--- MITgcm/doc/tag-index	2007/05/10 16:55:58	1.812
+++ MITgcm/doc/tag-index	2007/08/17 20:51:27	1.859
@@ -1,10 +1,180 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.812 2007/05/10 16:55:58 heimbach Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.859 2007/08/17 20:51:27 jmc Exp $
 $Name:  $
 
     Notes on tags used in MITgcmUV
     ==============================
 
+o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
+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
+ - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value). 
+   It is turned off by default (=-1.), because it changes the results.
+ - make it possible to read AREA from a file, too.
+
+checkpoint59c
+o add S/R and diagnostics for oceanic mixed-layer depth
+o move GMRedi call after all vertical mixing schemes (including KPP)
+o pkg/thsice: 
+ - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
+  (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
+o pkg/obcs:
+ - bug fix for balance code
+o pkg/seaice:
+  - allow values of SEAICE_elasticParm > 1
+  - add new parameter SEAICE_evpTauRelax as an alternative 
+    to SEAICE_elasticParm
+  - make lsr boundary conditions free slip (by default), changes result
+  - add code for no slip boundary conditions for lsr
+  - set minimum of zeta to zero (and not 4e8) (changes results)
+  - add a cap on AREA after advecting AREA if seaice_growth is not called
+o change calculation of Visbeck K:
+  - no longer depend on tapering scheme; instead, compute slope (limited 
+    by GM_maxSlope). this is equivalent to what was comuted before with
+    clipping or linear tappering.
+  - fix vertical averaging (wrong by 1/2 level)
+  - leave the old version (but will not be maintained) within
+    #ifdef OLD_VISBECK_CALC / #endif
+  - update output of exp. ideal_2D_oce
+o change error catch in calc_r_star to improve vectorization
+o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
+  add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
+o adjoint:
+  Re-organized adjoint checkpointing according to Matt Mazloff
+  (but with modifs/completions/cleanups)
+  Storing is now bundled into large arrays to optimized I/O
+  (and second step in cleanup of the_main_loop)
+
+checkpoint59b
+o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
+  - export/import (between ocean & coupler) fields needed for ocean DIC.
+o pkg/seaice: 
+  - get rid of three more exchanges seaice_calc_viscosities (required 
+    different loop boundaries in seaice_lsr and seaice_ocean_stress)
+  - bug fix in seaice_ocean_stress (update of lab_sea required)
+  - reduce loop boundaries to necessary minimum also in seaice_evp
+  - go back to the old way of computing deltaC/Z as the adjoint likes that 
+    better
+o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
+  passive tracer to an Age Tracer) + update output.txt
+o pkg/exf:
+  - implement A-grid / C-grid selection for wind-stress input files.
+  - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
+  for now, in exf_bulk_largeyeager04.F only :
+  - change implementation for case where windspeed + 2. components wind-stress
+    are read-in. AND use rhoConstFresh to convert evap.
+o pkg/seaice:
+  - use correct EXCH_UV for wind-forcing (on A-grid).
+  - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
+    SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
+o pkg/exf:
+  - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
+  EXF_INTERPOLATION: 
+  - merge global_with_exf/code version of exf_interp_read.F
+    to the main code ; 
+  - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when 
+    reading the file ; Important: This options needs to be defined to recover 
+    previous code.
+    otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
+  - no longer loose real*8 precision along the way when using exf_iprec=64.
 o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
+  - change discretisation of evp-solver in order to avoid another exchange
+    (changes lab_sea) and clean up a little
+  - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS) 
+    help the adjoint (this also changes the results slightly)
+  - add a few "_d 0" where they had been missing in seaice_evp.F
+  - cleaning up: remove unused seaice_calc_rhs.F
 o pkg/exf: some cleaning-up:
   - change various "constants" into runtime parameters
   - cleaned-up Large&Yeager04 routine which should eventually
@@ -18,7 +188,7 @@
 o pkg/thsice:
  fix few little problems, in thsice_calc_thickn.F:
   - growth vertically (and not laterally) if iceFrac == iceMaskMax
-  - melt laterally only if hIce < hThinIce (as the comments say)
+  - melt only laterally if hIce < hThinIce (as the comments say)
   and in thsice_extend.F:
   - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
   - start to form ice as soon as the minimum ice-volume is reachable.