--- MITgcm/doc/tag-index	2007/09/28 07:46:13	1.884
+++ MITgcm/doc/tag-index	2007/11/28 00:18:16	1.912
@@ -1,9 +1,111 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.884 2007/09/28 07:46:13 mlosch Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.912 2007/11/28 00:18:16 dimitri Exp $
 $Name:  $
 
     Notes on tags used in MITgcmUV
     ==============================
 
+o added pkg/salt_plume
+o script to test restart (for now, in MITgcm_contrib/jmc_script)
+o pkg/seaice: new read/write pickup version. 
+  read meta file and write only fields which are needed to restart.
+  ( same logic as main pickup file ; also using pickupStrictlyMatch )
+o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
+o lab_sea.hb87: modify the domain & update output.hb87.txt :
+  lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
+  at j=1 & j=Ny+1 : this case is not treated correctly in the restart
+  process. Fixed here by closing the domain at the Northern boundary.
+o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
+o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
+  a set of consecutive levels in/from a 3-D array.
+o pkg/ptracers: 
+  use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
+  to-do: fix pkg/diagnostics when large number of diagnostics are defined.
+
+checkpoint59j
+o in pkgs: dic, obcs, offline, rbcs:
+  standard way to compute coeff. for time interpolation between 2 time reccords
+  which retains full precision (& make results less dependent on compiler).
+  update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
+o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
+  packages instead of reading ice cover and wind speed separately
+o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
+ (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
+  to allow to compile customized code before the update)
+o cleaning-up: 
+  - fix CPP instruction syntax in pkg/obcs
+  - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
+    add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
+  - fix some threads issue in IO parts.
+o pkg/dic:
+  - add tons of "_d 0" (--> much better testreports !)
+   and then update outputs of tutorial_global_oce_biogeo
+o pkg/mom_fluxform:
+  add a special version of momentum advection intended to conserve momentum
+  next to a bathymetry step or a coastline edge. (default = off = #undef)
+o new read/write pickup version:
+  - for now, only implemented for main (mdsio) pickup file.
+  - write out only what is needed to restart; merge pickup_nh , pickup_ph
+    and main pickup together.
+  - read meta file; read only what is needed to restart; stop if a field
+    is missing (if pickupStrictlyMatch=T, = the default) or try to restart
+    if it make sense (even if the restart is not perfect).
+  - if no meta file, assume that pickup to read corresponds exactly to
+    a pickup that would currently be written.
+  - read pickup written in the old format (until checkpoint59i) if it
+    recognizes an old meta file (no field-list).
+  - add a meta file in exp. which starts from a pickup: 2 cases:
+    a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
+     e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
+    b) a meta file describing the content of the associated pickup file
+     e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
+o pkg/mdsio & pkg/rw:
+  - new routine to read a meta file ; new set of routine to read
+    Multiple-fields file (with meta file).
+o added open boundary conditions capability for seaice
+    HSNOW, HSALT, UICE, and VICE
+
+checkpoint59i
+o adjoint:
+  * fix multiDimAdvection adjoint 
+    (partial recomputation problem by TAF for fVerT(:,:,kDown)
+    and comlev1 size definition (maxpass vs. max. number of tracers)
+  * verification/global_ocean.90x45x15 adjoint now tests
+    NLFS and multiDimAdvection using DST3 (=30)
+  * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
+o pkg/kpp: add "_d 0" to real constant (if missing); 
+  update output of exp: natl_box (10.digits); vermix (std, 7.digits)
+  and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
+o prepare for "clever pickup" implementation: add new header file "RESTART.h"
+  for internal parameters related to restart process (formerly from PARAMS.h)
+  and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
+o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
+  as argument. (only atm2d & obcs write_pickup have not yet been updated)
+o pkg/monitor:
+  - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
+  - fix mon_stats_rs (statistics over the full domain, even where field is zero)
+  - account for deep Atmosphere factor and density factor (anelastic)
+o added open boundary conditions capability for seaice HEFF and AREA
+o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
+  thermodynamics
+  - requires a little reorganization, which affects the testreport results 
+    of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
+    so that now the conservative form is tested
+  - add a few comments
+o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
+o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
+o add new diagnostics to seaice: advective, diffusive fluxes (only for
+  multidim-advection, for scheme 2 they are not filled) and transports, 
+  thermodynamic growth rates
+o change units of EmPmR (inside the code, + within coupling interface)
+  from m/s to kg/m2/s (mass flux) but leave input file unchanged.
+  Affects results @ truncation level (cg2d match) and update output of 
+   experiments: lab_sea(6), global_ocean.90x40x15(10),
+  global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
+  + adjoint results: global_ocean_ebm(11) and lab_sea (12).
+  Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
+  Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
+
+checkpoint59h
 o pkg/exf: 
   - improve vectorization by moving if-statement out of loops in
     exf_mapfields, exf_radiation