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fix for case where pkg/generic_advdiff is disable (e.g., exp. adjustment.cs-32x32x1)
Add tracer identity as argument of gmredi_calc_diff.F
Added comments, which describe the changes made in kpp_calc_diff_s & _t.F on April 23, 2007. These routines no longer update the vertical diffusivity array (passed as argument) but are (re-) setting those arrays. Also changed order GMREDI_CALC_DIFF & KPP_CALC_DIFF_T in calc_diffusivity.F and ptracers_calc_diff.F since now the order matters.
reduce number of "warning: unused variable"
o bug fixes for vertical diffusivity computations when both KPP and
3D diffusivity arrays are used.
latitudinal dependence of Bryan and Lewis, 1979 fixed and reworked as per JM suggestions
latest changes are so good (specially from testing on faulks with ifort) that we will keep them confidential for now. Go back to previous version.
o Added capability for latitudinal dependence of Bryan and Lewis, 1979 vertical diffusivity, similar to that in MOM4; vertical diffusivity is specified using diffKrBL79* diffKrBLEQ* and KbryanLewisLatTransition
Modified capability for 3D specification of background vertical diffusion
coefficient as per JM requests. 3D diffusion is now specified by
(i) #define ALLOW_3D_DIFFKR in CPP_OPTIONS.h and
(ii) specifying file diffKrFile in runtime "data" file that contains
the 3D vertical diffusivity coefficients.
o Added capability for 3D specification of vertical diffusion coefficient.
This is done by specifying files diffKr3dSfile and diffKr3dTfile that
contain the 3D vertical diffusivity coefficients.
Modified files: doc/tag-index model/inc/PARAMS.h
model/src/calc_3d_diffusivity.F, calc_diffusivity.F, ini_mixing.F,
ini_parms.F, and set_defaults.F
Added missing file verification/tutorial_global_oce_latlon/run/.cvsignore
Change arrays for total vertical diffusivity (2.D explicit, 3.D implicit)
towards separation of Explicit & Implicit vertical diffusivity
allow to set a vertical profile of vertical diffusivity for T & S
o prepare addition of new packages GGL90 and OPPS - new parameters useGGL90 and useOPPS - include call to the new routines at the (hopefully) right places
o added call to my82_calc_diff, this gives the Mellor+Yamada scheme a chance to work (o:
o add calls for two new packages
- pp81 (Packanowski and Philander, 1981), Richardson number and
stratification dependent mixing
- my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
prepare splitting of thermodynamics: store convective counter in common block
Added vertical diffusivity profile (T/S) due to Bryan and Lewis, 1979. New parameters: diffKrBL79surf - surface diffusivity diffKrBL79deep - deep diffusivity diffKrBL79Ho - turning depth for arctan function diffKrBL79scl - depth scale for arctan function This diffusivity is added to all other diffusivities. The defaults are set so as to give zero diffusivity.
o first check-in for the "branch-genmake2" merge
o verification suite as run on shelley (gcc 3.2.2):
Wed Oct 8 23:42:29 EDT 2003
T S U V
G D M c m s m s m s m s
E p a R g m m e . m m e . m m e . m m e .
N n k u 2 i a a d i a a d i a a d i a a d
2 d e n d n x n . n x n . n x n . n x n .
OPTFILE=NONE
Y Y Y Y 13 16 16 16 0 16 16 16 16 16 16 16 16 13 12 0 0 pass adjustment.128x64x1
Y Y Y Y 16 16 16 16 0 16 16 16 16 16 16 0 0 16 16 0 0 pass adjustment.cs-32x32x1
Y Y Y Y 16 16 16 16 0 16 16 16 16 16 16 22 0 16 16 22 0 pass adjust_nlfs.cs-32x32x1
Y Y Y Y -- 13 13 16 16 13 13 13 13 16 16 16 16 16 16 16 16 N/O advect_cs
Y Y Y Y -- 22 16 16 16 16 16 16 13 16 16 16 16 16 16 16 16 N/O advect_xy
Y Y Y Y -- 13 16 13 16 16 16 16 16 16 16 22 16 16 16 16 16 N/O advect_xz
Y Y Y Y 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 pass aim.5l_cs
Y Y Y Y 14 16 16 16 16 16 16 16 16 13 16 16 16 16 16 13 16 pass aim.5l_Equatorial_Channel
Y Y Y Y 16 16 16 16 16 16 16 16 16 16 16 13 16 16 13 13 16 pass aim.5l_LatLon
Y Y Y Y 13 16 16 16 16 16 16 16 16 16 13 12 13 13 16 13 16 pass exp0
Y Y Y Y 14 16 16 16 16 16 16 16 22 16 16 16 13 16 16 22 16 pass exp1
Y Y Y Y 13 13 16 13 16 16 16 16 16 13 13 16 16 13 13 13 13 pass exp2
Y Y Y Y 16 16 16 16 16 16 16 16 22 16 16 16 16 16 16 16 16 pass exp4
Y Y Y Y 16 16 16 16 16 16 16 16 16 16 16 22 16 16 16 22 16 pass exp5
Y Y Y Y 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 pass front_relax
Y Y Y Y 14 16 16 13 13 16 16 13 13 16 13 13 16 12 13 13 16 pass global_ocean.90x40x15
Y Y Y Y 10 16 16 13 13 16 13 16 16 13 13 13 13 16 16 13 16 FAIL global_ocean.cs32x15
Y Y Y Y 6 11 12 13 13 12 13 16 13 9 9 9 9 10 9 9 11 FAIL global_ocean_pressure
Y Y Y Y 14 16 16 13 16 16 16 13 13 13 13 13 16 12 16 13 16 pass global_with_exf
Y Y Y Y 14 16 16 16 16 16 16 16 16 11 13 22 13 16 16 9 16 pass hs94.128x64x5
Y Y Y Y 13 16 16 16 16 16 16 16 16 11 16 16 16 13 16 22 13 pass hs94.1x64x5
Y Y Y Y 14 16 16 16 16 16 16 16 16 13 16 13 13 16 16 22 13 pass hs94.cs-32x32x5
Y Y Y Y 10 10 16 13 13 16 16 16 22 16 13 13 13 13 13 22 13 FAIL ideal_2D_oce
Y Y Y Y 8 16 16 16 16 16 16 16 16 13 13 8 16 16 16 16 16 FAIL internal_wave
Y Y Y Y 14 16 16 16 16 16 16 16 16 13 13 22 13 13 13 22 16 pass inverted_barometer
Y Y Y Y 12 16 16 16 16 16 16 16 16 16 13 12 13 13 13 13 13 FAIL lab_sea
Y Y Y Y 11 16 16 16 16 16 16 16 13 13 13 12 13 16 13 12 13 FAIL natl_box
Y Y Y Y 16 16 16 16 16 16 16 16 22 16 16 16 16 16 16 16 16 pass plume_on_slope
Y Y Y Y 13 16 16 16 16 13 16 16 16 16 16 16 16 13 16 16 16 pass solid-body.cs-32x32x1
Extended calculation to full overlap (needed to avoid partial recomputation in adjoint mode). CVS ----------------------------------------------------------------------
Bringing comments up to data and formatting for document extraction.
Modifications related to split into thermodynamics.F, dynamics.F o missing initialisations in dynamics.F added o some fields no longer needed in dynamics/thermodynamics deleted o split of calc_diffusivity.F into calc_viscosity.F (plus split of kpp_calc_diff.F into kpp_calc_visc.F) o Modifications of some store directives for TAF
Extended iMin,jMin range for calc_common_factors, calc_diffusivity.
Merge from branch pre38: o essential mods for cubed sphere o debugged atmosphere, dynamcis + physics (aim) o new packages (mom_vecinv, mom_fluxform, ...)
Made sure each .F and .h file had the CVS keywords Header and Name at its start. Most had header but very few currently have Name, so lots of changes!
Change variable name useKPP, useGMRedi.
Moved explicit contributions from GM/Redi and KPP to diffusivity to called routines.
Added IVDC (Implicit Vertical Diffusion Convection). Also facilitated a "convection counter" that is output through "diags".
Modifications/additions for KPP mixing scheme. Instigated by Dimitri.
Changes to allow for atmospheric integration builds of the code
Isomorphism consistency changes
Changes to support r as a vertical coordinate
Added code to bring "salt" up-to-date with "theta". One caveat is that implicit diffusion of salt is done with the diffusivity of theta. We'll sort this out later. In explicit mode, diffKzS is used.
Fixed problems with _RS -> REAL*4 and with reading in intial hydrography
Changes to support topography, hydrography and forcing from files
Implemented implicit vertical diffusion (tracers only). Involved introducing a "total" diffusivity array (local 3D) calculated by calc_diffusivity(). Made some small changes to time-stepping algorithm. Switched on by setting implicitZdiffusion. (note: *Not* fully tested with topography. But when switched off this does produce identical results)
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