--- MITgcm/doc/tag-index	2007/09/14 02:07:37	1.871
+++ MITgcm/doc/tag-index	2007/10/15 00:30:04	1.892
@@ -1,16 +1,77 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.871 2007/09/14 02:07:37 dimitri Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.892 2007/10/15 00:30:04 jmc Exp $
 $Name:  $
 
     Notes on tags used in MITgcmUV
     ==============================
 
+o pkg/monitor:
+  - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
+  - fix mon_stats_rs (statistics over the full domain, even where field is zero)
+  - account for deep Atmosphere factor and density factor (anelastic)
+o added open boundary conditions capability for seaice HEFF and AREA
+o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
+  thermodynamics
+  - requires a little reorganization, which affects the testreport results 
+    of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
+    so that now the conservative form is tested
+  - add a few comments
+o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
+o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
+o add new diagnostics to seaice: advective, diffusive fluxes (only for
+  multidim-advection, for scheme 2 they are not filled) and transports, 
+  thermodynamic growth rates
+o change units of EmPmR (inside the code) from m/s to kg/m2/s (mass flux) but
+  leave input file unchanged. Affects results @ truncation level (cg2d match)
+  and update output of experiments: lab_sea(6), global_ocean.90x40x15(10),
+  global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
+  + adjoint results: global_ocean_ebm(11) and lab_sea (12).
+  Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
+
+checkpoint59h
+o pkg/exf: 
+  - improve vectorization by moving if-statement out of loops in
+    exf_mapfields, exf_radiation
+  - exf_bulkformulae.F: introduce 2D fields and vectorize code
+o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
+o testreport: 
+  - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE 
+    monitor & update offline_exf_seaice exp. output.
+  - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
+o pkg/seaice:
+  - bug fix in the evp solver: boundary conditions were affected be
+    masking of zMax/zMin (changes results)
+  - minor bug fix in boundary conditions in seaice_calc_strainrates 
+    (changes results for no_slip)
+  - seaice_lsr.F: make interpolation of eta dependent on boundaries
+  - replace hardcoded lower limit for zeta (zMin) by runtime parameter
+  - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
+    stress formulation and no-slip boundary conditions
+o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
+  in gad_calc_rhs.F ; add few safety stops in initialisation phase.
+o pkg/seaice: a first HSALT time stepping equation has been checked in
+o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
+  in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
+  without requiring DO-IF statements
+o pkg/thsice:
+  use continuous power-law function for partition of energy between lateral
+  melting/freezing and thinning/thickening ; old code using step function
+  still available with #undef THSICE_FRACEN_POWERLAW
+  update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
+o testreport: change AD testing : check against results/output_adm.txt
+  using same scripts as for forward test.
+
+checkpoint59g
+o adjoint testing: in preparation for changing testreport:
+  - output format: cost and grad written on separated lines
+  - ad output results in directory "results" (instead of "results_ad")
+o pkg/seaice: adding ice salinity HSALT as a prognostic variable
 o pkg/seaice: changes for using pkg/seaice with pkg/obcs
 o pkg/ecco: allow user defined cost function contributions 
 o testreport:
   Allow to choose (per experiment) the list of tested output variables
    and the main variable (used to issue a pass/FAIL ) ;
   - for now, done by adding the specific list in file: [exp]/input/tr_checklist
-  - default is unchange: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
+  - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
   Also modify printing of summary:
    a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
    b) echo the list of tested variables in the individual summary.txt of
@@ -273,7 +334,9 @@
      ATMOSPHERIC_LOADING is #define).
 o pkg/kpp: replaced _KPP_RL with _RL
 o bug fixes for vertical diffusivity computations when both KPP and
-    3D diffusivity arrays are used.
+    3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
+    are no longer updating the vertical diffusivity array
+    (passed as argument) but are (re-) setting those arrays.
 o pkg/seaice: fix bug in evp solver, while doing that
   - change (improve?) discretization of stress computations for both
     cgrid-lsr and evp solver