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remove unused variable
add a comment about potential instability and possible fix
Add kpp to verification.
Include explicitly AUTODIFF_OPTIONS.h (in case we don't use ECCO_CPPOPTIONS.h) and put storage dir within #ifdef ALLOW_AUTODIFF_TAMC
avoid unused variables (+ cleaning some comments)
An Nguyen's extensions to salt_plume package (carry corresponding heat flux along with salt redistribution)
prep for saltplume code change: clean up: reformulate 1-(1-abc) to abc
should never call any of the DIAGNOSTICS_[]FILL routine if useDiagnostics=F
move flag "inAdMode" from PARAMS.h to AUTODIFF_PARAMS.h
avoid unused variables
fixing diagnostics_fill calls
modif for vertical profile of (background) viscosity: for now, just uses 1rst value: viscArNr(1)
add double diffusive contributions as a hack, turned off by default for now, and the code can be excluded with a CPP-flag EXCLUDE_KPP_DOUBLEDIFF just as EXCLUDE_KPP_SHEAR_MIX
Add run-time flag to remove limit on hbl under stable conditions (default behavior unchanged)
Fix vertical indices of diffusivities in subroutine RI_IWMIX
Update tamc.h for single-prec comlev option
Removing KPPmld diagnostic
Add Bulk Richardson number diagnostics
Add missing comma (didn't compile if ALLOW_KPP_VERTICALLY_SMOOTH defined)
replace calls to "FIND_RHO" by new version "FIND_RHO_2D".
o pkg/kpp: added saltplume diagnostics
making pkg/kpp ALLOW_SALT_PLUME code compatible with pkg/plume
add _d 0 to Real constant.
exchange order of loops (move i-loop into k-loop) in one instance to improve vectorization, can speed up routine by 50% on a vector machine (thanks to Jens-Olaf Beismann)
added the salt plume scheme (ALLOW_SALT_PLUME) to pkg/kpp (code conttributed by An Nguyen)
Fix mismatch in parameter lists in KPPMIX, RI_IWMIX
add standard argument (myThid, myIter) to few S/R.
add more code to have only Ri-number based mixing in shelf ice caverns add myThid to all kpp routines (long overdue)
undo previous modifs which were producing a TAF seg-fault.
Begin modifications for heterogeneous bcs in kpp - zero diff arg list changes 1
replaced _KPP_RL with _RL
o bug fixes for vertical diffusivity computations when both KPP and
3D diffusivity arrays are used.
removing some superfluous "#include *.h"
FRUGAL_KPP option removed due to popular undemand
o added diagnostics to pkg/kpp, including computation of mixed layer depth based on a temperature/density criterion o updated verification/natl_box to test the new pkg/kpp diagnostics
... and an example on how it may work: Switching of shear instability in adjoint mode.
allow to set a vertical profile of vertical diffusivity for T & S
replace pMask by maskC
o Additional storing in an attempt to fix TAMC problem with adjoint of KPP code. (no success...) Identical code works fine with TAF.
Include KPP option EXCLUDE_KPP_SHEAR_MIX to exclude interior shear instability mixing.
o convert all comments with single quotes (such as "can't", "don't", etc.)
to unabbreviated form (eg. "do not") since these unmatched quotes
tend to break the Fortran parser used to generate the HTML-ified
code browser (see: http://mitgcm.org/dev_docs/code_reference/)
Bug fix for merging between c50 and KPP. ikey was passed from thermodynamics to kpp_calc via common block rather than being recomputed in kpp_calc, in contradiction with new key itdkey. New key ikppkey created, and tamc.h headers updated.
Bug fix for merging between c50 and KPP. ikey was passed from thermodynamics to kpp_calc via common block rather than being recomputed in kpp_calc, in contradiction with new key itdkey. New key ikppkey created, and tamc.h headers updated.
added more storing to avoid more recomp.
Added more storing to avoid more recomp. in kpp_routines.F, gmredi_calc_tensor.F
merging c44 and e27
Merging from release1_p12: o Modifications for using pkg/exf with pkg/seaice - improved description of the various forcing configurations - added basic radiation bulk formulae to pkg/exf - units/sign fix for evap computation in exf_getffields.F - updated verification/global_with_exf/results/output.txt o Added pkg/sbo for computing IERS Special Bureau for the Oceans (SBO) core products, including oceanic mass, center-of-mass, angular, and bottom pressure (see pkg/sbo/README.sbo). o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F to avoid negative values in shallow regions. - updated verification/natl_box/results/output.txt - updated verification/lab_sea/results/output.txt o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F o Added useSingleCpuIO option (see PARAMS.h). o Updated useSingleCpuIO option in mdsio_writefield.F to work with multi-field files, e.g., for single-file pickup. o pkg/seaice: - bug fix in growth.F: QNET for no shortwave case - added HeffFile for specifying initial sea-ice thickness - changed SEAICE_EXTERNAL_FLUXES wind stress implementation o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf, kpp_transport_t.F, forward_step.F, and the_main_loop.F o pkg/seaice: - adjoint-friendly modifications - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
o Merging pkg/exf and pkg/seaice from cvs tag ecco_ice2
02/12/03 Added pkg/seaice and modified pkg/exf as per release1_p12_pre
Modified Files: eesupp/src/eeboot_minimal.F model/src/cg2d.F
model/src/do_coupled_ucla.F pkg/kpp/kpp_calc.F
pkg/kpp/kpp_routines.F
o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F to avoid negative values in shallow regions. o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F o Added useSingleCpuIO option (see PARAMS.h). ---------------------------------------------------------------- Modified Files: Tag: release1 doc/tag-index eesupp/src/ini_procs.F model/inc/PARAMS.h model/src/ini_parms.F model/src/set_defaults.F pkg/kpp/kpp_do_diags.F pkg/kpp/kpp_readparms.F pkg/kpp/kpp_routines.F pkg/mdsio/mdsio_writefield.F pkg/sbo/README.sbo pkg/sbo/sbo_calc.F pkg/sbo/sbo_diags.F verification/lab_sea/code/CPP_OPTIONS.h verification/lab_sea/input/.genmakerc verification/lab_sea/input/data.pkg Added Files: Tag: release1 eesupp/src/gather_2d.F eesupp/src/scatter_2d.F verification/lab_sea/input/data.sbo
Added lower bound diffusivity to kpp_routines.F (see !!!NOTE!!!).
checkpoint47f_post
Merging from release1_p10:
o modifications for using pkg/exf with pkg/seaice
- pkg/seaice CPP options SEAICE_EXTERNAL_FORCING
and SEAICE_EXTERNAL_FLUXES
- pkg/exf CPP options EXF_READ_EVAP and
EXF_NO_BULK_COMPUTATIONS
- usage examples are Experiments 8 and 9 in
verification/lab_sea/README
- verification/lab_sea default experiment now uses
pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf
o modifications for using pkg/exf with pkg/seaice
- pkg/seaice CPP options SEAICE_EXTERNAL_FORCING
and SEAICE_EXTERNAL_FLUXES
- pkg/exf CPP options EXF_READ_EVAP and
EXF_NO_BULK_COMPUTATIONS
- usage examples are Experiments 8 and 9 in
verification/lab_sea/README
- verification/lab_sea default experiment now uses
pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf
Commiting old bug fixes to ecco-branch
o cleaned up the use of rhoNil and rhoConst.
- rhoNil should only appear in the LINEAR equation of state, everywhere
else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst
and the dynamical equations are all divided by rhoConst
o introduced new parameter rhoConstFresh, a reference density of fresh
water, to remove the fresh water flux's dependence on rhoNil. The default
value is 999.8 kg/m^3
o cleanup up external_forcing.F and external_forcing_surf.F
- can now be used by both OCEANIC and OCEANICP
o Include a new diagnostic variable phiHydLow for the ocean model
- in z-coordinates, it is the bottom pressure anomaly
- in p-coordinates, it is the sea surface elevation
- in both cases, these variable have global drift, reflecting the mass
drift in z-coordinates and the volume drift in p-coordinates
- included time averaging for phiHydLow, be aware of the drift!
o depth-dependent computation of Bo_surf for pressure coordinates
in the ocean (buoyancyRelation='OCEANICP')
- requires a new routine (FIND_RHO_SCALAR) to compute density with only
Theta, Salinity, and Pressure in the parameter list. This routine is
presently contained in find_rho.F. This routine does not give the
correct density for 'POLY3', which would be a z-dependent reference
density.
o cleaned up find_rho
- removed obsolete 'eqn' from the parameter list.
o added two new verification experiments: gop and goz
(4x4 degree global ocean, 15 layers in pressure and height coordinates)
Merging from release1_p5 o Adjoint-related bug fixes in kpp: - kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix - kpp_routines: store of Rib avoids partial recomputation bug of TAF.
Adjoint-related bug fixes: o kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix o kpp_routines: store of Rib avoids partial recomputation bug of TAF.
Bug fix in S/R ri_iwmix (benign bug); spotted by D. Menemenlis.
Modifications and additions to enable automatic differentiation. Detailed info's in doc/notes_c37_adj.txt
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!
Merged changes from branch "branch-atmos-merge" into MAIN (checkpoint34) - substantial modifications to algorithm sequence (dynamics.F) - packaged OBCS, Shapiro filter, Zonal filter, Atmospheric Physics
Replaced some storage for TAMC by cheap recomputation.
Re-wrote calc_phi_hyd() - use theta and salt as arguments (necessary for staggered time-step) - calls find_rho() from inside - find_rho() also takes theta,salt as arguments - uses different formulation for 'OCEANIC' and 'ATMOSPHERIC' modes - "finite volume" (non-energy conserving) form supplied in comments
Modified and fixed version. Tested with verification/natl_box.
KPP package without flag kppPackageIsOn.
Updated version by D. Menemenlis. Takes new unit and sign conventions for forcing fields into account. Includes changes of Ralf in ecco_c30_05.09. Yet to be fully tested.
Packaged KPP mixing scheme.
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