--- MITgcm/doc/tag-index	2007/06/06 14:37:14	1.832
+++ MITgcm/doc/tag-index	2007/09/14 02:07:37	1.871
@@ -1,10 +1,149 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.832 2007/06/06 14:37:14 mlosch Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.871 2007/09/14 02:07:37 dimitri Exp $
 $Name:  $
 
     Notes on tags used in MITgcmUV
     ==============================
 
+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,
+  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:
+ - added option ALLOW_PROFILES_GENERICGRID
+     -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
+     that interpolation information (grid points and coefficients) is provided 
+     within the netcdf input files.
+     -> sample matlab scripts can be found in MITgcm_contrib/gael
+     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
+   requires a new routine: seaice_diagnostics_fill.F
  - make sure that seaice does not move if not forced (pressure replacement
    method, Hibler and Ip, 1995), changes results
  - and new damping criterion for EVP solver according to Hunke, JCP, 2001