--- MITgcm/doc/tag-index	2005/10/14 12:45:43	1.573
+++ MITgcm/doc/tag-index	2006/01/11 06:04:11	1.598
@@ -1,9 +1,99 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.573 2005/10/14 12:45:43 mlosch Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.598 2006/01/11 06:04:11 edhill Exp $
 $Name:  $
 
     Notes on tags used in MITgcmUV
     ==============================
 
+o add "--embed-source" option to genmake2 which, when the supporting 
+  tools can be compiled (as determined by genmake2) will turn on the 
+  embed_files package which then embeds the entire MITgcm source code 
+  (*.[fFhc] + Makefile) used for the build within the executable
+  - requested by CNH but off by default
+  - adds a paltry <9MB to the mitgcmuv executable in most cases
+  - only writes the output when useEMBEDSRC in eedata is true
+o clean up 3-dim. relaxation codes:
+  * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
+  * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
+  * Thanks to Tom Haine for testing!
+
+checkpoint57z_post
+o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
+  affects output (@ truncation level) of exp. plume_on_slope ; updated.
+o fix the pickup behavior for obcs in combination with ptracers
+o fix a bug in ptracers_external_fields_load
+o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
+  affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
+o transfered surface NH pressure to eta field (if exactConserv).
+o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
+     and update lab_sea output.txt file.
+o completing 3-dim. relaxation code: additional term
+     1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
+  in S/R EXTERNAL_FORCING_T (file external_forcing.F)
+  * At compile time, in "EXF_OPTIONS.h" set
+      #define  ALLOW_CLIMTEMP_RELAXATION
+      #define  ALLOW_CLIMSALT_RELAXATION
+  * At runtime in "data", under &PARM03 set (e.g., units in seconds)
+      tauThetaClimRelax3Dim = 15552000.0,
+      tauSaltClimRelax3Dim  = 15552000.0,
+  * 3 cases:
+      1) Use a constant-in-time 3-dim. field
+      2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
+      3) Real-time relax. to time-evolving prescribed field
+o Adding Laplacian-type smoothness constraint on 
+  initial and boundary (forcing) controls (ic, bc)
+  * enable at compile-time via 
+    ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
+  * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
+  * Absolute scale somewhat unclear so far
+  * no area weighting was included since no other cost term does so far
+
+checkpoint57y_post
+First step for a NLFS adjoint
+o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
+o new init. routines for calc_r_star, calc_surf_dr
+o still need to deal with ini_masks_etc
+o testreport seemed happy
+checkpoint57y_pre
+
+o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
+o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
+o add new offset feature to offline pkg (plus minor cleanup)
+o cfc fixes for final year of integration
+o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
+  be in GCHEM_OPTIONS).
+
+checkpoint57x_post
+o fix testreport Pb in multiple test experiment.
+o cleanup our namelist syntax in verification:
+  - make it more F95 standards compliant (some work still needed)
+  - allows the vast majority of our tests to work with gfortran
+o Non-Hydrostatic:
+ - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
+ - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
+o Allow to apply AB on T,S rather than on AB(gT,gS):
+ - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
+ - use the same arrays (gtNm,gsNm) to hold tracer field at previous
+   time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
+ - need a "clever" read_pickup to restart from the other AB formulation
+o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h 
+o remove some unused variables (reduces number of compiler warnings)
+o adjoint
+  * Disable useVariableViscosity for adjoint for time being
+    (there are a number of extensive recomputations)
+  * Initialize certain variables needed for adjoint
+
+checkpoint57w_post
+o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
+             fix the singleCpuIO RS version of MDSWRITEFIELD
+   and add a WARNING if using globalFiles=T with multi-processors.
+o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
+  using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
+o tracer advection scheme:
+  add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get 
+   those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile, 
+   was not very convenient).
+  add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
+   (further tests needed for the implicit DST & Flux-Limiter schemes).
 o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
   and sRef for convenience, handy, when you want to initialize
   ptracers in a large domain with a constant non-zero value. Also,