--- MITgcm/doc/tag-index	2013/12/19 01:06:09	1.1950
+++ MITgcm/doc/tag-index	2014/02/13 00:12:27	1.1967
@@ -1,12 +1,90 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1950 2013/12/19 01:06:09 dimitri Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1967 2014/02/13 00:12:27 jmc Exp $
 $Name:  $
 
     Notes on tags used in MITgcmUV
     ==============================
 
-o useSingleCpuInput separates single-CPU input from single-CPU output
-o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the 
-  SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8
+o verification/MLAdjust:
+  - rename secondary test suffix:
+     1.leith  -> A4FlxF  + switch to flux-form & add side-drag
+     0.leithD -> AhFlxF  + switch to flux-form
+     0.smag   -> AhVrDv  (use Vorticity-Div. visc form) + add side-drag
+     0.leith  -> AhStTn  (use Strain-Tension visc form) + add side-drag
+o pkg/mom_vecinv:
+  - remove unused arguments from S/R MOM_VI_HDISSIP & MOM_HDISSIP (as it used
+    to be before mom_calc_visc.F)
+  - skip the call to MOM_CALC_TENSION & MOM_CALC_STRAIN if not needed.
+  - add 2nd copy of vort3 & strain that knows about lateral BC (free/no slip):
+    this is simpler for the adjoint and for diagnostics.
+o model/src + pkg/momentum:
+  - add input files for  2-D additional Western and Southern cell-edge wall
+     (e.g., to add "thin-wall" where it is =1).
+  - fix sideDrag option for thin-walls with Non-Lin Free-Surf
+    using 2nd hFacZ that is computed from initial (fix domain) hFac
+  - known limitations of thin wall implementation: not yet coded for sigma
+    coords; not working with CD-scheme neither.
+o pkg/seaice:
+  - rename recently introduced parameters from (wrong name) AB to
+    BDF (backward difference time discretisation)
+  - retire runtime parameters SEAICEuseAB2, SEAICE_abEps
+o tools/adjoint_options:
+  - remove setting of "OPENAD=true" (now set by command line "genmake2 -oad")
+
+checkpoint64t (2014/02/01)
+o pkg/thsice
+  - corrected store directive fixes thsice adjoint gradient checks
+o genmake2 & testreport:
+  - add genmake2 option "-oad" to generate a Makefile for OpenAD built and
+    in this case, use tools/adjoint_options/adjoint_oad as default AD optfile.
+    Update testreport accordingly. No need to set "export OPENAD=true"
+    in adjoint_options/adjoint_oad anymore (will be removed later).
+o pkg/shelfice:
+  - put T & S shelfice forcing into model surfaceForcing_T,_S (for now,
+    only if SHELFICEboundaryLayer=F); Change model/src/external_forcing.F
+    so that surface forcing applies to k=kSurf if using pkg/shelfice.
+o pkg/ctrl, pkg/grdchk, pkg/ecco:
+  - Changes to make GENARR more modular (i.e. invisible if not used)
+o model/src/temp_integrate.F and salt_integrate.F
+  - re-include store directives that were removed on Dec 27th.
+o model/src/external_forcing_surf.F
+  - add storage directives for EmPmR and PmEpR to avoid recomputation of
+    seaice_model in the adjoint that is problematic when seaice_model is
+    turned off in the adjoint. The resolved issue dated back to July when
+    EXTERNAL_FORCING_SURF call was moved.
+    Update global_ocean.cs32x15/*/output_adm.seaice_dynmix.txt accordingly.
+o pkg/exf/exf_check.F
+  - fix a small bug again (originally found by Wentao Liu, now found again)
+  - streamline error output
+o pkg/streamice and aim_v23:
+  - replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that
+    Apple's /usr/bin/cpp knows what to do:
+    Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
+    Target: x86_64-apple-darwin13.0.0
+
+checkpoint64s (2014/01/05)
+o tools/adjoint_options:
+  - switch to fastopt.net TAF server (instead of default fastopt.de) for
+    AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default).
+o model/src:
+  - remove some unnecessary TAF storage directives in forward_step.F and
+    in dynamics.F (note: not always removed by TAF, e.g., double storage
+    of kappaRU,kappaRV in former version of dynamics.F).
+o model/src & pkg/ptracers:
+  - call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F
+    salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F)
+    and remove ptracers_dwnslp_apply.F & ptracers_implicit.F
+  - call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F)
+  - add fZon & fMer as output argument of S/R GAD_CALC_RHS.
+  - update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad).
+o useSingleCpuInput separates single-CPU input from single-CPU output;
+    for now only implemented for in exf_interp_read.F
+o verification/advect_xy:
+  - fix missing EXCH call in local version of ini_salt.F and update output.
+o momentum diagnostics:
+  - fix which deltaT is used in Total-Tendency diagnostics.
+  - fix typo in diagnostics for momentum tendency from AB.
+o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the
+    SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8
 
 checkpoint64r (2013/12/08)
 o verification/*/results:
@@ -112,7 +190,7 @@
 o pkg/cost:
   - define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL
     (instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads:
-    o this fixes global-sum value if multi-threads (since GLOBAL_SUM_TILE_RL
+    o this fixes global-sum value if multi-threads (since GLOBAL_SUM_RL
       cannot be applied to var in common block).
     o allows to get results independent of tile-per-proc setting (if using
       slower GLOBAL_SUM_SEND_RECV option).