--- MITgcm/doc/tag-index	2009/06/24 08:05:07	1.1130
+++ MITgcm/doc/tag-index	2009/11/10 09:34:04	1.1191
@@ -1,9 +1,209 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1130 2009/06/24 08:05:07 mlosch Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1191 2009/11/10 09:34:04 mlosch Exp $
 $Name:  $
 
     Notes on tags used in MITgcmUV
     ==============================
 
+o pkg/seaice
+ - fix diagnostics of principal stress components for EVP
+ - add optional diagnostics of non-linear convergence for LSOR solver
+ - make maximum zeta a runtime parameter
+o model/src (3-d solver):
+  Undo modif from Dec 12, 2005 (solve_for_pressure.F cvs version v.49),
+   which consisted in removing the Surf. Non-Hydrostatic pressure from the
+   whole column and adding it to Eta (inspired from Casualli, 1999):
+   Only affects 3-D solver initial guess and only if using ExactConserv,
+   but tests did show a degradation of solver convergence. For this reason,
+   decide to disable this piece of code.
+   to recover previous version, just set zeroPsNH = exactConserv (line 78).
+  Update output of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW
+o pkg/ggl90: 
+ - fix previous modif (unfortunatly has not been documented here).
+o pkg/seaice/autodiff:
+ - add CPP flag to include clipping of zeta in EVP code;
+   although clipping of zeta is not necessary for EVP and not recommended
+   it was done by default, now clipping is disabled by default
+ - modify computation and store zetaC/Z in seaice_evp for TAF
+ - add CPP-flag SEAICE_ALLOW_CLIPVELS (undefined by default)
+ - change seaice_calc_viscosities/strainrates for better
+   vectorization after AD by TAF
+ - rearrange common blocks in SEAICE.h once again for easier dumps of
+   adjoint output, adjust adcommon.h and g_common.h
+ - change flux form of default advection scheme for better vectorization
+   of adjoint code
+ - modify lab_sea/input.lsr to test the flux form of default advection 
+   scheme
+o autodiff: fix seaice fields in g_common.h (left over from 3 to 1 level
+  transition in checkpoint61r)
+
+checkpoint61x
+o adjoint: adding two new verification experiments
+  * tutorial_global_biogeo: an online dic sensitivity experiment 
+    (work with G. Forget)
+  * tutorial_dic_adjoffline: an offline dic sensitivity experiment
+    (an update of the Dutkiewicz et al., 2006 paper)
+  Both use the same CO2FLUX cost function, but different controls
+  Gradient checks look good, but some recomp. could still be traightened out
+  Should add xx_dic control variable to test at some point
+o model/src:
+  add run-time parameters to check and/or mask initial Temp & Salt
+o pkg/ptracers:
+  apply zonal filter (if used) to all passive tracers
+
+checkpoint61w
+o adjoint:
+  * update and finish work on adjoint of dic package (G. Forget)
+  * start adjoint of offline package
+  * bug fix for cube-sphere TLM code (active_file_g.F)
+o tutorial_global_oce_optim:
+  now tested with 4 tiles (change data.grdchk and update output_adm.txt)
+  and add SIZE.h_mpi for MPI testing
+o pkg autodiff
+ - fix bug in autodiff_restore
+ - make genmake2 remove comments and empty lines from ad_input_code.f in 
+   order to reduce file size (new script file remove_comments_sed)
+o allows to specify vertical profile of vertical viscosity (viscArNr)
+o pkg autodiff
+  autodiff_ini_model_io: comment out writing of grid information to netcdf 
+  files, because at this time the grid fields are a bunch of zeros 
+  (this is analogous to ini_mnc_vars.F) 
+o pkg seaice/autodiff:
+ left-over from removing the 3-time-level fields: 
+ - small rearrangement of common blocks (SEAICE.h)
+ - fix field declaration in order to get meaningful output in 
+   adseaice.*.nc (adcommon.h) 
+o pkg obcs:
+ - go through NH code only if nonHydrostatic=T
+ - fix restart for Orlanski (Hydrostatic; still to fix NH+Orlanski restart)
+ - move call to OBCS_CALC before SEAICE_MODEL which needs seaice-obc fields
+   => Update output of experiment seaice_obcs
+ - useOBCSbalance: code is wrong with multi-tile / proc: add a stop.
+ - fix NH+Orlanski restart (add wvel OBC value in pickup file)
+ - fix restart for useOBCSprescribe + useEXF
+o pkg ctrl
+ - make obcs as control parameter work also with useSingleCPUio
+ - replace a few sny and snx by Ny and Nx to be consistent with
+   ctrl_set_globfld_x/yz.F
+o pkg seaice
+ - re-introduce global field frWtrAtm for the case of 
+   ALLOW_MEAN_SFLUX_COST_CONTRIBUTION defined (SEAICE.h, seaice_growth.F)
+ - catch the case of an empty filename in seaice_cost_init_fixed.F
+o pkg ecco:
+ - small bug fixes in the_main_loop
+  . fix order of monitor arguments
+  . change SEAICE_MULTILEVEL to SEAICE_MULTICATEGORY
+  . move include DYNVARS.h up outside the ALLOW_AUTODIFF_TAMC block so
+    that ALLOW_ECCO_FORWARD_RUN works with NONLIN_FRSURF
+ - replace cos(yc*deg2rad) by _rA in cost_mean_heat/saltflux.F, fix the 
+   imbalance diagnostics for wmean_h/sflux = 0 
+ - add actual values to f_obcsn/s/w/e in ecco_cost_final.F
+ - catch the case of empty filenames in ecco_cost_init_fixed.F 
+   and ecco_readparms.F
+ - fix the logic of wsalt=0.and.wsalt2=0 to wsalt=0.or.wsalt2=0 (and theta)
+   to make this statement meaningfull in ecco_cost_weights.F
+o pkg zonal_filt:
+  - change ZONAL_FILTER S/R interface (allows to filter 2-D fields)
+  - when using rStar, filter uVel*hFacW instead of uVel
+   (tested without topography: fix a Pb of growing instability with NLFS)
+o pkg/aim/thsice:
+ -Add capacity to read a Q-Flux to be applied in slab-mixed layer thsice_slab_ocean.F
+  (works as SST restoring)
+o pkg/thsice:
+ -add specific parameter for salt restoring in slab mixed-layer
+   (by default equal to the temperature restoring)
+
+checkpoint61v
+o pkg/kpp:
+ -add double diffusive contributions as a hack, turned off by default 
+  for now, and the code can be excluded with a CPP-flag 
+  EXCLUDE_KPP_DOUBLEDIFF just as EXCLUDE_KPP_SHEAR_MIX
+ -add a verification experiments to "vermix" to test this code
+o pkg/mom_common:
+  Move computation of length scales to mom_init_fixed.F (avoid recomputation
+  at each time-steps*levels).
+o pkg/layers:
+  Created a new package for computing volume fluxes in temperature or
+  [not yet implemented] density layers, e.g. for calculating residual
+  overturning circulations. 
+o pkg/diagnostics: 
+  implement a RS type version for the set of DIAGNOSTICS-FILL subroutines
+o fix few RS/RL type mismatch (check with ifort 11.1 "-warn all" option)
+o pkg/mdsio (& pkg/rw): rework high level S/R interface:
+  To avoid mixing type (RS/RL) of input/output array argument,
+  replace single mixed-type array with a pair from each type (RS/RL).
+o setting pickupSuff force to start from a pickup (even if nIter0=0): this
+  is now implemented for all pkgs (previously only done for the main pickup) 
+
+checkpoint61u
+o pkg/obcs:
+  - change OB?eta from _RS to _RL and put them into a separate commen block
+  - add code to read OB?eta from a file via obcs_prescribe_read: the code
+    compiles and does not destroy any other experiments, the data is read
+    properly, but the code is not tested in actual applications
+o ini_mnc_vars.F: if available (ALLOW_CAL), use startTime_1 and 2 to 
+  create a meaningful unit attribute for the time coordinate variable 
+o pkg/ebm: add plenty of missing "_d 0" ;
+   update results of experiment global_ocean_ebm (fwd + adjoint tests) 
+  Notes: several pieces of code only works for (very) specific set up
+   (domain size, lat range, etc ...); should be documented & stop if one 
+   of those assumptions is not meet.
+o pkg/seaice: add missing "_d 0" in HSNOW initialisation
+   update results of experiments: lab_sea (3 fwd tests + 2 adjoint tests) 
+      and offline_exf_seaice (seaicetd + adjoint).
+o add missing "_d 0" in ShortWave flux penetration (S/R SWFRAC):
+   update results of experiments: lab_sea (4 fwd tests + 3 adjoint), 
+    seaice_obcs, global_ocean.cs32x15 (icedyn & thsice) and natl_box (x2).
+o few changes to pass when compiling with strick checking of arguments 
+   across S/R (allow to find few bugs in S/R calls).
+o pkg/seaice:
+ - seaice_evp: move if-statement out of loop (TEM) at the cost of 11 new 
+   2d-fields, for slightly better performance
+
+checkpoint61t
+o pkg/seaice: 
+ - remove unused variables in seaice_evp
+ - reduce number of SQRT in seaice_evp and seaice_calc_viscosities
+o eeset_parms.F, open_copy_data_file.F & ini_parms.F:
+   named file replacing SCRATCH files (for TARGET_BGL & TARGET_CRAYXT):
+   each processor opens a different file (a fix from Matt).
+o cg2d:
+   use simple EXCH (overlap size = 1 and ignore corners), like in cg3d.F :
+   this reduces number of EXCH calls by 2 when using exch2.
+   For now, keep previous size array for gc2d_nsa.F to avoid Pb with store 
+   directives and missing simple EXCH (exch_s3d_rx) adjoint code.
+o pkg/thsice: 
+   add code for Near Infra-Red albedo (from Jeff)
+   (turned on with run-time flag: thSIce_calc_albNIR, in data.ice).
+o ini_model_io:
+   move (from packages_readparms.F & initialise_fixed.F) to ini_model_io.F
+   MNC & MONITOR initialisation calls; move MNC calls from {pkg}_readparms.F
+   to {pkg}_init_fixed.F for {pkg}= kpp, seaice & shelfice.
+
+checkpoint61s
+o pkg/exch2 (exch2_rxN_cube*):
+   remove last BARRIER (no need to synchronise after getting data from shared
+   buffer (get) as long as any change to buffer (put,recv) is between BARRIER)
+o change tiling of natl_box (from 2 to 4 tiles) to get it tested with MPI+MTH
+  and generate new output (for the 2 tests) using default rotationPeriod.
+o pkg/exch2:
+  - always call exch2_*_cube, not exch-1 anymore, if useCubedSphereExchange=F
+    (was already the case with AUTODIFF_EXCH2 defined)
+  - add bj in exch2 arrays and S/R.
+  - can now use pkg/exch2 for regular (non CS) set-up; switch test experiment
+    MLAdjust to exch2 (identical results except with MPI -> truncation diff);
+o add pkg/longstep for ptracer timestep a multiple of U/V/T/S timestep
+  - adds deltaT argument to the subroutines TIMESTEP_TRACER DWNSLP_APPLY
+    GAD_ADVECTION GAD_CALC_RHS GAD_IMPLICIT_R GAD_SOM_ADVECT
+  - verification experiment natl_box.longstep
+o build_options: ifort+mpi_aces optfile (following Constantinos advise):
+  allow different versions of ifort (8 or 9) and different versions
+   of mpi (mpich or mpich2) to be used with the same optfile.
+  requires to load a netcdf module and set MPI_INC_DIR (see comments inside
+   optfile). Change testing scripts (example_scripts/ACESgrid) accordingly.
+o pkg/seaice: 
+  fix previous modif (3-level field removed) for old-pickup reading 
+
+checkpoint61r
 o pkg/seaice: 
  - clean up the 3-time levels of UICE,VICE,HEFF,AREA in three steps:
   1. introduce fields for time step (N-1)
@@ -14,6 +214,8 @@
      pkg/obcs/obcs_apply_uvice.F.
  - completely remove code for leap-frog time stepping for second order
    advection
+ - adjusted adjoint accordingly;
+   gradient checks have improved by an order of magnitude!
  
 checkpoint61q
 o pkg/seaice: fix bug in free slip boundary conditons for LSOR solver