--- MITgcm/doc/tag-index	2006/11/20 20:06:43	1.747
+++ MITgcm/doc/tag-index	2007/04/17 16:15:27	1.790
@@ -1,9 +1,162 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.747 2006/11/20 20:06:43 dimitri Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.790 2007/04/17 16:15:27 mlosch Exp $
 $Name:  $
 
     Notes on tags used in MITgcmUV
     ==============================
 
+o pkg/exf:
+  move exf header files from lower_case.h to UPPER_CASE.h ; 
+  add missing cvs Header & Name
+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
+
+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 runoff1 into the appropriate common block
+o fix multi-category seaice:
+ - change cpp flag SEAICE_MULTILEVEL to more meaningful name: 
+   SEAICE_MULTICATEGORY
+ - fix short wave heat flux
+o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
+   and allow to use EVP solver. Change forward lab_sea: test both EVP 
+   solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
+o Initial check-in of lab_sea adjoint
+  (very similar to natl_box_adjoint/code_seaice)
+  * used C-grid and EVP solver
+  * used KPP, GM/Redi
+  * uses inAdExact=.TRUE.
+  * gradient checks fail for both ADM and TLM
+    due to sensitive snow melt code in seaice_grwoth (look for "JZ")
+    f.d. gradients actually seem more problematic than ADM, TLM gradients;
+    issue is related to forward mismatch between g77 an ifort
+o pkg/seaice: overhaul of thermodynamics
+ - growth.F and groatb.F are replaced by new routine seaice_growth.F
+ - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
+ - move a few global fields out of SEAICE.h into seaice_growth.F and
+   make them 2D (FICE/QNETO/ ...)
+ - remove FO (it is the same as QNETO)
+ - introduce a few local fields to avoid modifying external fields such
+   as atemp, etc.
+
+checkpoint58s_post
+o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
+  changed exf_set_gen.F so that
+    genperiod=0 means input file is one time-constant field and
+    genperiod=-12 means input file contains 12 monthly means
+o CG2D: use pre-computed solver main-diagonal (stored in common block);
+  this affects truncation error ; generate new output file for exp. which
+  fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
+    global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
+    ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
+    MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
+    tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
+    vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
+o start implementation of deep-atmosphere and anelastic formulation
+o verification: remove 2nd copy of input files and use script "prepare_run"
+  to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
+o mom_common/vecinv/fluxform: fix a few initialisation isssues
+o profiles: fix for multithreaded case
+
 o diagnostics: rename few diags:
   s/'PRESSURE'/'RCENTER '/g
   s/'TICE    '/'oceFreez'/g