--- MITgcm/doc/tag-index	2004/07/05 23:56:43	1.321
+++ MITgcm/doc/tag-index	2004/09/24 12:38:00	1.354
@@ -1,9 +1,140 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.321 2004/07/05 23:56:43 jmc Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.354 2004/09/24 12:38:00 mlosch Exp $
 
     Notes on tags used in MITgcmUV
     ==============================
 
-tag before changing staggerTimeStep
+o more obcs stuff
+  - added obcs_external_fields_load as an alternative to the EXF-pkg option
+    for reading boundary values. This routine is called from 
+    obcs_prescribe_read
+  - updated obcs_check
+
+checkpoint55c_post
+o obcs stuff
+  - new runtime flags useOBCSprescribe, useOBCSbalance
+  - re-arranged obcs_calc
+  - moved exf_getobcs to obcs_prescibe_read
+    obcs_prescibe_read is called after ORLANSKI stuff
+    and independent of it (executable can contain all).
+  - updated obcs_check
+  - added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE.
+    These may be necessary only if tangential velocities are
+    prescribed at OB, not sure, needs testing.
+o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments
+  which simplifies the calls and passes the ifc check-bounds test
+
+checkpoint55b_post
+o add a 2D scalar, Z location, exchange_2 routine.
+o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows
+  to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]
+  affects advect_cs results (for the wrong reason): update output.txt
+o use a more standard discretization for biharmonic viscosity ; 
+ (original version still available with #define MOM_VI_ORIGINAL_VISCA4 )
+  affects results of dome set-up: update output.txt 
+o fix gad_advection.F (CubedSphere part), back to version 1.23
+o fix bug in mom_vi_del2uv.F (CubedSphere part).
+
+checkpoint55a_post
+o merged code to 
+  * prescribe/read time-dependent open boundaries
+    (works in conjunction with exf, cal)
+  * sponge layer code for open boundaries
+  * each boundary N/S/E/W now has its own CPP option
+    (healthy for the adjoint)
+
+checkpoint55
+o up-to-date adjoint of previous breaks
+  - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix
+  - global_ocean_ebm: adjoint still needs fix (TLM ok)
+  - global_ocean.90x40x15: extended GMREDI_OPTIONS.h
+  - carbon: * remove tr1-related adjoint verification
+            * add ptracer as control variable
+o remove all tr1-related code (ALLOW_PASSIVE_TRACER)
+  (adjoint stuff still has some tr1 'names', but all use ptracer arrays)
+
+checkpoint54f_post
+o in verification/carbin/ remove experiment related to
+  ALLOW_PASSIVE_TRACER (array tr1 etc)
+  code_ad/ input_ad/ results_ad
+
+o add two new packages
+  - ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993)
+    + subject to optimization (memory)
+  - opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997)
+    + subject to reordering (many GOTOs in the original code)
+    + so far opps is called for every (i,j) point, and then operates in
+      the vertical; one may want to reorder the scheme in order operate in
+      horizontal slabs at the cost of (a lot of) memory, at least ten new 3D 
+      fields)
+o overhaul of IO so that we now have flags for MDSIO and/or MNC
+  - all verification tests compile and run with linux_ia32_g77
+  - defaults are compatible with current input files--nothing 
+    should change if you were not previously using MNC
+  - MNC output has been added in numerous places (eg. timeave)
+    but there are still a few writes not yet do-able with MNC
+    (this is in progress)
+  - flags now allow for either/or/both use of MDSIO and MNC and 
+    documentation will soon follow
+  - numerous small formatting cleanups for ProTeX
+o add version info (via BUILD_INFO.h) to MNC and stdout
+
+checkpoint54e_post
+o add two new packages
+  - pp81 (Packanowski and Philander, 1981), Richardson number and 
+    stratification dependent mixing
+  - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
+  - these scheme operate in a similar manner as KPP (without ghat, of 
+    course), however there is only one diffusivity that is used for both
+    temperature and salinity (and passive tracers)ç
+o add offline package
+o add "verification/dic_example" which contains a dic-gchem-ptracer setup
+  provided by Stephanie Dutkiewicz
+o genmake2: add ability to search for C compilers and cleanup test output
+  - fixes recent SX-6 problems and should help with others (eg. HP-UX)
+
+checkpoint54d_post
+o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed
+o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong, 
+  leading to additional shift by 5 days each year of integration
+   (i.e. leading to considerable offset over the years)
+o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep
+o start with no AB and no initial filtering (staggerTimeStep):
+  change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5
+o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F
+  (external loading & cpl import/export stay in forward_step.F)
+o update coupling interface to work with new staggerTimeStep
+o change MDSIO ptracers_pickup.
+o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F);
+o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")
+o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)
+
+checkpoint54c_post
+o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr
+  this affects (truncation error) output.txt of test-exp:
+   global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box
+o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array)
+o change Qnet to always be the net heat flux, (+upward).
+  affects (truncation error) output of natl_box exp.: updated
+o define the max number of passive tracers in PTRACERS_SIZE.h
+o start to test mnc routinely in exp0
+o add sea-ice loading (sIceLoad) as a new forcing field.
+
+checkpoint54b_post
+o add testreport "-j JOBS" option for parallel builds (tested and pretty 
+   impressive on Altix and Opteron systems)
+o diagnostics can now write NetCDF files through the mnc package
+o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output
+o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added 
+o staggerTimeStep & NLFS: rescale T & S surface tendencies.
+  affects (truncation error) output of lab_sea & natl_box exp.: updated
+o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
+
+checkpoint54a_post
+o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).
+o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)
+o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)
+o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)
+  + internal_wave (shift in writing cg2d_ini_res)
 checkpoint54a_pre
 
 o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice