--- MITgcm/doc/tag-index	2014/09/17 20:58:54	1.2066
+++ MITgcm/doc/tag-index	2014/10/06 14:12:28	1.2078
@@ -1,19 +1,92 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.2066 2014/09/17 20:58:54 gforget Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.2078 2014/10/06 14:12:28 gforget Exp $
 $Name:  $
 
     Notes on tags used in MITgcmUV
     ==============================
 
-o pkg/ecco :
-   - remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F)
-   - remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F)
-   - update cost_forcing_gen calls in cost_forcing.F
-   - update cost_genctrl call in ecco_cost_driver.F
-   - update ecco_ad_diff.list accordingly
+o pkg/ecco: increase modularity and improve logic
+  - ecco_toolbox.F (new) : basic operations that are often used
+     (for now, ecco_toolbox.F simply contains function ecco_zero).
+  - cost_gencal.F (new) : determine filnames and records.
+  - cost_gendif.F (new) : compute masked model-data difference.
+  - cost_genread.F : use ecco_zero to initialize field to 0s.
+  - cost_generic.F : use spzeroloc rather than hard-coded -9999,
+    and exploit the above functions leading to more compact code.
+  - ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj,
+    using_ers, using_gfo, using_mdt is now only defined within gencost)
+o pkg/ecco: extend generic cost capabilities
+  - pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost
+    capabilities via gencost_preproc (+ _c,_i,_r related params), 
+    gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod,
+    gencost_outputlevel arguments to cost_generic
+  - pkg/ecco/cost_genread.F (new) : interface between cost_generic
+    and active_read, making room for gencost_preproc to take effect.
+    Added preproc code ('climmon') to replace GENERIC_BAR_MONTH.
+  - pkg/ecco/cost_generic.F :
+    compute and store misfit maks*(model-data) in localdif that is
+    then used in cost and for output, output misfit if outlev.GT.0
+  - pkg/ecco/cost_averagesfields.F : depend on gencost_barskip
+    rather gencost_barfile for deciding whether to write barfile
+  - pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd
+  - pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from
+    ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip
+  - pkg/ecco/ecco_summary.F : report gencost variables
+  - pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs
+o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA
+o pkg/ecco: internal re-organization
+  - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl 
+    (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,
+    mv relevant variables definition from ecco_cost.h to ecco.h, 
+    make sure gencost routines only include ecco.h)
+  - throughout : add missing CCP switches, rm unused variables,
+    and rm un-necessary CPP switches
+  - throughout gencost routines : replace modelstartdate with 
+    gencost_startdate when needed
+  - cost_bp_read.F : use arguments, instead of common blocs
+    so that it can be used also by (new) cost_gencost_bpv4.F 
+  - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0
+  - ecco_phys.F : compute etanFull
+  - ecco_readparms.F : rename using_topex as using_tpj, add
+    bpv4-grace to gencost list, initialize added parameters
+  - ecco_summary.F : include SIZE.h needed for augmented ecco.h
+
+checkpoint65e (2014/09/28)
+o pkg/obcs:
+  - replaced the just-added CPP options with run-time variables
+    (see pkg/obcs/OBCS_PARAMS.h for details)
+o pkg/obcs:
+  - add additional CPP options for sponge boundary layers
+    (see pkg/obcs/OBCS_OPTIONS.h for details)
+o pkg/atm_phys:
+  - implement simple (obliquity only, assuming circular planet orbit)
+    seasonal cycle for incoming insolation ; used when run-time parameter
+    "select_incSW" is set to 1 ; by default (=0), uses old unchanged formula.
+o pkg/exf, pkg/ecco, pkg/ctrl:
+  - add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets
+  - activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip
+  - implement gentim2d for xx_tauu, xx_tauv
+o pkg/ctrl, pkg/ecco :
+  - fix and complement the generic controls implementation
+o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F,
+    pkg/shelfice/shelfice_thermodynamics.F,
+    verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F,
+    verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F :
+  - add weight in CTRL_GET_GEN calls
+o pkg/ctrl :
+  - ctrl_get_gen.F : add weight as input parameter, and apply
+    it directly rather than using smooth_correl2Dw (to be retired).
+  - ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call
 o pkg/ctrl :
-   - add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F)
-   - add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F)
-   - update ctrl_ad_diff.list accordingly
+  - introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F,
+    ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F)
+  - re-activate ctrl_summary (call in ctrl_init.F)
+o pkg/ctrl/ctrl_cost_gen.F :
+  - fix CCP brackets, remove un-necessary myiter, mytime
+o pkg/ecco, pkg/ctrl :
+  - remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F)
+  - remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F)
+  - add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F)
+  - add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F)
 
 checkpoint65d (2014/09/15)
 o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F :