--- MITgcm/doc/tag-index	2012/04/02 04:34:07	1.1641
+++ MITgcm/doc/tag-index	2012/11/09 14:12:43	1.1764
@@ -1,9 +1,693 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1641 2012/04/02 04:34:07 dimitri Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1764 2012/11/09 14:12:43 mlosch Exp $
 $Name:  $
 
     Notes on tags used in MITgcmUV
     ==============================
 
+o pkg/seaice:
+  - move computation of eta at Z-points into calc_viscosities
+    + introduce global field etaZ
+    + add different methods for computing etaZ, for now the old
+      method (simple averages of eta to Z-points) is hardwired
+    + replace etaMeanZ by etaZ in seaice_lsr, seaice_calc_residual, 
+      seaice_preconditioner
+  - simplify computations for SEAICE_ZETA_SMOOTHREG
+  - seaice_preconditioner: 
+    + replace one remaining press by pressLoc (mistake)
+    + adjust printing of residuals
+  - improve I/O of diagnostics of JFNK in seaice_jfnk.F:
+    + add (SEAICE.h) and rename some counters (initiliased in 
+      seaice_init_fixed.F)
+    + add _BEGIN/END_MASTER (myThid)  around print statements
+    + print total number of iterations and failures over SEAICE_monFreq
+      interval to STDOUT
+  - move control over output-messages by fgmres to seaice_jfnk to save
+    some operations
+  - move resetting initial guess for fgmres outside of seaice_fgmres_driver
+    in order to make restarts with sol .ne. zero (fgmres with restarts)
+    (seaice_jfnk.F, seaice_fgmres.F)
+  - seaice_calc_l/rhs.F: replace maskW/S by maskInW/S; this fixes
+    a serious convergence problem when open boundaries are involved
+o pkg/ggl90: fix computation of control volumes for the case of 
+  ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes
+  up half a grid cell from C-centered to W-centered (pointed out by C. Eden)
+o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC
+o pkg/autodiff
+  - Add inAdMode switch for SEAICEuseDYNAMICS:
+    SEAICEuseDYNAMICSinAdMode 
+    (extend logic in ADAUTODIFF_INADMODE_SET)
+o pkg/seaice
+  - Step 1 of merging ice-thickness distribution (ITD) code from
+    MITgcm_contrib/torge/itd/ (author: Torge Martin)
+    The code implements concept laid out in Thorndike et al. (1975);
+    code is enabled via CPP flag SEAICE_ITD
+    nITD (in SEAICE_SIZE.h) defines number of ice thickness categories;
+    code is not complete yet!!
+  - SEAICE_SIZE.h now included in almost all seaice routines
+o verification (using seaice):
+  - switch back seaice-dynamics (+ lower SOLV_MAX_ITERS) in ADM exp.
+    global_ocean.cs32x15.seaice ; update results.
+  - compile B-grid dynamics in FW test exp 1D_ocean_ice_column ;
+  - compile C-grid dynamics with #define SEAICE_ALLOW_JFNK in FW test exp
+    offline_exf_seaice (previously compiling B-grid).
+o pkg/exf:
+  - fix some STOP conditions in exf_check.F (from Aug 28, modifs did not allow
+    to specify neither just 1 comp of wind or wind-stress, nor no surface momentum
+    forcing): just replace CPP option ALLOW_ATM_WIND with run-time param useAtmWind.
+o pkg/layers (adjust changes from Sept 19):
+  - do snap-shot output and fill diagnostics from inside iLa loop (layers_calc.F)
+    this allows to remove "layers_maxNum" dimension from all layers arrays.
+o pkg/layers (adjust changes from Sept 19):
+  - remove ALLOW_LAYERS_OUTPUT ; fix snap-shot and time-ave output ;
+  - snap-shot extended to all type of layers (not just the 1rst type);
+  - remove layers variables when corresponding CPP option is undef.
+o pkg/layers:
+  - rename pkg/layers variable and add new output (layer exist & un-weighted
+    velocity in layer)
+o pkg/seaice:
+  - simplify (?) ocean-drag coefficent computations by using
+    the same routine in all three solvers (saves some code lines)
+  - remove global fields DRAGA and DRAGS from C-grid code and
+    declare them locally in lsr.F (the only place where they are
+    still used)
+  - update AD output of lab_sea.evp (very sensitive anyway).
+o pkg/seaice: add Jacobian-free Newton Krylov solver for ice dynamics
+  (Lemieux et al. 2010, 2012). Turn on with the usual SEAICE_ALLOW_JFNK
+  and SEAICEuseJFNK=.true. A few things to note:
+  - involves a FGMRES, that is parallel but very inefficient,
+    because of many scalar products (global sums) in the Gram-Schmidt
+    orthogonalization method. Needs to be replaced. Original code
+    from J.-F. Lemieux
+  - preconditioner for FGMRES is a stripped down version of LSOR
+  - SOLV_MAX_ITERS is now used for LSOR as a solver and as a
+    preconditioner. For the preconditioner, the default is set to 10.
+  - Jacobian times vector is computed with finite differences
+  - marginally related to JFNK-solver: add a smooth regularization for
+    zeta with tanh that will improve convergence (Lemieux and Tremblay,
+    2009) for any implicit solver (not implemented for EVP because EVP
+    does not need this regularization in the first place). Define
+    SEAICE_ZETA_SMOOTHREG in SEAICE_OPTIONS.h to use.
+o eesupp/src:
+  - check in genmake2 that intrinsic S/R flush is available.
+  - add S/R to flush IO unit (if intrinsic S/R flush is available)
+  - flush standard & error msg unit before MPI termination
+  - if debugMode, flush IO unit after printing msg
+o pkg/ctrl:
+  - ctrl_unpack.F, ALLOW_GENARR3D_CONTROL code: fix missing argument in call
+    to ctrl_set_unpack_xyz.
+
+checkpoint64 (2012/10/09)
+o pkg/shelfice
+  - in mom_fluxform.F, mom_vecinv.F:
+    CALL SHELFICE_V_DRAG(bi,bj,k,vFld,KE,KappaRU,vF,myThid)
+    Bug fix KappaRU -> KappaRV
+    does not change verification/isomip but may change other setups
+    (presumably constant KappaRU=KappaRV)
+  - fix diagnostics SHIU/Vdrag (thanks to Tom Millgate)
+o pkg/obcs:
+  - fixed some indexing bugs in obcs_seaice_sponge.F
+  - added obcs relaxation subroutines for HSALT and HSNOW
+  - changes verification/seaice_obcs/results/obcs_seaice_sponge.F
+o pkg/seaice:
+  - add "multicategory" parameterization for snow in analogy to ice,
+    default is off for now.
+o pkg/obcs:
+  - added obcs_seaice_sponge.F for obcs relaxation of seaice variables;
+    see verification/seaice_obcs/input.seaiceSponge for example application.
+  - remove local commom bloc "OBCS_GLOBAL" in obcs_readparms.F and do all the OB
+    index setting by master-thread. This fix multi-threads Pb in previous modifs.
+o pkg/layers :
+  - add diagnostics to pkg/layers
+  - move the meat of pkg/layers from layers_calc.F to layers_fluxcalc.F
+    (from R.Tulloch). Layers_calc.F now calls layers_fluxcalc.F accordingly.
+o pkg/generic_advdiff/gad_implicit_r.F :
+  - fix ADVr diagnostics in case of both implicit vertical advection and diffusion.
+o pkg/seaice/seaice_growth.F:
+  - fix SItflux diagnostics in virtual salt flux + balanceEmpmr case.
+o pkg/obcs:
+  - change default setting of OBCS_UVICE_OLD from defined to undef;
+  - use new parameter OB_indexNone for null index value (instead of hard-coded 0)
+    in all pkg/obcs code and in other pkgs; remove k loop in obcs_check_depths.F;
+  - pass OB_indexNone as (new) argument to S/R CTRL_MASK_SET_[X,Y]Z;
+  - change OB null index value (OB_indexNone) to -99 ; this fix the problem
+    with Southern & Western OB at a tile edge (at least in a simple set-up).
+o pkg/obcs:
+  - change settings of OB index in case OB coincides with tile edge (shared by
+    2 tiles), so that common OB location is registered by both tiles (instead of
+    only 1). However, for Southern and Western OB, index value = 0 is not
+    recognized as valid OB index (=default null value) and needs to be fixed.
+  - modify accordingly OBCS_BALANCE_FLOW and OBCS_MONITOR (avoid double counting)
+  - new parameter "OB_indexNone" for null index value (for now, still zero)
+    to replace hard-coded null index value of zero.
+o pkg/exch2:
+  - improve W2_USE_E2_SAFEMODE (faster) and W2_E2_DEBUG_ON:
+    always check buffer-size (but outside the loop); move checking for valid
+    index from W2_USE_E2_SAFEMODE to W2_E2_DEBUG_ON; in W2_E2_DEBUG_ON,
+    print each tile and point connection only if |W2_printMsg|>= 2 and 3.
+o pkg/ctrl (pack & unpack):
+  - in ctrl_pack.F & ctrl_unpack.F, use the same local file-name variable
+    (locally defined) for different variables (+ remove the variable-specific
+    file name in CTRL_GENARR.h). For now, only implemented for GENARR2/3D_CONTROL
+    (to be extended to other local file names in ctrl.h).
+o pkg/flt:
+  - add a FLT_Iter0 option (similar to PTRACERS_Iter0).
+o pkg/mdsio:
+  - fix missing STOP in mdsio_readvec_loc.F (case ioUnit=0) when file is missing
+o tools/genmake2:
+  - add similar dependences for target EXE_AD & EXE_FTL as we have for EXECUTABLE
+    (added by Alistair in version 1.51 for building without make depend);
+  - remove Header files list (H_SRC_FILES) from the dependence of targets
+     ad_input_code.f & ftl_input_code.f (not clear why it was added in the first
+    place in version 1.23): this save going through staf when unrelated header
+    file has been modified.
+   Note: for an intermediate target (e.g., ad_input_code.f or adtaf) without
+    "make depend" step, still need to do "make links" before "make adtaf".
+o eesupp/src (+ few pkg src files) & genmake2:
+  - finish to remove ALWAYS_USE_MPI in source code that TAF does not see;
+  - no longer set ALWAYS_USE_MPI in Makefile (was done by genmake2).
+  - improve genmake2 checking for ALLOW_${PKG} in CPP_OPTIONS.h files (distinguish
+     upper/lower case ; account for space between "#" and undef/define)
+o pkg/flt (with exch2):
+  - cleaning: fix so that it compiles; move remaining MPI calls out of flt_exch2.F;
+  - simplify threads synchronisation; fix (many issues) multi-threaded with MPI.
+
+checkpoint63s (2012/09/05)
+o pkg/ecco:
+  - remove #ifdef ALLOW_SMOOTH_CORREL3D brackets.
+  - add more relevant #ifdef ALLOW_SMOOTH ones.
+  - sort out useAtmWind, useSMOOTH, ctrlSmoothCorrel2D.
+o pkg/ctrl:
+  - CTRL_OPTIONS.h : document CPPs related to smoothing; ALLOW_SMOOTH_CORREL2D/3D,
+    ALLOW_CTRL_SMOOTH, ALLOW_SMOOTH_CTRL2D, ALLOW_SMOOTH_CTRL3D.
+  - ctrl.h : document run time params doInitXX, doMainPack, doMainUnpack, doPackDiag,
+    doSinglePrecTapelev (audodiff param!), ctrlSmoothCorrel2D (new) and
+    ctrlSmoothCorrel3D (new).
+    The added ctrlSmoothCorrel2D/3D replace the old ALLOW_SMOOTH_CORREL2D/3D CPP.
+  - ctrl_readparms.F : initialise ctrlSmoothCorrel2D/3D and read from namelist.
+  - ctrl_init.F ctrl_pack.F ctrl_unpack.F : switch off ustress/vstress
+    controls when useAtmWind, and vice versa.
+  - ctrl_map_ini_ecco.F : UVEL0, VVEL0, edtaux, edtauy cannot be smoothed as tracers.
+  - ctrl_get_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL2D with
+      #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel2D, IF useSMOOTH.
+  - ctrl_map_ini_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL3D with
+      #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel3D, IF useSMOOTH.
+  - ctrl_set_pack_xy[z].F, ctrl_set_unpack_xy[z].F:
+    replace ALLOW_SMOOTH_CORREL2D/3D brackets with ctrlSmoothCorrel2D/3D.
+o pkg/smooth:
+  - remove un-necessary includes.
+  - remove ALLOW_SMOOTH*D and ALLOW_SMOOTH_CORREL*D brakets.
+    Those CPP options were never defined, and not necessary.
+o model/src:
+  - fix CPP brackets in ini_mixing.F (GM_background_K belongs to gmredi).
+  - standard treatment of useSMOOTH.
+o pkg/autodiff:
+  - add LOGICAL useGGL90inAdMode, useGGL90inFwdMode, useSALT_PLUMEinAdMode,
+    useSALT_PLUMEInFwdMode allowing to switch off ggl90 and salt_plume adjoint.
+o pkg/exch2:
+  - add "if usingMPI" where it was missing (in exch2_rx?_cube*.template)
+    + start to remove ALWAYS_USE_MPI in source code that TAF does not see.
+  - make new S/R W2_MAP_PROCS out of w2_eeboot.F to setup exch2 CommonFlag
+    and tiles to process mapping.
+  - re-arrange 3 header files (W2_EXCH2_PARAMS.h, _BUFFER.h & _TOPOLOGY.h)
+    moving /EXCH2_FILLVAL_RX/ & /W2_EXCH2_COMMFLAG/ to W2_EXCH2_TOPOLOGY.h;
+    rename "exch2_tProc" to "W2_tileProc" and move seting of e2FillValue_RX
+    from w2_eeboot.F to w2_readparms.F.
+o eesupp/src:
+  - set exchNeedsMemsync & exchUsesBarrier according to "usingMPI" (instead of
+    ALWAYS_USE_MPI) + moved from ini_communication_patterns.F to eeset_parms.F;
+    also move setting of exchCollectStatistics from exch_init.F to eeset_parms.F
+  - in eedie.F and all_proc_die.F, always call MPI_FINALIZE when ALLOW_USE_MPI
+    is defined (remove condition on usingMPI) to match cases where MPI_INIT
+    has been called.
+  - fix bug I put in previous modif of exch_sm_3d_rx.template (not much used);
+  - change default (non-MPI) value of myPid (from 1 to 0) to match MPI settings
+    (so that on 1 proc, get same myPid independently of usingMPI)
+  - add a stop if multi-procs but usingMPI=F ; stop also if usingMPI=T and
+    useCubedSphereExchange with EXCH-1 (safer).
+  - add "if usingMPI" where it was missing (+ start to remove ALWAYS_USE_MPI).
+o pkg/ggl90:
+  - fix bug in filling corner mask array "mskCor" (FILL_CS_CORNER_TR_RL call)
+    used in ALLOW_GGL90_SMOOTH code.
+o pkg/flt:
+  - fix typo in FLT_WITHOUT_Y_PERIODICITY (the effect was to ignore stopping
+    floats at the Southern end of the domain).
+o eesupp/inc:
+  - add a list of CPP-options which can be set by Makefile (DEF_IN_MAKEFILE.h);
+    but not used (and not to be used) anywhere, just for documentation.
+o pkg/autodiff, exf, ptracers & seaice (AD & TL output):
+  - comment out the very nasty "writeBinaryPrec = writeStatePrec" line, since:
+    a) can damage previously written records in any other multi-record files.
+    b) if needed, can easily do it cleanly, by calling S/R WRITE_REC_3D_RL/S.
+o tools/genmake2:
+  - define variable MAKE within Makefile and use it in place of 'make';
+  - update AD_CONFIG.h (if needed) before building any of the executable
+    (forward, adjoint or tangent-lin); this involves a 2nd invocation of make;
+    and add the usual #ifndef/#define AD_CONFIG_H in AD_CONFIG.h;
+  - always print usual warning comment 'this file is automatically generated'
+    from script convert_cpp_cmd2defines (+ remove this warning from genmake2).
+o pkg/cheapaml:
+  - updated to correspond to the code used in accepted paper (Nico Wienders).
+o pkg/exf:
+    added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch.
+    ALLOW_ATM_WIND now just sets the useAtmWind default (see exf_readparms.F)
+    and force defines ALLOW_BULKFORMULAE (EXF_OPTIONS.h).
+o pkg/exf, autodiff, ctrl, ecco and seaice:
+    remove ALLOW_ATM_WIND brackets, or replace them with useAtmWind ones.
+o pkg/ctrl, ecco:
+    allow to compile both ALLOW_U/VSTRESS_CONTROL and ALLOW_U/VWIND_CONTROL.
+    Depending on useAtmWind, one is inactive, and the other is active (see
+    exf_getffields.F/exf_getsurfacefluxes.F).
+o tools/genmake2:
+  - improve error msg when failing in 2nd test of check_for_broken_Ff
+  - fix option '-makefile' short-name (-mf according to genmake2 -help)
+  - source local config file "genmake_local" just after processing the genmake2
+    command arguments (previously done before processing arg).
+o pkg/grdchk:
+  - add a call to TURNOFF_MODEL_IO for Tangent-Linear run (in this case, call
+    to this routine from cost_final has been dropped in g_cost_final)
+  - improve printed information (more explicit msg, no longer using "print *,"
+     fix fcpertminus printed value).
+o model/src:
+  - move call to COST_INIT_VARIA out of packages_init_variables.F directly
+    into initialise_varia.F (just after calling PACKAGES_INIT_VARIABLES):
+    this prevents getting cost-funct reset in adinitialise_varia recomputations.
+o pkg/dic:
+  - move initialisation of "freefe" array from from dic_biotic_forcing.F to
+    fe_chem.F: this prevents TAF from dropping this initialisation in TLM code.
+o pkg/grdchk:
+  - grdchk_main.F : added CALL GLOBAL_SUM_INT( ierr , myThid )
+  - grdchk_getadxx.F etc. : omit I/O if ierr.EQ.0
+o pkg/autodiff/ctrl/grdchk :
+  - attempt to sort out what works and what does not,
+    with regard to I/O, and to warn/stop accordingly.
+o pkg/grdchk:
+  - attempt to fix grdchk in the case of useSingleCpuIO.
+  - "if ( myProcId .EQ. grdchkwhichproc .AND. ierr .EQ. 0 )"
+   statements were moved from grdchk_main.F and into
+   grdchk_getadxx.F grdchk_getxx.F grdchk_setxx.F.
+  - a global sum is applied to record numbers icvrec/layer
+   out of grdchk_loc so that they be passed to I/O routines.
+o pkg/smooth:
+  - fix recomputation that appeared with nlfs : use smooth_recip_hFacC,
+    smooth_hFacW, smooth_hFacS (copied at init_fixed) in 3d case.
+o verification/testreport:
+  - add option '-tlm' for Tangent-Linear test (-adm,-oad,-tlm are all exclusive);
+  - can also use compressed (gzip) reference output file;
+  - change format (in pkg/grdchk) of TLM output (+ add forward gradient)
+    to be easier to collect by testreport.
+  - update existing TLM output (half out-of-date by more than 3 yrs).
+  - report NETCDF & LAPACK settings (from genmake2) in output dir.
+  - report run-time in each individual summary (previously only for AD test);
+    for TLM test, add also TAF version.
+  - add daily TLM test on (old) aces cluster + weekly test on baudelaire.
+
+checkpoint63r (2012/08/15)
+o tools/genmake2:
+  - fix Makefile for target ftlall (+ update files to clean after make ftlall)
+o pkg/ecco/ecco_cost_final.F :
+  - fix fc print statements (to stdout and costfunction0000) so
+    that the printed value is always after the global sum.
+o pkg/seaice/seaice_dynsolver.F :
+  - fix ice strength assymptote at SEAICE_area_max<1
+    (no change for the standard case of SEAICE_area_max=1)
+o some cleaning:
+  - pkg source files: ensure that all *.F files from each pkg included the
+    corresponding ${PKG}_OPTIONS.h file (except stand-alone src file which
+    only includes CPP_EEOPTIONS.h); fix S/R CTRL_SMOOTH ; update AD experiment
+    code_ad/*.F src files; add new option-file in pkg/admtlm + corresponding
+    includes;
+  - model/src: add PACKAGES_CONFIG.h wherever ALLOW_AUTODIFF[_TAMC] is used.
+  - ALLOW_DIFFKR_CONTROL: add a stop in S/R CTRL_CHECK in case ALLOW_3D_DIFFKR
+    is undef; also define /DYNVARS_DIFFKR/ common block in DYNVARS.h when
+    ALLOW_DIFFKR_CONTROL is defined, to allow to compile and reach this stop.
+  - update option-file CPP_OPTIONS.h of all AD experiments:
+    * no longer include PACKAGES_CONFIG.h ;
+    * includes ECCO_CPPOPTIONS.h if PACKAGES_CONFIG.h has been included ;
+    * def/undef ALLOW_3D_DIFFKR independently of ALLOW_DIFFKR_CONTROL (before
+      including ECCO_CPPOPTIONS.h).
+o pkg/cost, pkg/ctrl, pkg/ecco option-file:
+  - clean-up and split content of old pkg/ecco/ECCO_CPPOPTIONS.h file into
+    separated pkg option-file (done according to old doc from ECCO_CPPOPTIONS.h,
+    not necessary accurate).
+  - add a template for option-file ECCO_CPPOPTIONS.h, mostly empty, in
+    pkg/autodiff, i.e., the 1rst pkg to compile for adjoint built, with lines to
+    deliberately break compilation (a remainder that it needs to be customized)
+  - in pkg/ecco, includes ECCO_OPTIONS.h instead of COST_OPTIONS.h
+  - rename COST_CPPOPTIONS.h to COST_OPTIONS.h
+  - rename CTRL_CPPOPTIONS.h to CTRL_OPTIONS.h
+o tools/genamke2:
+  - check for lapack.
+o pkg/cost and pkg/ecco : attempt to sort out some of the limiting intricacies.
+  - pkg/cost.cost_final.F : allow for use of pkg/ecco and pkg/cost cost functions
+    jointly. The exclusive ifdefs were removed, to add costs terms (when defined)
+    from both packages.
+  - the fc global sum in pkg/ecco/ecco_cost_final.F was removed accordingly.
+  - for objf_atl we use either the pkg/ecco or the pkg/cost term depending on CPPs.
+  - pkg/ecco and model/src : add CPP brackets around pkg/cost and pkg/ctrl includes
+    of "CTRL_SIZE.h" "ctrl.h" "ctrl_dummy.h" "optim.h" / "cost.h" accordingly.
+o pkg/cost : add comments to explain special and/or untested setups.
+o pkg/exf:
+  - use EXF_OPTIONS.h to set pkg/exf options except if done in ECCO_CPPOPTIONS.h
+    (previously, ALLOW_AUTODIFF_TAMC was controling this switch).
+o verification/*/code_ad:
+  mimimal cleaning of AD experiments ECCO_CPPOPTIONS.h option-file:
+  - reccord when this file is included (define ECCO_CPPOPTIONS_H)
+  - remove the most obvious obsolete features (e.g., #define ALLOW_COST not
+    allowed since Oct 2003 in any option-file except in PACKAGES_CONFIG.h)
+o pkg/seaice :
+  - added possibility to change ice strength/PRESS0 relationship to
+    HEFF, according to the following run time parameters
+    SEAICEpresPow0 :: HEFF exponent for ice strength below SEAICEpresH0 (integer, >0)
+    SEAICEpresPow1 :: HEFF exponent for ice strength above SEAICEpresH0 (integer, >0)
+    SEAICEpresH0   :: HEFF threshold for ice strength            (m)
+o pkg/ggl90 :
+  - added run time flag mxlSurfFlag to include the code that ensure
+    mixing between first and second level (previously included as a comment)
+o verification/1D_ocean_ice_column/input_ad/data.autodiff :
+  - add test of newly added dumpAdByRec=T option where
+    we write all records to one file per variable.
+o verification/global_ocean.cs32x15/code_ad/CPP_OPTIONS.h :
+  - switch to #define ALLOW_BALANCE_RELAX and ALLOW_BALANCE_FLUXES
+    to check that this code is ok with taf and compiles in adjoint.
+o pkg/autodiff :
+  - added run time param dumpAdByRec : ad dump format switch.
+    If true then write all records to one file per variable.
+    Else write one file per record (remains the default).
+  - revise seaice_ad_dump.F and exf_adjoint_snapshots_ad.F accordingly.
+o pkg/seaice:
+ - Added SEAICEuseTILT run time switch : if set to
+   false then omit the tilt term in seaice dynamics.
+ - Fix free drift calculation.
+o pkg/shelfice:
+  When initializing SHELFICEDragQuadratic, set default to be
+  consistent with shiCdrag in case SHELFICEuseGammaFrict is used,
+  but retain option to set it independently
+  (inconsistenty spotted by Veronique Dansereau)
+o eesupp/inc:
+  - in EEPARAMS.h, add real-type constant for some frequently used simple number
+     (0,1,2,1/2), with name explicitly referring to RS/RL type.
+o model/src:
+  - move balancing of relaxation terms to new S/R balance_relax.F.
+o pkg/autodiff:
+  re-write active I/O high-level (control) S/R:
+  - rename  S/R ACTIVE_READ/WRITE_RL to ACTIVE_READ/WRITE_3D_RL
+  - add 1 more argument (useCurrentDir) to replace the "_LOC" 2nd set of S/R.
+  - use standard pkg/mdsio I/O routines (MDS_READ/WRITE_SEC_XZ/YZ  and
+    MDS_READ/WRITE_FIELD); change loops to multi-threads.
+  - update and merge active_file_control_slice.flow into active_file_control.flow
+  - update the calls in lower level S/R (active_file.F, active_file_g.F and
+    active_file_ad.F) keeping the argument list and function unchanged.
+  - also update lower-level "_LOC" version (call same S/R with "useCurrentDir
+    =.TRUE.") and remove high-level (control) _loc version (not called anymore).
+  - new low-level active I/O routines, one for each type (RL/RS), for active var
+    of various (XY,XZ,YZ) shape and level number (arguments: arrShape, myNr);
+    fix ctrl_init_wet.F & ecco_cost_weights.F by calling the new S/R with the
+    right type.
+o autodiff and RS=real*4:
+  - call the right type (_RS instead of _RL) of S/R in few output S/R (pkg/exf
+    ad-monitor and snapshots); disable arrType='RS' in mdsio_gl*.F ;
+  - change argument type of 3-D mask argument to _RS to match type in the call
+    (in seaice_cost*.F, ctrl_*_gen.F and *ctrl_bound.F); to be continued.
+o pkg/thsice:
+  - re-anable balanceEmPmR when useSEAICE=T with useThSIce=T.
+  - option to correct ocean fresh-water flux for imbalance of Atmos+Land
+    fresh-water flux: uniform correction or proportional to local precip.
+o pkg/ctrl:
+  - new header file CTRL_SIZE.h for parameters maxCtrlArr2D, maxCtrlArr3D
+  - redefine CPP option ALLOW_BOTTOMDRAG_CONTROL to
+                        ALLOW_BOTTOMDRAG_CONTROL_NONGENERIC
+  - verification/hs94.1x64x5/ tests ALLOW_GENARR{2D,3D}_CONTROL
+
+checkpoint63q (2012/07/30)
+o pkg/autodiff:
+  note about monitor and snap-shot of ad-variables:
+  a) need to apply ADEXCH before monitor or output of ad-vars to include
+   overlap contributions (was done for adjDump but missing for monitor).
+  b) since ADEXCH implies adding overlap values to interior array, machine
+   truncation error is expected when adding an ADEXCH call in the middle of
+   the time-stepping (although mathematically identical).
+  modifs:
+  - fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars
+    declaration (adEddyPsiX,adEddyPsiY in adcommon.h).
+  - add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how  to
+    apply ADEXCH before monitor or snap-shot of ad-variables:
+       =0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy.
+  - implement new method (copy+adexch) for snap-shot and monitor of main model
+    ad-vars (initially not used by default -> output unchanged).
+  - change default (set to 2) to use new method and update few output_adm.txt
+    with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo
+    and both tutorial_tracer_adjsens tests).
+  - switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice)
+    and turn off momDissip_In_AB in the 2 other (needed for stable AB-3).
+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)
+  - 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