--- MITgcm/doc/tag-index	2012/03/18 23:29:55	1.1626
+++ MITgcm/doc/tag-index	2012/06/22 18:31:45	1.1673
@@ -1,9 +1,191 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1626 2012/03/18 23:29:55 jmc Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1673 2012/06/22 18:31:45 jmc Exp $
 $Name:  $
 
     Notes on tags used in MITgcmUV
     ==============================
 
+o verification (atmospheric set-up):
+  - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
+o pkg/profiles : refine profiles and files handling.
+o model/src and pkg/ecco : introduce run-time switch usePROFILES.
+o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
+  - changes to use model/src/the_main_loop.F rather than the ecco version
+    in ecco type adjoint runs.
+o model/src:
+  - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
+  - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
+  - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
+o model/src:
+  - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
+    update output of test experiment bottom_ctrl_5x5.
+o pkg/generic_advdiff:
+  - implement vertical bi-harmonic diffusion (for now, only for T & S and
+    only explicitly).
+o verification/bottom_ctrl_5x5/
+  update reference output (results changed quite some time ago,
+  not sure when; but new reference results look ok in terms of grdchk)
+o verification/1D_ocean_ice_column/
+  For verification purposes, the exact adjoint rather than an approx.
+  should be used (e.g., to comare against F.D. or TLM).
+  removed autodiff_inadmode*_ad.F routines in code_ad/
+  Update results/ accordingly.
+o pkg/cal:
+  - change cal_getdate.F so that output date is function of input time only
+    (less ambiguous, not mixed up with input iteration number).
+  - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
+o pkg/diagnostics:
+  - implement calendarDumps also for stats-diags
+  - implement calendarDumps also for snap-shot output (negative freq)
+  - for now, ignores calendarDumps if non-zero phase-lag.
+
+checkpoint63n (2012/06/04)
+o model/src:
+  - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
+    between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
+  - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
+    similar to calc_r_star.F); update results of experiment internal_wave and
+    tutorial_global_oce_in_p (affected @ truncation level).
+o pkg/shelfice:
+  - add parameterisation of advective-diffusive flux into the ice shelf
+    according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
+  - simply eps3/3a computation
+o eesupp:
+ - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
+   between tiles, just fill-in edges assuming locally periodic subdomain) and
+   add corresponding exchange subroutines (EXCH0);
+ - new CG-solver version (_EX0) for disconnected-tiles special case.
+o model/src (CG-solvers):
+ - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
+   (similar final residual output and max-Iter number as with standard version);
+ - allows to store and use lowest-residual solution (standard & _SR versions);
+ - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
+ - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
+o eesup/src:
+ - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
+   ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
+o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
+
+checkpoint63m (2012/04/27)
+o pkg/shelfice:
+ - account for partical cells in surface level below ice-shelf for hydrostatic
+   pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
+o ad test experiments:
+ - update and rename to "ad_optfile.local" local AD-optfile specific to a
+   particular adjoint verification experiment (in verification/*/code_ad/)
+o pkg/seaice & pkg/exf:
+ - Part two of ECCO-CLIVAR code merges.
+   Completes merge of seaice area relax. code.
+   Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
+   to be set in EXF_OPTIONS.h since this pkg controls its I/O
+   (and avoids second CPP option in SEAICE_OPTIONS.h)
+ - change default value of costIceStart & costIceEnd to a valid date.
+ - add snowPrecip to HSNOW in seaice_growth
+o pkg/ptracers:
+ - move ptracers summary and setup check into separated S/R ; add a check for
+   valid PTRACERS_Iter0 value (error+stop or just warning).
+o pkg/cal (+ pkg/ecco):
+ - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
+   as input; and for AD, unless both are not differentiable (e.g., k index)).
+o model/src:
+ - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
+   is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
+   temporary set to usingZCoords value (to be changed to F when using shelfice).
+ - hydrostatic pressure: implement partial cell near the surface also for
+   Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
+   usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
+o pkg/ctrl/ctrl_init.F:
+ - add a formal parameter to s/r ctrl_init_rec to print
+   xx_$(ctrl_valiable)_file for easier debugging
+ - move call of cal_* routines into the if-block where they are really
+   needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
+   to specify a startdate
+o pkg/seaice:
+ - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
+   global_ocean.cs32x15/code versions).
+ - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
+   verification experiment global_ocean.cs32x15.seaice and update results.
+o pkg/exf:
+ - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
+   (according to useExfYearlyFields).
+o pkg/cal:
+ - move calendar setting & summary (previously in cal_readparams.F) into new
+   S/R CAL_INIT_FIXED to be called later in the initialisation process, once
+   length of the simulation is set (after SET_PARMS call); This is an attempt
+   to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
+ - For safety: keep a record of pkg/cal parameter settings status
+           to allow to STOP if one pkg/cal S/R is called too early.
+ - add a stop in all basic pkg/cal subroutines if called before setting is done.
+ - modify cal_getdate.F: stop when nothing was returned;
+   if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
+   this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
+
+checkpoint63l (2012/04/04)
+o pkg/bbl:
+  - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
+    update global_with_exf output.yearly.txt file.
+o pkg/cal:
+  - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
+  - remove 2 unsused and very short (1 line only) functions ;
+  - remove unsused subroutines from AD-Diff list.
+o model/src:
+  - start to implement clean wait to stop in initialization S/R (config_check.F,
+     packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
+o folowing PRINT_MESSAGE changes:
+  - remove reminder multiple print to the same file (STDOUT) when multi-threads.
+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