--- MITgcm/doc/tag-index	2006/05/30 22:49:21	1.662
+++ MITgcm/doc/tag-index	2006/08/29 18:10:03	1.721
@@ -1,9 +1,172 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.662 2006/05/30 22:49:21 mlosch Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.721 2006/08/29 18:10:03 dfer Exp $
 $Name:  $
 
     Notes on tags used in MITgcmUV
     ==============================
 
+o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
+
+checkpoint58o_post
+o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
+  remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
+o change controling S/R for writing pickup file (new S/R do_write_pickup)
+  and clean-up reading/writing of pickup files.
+o fix local version of read/write pickup (NH part) in rotating_tank/code
+o simplify EXCH interface:
+ - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
+ - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
+o added the regrid package
+o shelfice: 
+ - add a simple boundary layer scheme to reduce noise
+ - fix the indexing in shelfice_u/v_drag so that there will be actually drag
+
+checkpoint58n_post
+o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to 
+   local variable (not in common block).
+o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass. 
+  - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more); 
+  - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
+    to work with SingleCpuIO.
+o add "_d 0" to real constant of pkg/cfc subroutines ; 
+   update exp. cfc_exemple & tutorial_cfc_offline output files.
+o multi-threading and IO:
+  - all threads call READ_FLD S/R (needed if using SingleCpuIO): 
+    (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
+  - barrier before and after reading.
+  - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
+  - avoid using MDS_WRITELOCAL for LAND pkg output.
+  - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
+    common-block variables ; Allows multi-threading with master-thread IO.
+o change default MAX_NO_THREADS from 32 to 4 ; 
+  and stop cleanly when MAX_NO_THREADS is too small. 
+o add S/R BAR_CHECK to check multi-threaded barrier synchronization
+
+checkpoint58m_post
+o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
+   and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
+o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
+   keep global_ocean.90x40x15 (for AD testing) with former secondary test 
+   (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
+o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
+    add MITgcm_tutorials (= code + all the tutorials)
+o ecco, option to compute cost for total ssh (mean+anom)
+o consistent with addition of ptracer and ssh in pkg/profiles
+o profiles: adding ptracer and ssh
+o testreport: change multi-test output-file name 
+  (from output.txt.{name} to output.{name}.txt)
+o profiles: now ok for mutli-tiles case
+o seaice: add 4 parameters for different advection schemes for area, 
+  (effective) seaice thickness, enthalphy, and snow height. Their default
+  is the standard parameter SEAICEadvScheme
+o calc_gw: 
+ - add cosFacU in zonal viscous flux (harmonic.visc.).
+ - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
+   of tutorial_plume_on_slope.
+o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
+o calc_gw: true flux-form, account for horizontal grid spacing.
+  update rotating_tank results, but not plume_on_slope (affected at 
+  truncation level, 11 digits).
+
+checkpoint58l_post
+o calc_gw: 
+ - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
+ - remove side-drag for now (need to fix it); update plume_on_slope results.
+ - fix for partial-cell & non-uniform dz; update plume_on_slope results.
+o commit code to make SST/SSS weights spatially variable
+  (based on either variable in-situ or variable initial T/S weights)
+o pkg/ecco:
+  * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
+    now based on horizontally varying weights wthetaLev, wsaltLev
+  * cost_averagesflags now returns year indices in addition to day, month
+  * sflux balance is performed on annual basis 
+    (sflxumm, sfluxmm2, bal_sfluxmm)
+  * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
+    including separate counting and multipliers
+o pkg/rbcs
+  * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
+
+checkpoint58k_post
+o testreport:
+ - always build in dir. "build" (if not there, mkdir build instead of building 
+   & running in input)
+ - run in dir run (if it exists), in build otherwise.
+ - call prepare_run (if input/prepare_run exists)
+ - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
+o pkg/exf modifications to interpolation and rotation routines for more
+   reasonable treatment of North Pole singularity: for tracers North Pole
+   value is set to northernmost zonal-mean value, for zonal velocity it is
+   set to zero, and for meridional velocity it is set to northernmost value.
+o pkg/exf/exf_check_range.F
+ - add tile index to diagnostics and move stop statement to the very 
+   end of the routine. 
+o pkg/diagnostics: (diagnostics_main_init.F)
+  define title of isomorphic variables according to the current config.
+o pkg/thsice with pkg/seaice dynamics:
+- fix domain of computation (interior only, required for exf) and do exchanges
+- seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
+o towards a standard way of dealing with multi-threading in MONITOR
+  and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
+o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith) 
+   to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
+o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
+o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
+o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
+   (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
+o tracer advection: 
+ - clean-up and simplify calc_common_factors.F
+ - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer 
+   advection subroutine (but still not used within DST advection S/R)
+o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
+
+checkpoint58j_post
+o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
+  from file (collects calls previously in FORWARD_STEP)
+o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
+o adjoint store dir. adjusted accordingly
+o genmake2
+  replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
+
+checkpoint58i_post
+o pkg/seaice: add parameter that allows to scale/turn off effect of seaice 
+  on wind stress (SEAICEstressFactor defaults to 1.)
+o Total number of Timers is finite (<=40): comment out 2 non-essential one
+  in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
+o vector_invariant: fix highOrderVorticity(=4.th.Order) advection 
+  on CS-grid: no longer loosing mass.
+o exf & curvilinear-grid: no longer modify longitude xC & xG.
+o pkg/ggl90: fix sloppy output and fix a bug
+o pkg/seaice: added SEAICEuseEVPpickup parameter
+  - Set to false in order to start EVP solver with
+    non-EVP pickup files when using SEAICEuseEVP
+  - fix sign error in diffusion in seaice_calc_rhs
+
+checkpoint58h_post
+* Modifications for bottom topography control
+  o replace hFacC by _hFacC at various places
+  o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
+  o add non-self-adjoint cg2d_nsa
+  o update autodiff support routines
+  o re-initialise hfac after ctrl_depth_ini
+  o works for 5x5 box, doesnt work for global_ocean.90x40x15
+* Adding verification for 5x5 box (4-layer) bottom topography control
+
+checkpoint58g_post
+o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
+   used for mean seasonal cycle, mean diurnal cycle); add an example
+   in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
+o pkg/ggl90: 
+  - add parameter (minimum surface kinetic energy)
+  - fix bug (avoiding division by zero)
+o couple pkg/thsice to pkg/seaice:
+  - modify advection in seaice to accomodate new scalar fields to be advected
+  - only muliDimAdection scheme work with seaice/thsice
+  - mapping of thsice-variables to seaice-variables, back and forth
+  - does not break the verification experiments, but does not give the
+    desired results either
+o pkg/seaice
+  - make (default) second order advection a bit less confusing?
+
+checkpoint58f_post
 o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice 
   to pkg/seaice): 
   - new routines thsice_map_exf and thsice_get_exf provide the interface
@@ -16,6 +179,8 @@
     exf_radiation, exf_wind
   - add new parameters and constants: longwave emissivity for ocean, ice 
     and snow, evaporation parameters over ice
+  - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
+    either wind from stress or stress from wind
 o pkg/thSIce:
 - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
 - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND