak@cheyenne1.cheyenne.ucar.edu> * Use Stanley (2020) variance; scheme off at coast * Comment clean-up * Remove factor of 0.5 in Tvar * Don't calculate Stanley diagnostics on halo * Change start indices in stanley_density_1d * Stanley param in MOM_isopycnal_slopes (JCSDA-internal#22) Stanley param in MOM_isopycnal_slopes and thickness diffuse index fix * Set eady flag to true if use_stored_slopes is true * Cleanup, docs, whitespace * Docs and whitespace * Docs and whitespace * Docs and whitespace * Whitespace cleanup * Whitespace cleanup * Clean up whitespace * Docs cleanup * use_stanley * Update MOM_lateral_mixing_coeffs.F90 * Adds link to another TEOS10 module * Set Stanley off for testing * Line continuation Co-authored-by: Phil Pegion <38869668+pjpegion@users.noreply.github.com> Co-authored-by: Philip Pegion <Philip.Pegion@noaa.gov> Co-authored-by: Jessica Kenigson <jessicak@cheyenne6.cheyenne.ucar.edu> Co-authored-by: Jessica Kenigson <jessicak@cheyenne3.cheyenne.ucar.edu> Co-authored-by: jkenigson <jkenigso@gmail.com> Co-authored-by: jskenigson <jessica.kenigson@colorado.edu> Co-authored-by: Jessica Kenigson <jessicak@cheyenne1.cheyenne.ucar.edu> Co-authored-by: Jessica Kenigson <jessicak@cheyenne5.cheyenne.ucar.edu> Co-authored-by: Philip Pegion <ppegion@Philips-MacBook-Pro.local> Co-authored-by: Jessica Kenigson <jessicak@cheyenne4.cheyenne.ucar.edu>
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Pulling in the latest dev/master from GFDL to stay in sync.
Luckily this is an easy one and requires no soca changes and doesn't change our answers.
Tested as well on Discover with gcc/intel17