merge Brankart#7
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pjpegion merged 176 commits intopjpegion:stoch_eosfrom Sep 17, 2020
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This is done via parameter RE_AH: if nonzero, the biharmonic coefficient is scaled so that the biharmonic Reynolds number is equal to this.
grid_Re_Kh = (U sqtr(dx2))/Kh grid_Re_Kh = (U dx3)/Ah where dx2 is the harmonic mean of the squares of the grid [L2], and dx3 is the harmonic mean of the squares of the grid^(3/2) [L3]
Hoping this will fix the floating point exception in symmetric mode.
This PR add two hard-coded parameters (AH_min and KH_min) to avoid dividing by zero when computing the Biharmonic and Laplacian grid Reynolds numbers, respectively. It also fixed the size of an array used in the Biharmonic Re calculation.
* Follow Bob's suggestion throughout the code: - remove unnecessary halo updates - change loop indices - make expressions rotationally symmetric - fix bugs in vort_xy_dy and grid_sp_v2 * clean the code by deleting commented lines
There were a few mistakes in the Leith AH coefficient calculation that are now fixed. * Use inv_PI6 instead of inv_PI5 * Use Del2vort_q instead of vert_vort_mag
Add option to control Biharmonic coeff. via grid Reynolds number
Improve Leith schemes
Add tidal diffusivities into Kd_int
Brankart PGF update
…didate-ncar-2020-08-11 Dev master candidate NCAR 2020-08-11
…actor OBC: segment parser refactoring
Properly set vertex_shear in set_diffusivity_init
Clean up pass_var for tracer reservoirs.
Tracer concentrations were being posted at the same time as the transport diagnostics. This leads to some unexpected behavior (e.g. SST and 3D temperature are not consistent) because the concentrations are potentially being posted at an intermediate state. In addition to fixing this problem for all tracers, the subroutine has been renamed to be more descriptive of what kinds of diagnostics might fall into this category.
…_concentration_post
Careless me left out 'subroutine' in the declaration of post_tracer_diagnostics_at_sync
Corrected an obvious syntax error in a subroutine declaration.
…6 into move_tracer_concentration_post
Adds a tracer diagnostic for the intermediate state of tracer concentrations right after horizontal transport (advection and diffusion) has occurred. For cases where DIABATIC_FIRST = False, this will definitely not be identical to the tracer concentration diagnostic that is posted when the MOM6 state is 'synchronized' (e.g. all forcing terms within a MOM6 timestep have been calculated and applied).
…n_post Post tracer concentration when synced
This patch attempts to detect if a new diagnostic has been added, which
was previously interpreted as a regression.
Previously, any diff in chksum_diag between a PR and dev/gfdl was
interpreted as a regression. This included new diagnostics, which do
not actually change any existing answers.
This patch only raises an error (blocking the merge) if there are
detected changes in dev/gfdl's chksum_diag.
If the diff only reports new lines in chksum_diag from the PR, then it
reports in the log as a WARN and reports as a PASS to the CI (currently
Travis).
This patch also fixes a minor typo in the .restart test ($$* should have
been $*). Several Make variables using shell-style brackets {} were
also replaced with Make brackets ().
Testing: Warn on new diagnostic in regression
…kenigson-brankart
- Commit b67d3c6 added back two submodules that still exist on the NCAR branch but no longer are used in the GFDL branch and soon will be expunged on the main branch too. This removes the submodules as was done in NOAA_GFDL/MOM6#1139.
- Following suggestions from @Hallberg-NOAA for PR mom-ocean#1193, I've copied the more completely-documented declaration lines from PressureForce_FV_Bouss() to thickness_diffuse_full(). - Similarly to the other module made a change of an intermediate variable to its reciprocal. - Corrected missing OpenMP directives for some local variables.
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Corrected the descriptions of 60 variables
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Merge in Alastair's branch into my branch.