--- MITgcm/doc/tag-index	2008/02/13 07:43:39	1.957
+++ MITgcm/doc/tag-index	2008/05/09 22:39:42	1.990
@@ -1,9 +1,106 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.957 2008/02/13 07:43:39 mlosch Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.990 2008/05/09 22:39:42 dfer Exp $
 $Name:  $
 
     Notes on tags used in MITgcmUV
     ==============================
 
+o Freshen up a bit hs94.1x64x5, notably: 
+  remove rotationPeriod and tRef=5*0. (adjoint only), and add exactConserv=.TRUE.
+o pkg/generic_advdiff:
+  change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
+  applies to files where Temperature & Salinity 2nd Order moments are used.
+o pkg/ptracers: add second-order moment advection schemes (80 and 81);
+  this uses a dynamically allocated internal state data structure
+  (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h) 
+  and requires a fortran 90 compiler
+
+checkpoint59q
+o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
+   (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
+o Refresh tutorial_global_oce_biogeo, notably:
+  - change bathymetry (put back seamounts in ACC, use hFacs)
+  - change EOS (POLY3 --> JMD95Z)
+  - use Bryan-Lewis vertical diffusivity
+  - use multidimensional advection
+  - remove old virtual virtual in dic pkg, now done through ptracer pkg
+  - change a couple of parameters in dic pkg
+o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
+o pkg/obcs: change default to OBCSfixTopo = .true., 
+  - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
+  - replace "debugMode" with "debugLevel .GE. debLevB"
+o implementation of TAF directives for gchem,cfc,dic 
+o remove "exp5" (replaced by tutorial_deep_convection).
+o pkg/obcs: add code to fix topography gradients normal to open boundaries;
+  this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
+  the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
+  --> changes results in exp4, seaice_obcs
+o tutorial_deep_convection :
+  update the set-up and increase resolution and domain size ; start
+  from pseudo initial conditions = output at t=120mn in order to see
+  something happening when running testreport.
+o pkg/seaice: add os7mp as an advection scheme
+              add check for advection schemes
+              add a flag for restoring T and S underneath sea ice
+o pkg/my82: add netcdf-support and diagnostics 
+o thsice pkg:
+  - Now hsMax limits snow height by turning it into ice following
+    flooding scheme (and now conserving energy)
+  - Slight rewriting of the formula in thsice_calc_thick.F
+  - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
+  --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice 
+
+checkpoint59p
+o gchem / dic / cfc :
+  - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
+  - add new parameter files: "data.dic" & "data.cfc" ;
+  - various re-arrangement in initialisation & header file ;
+  - fix tutorial_global_oce_biogeo for multi-threaded test.
+o pkg/dic: test for "pickup_dic" file when restarting ;
+  if no pickup-file, can restart with a re-initialised pH (same as it did
+  before) providing pickupStrictlyMatch is set to False.
+o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
+  + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
+o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
+  and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
+o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
+ & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
+   (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
+o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
+   scheme to use for vorticty-term ;
+ - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F 
+   (with default selectVortScheme, return to original discretisation)
+ - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
+o pkg/seaice: add a line to the summary to indicate grid type (B/C)
+o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
+  bottom ; only used with variable horizontal viscosity and non-hydrostatic.
+  also fix diagnostics VISCAHW & VISCA4W.
+
+checkpoint59o
+o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
+o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
+  move a few statemens out the main loop into separate loops
+o pkg/shelfice: 
+  - sort out freshwater flux; convert freshwater fluxes to mass fluxes 
+    (kg/m^2/s), does not break tests, because in verification/isomip,
+    rhoConstFresh=rhoConst (by accident)
+  - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
+  - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
+    new file model/src/seawater.F, so that they are available for all pkgs.
+  - convert potential temperature into in-situ temperature. This changes the
+    isomip tests => update tests
+o add a flag writePickupAtEnd (default=true) to be able to suppress 
+  writing a pickup at the last timestep
+o tools/mpack-1.6 : 
+  - disable automake (not working) and autoconf (not needed).
+  - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
+    also cleaner with much less compilation warnings.
+o pkg/profiles: 
+  rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
+  (for "less than 32 characters name" compiler requirement)
+o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
+  conditions that have a different sampling frequency than S/T/U/V obcs
+o pkg/diagnostics (stats-diags): 
+  - fix global Min/Max in case 1 processor get only empty tiles
 o genmake2: replace (4 times)
      make genmake_tc_1.o >> genmake_warnings 2>&1
   with