--- MITgcm/doc/tag-index	2001/07/13 18:08:14	1.41
+++ MITgcm/doc/tag-index	2002/03/14 15:23:50	1.68
@@ -1,7 +1,188 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.41 2001/07/13 18:08:14 heimbach Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.68 2002/03/14 15:23:50 jmc Exp $
 
     Notes on tags used in MITgcmUV
     ==============================
+
+o vertical grid option: allow to put the Interface at the middle between
+  2 cell-centers ; replace delZ in pkg/kpp by drF.
+o GM Advective form: Tracers are advected using the residual transport (=
+  Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.
+
+checkpoint44g_post
+o fix surface correction term in multiDimAdvection (affects plume_on_slope 
+  results) ; ifdef missing in thermodynamics.F
+
+checkpoint44f_pre,checkpoint44f_post
+o added PTRACERS package
+  This allows an arbitrary number of passive tracers to be integrated
+  forward simultaneously with the dynamicaly model.
+  + Implemented so far:
+    - basic forward algorithm (time-stepping, advection, diffusion, convection)
+    - I/O and checkpointing
+    - GM/Redi  *but*  using the GM/Redi coefficient of Salt
+  + Not implemented so far:
+    - KPP
+    - OBCS
+  + No specific example supplied (yet) but global_ocean.90x40x15 has the
+    necessary data.ptracer file. Simply use -enable=ptracers and uncomment
+    line in data.pkg.
+  + This package is disabled by default since it increases storage.
+
+
+o testscript: added -cleanup option
+o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter
+             b) enable to filter 2D fields.
+
+checkpoint44e_pre,post
+o re-wrote convective adjustment to use pre-calculated weights
+  Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F
+  Adds:    model/src/convective_weights.F, convectively_mixtracer.F
+  Original calls to convect() still in place.
+
+chkpt44d_pre,post
+o added missing EXCLUDE_MONITOR flags
+o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
+  (incompatible typ in MIN/MAX expressions caused problems
+  on IBM SP3)
+o in genmake added variable MAKEDEPEND
+  plus resetting for case SunOS
+o added timer_stats.c routine for IBM SP3
+o removed variables in dynamics
+!!! I forgot to create tag chkpt44d_pre !!!
+!!! But chkpt44d_pre = chkpt44c_post    !!!
+
+o real fresh water flux implemented with non-linear free-surface.
+
+chkpt44c_pre,post
+o few fix (mask in shap_s2, EmPmR in external_field_load, 
+  USE_NATURAL_BCS in solve_for_P); 
+o add arguments myIter & myTime to S/R obcs_calc & solve_for_P
+
+checkpoint44b_pre/_post
+o merge of relevant stuff from the ecco-branch:
+  - genmake: removed $S64 overwrite for case SunOS
+  - pkg/exf: update and corrections for field swapping and obcs
+  - pkg/ecco: parameter lists for the_model_main, the_main_loop
+              harmonized between ECCO and MITgcm
+  - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
+                  updated checkpointing_lev... lists for obcs
+  - model/src: minor changes in forward_step, plot_field
+               added directive for divided adjoint in the_main_loop
+  - pkg/mdsio: added mdsio_gl_slice
+
+o check parameters & config (chkpt44a_pre,post)
+o OBC and NonLin_FrSurf.
+
+checkpoint44
+o fix bug in mom_vi_del2uv
+o select when filters are applied ; add options to zonal_filter (data.zonfilt)
+o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
+o update AIM experiments (NCEP input files)
+o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
+o added some stuff for AD
+
+checkpoint43
+o added two new advection tests
+o added global 4x4 degree ocean test
+o added test of H&S94 with free surface on cube
+o some final mods for gradient check, adjoint,...
+
+checkpoint42
+  Fixed AD-related problems:
+o Store directives up-to-date with re-arranged Adams-Bashforth
+  (mainly thermodynamics.F)
+o New store directives for multi-dim. advection schemes
+  * new CPP flag ALLOW_MULTI_DIM_ADVECTION
+  * new common block and key passkey
+  (mainly gad_advection.F)
+o Modified store directives for split of dynamics/thermodynamics
+  for the case ALLOW_KPP
+o Cleaned argument list for timestep_tracer.F
+
+checkpoint41
+o re-formatted/added comments in prologues of key subroutines
+  to work with protex
+
+checkpoint40
+o moved calc_gs, calc_gt and calc_tr1 back to model/src
+o added FLT (floats) package from Arne along with demo. experiment
+o re-arranged Adams-Bashforth scheme for tracers to allow easier
+  implementation of forward-in-time forcing terms
+o more mods for non-linear free-surface including new variable
+o modified multi-dim method to work on cube
+o bug fix in KPP (from DM)
+
+checkpoint40pre9
+o added DST advection schemes
+o fix MPI bug on SGI's
+o modifications for non-linear free-surface
+o fixed conditionals for fixed flow/passive tracer only mode
+o added tension/strain form of stress tensor
+o changes to commenting of arguments for TAF/TAMC
+o added/updated many matlab scripts
+o added multi-dimensional advection method for tracers
+  
+checkpoint40pre8
+o new package rw/
+  Added method for dumping intermediate local arrays:
+  mdsio_writetile - same as mdsio_writefield except works from inside
+                    bi,bj loop
+  mdsio_writelocal - same as mdsio_writetile except works for local
+                     arrays
+  write_local_r? - higher-level wrapper for mdsio_writelocal
+  Controlled by diagFreq. Defaults to zero (ie. no dumps)
+  Example given at end of mom_vecinv.F that dumps some local arrays.
+o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to
+  control flux-form versus vector invariant code.
+  Switch is runtime flag vectorInvariantMomentum (defaults to false)
+  or genmake -DISABLE ...
+o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F
+  (additional storing is now needed for case vecinv;
+  currently nothing implemented to switch this storing off
+  in case fluxform is used since no CPP flag available).
+
+checkpoint40pre7
+o bug fix in dynamics.F
+  calc_viscosity called before k=1,Nr loop.
+o added some #ifdef's ALLOW_PASSIVE_TRACER
+o cleaned initialisations in ctrl_map_ini
+  related to TAF
+
+checkpoint40pre6
+o split dynamics into thermodynamics & dynamics
+o corresponding split of calc_diffusivity into
+  calc_diffusivity, calc_viscosity
+  (kpp_calc_diff, kpp_calc_visc).
+o Added diffkr, kapgm to control variables
+o bug fix in gmredi_slope_limit for ldd97
+
+checkpoint40pre5
+o proper initialization of Adams-Bashforth time stepping
+  + uses forward step for very first step of model (iter=0)
+o re-generated *all* output since almost all output is modified by this
+  change (sorry but we've been putting this one off for about 2 years)
+  + natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were
+    *not* regenerated since they are already out of date and I don't
+    want to create the impression that they are suddenly working.
+o removed KAP stuff for DEC's
+o modified/added many .cvsignore files in */code and */input
+o added new expt "solid-body.cs-32x32x1"
+  + this uses an alternative form of ini_curvilinear_grid.F which
+    is not necessarily any better than the current one...
+
+checkpoint40pre4
+o added re-initialisations of utrans,vtrans,rtrans in
+  calc_common_factors which are crucial for TAF.
+o extended iMin,jMin range for calc_common_factors,
+  calc_diffusivity
+o added option ALLOW_PASSIVE_TRACER
+o a few minor updates and fixes
+
+checkpoint40pre3
+o created calc_gtr1.F for gad package
+o split the_main_loop and re-introduced forward_step
+o some recomputations of nIter0 for TAMC
+
 checkpoint40pre2
 o Updated to latest branch of AJA, JMC
 o Added gradient check package