--- MITgcm/doc/tag-index	2009/09/30 16:03:49	1.1164
+++ MITgcm/doc/tag-index	2009/11/13 09:05:35	1.1194
@@ -1,9 +1,97 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1164 2009/09/30 16:03:49 mlosch Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1194 2009/11/13 09:05:35 mlosch Exp $
 $Name:  $
 
     Notes on tags used in MITgcmUV
     ==============================
 
+o pkg/seaice
+ - change (once again) the discretization for the evp solver: rather than
+   squaring the averages of strain rates, average the squares to give
+   a better approximation to VP behavior (in simple test); this breaks
+   verification experiments that use EVP (lab_sea and lab_sea.hb87)
+    --> update outputs
+o add CPP-flag (in mom_calc_visc.F) and TAF directive (in gmredi_slope_limit) 
+  to improve vectorization of adjoint code on TARGET_NEC_SX
+o verification/vermix:
+  - change vermix to a more "classical" 1d column with high vertical 
+    resolution, seasonal heat flux forcing and constant wind forcing 
+    --> update outputs
+o pkg/seaice
+ - fix diagnostics of principal stress components for EVP
+ - add optional diagnostics of non-linear convergence for LSOR solver
+ - make maximum zeta a runtime parameter
+o model/src (3-d solver):
+  Undo modif from Dec 12, 2005 (solve_for_pressure.F cvs version v.49),
+   which consisted in removing the Surf. Non-Hydrostatic pressure from the
+   whole column and adding it to Eta (inspired from Casualli, 1999):
+   Only affects 3-D solver initial guess and only if using ExactConserv,
+   but tests did show a degradation of solver convergence. For this reason,
+   decide to disable this piece of code.
+   to recover previous version, just set zeroPsNH = exactConserv (line 78).
+  Update output of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW
+o pkg/ggl90: 
+ - fix previous modif (unfortunatly has not been documented here).
+o pkg/seaice/autodiff:
+ - add CPP flag to include clipping of zeta in EVP code;
+   although clipping of zeta is not necessary for EVP and not recommended
+   it was done by default, now clipping is disabled by default
+ - modify computation and store zetaC/Z in seaice_evp for TAF
+ - add CPP-flag SEAICE_ALLOW_CLIPVELS (undefined by default)
+ - change seaice_calc_viscosities/strainrates for better
+   vectorization after AD by TAF
+ - rearrange common blocks in SEAICE.h once again for easier dumps of
+   adjoint output, adjust adcommon.h and g_common.h
+ - change flux form of default advection scheme for better vectorization
+   of adjoint code
+ - modify lab_sea/input.lsr to test the flux form of default advection 
+   scheme
+o autodiff: fix seaice fields in g_common.h (left over from 3 to 1 level
+  transition in checkpoint61r)
+
+checkpoint61x
+o adjoint: adding two new verification experiments
+  * tutorial_global_biogeo: an online dic sensitivity experiment 
+    (work with G. Forget)
+  * tutorial_dic_adjoffline: an offline dic sensitivity experiment
+    (an update of the Dutkiewicz et al., 2006 paper)
+  Both use the same CO2FLUX cost function, but different controls
+  Gradient checks look good, but some recomp. could still be traightened out
+  Should add xx_dic control variable to test at some point
+o model/src:
+  add run-time parameters to check and/or mask initial Temp & Salt
+o pkg/ptracers:
+  apply zonal filter (if used) to all passive tracers
+
+checkpoint61w
+o adjoint:
+  * update and finish work on adjoint of dic package (G. Forget)
+  * start adjoint of offline package
+  * bug fix for cube-sphere TLM code (active_file_g.F)
+o tutorial_global_oce_optim:
+  now tested with 4 tiles (change data.grdchk and update output_adm.txt)
+  and add SIZE.h_mpi for MPI testing
+o pkg autodiff
+ - fix bug in autodiff_restore
+ - make genmake2 remove comments and empty lines from ad_input_code.f in 
+   order to reduce file size (new script file remove_comments_sed)
+o allows to specify vertical profile of vertical viscosity (viscArNr)
+o pkg autodiff
+  autodiff_ini_model_io: comment out writing of grid information to netcdf 
+  files, because at this time the grid fields are a bunch of zeros 
+  (this is analogous to ini_mnc_vars.F) 
+o pkg seaice/autodiff:
+ left-over from removing the 3-time-level fields: 
+ - small rearrangement of common blocks (SEAICE.h)
+ - fix field declaration in order to get meaningful output in 
+   adseaice.*.nc (adcommon.h) 
+o pkg obcs:
+ - go through NH code only if nonHydrostatic=T
+ - fix restart for Orlanski (Hydrostatic; still to fix NH+Orlanski restart)
+ - move call to OBCS_CALC before SEAICE_MODEL which needs seaice-obc fields
+   => Update output of experiment seaice_obcs
+ - useOBCSbalance: code is wrong with multi-tile / proc: add a stop.
+ - fix NH+Orlanski restart (add wvel OBC value in pickup file)
+ - fix restart for useOBCSprescribe + useEXF
 o pkg ctrl
  - make obcs as control parameter work also with useSingleCPUio
  - replace a few sny and snx by Ny and Nx to be consistent with