--- MITgcm/doc/tag-index	2007/07/19 15:34:50	1.851
+++ MITgcm/doc/tag-index	2007/09/15 01:38:59	1.872
@@ -1,9 +1,87 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.851 2007/07/19 15:34:50 dimitri Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.872 2007/09/15 01:38:59 dimitri Exp $
 $Name:  $
 
     Notes on tags used in MITgcmUV
     ==============================
 
+o pkg/seaice: adding ice salinity HSALT as a prognostic variable
+o pkg/seaice: changes for using pkg/seaice with pkg/obcs
+o pkg/ecco: allow user defined cost function contributions 
+o testreport:
+  Allow to choose (per experiment) the list of tested output variables
+   and the main variable (used to issue a pass/FAIL ) ;
+  - for now, done by adding the specific list in file: [exp]/input/tr_checklist
+  - default is unchange: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
+  Also modify printing of summary:
+   a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
+   b) echo the list of tested variables in the individual summary.txt of
+      each experiment.
+o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
+  threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
+  (but still depend on the tile decompostion of the domain).
+o pkg/seaice: change a discretization detail to make the B-grid code 
+  "more symmetric". This change is likely to remove all "ridges/leads" that 
+  where quasi-aligned with the grid in B-grid solutions. It may also be 
+  the solution to the stress coupling issues with the B-grid.
+o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
+  remove .cvsignore from input dir. (since testreport no longer run here).
+o pkg/thsice:
+ - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
+ - fix reshaping of sea-ice just after advection:
+   melt all the ice only if ice-volume is too small.
+ - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
+   prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
+ and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
+o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
+  tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
+o define mass2rUnit & rUnit2mass as units conversion factor, used for surface 
+  forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
+  (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
+  and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
+  of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
+  -> update output.txt
+o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
+ this affects truncation error: -> update output.txt of exp:
+  global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
+  ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
+
+checkpoint59f
+o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode) 
+o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in 
+  a bounded range (in forward mode)
+o pkg/ecco, ctrl, autodiff and mom_common:
+ internal parameter controls, completements of implementations
+o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
+o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
+  (not seem any difference in testing results).
+o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains 
+   at face corners.
+o pkg/generic_advdiff: 
+ - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
+  loop range indices for computing vertical advection tendency
+  and do the calculation in the interior only (no overlap) ;
+  for now, only implemented for SOM advection (to save CPU time).
+ - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
+o exch2 adjoint
+  First set of changes:
+  - add exch2 hand-written adjoint templates
+  - exch2 hand-written no longer use TAF-flag 'nownew_arg'
+    This will require cleanup in pkg/autodiff/*.F
+    (changed routines currently kept separate in verif. code/)
+  - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
+    that used to hide exch2 or cubed-sphere specific code
+    (commented via 'cph-exch2')
+o pkg/seaice
+  - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
+o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update 
+   output of global_ocean.cs32x15.thsice .
+
+checkpoint59e
+o exch2: new S/R that only use the cube-tracer (center-position) exchange:
+  for B-grid vector (not yet tested) and C-grid vector (<- only used
+  when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
+o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
+  (#ifdef ALLOW_SALT_PLUME)
 o gather_2d/scatter_2d: removed halo regions
 o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
   scheme and the corresponding test case (under front_relax dir). For now,