--- MITgcm/doc/tag-index	2012/07/06 15:32:20	1.1684
+++ MITgcm/doc/tag-index	2012/07/27 18:29:17	1.1696
@@ -1,9 +1,79 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1684 2012/07/06 15:32:20 jmc Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1696 2012/07/27 18:29:17 heimbach Exp $
 $Name:  $
 
     Notes on tags used in MITgcmUV
     ==============================
 
+o pkg/ctrl:
+  enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of
+  generic control variables via
+  #define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL
+  Only required customization should be S/R ctrl_map_ini_genarr.F
+  (routine in repository contains example)
+o pkg/exf:
+  - fix and refine checking of surface-relaxation setting when using EXF
+o verification (adjoint exp):
+  - reduce length of simulation by half for experiment global_ocean.cs32x15
+    (std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output.
+o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag)
+  - replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers
+    of KE that can occur with aggressive optimization
+  + put quadratic bottom drag calculation in separated loops (only done if
+    using bottomDragQuadratic)
+o model/src: CG2D_NSA
+  - clean-up:  stop if cg2dNormaliseRHS=T and AUTODIFF
+     and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE.
+  - in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens),
+     change cg2d residual target to be expressed in Wunits (=> do not normalise
+     RHS ; this fix global_max Pb with TAF); update output.
+o verification/tutorial_tracer_adjsens:
+   improve parameter consistency (and get rid of warnings):
+   - use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf);
+   - switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical)
+   - use staggerTimeStep (for stability) in som81; use default rotation period.
+o pkg/exch2:
+  - with empty facet: fix compact-format (W2_mapIO=1) definition (was previously
+    reset to 0 = 1 long line in X)
+o pkg/mdsio:
+  - fix reading of dimensions from meta file for large-size domain
+o model/src:
+  - fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long);
+  - to refine CS-grid check, add logical flag "hasWetCSCorners": true if using
+    Cubed-Sphere Exch with CS-corners inside the domain;
+    make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate
+    globalArea and to set hasWetCSCorners.
+  - add warning if usingCurvilinearGrid and momAdvection in flux-form (missing
+    metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form.
+  - re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if
+    useCDscheme and useCubedSphereExchange).
+o pkg/seaice/seaice_growth.F :
+  - compute the SEAICE_DISABLE_HEATCONSFIX term accordingly
+    for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0)
+    when the previous code was not correct.
+  - in all cases diagnoze the boundary condition mismatch to SIaaflux
+  - in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add
+    that term to QNET (essentially to set the melt/freeze water to 0degC).
+    when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed.
+o verification/global_ocean.cs32x15/input.seaice :
+  - add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget.
+  - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces).
+  - update results (output.seaice.txt) accordingly.
+o verification/lab_sea/input/data.seaice :
+  - remove SEAICEheatConsFix, which is now be tested
+    in global_ocean.cs32x15. The presently coded fix
+    is only consistent with real fresh water + nlfs.
+  - update results (output.txt) accordingly.
+o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd).
+o AD_CONFIG.h file:
+  - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;
+  - remove #include "AD_CONFIG.h" from all included OPTIONS files and
+    add it explicitly in each fortran src file where it is needed.
+    motivation: header file AD_CONFIG.h is generated/modified after "make depend"
+    thus introducing potentially wrong dependency; therefore, better to include
+    it only where it's really needed, and after any other included OPTIONS file
+    (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN
+    or ALLOW_TANGENTLINEAR_RUN).
+
 checkpoint63p (2012/07/06)
 o pkg/autodiff:
   - rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ;