--- MITgcm/doc/tag-index	2007/06/17 09:22:06	1.837
+++ MITgcm/doc/tag-index	2007/08/16 02:34:16	1.858
@@ -1,9 +1,83 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.837 2007/06/17 09:22:06 mlosch Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.858 2007/08/16 02:34:16 jmc Exp $
 $Name:  $
 
     Notes on tags used in MITgcmUV
     ==============================
 
+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,
+  only available with Skew-flux form and not yet tested in realistic set-up.
+  adjoint: store directives updated, but gradient checks deteriorated,
+  so maybe GM/Redi adjoint is now broken.
+o seaice adjoint
+  * add AREA, HEFF, HSNOW as control variable
+    (should not change lab_sea results)
+  * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
+o pkg/seaice:
+  * added computation of saltFlux in seaice_growth;
+    For time being, sea ice salinity is assumed constant
+    contribution of snow flooding to freshening of sea ice is neglected.
+    SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
+    defaults to 0.0 in order to maintain backward compatibility.
+    Typical values for SEAICE_salinity are 4 to 10 g/kg.
+  * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
+  * added SEAICE_availHeatFrac, which specifies fraction of surface level
+    heat content used to melt or grow ice
+  * commented out cap of HICE: it helps keep ice thinner
+  * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
+  * applied OBCS T/S mask to HEFFM sea ice mask
+
+checkpoint59d
+o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
+ for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
+ (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
+o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
+ and change default value of parameter "GM_Small_Number";
+ update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
+   global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
+   tutorial_global_oce_biogeo, tutorial_global_oce_latlon
+o pkg/ecco: cost function when applying pkg/smooth to controls
+o pkg/ctrl: add forcingPrecond run time parameter
+o pkg/seaice:
+ - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
+ - fix bug in metric terms of u-equation in LSR solver (implicit part), 
+   changes verification/lab_sea
+ - rearrange implicit part of u-equation in LSR solver to make it easier to
+   read, understand, and debug. This causes changes at the truncation level.
+ - fix (serious) bug in the boundary conditions (sign error in the implicit 
+   part) of the LSR solver. Changes all LSR results.
+ - fixed problem with HSNOW initialization to avoid thick snow when AREA
+   is initilized with small values - does not change lab_sea results.
+ - added HsnowFile initialization capability
+o pkg/smooth: addition to model/src and pkg/ctrl so allow 
+ initialization of pkg/smooth and application to control vector
 o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
 o dependencies: pkg/profiles requires pkg/cal
 o pkg/profiles:
@@ -15,7 +89,6 @@
      that allow you to prepare netcdf input files.
  - also modified: cleaner include statements, cleaner error print statements, 
    cleaner stops when error, and more tests of the netcdf input files consistency.
-
 o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
 o pkg/seaice:
  - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this