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Martin tries to clean up after himself: fix store directives for adjoint
make bio_export vectorize on SX8
avoid unused variables.
Fix init. of memory for taf store.
add argument "myThid" where missing
Moving dic options to DIC_OPTIONS.h
Merging DIC_ABIOTIC.h and DIC_BIOTIC.h
o don't allow negative biological activity (even if the nutrients have become negative). Need new GCHEM_OPTIONS.h macro: #define DIC_NO_NEG.
Cosmetic changes
o add new compile time option to go in GCHEM_OPTIONS.h: USE_QSW_UNDERICE and logical QSW_underice - so that if shortwave radiation/PAR already has ice fraction taken into account nothing more is done to it. Note that is USE_QSW is set AND seaice or thsice is used, then this will be automatic
o change Qsw: if using seaice or thsice, ice fraction is already taken into account o clean up seaice/thsice common blocks.
Add tons of "_d 0" (which changes the outputs)
o change check for Qsw too high, to be consistent with daily varying shortwave radiation (rather than 24hr averaged)
add missing cvs $Header:$ or $Name:$
bug: move the (1-fice) factor out of the k-loop
o clean up pkg/dic. o if using THSICE then use isemask for fice (still need to do this for other sea-ice packages)
o add (and change) flags so that pkg/dic can uses Qsw, Pload from FFIELDS. also ATMOSCO2 from the coupler (for times when coupled to an atmospheric model.
o add compile time flag (PAR_FROMSW) so that PAR needed in dic code is taken from Qsw (rather than insol algorithm or read from file). Also add some stop statements if silly combinations are attempted.
o changes to make dic code more adjoint friendly: - standardize how tracers are passed from dic_biotic_forcing to other subroutines - add a tanh function to take the place of min(x,y) in bio_export.F and fe_chem.F.
o dic code now does no calculations on the overlap regions
o add additional switches MINFE - to limit amount of free iron READ_PAR - reads PAR from file, rather than using insol.F
o include ice influence on air-sea fluxes, and more cleanup
o fix attentuation bug (bio-export), correct declarations (o2_surfforcing)
o clean up and add extra documentation
use drF instead of delZ
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
changes to keep current with gchem pkg, and to be adjointable
initial checking in biogeochemistry packages
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