--- MITgcm/doc/tag-index	2010/11/11 09:43:16	1.1332
+++ MITgcm/doc/tag-index	2011/03/07 08:23:57	1.1389
@@ -1,9 +1,252 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1332 2010/11/11 09:43:16 mlosch Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1389 2011/03/07 08:23:57 mlosch Exp $
 $Name:  $
 
     Notes on tags used in MITgcmUV
     ==============================
 
+o pkg/ecco: remove an obsolete initialization from ecco_cost_init_barfiles.F
+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
+   read in Interior mask from file. Check if Interior mask is consistent
+   with OB list of indices.
+o pkg/seaice
+ - beginning code for a seaice tracer package,
+   but currently only used for seaice age: SEAICE_AGE
+   SEAICE_num = 4
+   iTracer = 1: area-weighted ice age
+           = 2: volume-weighted ice age
+           = 3, 4: template for one-year vs. multi-year ice
+   data.seaice has new namelist SEAICE_PARM03 for arrays related to
+   SEAICE_num
+
+checkpoint62t (2011/03/05)
+o pkg/obcs:
+ - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
+   then normal component. This ensures that the normal component is set
+   correctly even when it conficts with tangential setting from an other OB.
+   Affects results of test-experiment seaice_obcs: update the output.txt
+o pkg/obcs:
+ - add code to monitor statistics of dynamical fields at OB.
+ - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
+   - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
+   - change default: balance the Net inflow through all OB (instead of balancing
+     each OB separately); keep the old method if setting OBC_balanceFacX < 0.
+ - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
+   to match Nortern OB inflow (OBCS_balanceFacN=0).
+o pkg/seaice:
+ - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
+o pkg/seaice (seaice_growth v 1.113):
+ - reverting seaice_growth to v 1.111 in order to have code with exact bit
+   compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
+   CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
+   runtime flag SEAICEareaFormula is kept but is inactive
+o model/src:
+ - add new param to scale curvilinear grid distance and area when using
+   a different sphere radius from the grid-files.
+ - test/check multi-threads EXCH applied to local variable (cg2d_x)
+o adjoint:
+ - enable adjoint of Stevens OB
+ - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
+   (a bit delicate because of potentially modified adj. common block structure;
+   current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
+
+checkpoint62s (2011/02/15)
+o pkg/seaice (seaice_growth v 1.112):
+ - introduce SEAICEareaFormula run time parameter, which selects the recipe for
+   computing the ice cover tendency from effective thickness tendencies. Include
+   Ian Fenty's formula.
+ - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
+   SEAICEareaFormula.
+ - simplify notations for the various d_HEFF/d_AREA terms.
+o pkg/gmredi:
+ - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
+   from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
+   add a verification test-run (front_relax.bvp) to test GM_useBVP.
+o pkg/seaice (seaice_growth v 1.111):
+ - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
+ - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
+   also melt ice.
+o pkg/seaice:
+ - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
+ - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
+o pkg/cheapaml:
+ - from Nico Wienders: New version of this package.
+o pkg/flt:
+ - add CPP options to prevent floats to re-enter the opposite side of
+   a periodic domain (default: keep periodicity)
+o pkg/gmredi:
+ - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
+   (needed for multi-dim advection).
+ - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
+o model/src:
+ - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
+o tutorial_tracer_adjsens
+ - extend to NLFS and replace maskC by hFacC
+   (change reference output accordingly)
+
+checkpoint62r (2011/01/24)
+o testreport:
+ - add option -deloutp (-do) to remove output file after successful run
+ - add option -mfile (-mf) for MPI machile-file and for each test-exp,
+   extract exact list of procs from this file ; adjust COMMAND by
+   replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
+o pkg/ecco: replace old ineffective way of penalizing deviations from
+  first guess (of obcs) with code by Matt Mazloff
+o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
+  exf/cal
+  - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
+    and handle case of obcs?period == 0
+    Not affected by these changes: There is still an inconsistency in
+    the computation of start/endrec for the obcs variables for ALLOW_CAL
+    defined (see comment by Menemenlis, 7-Mar-2003)
+  - make S/R ctrl_get_gen_rec return something meaningful even if
+    ALLOW_CAL is not defined
+  - ctrl_getobcs?: simplify code so that it does not need to use
+                   S/R exf_swapfields
+o testreport:
+   allow to test MPI with different number of processors for each experiment:
+   create file "SIZE.h.mpi" in each build dir.
+   Note: update of "-command" argument not yet implemented.
+o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
+  alleviate the need for additional 3D tapes when using
+  the non-inear free surface in the adjoint. This is done
+  by adding an 'update' of hfacc etc. to their current
+  value at the beginning of forward_step.F.
+o pkg/seaice
+  seaice_lsr: move stress-divergence computations out of outer pseudo-
+  timestepping loop
+o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
+  up, so that the calls of the ctrl_* subroutines are really at the end
+  of the routine.
+o pkg/gmredi:
+  allow to specify a 2-D horizontal map and a 1-D vertical profil
+  as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
+o pkg/seaice:
+  move lsr iterations from seaice_dynsolver to seaice_lsr.
+o pkg/seaice:
+  reduce memory footprint of seaice mutldim advection tapes,
+  by using a 2D tape independent of the generic_advdiff ones,
+  and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
+
+checkpoint62q (2010/12/29)
+o model/src:
+  - check horizontal grid-spacing for unset or zero/negative values.
+  - change AD test hs94.1x64x5 to be truly a 2-D set-up.
+o pkg/flt:
+  - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
+  - precision of input and output files set according to readBinaryPrec
+    and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
+  - initial float position from tiled file was not converted to index space
+    (looks like a bug): fixed to make it similar to initial pos. global file.
+o global_ocean.cs32x15:
+   change SIZE.h of AD set-up to get same tiling as with MPI.
+   Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
+o model/src:
+   add flag to control printing of domain fields (bathymetry, hFac ...) in
+   ini_mask_etc (call to plot_fieds_xy*).
+o pkg/thsice:
+   if useEXF, some forcing fields are not valid in overlap: fixed by computing
+   over the interior only + apply EXCH at the end (like with SEAICE advection).
+o pkg/mdsio:
+  - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
+    to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
+  - change barrier call for safe multi-threads access to 3-D shared buffer.
+  - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
+  - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
+    remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
+o pkg/flt:
+  - add fourth-order Runge-Kutta integration
+  - add basic exch2 support (only 1 facet supported so far!)
+o pkg/mdsio+rw:
+  new S/R to read local (or tile independent) vector (read counterpart of
+   mds_writevec_loc, and front-end write_glvec_rl/rs).
+o global_ocean.cs32x15: additional input_ad.seaice experiment
+    that uses pkg/seaice rather than pkg/thsice.
+    (using multidim advection for seaice)
+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