--- MITgcm/doc/tag-index	2012/06/07 17:17:04	1.1665
+++ MITgcm/doc/tag-index	2012/07/27 18:29:17	1.1696
@@ -1,9 +1,159 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1665 2012/06/07 17:17:04 jmc Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1696 2012/07/27 18:29:17 heimbach Exp $
 $Name:  $
 
     Notes on tags used in MITgcmUV
     ==============================
 
+o pkg/ctrl:
+  enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of
+  generic control variables via
+  #define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL
+  Only required customization should be S/R ctrl_map_ini_genarr.F
+  (routine in repository contains example)
+o pkg/exf:
+  - fix and refine checking of surface-relaxation setting when using EXF
+o verification (adjoint exp):
+  - reduce length of simulation by half for experiment global_ocean.cs32x15
+    (std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output.
+o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag)
+  - replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers
+    of KE that can occur with aggressive optimization
+  + put quadratic bottom drag calculation in separated loops (only done if
+    using bottomDragQuadratic)
+o model/src: CG2D_NSA
+  - clean-up:  stop if cg2dNormaliseRHS=T and AUTODIFF
+     and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE.
+  - in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens),
+     change cg2d residual target to be expressed in Wunits (=> do not normalise
+     RHS ; this fix global_max Pb with TAF); update output.
+o verification/tutorial_tracer_adjsens:
+   improve parameter consistency (and get rid of warnings):
+   - use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf);
+   - switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical)
+   - use staggerTimeStep (for stability) in som81; use default rotation period.
+o pkg/exch2:
+  - with empty facet: fix compact-format (W2_mapIO=1) definition (was previously
+    reset to 0 = 1 long line in X)
+o pkg/mdsio:
+  - fix reading of dimensions from meta file for large-size domain
+o model/src:
+  - fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long);
+  - to refine CS-grid check, add logical flag "hasWetCSCorners": true if using
+    Cubed-Sphere Exch with CS-corners inside the domain;
+    make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate
+    globalArea and to set hasWetCSCorners.
+  - add warning if usingCurvilinearGrid and momAdvection in flux-form (missing
+    metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form.
+  - re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if
+    useCDscheme and useCubedSphereExchange).
+o pkg/seaice/seaice_growth.F :
+  - compute the SEAICE_DISABLE_HEATCONSFIX term accordingly
+    for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0)
+    when the previous code was not correct.
+  - in all cases diagnoze the boundary condition mismatch to SIaaflux
+  - in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add
+    that term to QNET (essentially to set the melt/freeze water to 0degC).
+    when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed.
+o verification/global_ocean.cs32x15/input.seaice :
+  - add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget.
+  - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces).
+  - update results (output.seaice.txt) accordingly.
+o verification/lab_sea/input/data.seaice :
+  - remove SEAICEheatConsFix, which is now be tested
+    in global_ocean.cs32x15. The presently coded fix
+    is only consistent with real fresh water + nlfs.
+  - update results (output.txt) accordingly.
+o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd).
+o AD_CONFIG.h file:
+  - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;
+  - remove #include "AD_CONFIG.h" from all included OPTIONS files and
+    add it explicitly in each fortran src file where it is needed.
+    motivation: header file AD_CONFIG.h is generated/modified after "make depend"
+    thus introducing potentially wrong dependency; therefore, better to include
+    it only where it's really needed, and after any other included OPTIONS file
+    (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN
+    or ALLOW_TANGENTLINEAR_RUN).
+
+checkpoint63p (2012/07/06)
+o pkg/autodiff:
+  - rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ;
+  - create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters
+    which are now read from new parameter file "data.autodiff" (inAdExact
+    previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg)
+  - add file "data.autodiff" in all verification/*/input_ad/ directories.
+  - add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward
+    mode (used in global_ocean.cs32x15.seaice_dynmix test exp.)
+o verification/tutorial_tracer_adjsens/
+  - add extra sub-verification which uses "SOM" advection scheme
+    (2nd Order-Moment Advection Scheme, Prather Limiter) with
+      #define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h
+    and in data:
+      multiDimAdvection=.TRUE.,
+      tempAdvScheme=81,
+      saltAdvScheme=81,
+o model/src:
+  - introduce ALLOW_BALANCE_RELAX which allow the removal
+   of the global mean of relaxation terms by setting
+   balanceThetaClimRelax and balanceSaltClimRelax
+  - disable balanceEmPmR and balanceQnet in the case when useSeaice.
+   This case is now treated appropriately in seaice_growth.F
+o pkg/seaice:
+  - do balanceEmPmR and balanceQnet based on the net fluxes
+    (SItflux) that enter the ocean+ice system rather than QNET
+    and EMPMR. Works best in real fresh water.
+  - SIatmFW, SIatmQnet, and SItflux computations had to be moved
+    out of the diagnotics bloc, and stored in global arrays.
+
+checkpoint63o (2012/06/29)
+o vertical mixing schemes:
+  - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging)
+  - replace computation of density (in Function STATE1, opps_calc.F) by a call
+    to S/R FIND_RHO_SCALAR
+  - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC
+    and use it for N^2 calculation in ggl90_calc.F (save 2 density computations);
+    affects output (vermix.ggl90) at truncation level.
+o testreport:
+  - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles
+    (nSx,nSy) for the number of threads (from eedata.mth)
+o model/src:
+  - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part)
+    related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary).
+o verification/tutorial_tracer_adjsens/
+  - compile with ALLOW_CG2D_NSA
+  - run with nonlinFreeSurf=3
+  - update reference output_adm.txt
+o tools/genmake2:
+  - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
+    refine usePROFILES switching off (only when NetCDF is not available).
+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)