--- MITgcm/doc/tag-index	2011/03/10 09:35:14	1.1392
+++ MITgcm/doc/tag-index	2011/04/02 18:10:15	1.1405
@@ -1,9 +1,63 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1392 2011/03/10 09:35:14 mlosch Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1405 2011/04/02 18:10:15 jmc Exp $
 $Name:  $
 
     Notes on tags used in MITgcmUV
     ==============================
 
+checkpoint62v (2011/04/02)
+o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
+  (new velocity statistics after changing maskInW & maskInS definition)
+o pkg/generic_advdiff with OBCS:
+  use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
+  equivalent to assumption of no tracer gradient outside the OB region.
+  This will affect the results if using obcs+biharmonic diffusion.
+  update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
+o pkg/obcs:
+  change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
+  (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
+  in Interior region. No impact on solution but affects Velocity monitor stats.
+o pkg/ptracers (adjoint)
+  New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
+  tape file for each tracer
+o model/inc/src and pkg/autodiff: add parameters that allow to turn
+  of parts of the adjoint code at run time. For now, there are only
+  useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
+  parameters are set in data.pkg.
+  This is the lazy coward's version of doing this, but still useful for
+  debugging. In order to do it right, everything needs to be moved to
+  pkg/autodiff.
+o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
+  the end; this fixes the adjoint balancing code for open boundaries.
+o pkg/ctrl:
+  - change behavior of xx_${varname}period to be analogous to exf-conventions:
+    xx_${varname}period =   0.,  means time-independent control part
+    xx_${varname}period = -12., means one-year-periodic monthly control part
+  - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
+    clean up ctrl_init a little, remove unused variables
+  - ctrl_init: fixed the handling of the start/endrec for obcs-variables
+  - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
+
+checkpoint62u (2011/03/15)
+o model/src:
+  - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
+    h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
+  - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
+    INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
+o pkg/ctrl/obcs/ecco:
+  - remove obsolete, unused, and partially broken code:
+    ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
+    ALLOW_CTRL_OBCS_BALANCE
+  - put a stop statement into ecco/cost_obcsvol.F, but also add
+    cost_obcsvol to ecco_ad_diff.list
+o pkg/ecco: fix counting cost function contributions for obcs (code
+  by Matt M.) and diffkr for diagnostics
+o pkg/ecco, pkg/ctrl, pkg/grdchk:
+  add cost penalty terms for initial uvel, vvel, eta controls
+  and I/O for prior error files
+o pkg/mdsio:
+   move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
+   (new argument) to check for tiled file in mdsioLocalDir : this fix the
+   restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
 o pkg/ctrl:
  - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
    ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
@@ -11,13 +65,13 @@
  - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
 o pkg/ecco
  - enable adjoint of Stevens OB
-o pkg/ctrl/ecco/grdchk: 
+o pkg/ctrl/ecco/grdchk:
   - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
     Fortunately, we do not have any tests for the numerous cpp-flagged
     option of "obcs as control parameters" so we will never know
     if this is an improvement (but at least now things compile).
   - remove an obsolete initialization from ecco_cost_init_barfiles.F
-  - fix some problems within never used ifdefs to make the code compile 
+  - fix some problems within never used ifdefs to make the code compile
 o pkg/obcs:
  - Refine Interior mask definition to work with more complex OB (e.g.
    if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to