--- MITgcm/doc/tag-index	2010/01/12 00:23:23	1.1214
+++ MITgcm/doc/tag-index	2010/05/09 17:05:14	1.1265
@@ -1,9 +1,190 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1214 2010/01/12 00:23:23 jmc Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1265 2010/05/09 17:05:14 jmc Exp $
 $Name:  $
 
     Notes on tags used in MITgcmUV
     ==============================
 
+o model/src:
+  1rst version of a new driver S/R to turn-off output freq and flags after the
+  1rst forward sweep, to avoid over-writing output files during recomputations
+  (& grdchk); called from cost_final.F (and ctrl_init_ctrlvar.F ?).
+o model/src:
+  - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
+o pkg/exch2:
+  - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
+  - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
+o pkg/autodiff & exch2:
+  process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
+  (for now, only if ALLOW_EXCH2 is defined).
+o pkg/autodiff:
+  - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
+    (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
+   + clean-up comments (_RS is not always real*4)
+  - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
+  - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
+    was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
+o testreport (AD-tests):
+  no longer link files from dir "../input" (1rst link files from
+  "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
+
+checkpoint62f (2010/04/29)
+o model/src/the_main_loop.F:
+  adjust store directives for seaice evp and multicategory according to
+  pkg/ecco/the_main_loop.F
+o adjoint:
+  global_sum_ad was incomplete (noted many times by many people ;)
+  nice description by Jean U. as follows:
+  * allreduce(var) in global_sum.F can be interpreted as
+    reduce(sum) followed by broadcast of sum.
+  * The adjoint of that is
+    sum(adjoint) followed by broadcast(summed adjoint value)
+    or in other words, allreduce(sum, adjoint vars)
+  We were missing the sum(adjoint)!
+  Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
+  (noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset).
+  The fix should produce 16-digit accuracy between
+  single-CPU multi-tile (e.g. nSx=2, nPx=1) and
+  multi-CPU single-tile (e.g. nSx=1, nPx-2)
+  We'll probably change this yet again shortly
+o eesupp/src:
+  - fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?)
+o pkg/icefront
+  - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving
+    specification of addmass array based on a 2D field, which is added
+    at bottommost wet level at each horizontal location.
+o model/src:
+ horizontal grid initialisation (other than curvilinear): add code for Exch2 IO
+ layout; (not always compatible with delX,delY setting; commented out for now).
+o pkg/exch2:
+ change tile to processor setting (case nSy*nPy > 1): allows default model mapping
+ (myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config.
+
+checkpoint62e (2010/04/15)
+o pkg/obcs:
+  - fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert).
+o pkg/dic:
+  -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up;
+    (note: not presently tested in any forward verification exp.)
+   update tutorial_global_oce_biogeo AD output file.
+o pkg/exf:
+  - account for the variation of albedo as a function of zenith angle
+    by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h
+o build_options:
+ - rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas"
+o pkg/dic:
+  change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart:
+  - use binary pickup file for restart;
+  - initialise atmos-CO2 box from dic_pCO2 parameter;
+  - fix multi-threaded.
+o pkg/rbcs:
+ - clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ;
+   change (+ fix IO calls) type of array RBC_mask from _RL to _RS.
+ - add RBCS to exp4 passive tracer 01 (rbcs was previously untested)
+   and update output.txt
+o pkg/kpp:
+ - add diagnostics for KPP non-local flux of Temp, Salinity and pTracers;
+ - change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS
+   (= ratio of KPP non-local (salt) flux relative to surface-flux) when
+   using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat ');
+ - change pkg/offline to read-in average KPPghat*KPPdiffKzS from file
+   KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile).
+o pkg/offline:
+  fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor
+  (bug was added in version 1.10 on 2007-08-23).
+o pkg/offline:
+  - no need to specify periodicExternalForcing, etc ... to use offline pack
+  - offline input files no longer just single prec --> parameter offlineLoadPrec
+o verification/lab_sea:
+  change AD test to multi-tile setup and update all 4 AD output.
+  NOTE: while cost function values remain very similar,
+  gradients are very different, although gradient checks are self-consistent
+  Should try to get to the bottom of this (cost function summation order?)
+o pkg/dic:
+  in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid
+  a weakness of TAF that drops part of double precision in log10 derivative.
+  <= changes removed since problem has been fixed in current TAF version 1.9.71
+  update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo.
+o pkg/ecco:
+  add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F
+  update all 4 lab_sea AD output.
+
+checkpoint62d (2010/03/22)
+o build_options:
+  remove '-r8' (and '-i4') from linux_*pgf and linux_*ifort optfiles.
+o remove unbalanced quote (single or double) in commented line of source code
+  (may cause some warning with some preprocessor/makedepend versions).
+o pkg/seaice:
+  fix seaice_model.F for adjoint (gael) and update AD results of experiments
+   lab_sea (std + evp + noseaicedyn) and offline_exf_seaice.
+o testreport:
+  add option '-runonly' (short: '-ro') to just do the run part (without make).
+o eesupp: remove JAM communication code (obsolete).
+o add option to genmake2 & testreport to switch "_RS" type to "real*4"
+  (if allowed in CPP_EEOPTIONS.h); update default CPP_EEOPTIONS.h and return 
+  to default CPP_EEOPTIONS.h for exp. inverted_barometer & solid-body.cs-32x32x1
+  (update also the output).
+
+checkpoint62c (2010/03/02)
+o tools/build_options :
+   move (some) old optfiles from build_options/ to build_options/unsupported/
+o model/src and pkg/exf
+   surface relaxation -- separating data and data.exf options
+   The point is to ensure that we specify the surface relaxation
+   either in data or in data.exf (but not half and half) and to 
+   avoid an accidental relaxation to 0 (which happened if a time 
+   scale was specified but the file name was left empty)
+o model/src model/inc and pkg/mom_common
+   ALLOW_3D_VISCAH/ALLOW_3D_VISCA4 => 3D specification of Viscosity
+   => addition to the viscosity field as computed by others schemes
+o tools/build_options: 
+  - rename "_generic_mpi" -> "+mpi_generic" (like other "+mpi" optfile)
+    but keep the former optfile for few weeks for smooth transition
+o pkg/ecco
+  - allow user defined cost function contributions
+	CPP: ALLOW_USERCOST_CONTRIBUTION
+	USAGE: compute contributions in cost_usercost_all.F
+  - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
+      the two options are complementary.
+o pkg/smooth
+  - migration from contrib to the main repository
+
+checkpoint62b (2010/01/26)
+o pkg/monitor:
+  - change back mon_printstats_rl.F & mon_stats_rl.F and add a stop 
+    (in case someone forgot to update customized pieces of code)
+o nonHydrostatic:
+  - add Non-hydrostatic free-surface form (selectNHfreeSurf=1)(not fully tested);
+  - add a simple 2-D experiment (short_surf_wave) to test it.
+o pkg/icefront:
+   adding the shell of, and the hooks to, a new package that
+   will model melting and freezing of vertical glacier ice fronts
+o momentum:
+  add diagnostics of momentum tendency from Hydrostatic pressure gradient
+   (without surf.pressure term: would need a 2nd filling since implicit term).
+o add 3 "_d 0"s so that fizhi compiles with xlf on iblade, and replace
+  two " &end" by " &" (in fizhi-cs-*) because S/R NML_SET_TERMINATOR
+  cannot deal with the former
+o cleaning:
+  - remove all (except OpenAD) old TLM output from results_ad dirs.
+  - remove unused S/R (MDSWRITEMETA, DIAGNOSTICS_ADD2LIST, old DFILE IO S/R)
+  - comment out maskH definition (replaced by maskInC)
+o pkg/monitor:
+  - change mon_printstats_rl.F & mon_stats_rl.F (were similar to mon_writestats_rl
+    & mon_calc_stats_rl) to be the RL equivalent of mon_printstats_rs & mon_stats_rs.
+
+checkpoint62a (2010/01/15)
+o model/src:
+  - bottom pressure diagnostic: correct for r* (when nonlinFreeSurf >= 4)
+o pkg/diagnostics:
+  - add optional level number diagnostics (i.e., level number to be define
+    explictly with S/R DIAGNOSTICS_SETKLEV) with parser-code(10)="X".
+  - strictly check for valid parser-code(10) ;
+  - check if adding diag to the list from the right place.
+o pkg/longstep:
+  - change parameters and fix tracer conservation with rstar/nonlinear free surface
+o diagnostics:
+ - in all pkgs, replace remaining calls to old S/R DIAGNOSTICS_ADD2LIST with newer
+   S/R DIAGNOSTICS_ADDTOLIST ; fix seaice VICE diagnostics.
 o pkg/diagnostics:
  - Add option for writing vertical integral (sum of selected levels) of an output
     field instead of writing output field levels. Activate this option on a per