--- MITgcm/doc/tag-index	2010/10/16 19:33:41	1.1315
+++ MITgcm/doc/tag-index	2010/12/19 23:20:01	1.1353
@@ -1,9 +1,186 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1315 2010/10/16 19:33:41 heimbach Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1353 2010/12/19 23:20:01 jmc Exp $
 $Name:  $
 
     Notes on tags used in MITgcmUV
     ==============================
 
+o towards more F95 syntax for array specification in namelist:
+  - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
+    of all verification experiments.
+       e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
+      was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
+  - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
+o global_ocean.cs32x15: additional input.seaice experiment
+    that uses pkg/seaice rather than pkg/thsice.
+
+checkpoint62p (2010/12/17)
+o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
+    to THSICE_SIZE.h to avoid conflict with pkg/seaice.
+o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
+    allow for use of multim. advection in seaice adjoint.
+o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
+  - first attempt to close budgets by taking into account the freshwater
+    flux implied by the sublimation of snow and ice. So far only the
+    volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
+    SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
+o eesupp/src:
+  new S/R with new option (NML_EXTENDED_F77) to change array specification
+  from F95 standard to commonly accepted extended F77 form.
+  This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
+  and to revert back to the original syntax (with -DNML_EXTENDED_F77)
+  for less tolerant f77 compiler (e.g., pgf77, g77).
+o globalFiles:
+  commented out in parameter file "data" since it's not safe with MPI
+  (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
+  in this case); no longer commented out in restart test (tst_2+2).
+o add adTapeDir to specify a special directory where adjoint tapes are
+  written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
+  and cannot be used together with mdsioLocalDir.
+o nesting pkgs:
+  - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
+  - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
+  - add parameter files + utils dir + output from short run on beagle.
+o pkg/seaice:
+    fix seaice_growth.F store directives; update results of exp. lab_sea.ad
+o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
+  unnecessary copying in adjoint code, requires new parameter NMAX_ITER
+
+checkpoint62o (2010/11/25)
+o pkg/exf:
+  - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
+o pkg/seaice:
+  - seaice_ocean_stress: split a loop for better vectorization of the
+    adjoint code
+  - seaice_growth.F: fix bug in conservation of freshwater connected to
+    capping of heff, put contribution into d_HEFFbyNEG
+  - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
+    by something more sensible (parameters that are what their name implies)
+  - change some defaults, so that by default exf-parameters are used for
+    things like rhoAir, cpAir,latent/sensible heat parameters, in order
+    to reproduce the old results, many data.seaice now contain funny values
+    for cpAir and latent heat of sublimation
+o packages_readparms.F: move exf_readparms up in line so that
+    exf-parameters are visible for other packages (e.g. seaice)
+o debugMode & debugLevel=2:
+  - differentiate between debugMode & debugLevel=2:
+    debugMode: controls printing of debug messages (sequence of S/R calls).
+    debugLevel: controls printing of algorithm intermediate results and stats.
+  - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
+    => allows to print debug-stats without all sequence of call messages.
+  - switch control of debug print from debugLevel to debugMode in many S/R.
+o pkg/obcs (obcs-sponge):
+    fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
+    call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
+o pkg/generic_advdiff:
+  - record overlap minimum size for each advection scheme;
+  - refine criteria on overlap minimum size;
+  - check and stop (in gad_check) if overlap size is too small.
+o pkg/obcs:
+  - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
+    once, in ptracers_implicit.F)
+  - with seaice: remove test on empty file name in obcs_apply_seaice (always
+    apply OB values when tile has OB)
+o model/src, coriolis setting:
+  - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
+    useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
+    files (selectCoriMap=3) with any grid.
+  - add parameter "fPrime" for constant second Coriolis coeff (default=0).
+o pkg/seaice/seaice_growth.F:
+    a few cosmetic changes that reduce the number of lines of code
+o pkg/obcs: add boundary conditions following Stevens (1990)
+  - the code follows old MOM/NAOSIM code
+  - so far it is only implemented for the eastern and western boundaries
+    and NOT for pTracers
+o pkg/rbcs:
+  - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
+    beginning of the first rbcs forcing period.
+  - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
+    offline package, i.e., one file per time, labeled by iteration number;
+    deltaTrbcs sets the timestep with which the data was generated;
+    rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
+  - rbcsForcingCycle=0 makes forcing non-cyclic.
+  - make arithmetic safe for negative times and odd forcing periods.
+
+checkpoint62n (2010/11/09)
+o pkg/seaice:
+    fix masking in free-drift S/R ; update results of exp. lab_sea.fd
+o pkg/obcs:
+   New S/R to copy tracer value from the OB location to narrow band region
+    (width = same as overlap) beyond the OB: preserve OB value (needed for
+    high-order scheme) which were overwritten by EXCH call if in overlap
+    region. Applied to theta, salt, ptracer and advected seaice variables.
+   With seaice: use maskInC in similar way as in gad_advection.F,
+    in seaice_advection.F and advect.F.
+   Update output of experiment seaice_obcs and change exp4 to test OBCS with
+    4th order Adv.Scheme. for pasive salt and ptracer.
+o tools/genmake2:
+  - when looking for an optfile (not specified), only search for Fortran compiler
+    (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
+  - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
+    (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
+  - set default for CPP to "cpp -traditional -P" (was the case without specifying
+    an optfile, but otherwise default was just "cpp".
+  - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
+  - when "CC" is not set in the optfile, look for possible C compiler
+    (instead of just setting CC=cc)
+  - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
+    => add a ".F" to ".o" rule for source files with no "#include" (such as
+       port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
+  - move gfortran before g77 in list of possible Fortran compiler (consistent
+    with reference compiler switch from g77 to gfortran)
+o pkg/seaice:
+  o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
+    seaice_check that stops the model, when the CPP flag is used.
+  o seaice_growth.F: make capping of ice volume conserving by returning the
+    capped ice as freshwater to EmPmR. This does not change the verification
+    experiments but will change runs where the capping is acutally active
+o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
+  (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
+     global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
+     lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
+o tools/genmake2:
+  - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
+  - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
+  - clean previous genmake log files before anything else.
+  - change Makefile to remove testreport log files (*.tr_log) and genmake log
+    files only with "CLEAN" target (instead of "Clean");
+o pkg/generic_advdiff:
+  Change OBCS in multiDim advection (gad_advection.F):
+   Use maskInC to prevent intermediate update of tracer-field in OB regions,
+   thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
+   which were applying future time-step OB values.
+  This way, all explicit calculations use current-time-step OB values
+   (simpler and more consistent).
+  Affects results when set-up uses time-varying OBC and multi-dim advection;
+   update output of experiment seaice_obcs.
+o pkg/seaice:
+  move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
+   this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
+     SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
+  Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
+   but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
+   unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
+o pkg aim (2010/10/26):
+  - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
+    formulation with obliquity, eccentricity, ... as run-time parameters,
+  - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
+    upward shortwave radition at the surface (all-sky and clear-sky).
+o pkg/obcs:
+  - writing sections with globalFiles=T does not work: switch to tiled-files
+    when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
+  - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
+  - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
+
+checkpoint62m (2010/10/21)
+o pkg/seaice: vectorize seaice_solve4temp.F
+  - move iterations loops outside of i/j-loops
+  - requires 2D arrays for TB and effConduct
+  - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
+    modified in this routine
+  - a little bit of clean up, adjusting indentation, etc.
+  - replaced a few TEN**a by exp(a*log(10.)) in new code for better
+    performance and '**TWO' by '**2' (because TWO is a float),
+    replaced ONE, ZERO
 o eesupp/src:
    fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
 o pkg/seaice/seaice_growth.F
@@ -39,6 +216,10 @@
     experiments that have this flag undefined (not tested in verification);
     a little reorganization to save a few 2D fields and recomputations
   - 1st step of revisiting thsice adjoint (major recomp. sorted out)
+  - 2nd step:  fix some store dirs
+    o seems to work somewhat, i.e. using ifort but not g77
+    o likely cause are incomplete init. or recomputation
+    o start verification/global_ocean.cs32x15/input_ad.thsice
 o pkg/obcs: add support for exch2
   - the position of the boundary and prescribed values are specified using
     a global domain with exch2 facets stacked
@@ -400,8 +581,8 @@
     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
+     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