--- MITgcm/doc/tag-index	2004/12/09 09:03:32	1.406
+++ MITgcm/doc/tag-index	2004/12/17 05:03:43	1.417
@@ -1,8 +1,46 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.406 2004/12/09 09:03:32 mlosch Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.417 2004/12/17 05:03:43 jmc Exp $
 
     Notes on tags used in MITgcmUV
     ==============================
 
+o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC.
+o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon)
+  this is based directly on what the model compute, so that the content of
+  each diagnostics might be affected by switching options (e.g., implicitDiffusion)
+o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F)
+o clean up build options files for SunOS, in particular 
+  - remove -traditional from xmakedepend
+  - change -xarch=v9 to -xarch=native for f77
+  - restore use of make (not gmake)
+  - add CC=gcc if using g77
+o changes per discussion of AM, JMC, & EH3 today:
+  - move redundant "grid" variables out of "state" -- in preparation of 
+    creating proper CF-style coordinate variables and in recognition 
+    that any/all grid variables can be easily copied (eg. w/NCO) from 
+    the grid files into any of the other NetCDF files
+  - *always* output grid variables with MDSIO (this will eventually be 
+    changed)
+  - output MNC grid file if useMNC is true
+o every instance of _END_MASTER() has been found and replaced with 
+  _END_MASTER( myThid ) in order to satisfy certain picky Sun 
+  preprocessors
+o re-arrange diagnostics pkg initialisation:
+ - allow each package to extend the available diagnostics list
+ - add some checking and fix small problems (multi-threaded, ...)
+ - new S/R diagnostics_fill (replace fill_diagnostics):
+   look through the short list of active diag. (instead of the long list)
+   create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active
+
+checkpoint57a_post
+o this set of changes restores TAMC compatibility
+  tested for global_ocean.90x40x15 adjoint on trough
+  (what a pain)
+
+checkpoint57a_pre
+o some modifs in tools/build_options for sunos
+o call ctrl_pack for ctrl at end for optimcycle=0
+
+checkpoint57
 o add horizontal bi-harmonic viscosity for vertical velocity
   - new parameter viscA4W (defaults to viscA4)
   - affects only non-hydrostatic code
@@ -17,6 +55,8 @@
   and include in natl_box_adjoint
 o untangle a few ifdefs related to cost, ctrl, autodiff
   untangel a few ALLOW_ECCO_OPTIMIZATION
+o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)
+  (theta2, salt2 in ecco_cost_weights)
 
 checkpoint56c_post
 o OBCS as control variables