--- MITgcm/doc/tag-index	2004/12/09 09:03:32	1.406
+++ MITgcm/doc/tag-index	2005/02/09 17:34:19	1.448
@@ -1,8 +1,117 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.406 2004/12/09 09:03:32 mlosch Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.448 2005/02/09 17:34:19 edhill Exp $
 
     Notes on tags used in MITgcmUV
     ==============================
 
+o make genmake2 more portable by using ".$FS" instead of ".f" for more
+  of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys)
+o add coordinate variables to the MNC output from the diagnostics package
+o change MNC-flags default value: true when useMNC=TRUE
+o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F
+  the ability (off by default) to read the grid information using MNC 
+o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt
+o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging
+o do snap-shot diagnostics at the middle of the time-interval (instead of 
+  at the end).
+o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add
+  new test for AIM with thSIce + slab-ocean
+o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h)
+o move state variable diagnostics to the beginning of the time step ;
+  (note: still needs some work specially for snap-shot diagnostics)
+  duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z
+
+checkpoint57c_post
+o Change testing option (-ieee) to get closer agreement between g77 & ifort
+o generate new output.txt files on faulks with g77 & the new -ieee option
+checkpoint57c_pre
+
+o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF);
+  update output.txt of exp. global_ocean.90x40x15
+o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer 
+  results; update global_ocean_pressure & global_ocean.cs32x15 output.txt
+o add saltFlux(+File) forcing capability with periodicExternalForcing
+o allow to use pkg diagnostics for GM-Redi & ThSIce output
+o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc.
+o improvements for the MNC output from DIAGNOSTICS:
+  - correct handling of the unlimitied dimension
+  - all dims now have associated coordinate variables
+  - variables located at U, V, and Corner ("Z") points are now written
+    with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that 
+    *all* data points are output
+o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice
+o added pkg/seaice/seaice_monitor.F
+o mdsio_readfield.F can now read files visible only to master MPI process.
+o pkg/seaice: some test code for ice-modified ocean stress
+o exf_getffields interpolation defaults to bilinear for all scalar forcing
+  fields (remains bicubic for wind velocity and stress).  This avoids, e.g.,
+  spurious negative numbers for precipitation and humidity.  Will cause
+  some small numerical differences for integrations using pkg/exf/exf_interp.F.
+o pkg/ctrl/
+  * Add ctrlvec diagnostics in pack/unpack for nondimensional I/O
+    May be enabled via doPackDiag
+  *  introduce z-scaling of 
+     + gradient (doZscalePack) and 
+     + control (doZscaleUnpack)
+o pkg/mdsio/
+  * enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F
+  * N.B.: leave tiled I/O for tapelev (i.e. mds...vector)
+
+checkpoint57b_post
+o simplify options in diagnostics_fill arguments (remove weird combinations)
+o fix MNC coordinate variables so that they now contain per-face index
+  values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in 
+  general, EXCH2 grids are only aligned to a "local" coordinate system
+o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput)
+o Implement instantaneous output within pkg diagnostics:
+  setting a negative frequency in data.diagnostics produces
+ "snap-shot" output (as opposed to time-average if freq > 0)
+o move out off EQUIVALENCE all diagnostics that fizhi does not use ;
+  NOTE: change ptracer diagnostics name: use 2 characters to work with 
+        more than 9 tracers. Add also diagnostics of advect & diffus flux.
+o more CF compliance: convert all MNC 'iter' variables to 'T' so that it 
+  becomes the coordinate variable for the 'T' dimension
+o add CF-style coordinate variables to MNC
+  - just a first cut:  numbers are meaningless on the cubesphere and 
+    missing along the T axis but otherwise it works!
+o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX
+o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC.
+o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon)
+  this is based directly on what the model compute, so that the content of
+  each diagnostics might be affected by switching options (e.g., implicitDiffusion)
+o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F)
+o clean up build options files for SunOS, in particular 
+  - remove -traditional from xmakedepend
+  - change -xarch=v9 to -xarch=native for f77
+  - restore use of make (not gmake)
+  - add CC=gcc if using g77
+o changes per discussion of AM, JMC, & EH3 today:
+  - move redundant "grid" variables out of "state" -- in preparation of 
+    creating proper CF-style coordinate variables and in recognition 
+    that any/all grid variables can be easily copied (eg. w/NCO) from 
+    the grid files into any of the other NetCDF files
+  - *always* output grid variables with MDSIO (this will eventually be 
+    changed)
+  - output MNC grid file if useMNC is true
+o every instance of _END_MASTER() has been found and replaced with 
+  _END_MASTER( myThid ) in order to satisfy certain picky Sun 
+  preprocessors
+o re-arrange diagnostics pkg initialisation:
+ - allow each package to extend the available diagnostics list
+ - add some checking and fix small problems (multi-threaded, ...)
+ - new S/R diagnostics_fill (replace fill_diagnostics):
+   look through the short list of active diag. (instead of the long list)
+   create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active
+
+checkpoint57a_post
+o this set of changes restores TAMC compatibility
+  tested for global_ocean.90x40x15 adjoint on trough
+  (what a pain)
+
+checkpoint57a_pre
+o some modifs in tools/build_options for sunos
+o call ctrl_pack for ctrl at end for optimcycle=0
+
+checkpoint57
 o add horizontal bi-harmonic viscosity for vertical velocity
   - new parameter viscA4W (defaults to viscA4)
   - affects only non-hydrostatic code
@@ -17,6 +126,8 @@
   and include in natl_box_adjoint
 o untangle a few ifdefs related to cost, ctrl, autodiff
   untangel a few ALLOW_ECCO_OPTIMIZATION
+o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)
+  (theta2, salt2 in ecco_cost_weights)
 
 checkpoint56c_post
 o OBCS as control variables