--- MITgcm/doc/tag-index	2004/11/23 21:25:24	1.393
+++ MITgcm/doc/tag-index	2004/12/16 08:31:42	1.414
@@ -1,8 +1,106 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.393 2004/11/23 21:25:24 edhill Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.414 2004/12/16 08:31:42 mlosch Exp $
 
     Notes on tags used in MITgcmUV
     ==============================
 
+o clean up build options files for SunOS, in particular change -xarch=v9
+  to -xarch=native
+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
+  - to be done: no-slip lateral boundary conditions
+o switch back to "sflux = sflux - runoff" in exf_getforcing.F
+o implement Implicit Vertical advection for pTracers
+o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k)
+  (implemented also for implicit vertical diffusion & advection)
+o OBCS: extend application of tracer open boundary conditions
+  to a strip beyond the boundary of width Olx/Oly
+o add call monitor to TAF set of required calls (flow directives)
+  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
+  - update ctrl_ad_diff.list, obcs_ad_diff.list
+  - remove balance of obcs controls from default
+  - fix index bug nobcs in ctrl_init
+  - fix dummy fields filen in ctrl_pack
+  - add dummy weights for obcs
+o lsopt: comment out fort.94 output
+o optim: 
+  - remove unnecessary header files
+  - adjusted namelists
+  - add xerbla.F to Makefile
+o exf: 
+  - multiple modifications of exf_check_range
+  - unit change in exf_init_runoff from [m/year] to [m/s]
+o mdsio:
+  - i/o-vector change debugLevel from debLevA to debLevB
+
+checkpoint56b_post
+o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that
+  is called from DO_THE_MODEL_IO
+  - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE
+  - introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq)
+  - clean up PTRACERS_WRITE_TIMEAVE a little
+o add another verification experiment that tests both the cfc-pkg and
+  the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with 
+  reactive tendencies treated inline with regular timestepping
+o testreport previously did a lousy job of comparing small numbers, so
+  we (Ed and Martin) changed the  way the cut-off of 1.e-12 is
+  implemented in the little c-progam tmp_cmpnum.c which is embedded in
+  testreport. 
+o ptracers_monitor: bug fix for MPI
+
+checkpoint56a_post
+o GCHEM: finish reorganizating the package
+  - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency 
+    (introduces another 3D-array for each passive tracer, but only if
+    GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING
+    gchemTendency is not needed because the timestep is done separately)
+  - gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY
+  - GCHEM is now---more or less cleanly---separate from PTRACERS
+  - to bo done: handling of surfaceForcingPtr that is needed for KPP not
+    so clear to me how that should be done in a general way.
+o CFC: improve formatting of output in CFC_ATMOS
+o PTRACERS:
+  - rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so
+    that ALL experiments with ptracers enable can be checked. This makes
+    GCHEM_MONITOR obsolete.
+  - include a runtime parameter PTRACERS_monitorFreq that defaults to
+    monitorFreq
+  - set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true 
 o add PTRACERS (PTR0[1-5]) to testreport output
 o exf_check_range:
   * default changed to .TRUE.
@@ -25,7 +123,7 @@
     be replaced by a 3D array that is computed before thermodynamics; for 
     this, the tracer ID iTracer had to be included into the parameter list
     of ptracers_forcing
-  - set up forward_step for a call to gchem_forcing, that will replace 
+  - set up forward_step to call gchem_forcing, that will replace 
     gchem_forcing_int in ptracers_forcing
   - cleaning up
 o small cleaning of exch2: remove files that are also in eesupp/src