--- MITgcm/doc/tag-index	2007/07/27 22:22:37	1.855
+++ MITgcm/doc/tag-index	2007/10/28 21:39:40	1.900
@@ -1,9 +1,168 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.855 2007/07/27 22:22:37 heimbach Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.900 2007/10/28 21:39:40 jmc Exp $
 $Name:  $
 
     Notes on tags used in MITgcmUV
     ==============================
 
+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) 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).
+  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
+  - exf_bulkformulae.F: introduce 2D fields and vectorize code
+o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
+o testreport: 
+  - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE 
+    monitor & update offline_exf_seaice exp. output.
+  - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
+o pkg/seaice:
+  - bug fix in the evp solver: boundary conditions were affected be
+    masking of zMax/zMin (changes results)
+  - minor bug fix in boundary conditions in seaice_calc_strainrates 
+    (changes results for no_slip)
+  - seaice_lsr.F: make interpolation of eta dependent on boundaries
+  - replace hardcoded lower limit for zeta (zMin) by runtime parameter
+  - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
+    stress formulation and no-slip boundary conditions
+o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
+  in gad_calc_rhs.F ; add few safety stops in initialisation phase.
+o pkg/seaice: a first HSALT time stepping equation has been checked in
+o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
+  in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
+  without requiring DO-IF statements
+o pkg/thsice:
+  use continuous power-law function for partition of energy between lateral
+  melting/freezing and thinning/thickening ; old code using step function
+  still available with #undef THSICE_FRACEN_POWERLAW
+  update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
+o testreport: change AD testing : check against results/output_adm.txt
+  using same scripts as for forward test.
+
+checkpoint59g
+o adjoint testing: in preparation for changing testreport:
+  - output format: cost and grad written on separated lines
+  - ad output results in directory "results" (instead of "results_ad")
+o pkg/seaice: adding ice salinity HSALT as a prognostic variable
+o pkg/seaice: changes for using pkg/seaice with pkg/obcs
+o pkg/ecco: allow user defined cost function contributions 
+o testreport:
+  Allow to choose (per experiment) the list of tested output variables
+   and the main variable (used to issue a pass/FAIL ) ;
+  - for now, done by adding the specific list in file: [exp]/input/tr_checklist
+  - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
+  Also modify printing of summary:
+   a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
+   b) echo the list of tested variables in the individual summary.txt of
+      each experiment.
+o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
+  threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
+  (but still depend on the tile decompostion of the domain).
+o pkg/seaice: change a discretization detail to make the B-grid code 
+  "more symmetric". This change is likely to remove all "ridges/leads" that 
+  where quasi-aligned with the grid in B-grid solutions. It may also be 
+  the solution to the stress coupling issues with the B-grid.
+o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
+  remove .cvsignore from input dir. (since testreport no longer run here).
+o pkg/thsice:
+ - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
+ - fix reshaping of sea-ice just after advection:
+   melt all the ice only if ice-volume is too small.
+ - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
+   prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
+ and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
+o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
+  tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
+o define mass2rUnit & rUnit2mass as units conversion factor, used for surface 
+  forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
+  (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
+  and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
+  of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
+  -> update output.txt
+o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
+ this affects truncation error: -> update output.txt of exp:
+  global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
+  ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
+
+checkpoint59f
+o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode) 
+o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in 
+  a bounded range (in forward mode)
+o pkg/ecco, ctrl, autodiff and mom_common:
+ internal parameter controls, completements of implementations
+o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
+o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
+  (not seem any difference in testing results).
+o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains 
+   at face corners.
+o pkg/generic_advdiff: 
+ - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
+  loop range indices for computing vertical advection tendency
+  and do the calculation in the interior only (no overlap) ;
+  for now, only implemented for SOM advection (to save CPU time).
+ - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
 o exch2 adjoint
   First set of changes:
   - add exch2 hand-written adjoint templates
@@ -13,6 +172,10 @@
   - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
     that used to hide exch2 or cubed-sphere specific code
     (commented via 'cph-exch2')
+o pkg/seaice
+  - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
+o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update 
+   output of global_ocean.cs32x15.thsice .
 
 checkpoint59e
 o exch2: new S/R that only use the cube-tracer (center-position) exchange:
@@ -212,7 +375,9 @@
      ATMOSPHERIC_LOADING is #define).
 o pkg/kpp: replaced _KPP_RL with _RL
 o bug fixes for vertical diffusivity computations when both KPP and
-    3D diffusivity arrays are used.
+    3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
+    are no longer updating the vertical diffusivity array
+    (passed as argument) but are (re-) setting those arrays.
 o pkg/seaice: fix bug in evp solver, while doing that
   - change (improve?) discretization of stress computations for both
     cgrid-lsr and evp solver