--- MITgcm/doc/tag-index	2012/03/06 16:59:57	1.1612
+++ MITgcm/doc/tag-index	2012/04/02 04:34:07	1.1641
@@ -1,9 +1,144 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1612 2012/03/06 16:59:57 jmc Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1641 2012/04/02 04:34:07 dimitri Exp $
 $Name:  $
 
     Notes on tags used in MITgcmUV
     ==============================
 
+o pkg/bbl:
+  - modification so it can work with z*
+  - replace deltaT with dTtracerLev(k) for asynchronous time stepping
+  - global_with_exf/input.yearly verification; changes output.yearly.txt
+o eesupp/src:
+  - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
+    writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
+  - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
+    # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
+  - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
+  - when using MPI, always set usingMPI=T ; set default accordingly and stop
+    if not consistent.
+  - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
+    argument is zero (in case called within single-thread section).
+o pkg/fizhi:
+    clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
+    in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
+o pkg/exch2:
+  - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
+    activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
+  - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
+    but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
+    with bad ones coming from a not-yet-updated halo.
+    This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
+o pkg/frazil:
+    move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
+    http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
+o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
+o verification/lab_sea
+  * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
+  * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
+  * nTimeSteps 3 -> 4
+  * changed reference output accordingly
+o pkg/ctrl:
+  * fix ctrl_get_gen for xx_sst, xx_sss
+o pkg/fizhi:
+  - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
+    update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
+  - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
+    fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
+    clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
+o pkg/gmredi:
+  - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
+o pkg/fizhi:
+  - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
+    (old)aces open64 tuv test.
+o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
+o pkg/mom_vecinv:
+  - fix 1 loop range in mom_vecinv.F to be like all the other loops which
+    set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
+    with non-lin free-surf).
+o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
+  in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
+  some compilers (gfortran 4.6.0 on MacOS)
+o momentum:
+  - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
+    & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
+    fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
+
+checkpoint63k (2012/03/17)
+o model/src:
+   - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
+     flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
+   - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
+     (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
+o model/src: solve_*diagonal.F
+   - replace division with multiplication by inverse (similar to original version)
+     update output of AD exp. global_ocean.90x40x15.
+   - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
+     to enable the use of the vectorized & differentiable solve_tridiagonal.F
+   - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
+     vertical advection (to get solve_tridiagonal tested in AD mode).
+o pkg/seaice: ECCO-CLIVAR merge:
+  1. seaice AREA relaxation
+     * CPP option: SEAICE_ALLOW_AREA_RELAXATION
+     * runtime flag: SEAICE_tauAreaObsRelax
+  2. modified global mean cost imbalance code: CPP option
+      ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
+o another iteration on solve_*diagonal.F
+   Make choices independent of AUTODIFF
+   Default will be the adjoinable vectorized version.
+   Alternative choices are:
+   * non-adjoinable original version with low memory footprint:
+     #define SOLVE_DIAGONAL_LOWMEMORY
+   * still adjoinable but does not vectorize (k as inner-most loop):
+     #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
+o testreport
+ - add option to use a home made wrapper around "make"
+ - remove MITGCM_IEEE env. variable (no longer active)
+o pkg/shelfice
+ - improve computation of friction velocity for velocity dependent
+   exchange coefficients: include velocities into SHELFICEBoundaryLayer
+   block to average velocities vertically
+ - add TAF store directives for SHI_ALLOW_GAMMAFRICT
+o Modify diagonal solvers, now three versions (upon request):
+  #ifndef SOLVE_DIAGONAL_AUTODIFF
+    1. default version (dating back a while ago)
+  #else /* def SOLVE_DIAGONAL_AUTODIFF */
+  # ifdef SOLVE_DIAGONAL_KINNER
+    2. adjoinable version with k-innermost loop (G. Forget)
+  # else
+    3. adjoinable vectorized version of 2.
+  # endif
+  #endif /* SOLVE_DIAGONAL_AUTODIFF */
+  All flags are currently set within routines, but could/should be moved to CPP-options.
+  Array bounds for 1. are as before, for 2.,3. cover the entire domain
+  (could be changed for 1. too).
+o verification/lab_sea (fwd):
+  - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
+    use 7 categories (except hb87), new solve4temp params (except salt_plume),
+    constant salinity (=4) or variable salinity (salt_plume) done through
+    SItracer.
+o pkg/seaice:
+  - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
+  - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
+     SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
+    from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
+    SEAICE_freeze got retired) but already better than previously with
+    SEAICE_freeze=123456.7 deg.C;
+  - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
+    (safer multi-threaded setting); always set SEAICEuseEVP;
+  - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
+    SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
+    stop if multiple specifications for the same coeff; make sure default
+    SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
+o pkg/obcs:
+  - allow to switch to upwind 1rst order advection scheme for the advective
+    flux computation at the open-boundary; disabled for adjoint built.
+o pkg/ptracers:
+  - rename PTRACERS_RESTART.h -> PTRACERS_START.h
+  - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
+  - add parameter to decide when to start a tracer; use internal flag to
+    know which tracer to step-forward; switch this internal flag at the top
+    of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
+    for adjoint built.
 o pkg/seaice:
   - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
   - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;