--- MITgcm/doc/tag-index	2006/03/02 02:56:54	1.616
+++ MITgcm/doc/tag-index	2006/04/28 22:54:02	1.653
@@ -1,9 +1,129 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.616 2006/03/02 02:56:54 heimbach Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.653 2006/04/28 22:54:02 heimbach Exp $
 $Name:  $
 
     Notes on tags used in MITgcmUV
     ==============================
 
+o SEAICE_CGRID adjoint started
+  (all stores seem to be sorted out, but NANs in adjoint).
+
+checkpoint58d_post
+o upgrade simple test-experiment to tutorial example:
+ step.1: duplicate the experiment and (step.2) will remove the old copy.
+  tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
+  tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
+  tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
+  tutorial_global_oce_biogeo    <- copy of dic_example
+  tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
+  tutorial_plume_on_slope       <- copy of plume_on_slope
+  tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
+  tutorial_global_oce_optim     <- empty for now (David ?)
+  tutorial_global_oce_in_p      <- copy of global_ocean_pressure
+ some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
+o correct a sign problem in cost_scat.F
+o obcs and ptracers: fix boundary conditions for advections schemes 
+  with larger stencil 
+o thsice adjoint: start
+o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for 
+  completeness
+o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING 
+  and COSINEMETH_III, add comments in default CPP_OPTIONS.h
+o ptracers adjoint:
+  * avoid extensive recomputatations
+  * fix missing re-init. of gptr (missed by TAF)
+o obcs: add a flag (OBCSprintDiags, defaults is true) that allows 
+  me to turn off the excessive output to STDOUT that this package produces
+o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
+  and add those terms in Vector-Invariant formulation.
+o in ctrl pkg, if ALLOW_CAL, use monthly mean controls 
+  if the control period (xx_hfluxperiod etc) is 0
+o in profiles pkg, clean routines and fix details
+o in ecco pkg, reading ssh data: 
+  fix problem in case the model does not start at iter0=0
+o fix mnc-pickup/restart for ptracers
+o new package prifiles:
+  code to compute profile-based cost by Gael Forget
+  (modifs in ecco, ctrl, autodiff)
+o Benign bug fix in initialization (spotted by M. Mazloff) of
+  ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
+
+checkpoint58c_post
+o adjoint: finish NLFS adjoint and provide reference output in
+  verification/global_ocean.90x40x15/results_ad_nlfs
+o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the 
+  documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
+  SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only 
+  with SEAICE_CGRID defined.
+o move calendarDumps from "data" to "data.cal" and clean-up the code
+  with a simple call to pkg/cal S/R: CAL_TIME2WRITE
+o add useEXF & useCAL flags (for now, set in hard-coded way)
+o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
+  (were missing in NH mode, and wrong in quasihydrostatic mode).
+  waiting for Chris updated version of calc_gw to add those CALLs.
+o fix bug in quasihydrostatic S/R ;
+  add a test for this option: global_ocean.90x40x15.qshyd
+o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
+  (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
+o add on/off flag useOffLine for package OFFLINE
+o seaice: 
+  - modify advection so that it works also on the C-grid
+  - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes 
+    problem in multi-tile runs with C-grid
+  - add flags for clipping ice velocities and/or masking solver forcing
+  - fix drag (ocean on ice) formulation and a bug that caused noise in the
+    C-grid solver
+  - added a few comments to seaice_diffusion.F
+  - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
+    are now exclusive)
+  - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which 
+    required re-ordering the code a little:
+   + make DAIRN global variable (defined in SEAICE)
+   + move computation of the viscosities eta and zeta into a new separate
+     routine (because I need to recompute them in seaice_ocean_stress.F)
+
+checkpoint58b_post
+o AIM+thSIce: fix sign of Short-Wave through the Ice ; 
+  update output.txt of exp. aim.5l_cs.thSI
+o various mnc cleanups and improvements:
+  + shrink lookup tables by factor of ~4
+  + better error reporting when running out of lookup space
+  + able to handle longer path/file names (up to 500 chars)
+o adjoint:
+  - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
+  - TBD: "hidden" mom_vecinv recomp. in dynamics
+o change forcing_In_AB to affects both T,S forcing and Momentum forcing
+ (allow to differentiate between forcing components using new integer flags:
+  momForcingOutAB=1/0 & tracForcingOutAB=1/0)
+ and add new flag to put Dissipation tendency out of Adams-Bashforth.
+o ecco
+  - enable trend removal from SSH anomaly obs.
+o adjoint
+  - a fix for PmEpR when #undef EXACT_CONSERV
+  - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
+  - try to fix "hidden" recomp. in forward_step for NLFS
+    (NLFS seems broken sometimes after I checked it in)
+o seaice: 
+ - add c-grid version of the dynamic solver:
+   + three new routines that are the c-grid substitute lsr, dynsolver
+     and ostres
+   + put a few fields that were local to dynsolver into global common
+     blocks, so that I can move the computation of stresses etc into
+     seaice_lsr (saves coding but may break the adjoint).
+ - replace more hardwired parameters by runtime parameters
+ - add ice masks that mask the rhs of the implicit solvers where there
+   is no ice (commented out in seaice_dynsolver, because i am not sure
+   if this works properly), eventually this should replace the clipping
+   of ice velocities in seaice_dynsolver to +/-40cm/s.
+o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly 
+  include it only where its needed
+o move balancing of fluxes before the call of external_forcing_surf
+o seaice:
+  - correct units of turning angles (now they are really in degrees)
+  - move computation of GWATX/Y out of main routine into dynsolver
+  - initialize GWATX/Y in seaice_init
+o Apply mask on Fresh-Water flux (needed for SSH forcing).
+  update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual) 
+o seaice: add runtime flags for turning angles (default to zero)
 o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean 
   and trend from exf forcing and ctrl control adjustments
 o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF