--- MITgcm/doc/tag-index	2006/12/21 10:50:56	1.759
+++ MITgcm/doc/tag-index	2007/04/17 23:49:41	1.792
@@ -1,11 +1,123 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.759 2006/12/21 10:50:56 mlosch Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.792 2007/04/17 23:49:41 heimbach Exp $
 $Name:  $
 
     Notes on tags used in MITgcmUV
     ==============================
 
+o pkg/exf: 
+  - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
+    ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
+  - move exf header files from lower_case.h to UPPER_CASE.h ; 
+    add missing cvs Header & Name
+  - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
+o pkg/seaice:
+  - remove seaice_exch and seaice_exch_uv
+  - remove superfluous exchange of theta
+  - add myThid to seaice_budget_ocean/ice
+  - add new interface for atmospheric wind forcing (C-grid only)
+    + new routine
+    + two new field (taux, tauy for stress over ice)
+    + removed one global field (DAIRN) for C-grid case only
+o pkg/thsise
+  - 2nd set of modifs for thsice adjoint in conjunction with exf
+
+checkpoint58y_post
+o Added capability for latitudinal dependence of Bryan and Lewis, 1979
+  vertical diffusivity, similar to that in MOM4; turned on using
+  #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
+  diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
+o Added capability for 3D specification of background vertical diffusion
+  coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
+  in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
+  "data" file that contains the 3D vertical diffusivity coefficients.
+o ice dynamics (pkg/seaice) with thsice thermodynamics:
+  - add code within pkg thsice to advect & diffuse sea-ice fields
+  similar to (and will replace) what has been added in  seaice_advdiff.F,
+  but: - conserving Mass, Heat & Salt.
+       - better when using non-linear advection scheme (not yet fully tested)
+       - can also be used in atmospheric set-up (for now, only the diffusion).
+
+checkpoint58x_post
+o IO option for global-file compact format:
+  - add options when generating topology (utils/exch2/matlab-topology-generator)
+  - add I/O capability (pkg/mdsio).
+  - adapt utils/matlab/rdmds.m to read this format.
+  for now long-line format not yet supported by pkg/mdsio (& exch2).
+o shelfice: add a few diagnostics
+
+checkpoint58w_post
+o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
+  rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
+  (and replace horiVertRatio in NH code).
+  Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !) 
+                     and tutorial_plume_on_slope (sensitive to truncation)
+o seaice: if ALLOW_ATM_WIND is undefined use wind stress
+  directly to drive seaice model (C-grid only)
+o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
+ - reintroduce computation of wind from stress, 
+ - compute tau (in exf_bulkformulae.F) from windstress averaged to 
+   mass points to avoid tau = 0
+ - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
+o rdmnc.m: make it work with "global" files created with gluemnc
+o rdmnc.m : some improvements in dealing with singleton dimension
+  (tested on all testreport mnc output files).
+o genmake2: disable pkg/profiles if netcdf test fails.
+o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
+o move call to cal_readparms up to make calendar parameters/variable available
+  to all packages
+
+checkpoint58v_post
+o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
+  useDynP_inEos_Zc tested.
+o pkg/exf: changes to properly interpolate/mask/scale initial fields
+o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
+  and portions thereof.  See read_cs.txt for description and examples.
+o utils/matlab/cs_grid/bk_line: to compute transport through passages,
+  add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
+  following the great-circle arc between those 2 points.
+o trap un-initialized variable with pathscale compiler on weddell.mit.edu
+  (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
+o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
+ - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
+ - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
+ - still needs work (not working with some options ; efficiency to improve)
+   and serious testing.
+ - use this scheme for temperature & salinity in 2 advection test exp.:
+   advect_xy & advect_xz, respectively.
+
+checkpoint58u_post
+o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
+o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
+o testreport: add option "-skipdir" to skip some test.
+o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent 
+  momentum calculation.
+o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
+o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
+  remove checkpoint.F and the_correction_step.F (no longer used);
+  do the k loop inside CYCLE_TRACER (supposed to be more efficient).
+o add option (linFSConserveTr) to correct for tracer source/sink due to 
+  Linear Free surface
+o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
+o pkg/thsice: fix reading mnc-pickups
+
+checkpoint58t_post
+o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
+o pkg/mdsio:
+ - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
+   move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
+   mdsio_write_field.F (S/R MDS_WRITE_FIELD);
+ - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
+ - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
+   either MDS_READ_FIELD or MDS_WRITE_FIELD )
+ - new S/R (to replace MDSWRITEMETA), which allows to write more
+   informations (variable names, time ...) to meta files.
+ - modify rdmds.m to give back the meta file content.
+o pkg/diagnostics: change vertical interpolation to be safer, and more
+   flexible (define p-levels to interpolate to in data.diagnostics);
+  add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right 
+   diagnostic pointer.
 o pkg/seaice: more cleaning up of seaice_growth, added many comments
-o pkg/exf: put runoff0 and runoff into the appropriate common block
+o pkg/exf: put runoff0 and runoff1 into the appropriate common block
 o fix multi-category seaice:
  - change cpp flag SEAICE_MULTILEVEL to more meaningful name: 
    SEAICE_MULTICATEGORY