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-revision 1.433 by heimbach,
Tue Jan  4 22:08:07 2005 UTC
+revision 1.1400 by mlosch,
Tue Mar 15 16:51:37 2011 UTC
 Line 1
  $Header$
+ $Name$
      Notes on tags used in MITgcmUV
      ==============================
+ o pkg/ctrl:
+   - change behavior of xx_${varname}period to be analogous to exf-conventions:
+     xx_${varname}period =   0.,  means time-independent control part
+     xx_${varname}period = -12., means one-year-periodic monthly control part
+   - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
+     clean up ctrl_init a little, remove unused variables
+   - ctrl_init: fixed the handling of the start/endrec for obcs-variables
+   - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
+ checkpoint62u (2011/03/15)
+ o model/src:
+   - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
+     h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
+   - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
+     INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
+ o pkg/ctrl/obcs/ecco:
+   - remove obsolete, unused, and partially broken code:
+     ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
+     ALLOW_CTRL_OBCS_BALANCE
+   - put a stop statement into ecco/cost_obcsvol.F, but also add
+     cost_obcsvol to ecco_ad_diff.list
+ o pkg/ecco: fix counting cost function contributions for obcs (code
+   by Matt M.) and diffkr for diagnostics
+ o pkg/ecco, pkg/ctrl, pkg/grdchk:
+   add cost penalty terms for initial uvel, vvel, eta controls
+   and I/O for prior error files
+ o pkg/mdsio:
+    move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
+    (new argument) to check for tiled file in mdsioLocalDir : this fix the
+    restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
+ o pkg/ctrl:
+  - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
+    ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
+    unused and superfluous variables
+  - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
+ o pkg/ecco
+  - enable adjoint of Stevens OB
+ o pkg/ctrl/ecco/grdchk:
+   - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
+     Fortunately, we do not have any tests for the numerous cpp-flagged
+     option of "obcs as control parameters" so we will never know
+     if this is an improvement (but at least now things compile).
+   - remove an obsolete initialization from ecco_cost_init_barfiles.F
+   - fix some problems within never used ifdefs to make the code compile
+ o pkg/obcs:
+  - Refine Interior mask definition to work with more complex OB (e.g.
+    if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
+    read in Interior mask from file. Check if Interior mask is consistent
+    with OB list of indices.
+ o pkg/seaice
+  - beginning code for a seaice tracer package,
+    but currently only used for seaice age: SEAICE_AGE
+    SEAICE_num = 4
+    iTracer = 1: area-weighted ice age
+            = 2: volume-weighted ice age
+            = 3, 4: template for one-year vs. multi-year ice
+    data.seaice has new namelist SEAICE_PARM03 for arrays related to
+    SEAICE_num
+ checkpoint62t (2011/03/05)
+ o pkg/obcs:
+  - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
+    then normal component. This ensures that the normal component is set
+    correctly even when it conficts with tangential setting from an other OB.
+    Affects results of test-experiment seaice_obcs: update the output.txt
+ o pkg/obcs:
+  - add code to monitor statistics of dynamical fields at OB.
+  - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
+    - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
+    - change default: balance the Net inflow through all OB (instead of balancing
+      each OB separately); keep the old method if setting OBC_balanceFacX < 0.
+  - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
+    to match Nortern OB inflow (OBCS_balanceFacN=0).
+ o pkg/seaice:
+  - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
+ o pkg/seaice (seaice_growth v 1.113):
+  - reverting seaice_growth to v 1.111 in order to have code with exact bit
+    compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
+    CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
+    runtime flag SEAICEareaFormula is kept but is inactive
+ o model/src:
+  - add new param to scale curvilinear grid distance and area when using
+    a different sphere radius from the grid-files.
+  - test/check multi-threads EXCH applied to local variable (cg2d_x)
+ o adjoint:
+  - enable adjoint of Stevens OB
+  - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
+    (a bit delicate because of potentially modified adj. common block structure;
+    current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
+ checkpoint62s (2011/02/15)
+ o pkg/seaice (seaice_growth v 1.112):
+  - introduce SEAICEareaFormula run time parameter, which selects the recipe for
+    computing the ice cover tendency from effective thickness tendencies. Include
+    Ian Fenty's formula.
+  - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
+    SEAICEareaFormula.
+  - simplify notations for the various d_HEFF/d_AREA terms.
+ o pkg/gmredi:
+  - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
+    from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
+    add a verification test-run (front_relax.bvp) to test GM_useBVP.
+ o pkg/seaice (seaice_growth v 1.111):
+  - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
+  - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
+    also melt ice.
+ o pkg/seaice:
+  - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
+  - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
+ o pkg/cheapaml:
+  - from Nico Wienders: New version of this package.
+ o pkg/flt:
+  - add CPP options to prevent floats to re-enter the opposite side of
+    a periodic domain (default: keep periodicity)
+ o pkg/gmredi:
+  - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
+    (needed for multi-dim advection).
+  - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
+ o model/src:
+  - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
+ o tutorial_tracer_adjsens
+  - extend to NLFS and replace maskC by hFacC
+    (change reference output accordingly)
+ checkpoint62r (2011/01/24)
+ o testreport:
+  - add option -deloutp (-do) to remove output file after successful run
+  - add option -mfile (-mf) for MPI machile-file and for each test-exp,
+    extract exact list of procs from this file ; adjust COMMAND by
+    replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
+ o pkg/ecco: replace old ineffective way of penalizing deviations from
+   first guess (of obcs) with code by Matt Mazloff
+ o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
+   exf/cal
+   - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
+     and handle case of obcs?period == 0
+     Not affected by these changes: There is still an inconsistency in
+     the computation of start/endrec for the obcs variables for ALLOW_CAL
+     defined (see comment by Menemenlis, 7-Mar-2003)
+   - make S/R ctrl_get_gen_rec return something meaningful even if
+     ALLOW_CAL is not defined
+   - ctrl_getobcs?: simplify code so that it does not need to use
+                    S/R exf_swapfields
+ o testreport:
+    allow to test MPI with different number of processors for each experiment:
+    create file "SIZE.h.mpi" in each build dir.
+    Note: update of "-command" argument not yet implemented.
+ o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
+   alleviate the need for additional 3D tapes when using
+   the non-inear free surface in the adjoint. This is done
+   by adding an 'update' of hfacc etc. to their current
+   value at the beginning of forward_step.F.
+ o pkg/seaice
+   seaice_lsr: move stress-divergence computations out of outer pseudo-
+   timestepping loop
+ o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
+   up, so that the calls of the ctrl_* subroutines are really at the end
+   of the routine.
+ o pkg/gmredi:
+   allow to specify a 2-D horizontal map and a 1-D vertical profil
+   as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
+ o pkg/seaice:
+   move lsr iterations from seaice_dynsolver to seaice_lsr.
+ o pkg/seaice:
+   reduce memory footprint of seaice mutldim advection tapes,
+   by using a 2D tape independent of the generic_advdiff ones,
+   and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
+ checkpoint62q (2010/12/29)
+ o model/src:
+   - check horizontal grid-spacing for unset or zero/negative values.
+   - change AD test hs94.1x64x5 to be truly a 2-D set-up.
+ o pkg/flt:
+   - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
+   - precision of input and output files set according to readBinaryPrec
+     and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
+   - initial float position from tiled file was not converted to index space
+     (looks like a bug): fixed to make it similar to initial pos. global file.
+ o global_ocean.cs32x15:
+    change SIZE.h of AD set-up to get same tiling as with MPI.
+    Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
+ o model/src:
+    add flag to control printing of domain fields (bathymetry, hFac ...) in
+    ini_mask_etc (call to plot_fieds_xy*).
+ o pkg/thsice:
+    if useEXF, some forcing fields are not valid in overlap: fixed by computing
+    over the interior only + apply EXCH at the end (like with SEAICE advection).
+ o pkg/mdsio:
+   - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
+     to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
+   - change barrier call for safe multi-threads access to 3-D shared buffer.
+   - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
+   - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
+     remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
+ o pkg/flt:
+   - add fourth-order Runge-Kutta integration
+   - add basic exch2 support (only 1 facet supported so far!)
+ o pkg/mdsio+rw:
+   new S/R to read local (or tile independent) vector (read counterpart of
+    mds_writevec_loc, and front-end write_glvec_rl/rs).
+ o global_ocean.cs32x15: additional input_ad.seaice experiment
+     that uses pkg/seaice rather than pkg/thsice.
+     (using multidim advection for seaice)
+ o towards more F95 syntax for array specification in namelist:
+   - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
+     of all verification experiments.
+        e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
+       was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
+   - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
+ o global_ocean.cs32x15: additional input.seaice experiment
+     that uses pkg/seaice rather than pkg/thsice.
+ checkpoint62p (2010/12/17)
+ o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
+     to THSICE_SIZE.h to avoid conflict with pkg/seaice.
+ o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
+     allow for use of multim. advection in seaice adjoint.
+ o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
+   - first attempt to close budgets by taking into account the freshwater
+     flux implied by the sublimation of snow and ice. So far only the
+     volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
+     SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
+ o eesupp/src:
+   new S/R with new option (NML_EXTENDED_F77) to change array specification
+   from F95 standard to commonly accepted extended F77 form.
+   This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
+   and to revert back to the original syntax (with -DNML_EXTENDED_F77)
+   for less tolerant f77 compiler (e.g., pgf77, g77).
+ o globalFiles:
+   commented out in parameter file "data" since it's not safe with MPI
+   (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
+   in this case); no longer commented out in restart test (tst_2+2).
+ o add adTapeDir to specify a special directory where adjoint tapes are
+   written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
+   and cannot be used together with mdsioLocalDir.
+ o nesting pkgs:
+   - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
+   - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
+   - add parameter files + utils dir + output from short run on beagle.
+ o pkg/seaice:
+     fix seaice_growth.F store directives; update results of exp. lab_sea.ad
+ o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
+   unnecessary copying in adjoint code, requires new parameter NMAX_ITER
+ checkpoint62o (2010/11/25)
+ o pkg/exf:
+   - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
+ o pkg/seaice:
+   - seaice_ocean_stress: split a loop for better vectorization of the
+     adjoint code
+   - seaice_growth.F: fix bug in conservation of freshwater connected to
+     capping of heff, put contribution into d_HEFFbyNEG
+   - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
+     by something more sensible (parameters that are what their name implies)
+   - change some defaults, so that by default exf-parameters are used for
+     things like rhoAir, cpAir,latent/sensible heat parameters, in order
+     to reproduce the old results, many data.seaice now contain funny values
+     for cpAir and latent heat of sublimation
+ o packages_readparms.F: move exf_readparms up in line so that
+     exf-parameters are visible for other packages (e.g. seaice)
+ o debugMode & debugLevel=2:
+   - differentiate between debugMode & debugLevel=2:
+     debugMode: controls printing of debug messages (sequence of S/R calls).
+     debugLevel: controls printing of algorithm intermediate results and stats.
+   - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
+     => allows to print debug-stats without all sequence of call messages.
+   - switch control of debug print from debugLevel to debugMode in many S/R.
+ o pkg/obcs (obcs-sponge):
+     fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
+     call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
+ o pkg/generic_advdiff:
+   - record overlap minimum size for each advection scheme;
+   - refine criteria on overlap minimum size;
+   - check and stop (in gad_check) if overlap size is too small.
+ o pkg/obcs:
+   - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
+     once, in ptracers_implicit.F)
+   - with seaice: remove test on empty file name in obcs_apply_seaice (always
+     apply OB values when tile has OB)
+ o model/src, coriolis setting:
+   - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
+     useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
+     files (selectCoriMap=3) with any grid.
+   - add parameter "fPrime" for constant second Coriolis coeff (default=0).
+ o pkg/seaice/seaice_growth.F:
+     a few cosmetic changes that reduce the number of lines of code
+ o pkg/obcs: add boundary conditions following Stevens (1990)
+   - the code follows old MOM/NAOSIM code
+   - so far it is only implemented for the eastern and western boundaries
+     and NOT for pTracers
+ o pkg/rbcs:
+   - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
+     beginning of the first rbcs forcing period.
+   - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
+     offline package, i.e., one file per time, labeled by iteration number;
+     deltaTrbcs sets the timestep with which the data was generated;
+     rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
+   - rbcsForcingCycle=0 makes forcing non-cyclic.
+   - make arithmetic safe for negative times and odd forcing periods.
+ checkpoint62n (2010/11/09)
+ o pkg/seaice:
+     fix masking in free-drift S/R ; update results of exp. lab_sea.fd
+ o pkg/obcs:
+    New S/R to copy tracer value from the OB location to narrow band region
+     (width = same as overlap) beyond the OB: preserve OB value (needed for
+     high-order scheme) which were overwritten by EXCH call if in overlap
+     region. Applied to theta, salt, ptracer and advected seaice variables.
+    With seaice: use maskInC in similar way as in gad_advection.F,
+     in seaice_advection.F and advect.F.
+    Update output of experiment seaice_obcs and change exp4 to test OBCS with
+th order Adv.Scheme. for pasive salt and ptracer.
+ o tools/genmake2:
+   - when looking for an optfile (not specified), only search for Fortran compiler
+     (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
+   - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
+     (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
+   - set default for CPP to "cpp -traditional -P" (was the case without specifying
+     an optfile, but otherwise default was just "cpp".
+   - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
+   - when "CC" is not set in the optfile, look for possible C compiler
+     (instead of just setting CC=cc)
+   - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
+     => add a ".F" to ".o" rule for source files with no "#include" (such as
+        port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
+   - move gfortran before g77 in list of possible Fortran compiler (consistent
+     with reference compiler switch from g77 to gfortran)
+ o pkg/seaice:
+   o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
+     seaice_check that stops the model, when the CPP flag is used.
+   o seaice_growth.F: make capping of ice volume conserving by returning the
+     capped ice as freshwater to EmPmR. This does not change the verification
+     experiments but will change runs where the capping is acutally active
+ o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
+   (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
+      global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
+      lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
+ o tools/genmake2:
+   - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
+   - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
+   - clean previous genmake log files before anything else.
+   - change Makefile to remove testreport log files (*.tr_log) and genmake log
+     files only with "CLEAN" target (instead of "Clean");
+ o pkg/generic_advdiff:
+   Change OBCS in multiDim advection (gad_advection.F):
+    Use maskInC to prevent intermediate update of tracer-field in OB regions,
+    thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
+    which were applying future time-step OB values.
+   This way, all explicit calculations use current-time-step OB values
+    (simpler and more consistent).
+   Affects results when set-up uses time-varying OBC and multi-dim advection;
+    update output of experiment seaice_obcs.
+ o pkg/seaice:
+   move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
+    this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
+      SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
+   Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
+    but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
+    unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
+ o pkg aim (2010/10/26):
+   - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
+     formulation with obliquity, eccentricity, ... as run-time parameters,
+   - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
+     upward shortwave radition at the surface (all-sky and clear-sky).
+ o pkg/obcs:
+   - writing sections with globalFiles=T does not work: switch to tiled-files
+     when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
+   - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
+   - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
+ checkpoint62m (2010/10/21)
+ o pkg/seaice: vectorize seaice_solve4temp.F
+   - move iterations loops outside of i/j-loops
+   - requires 2D arrays for TB and effConduct
+   - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
+     modified in this routine
+   - a little bit of clean up, adjusting indentation, etc.
+   - replaced a few TEN**a by exp(a*log(10.)) in new code for better
+     performance and '**TWO' by '**2' (because TWO is a float),
+     replaced ONE, ZERO
+ o eesupp/src:
+    fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
+ o pkg/seaice/seaice_growth.F
+   Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
+   merging process. The merged routine has two branches, and one activates the 'evolution'
+   branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
+   In summary, here is what the '10/10 revision' did consist of
+     part 1: seaice_growth.F revisions 1.71 to 1.75
+       - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
+         The emphasis here was on improving readability (e.g. by trying to use meaningful
+         variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
+     part 1.5:
+       - revising the lab_sea experiment to make it a more useful (i.e. stable
+         and representative of an actual model run). This was done by generating a
+         (winter) pickup to start from, switching back the main experiment dynamic
+         solver from evp to lsr, having one of the experiments use the free drift solution.
+     part 2: seaice_growth.F revisions 1.76 to 1.85
+       - Sorting out hard-coded constants that prevented heat and fresh water conservation.
+       - Sorting out the various fields units and sign (set early on and reset at the end)
+         to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
+         fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
+       - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
+         and simplifying logical expressions to further improve readibility.
+     part 3: seaice_growth.F revisions 1.86 to 1.89
+       - Re-organize the blocks of code more logically.
+       - Merging the '_if.F' pieces that add something new.
+ o pkg/thsice:
+   - vectorize thsice_solve4temp and thsice_get_exf.
+     Problem: thsice_solve4temp has an unvectorizable statement that
+     might also be problematic for TAF
+   - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
+     does not change the verifcation experiment, but will change all
+     experiments that have this flag undefined (not tested in verification);
+     a little reorganization to save a few 2D fields and recomputations
+   - 1st step of revisiting thsice adjoint (major recomp. sorted out)
+   - 2nd step:  fix some store dirs
+     o seems to work somewhat, i.e. using ifort but not g77
+     o likely cause are incomplete init. or recomputation
+     o start verification/global_ocean.cs32x15/input_ad.thsice
+ o pkg/obcs: add support for exch2
+   - the position of the boundary and prescribed values are specified using
+     a global domain with exch2 facets stacked
+     - in x for N,S boundaries (like W2_mapIO=-1)
+     - in y for E,W boundaries (so E,W boundaries do not overlap)
+ o pkg/mdsio: add support for writing global sections with exch2
+     file layout is as for obcs described above:
+     - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
+     - for y-z sections, facets are stacked in y
+ o pkg/thsice:
+    - change a few routines for better vectorization: thsice_albedo.F,
+      thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
+      not affected, but in particular the latter routine has changed
+      dramatically (not necessarily easier to read now).
+    - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
+    iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
+ o verification/lab_sea:
+   - overhaul of the forward model experiments. The main motivation
+     for this revision is that lab_sea has proven quite fragile (when
+     changing the sea-ice code, and switching platforms) to a point
+     when failures were very hard to attribute to specific code problems.
+   - the suspected reason for this fragility is noise amplification by evp so,
+     to start with, we decided to replace evp with lsr in the main experiment.
+   - the input.lsr experiment thus became obsolete and was removed.
+   - it was replaced with the input.fd experiment that uses an
+     analytical "free drift" solution as the ice velocity field.
+   - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
+     will hopefully allow us to discriminate problems due to dynamic solvers
+     from problems due to the thermodynamic code. input.salt_plume (lsr) allows
+     us to test additional options, along with the salt plume package.
+   - Finally a pickup was generated (at the end of a one year run) to
+     make the tests more representative of an actual model run. Previously
+     the tests starting point was a 1m thickness of ice everywhere.
+ o pkg/seaice:
+   - introducing S\R seaice_freedrift.F that compute the
+     analytical solution to an approximate ice momentum
+     equation (i.e. the simple stress/coriolis balance).
+   - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
+     of the free drift velocity field, and enable its use.
+     To actually use the free drift solution as the model ice
+     velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
+ o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
+ checkpoint62l (2010/10/04)
+ o pkg/seaice:
+   -fix the USE_ORIGINAL_SBI version (for variable freezing point);
+   -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
+    version (with USE_ORIGINAL_SBI undef);
+ o add hooks for new packages OASIS, the package will follow
+   (hooks exclude the seaice pkg for now)
+ o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
+   Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
+   rather than mdsio_readvector.F/mdsio_writevector.F, within
+   adread_adwrite.F to read/write adjoint-related tapes to disk.
+ o eesupp and pkg/mdsio: ALLOW_WHIO
+   Option to write/read 2D fields to files including tiles halos.
+   The main purpose is for adjoint related "tape I/O".
+   The secondary purpose is for debugging phases.
+   A word on those rather specifically intended purposes.
+   The code was meant to be stripped down to the bare minimum.
+   Typically, there is a unique and basic mapping to the global
+   buffer (tile by tile, then proc by proc, then level by level), and
+   byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
+   meant to generate user friendly outputs of various shapes and forms.
+   Rather it is intended, for the knowledgeabale developers,
+   to be largely independent of the many mdsio options, to allow
+   outputs of tiles+halos in debugging phases and in adjoint runs,
+   and to allow some flexibility in tuning (adoint) I/O depending on each
+   file system behavior. With regard to tuning, most of the potential knobs
+   (to leave files open, to allocate the I/O indep. of usesinglecpuio,
+   to specify directories, to specify the typical size of I/O calls, etc.)
+   are not yet included, and will be added if they prove useful.
+ o pkg/seaice:
+    fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
+ o pkg/seaice:
+    new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
+    code (seaice_budget_ice_if.F) which enable to recover old standard
+    code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
+    temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
+ o model/src (rStar):
+    use simple average (not area weighted) of rStarFac at U,V point when using
+    vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
+    update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
+ checkpoint62k (2010/09/17)
+ o adjoint
+    * changed verification/global_ocean.cs32x15 ; adjoint now tests
+      Adams-Bashforth 3 + NLFS + RSTAR
+    * some more modifs required for ECCO-GODAE v4
+ o pkg/seaice
+    add SEAICE_AGE_VOL option to use volume instead of area for
+    integrating SEAICE_AGE
+ o model/src:
+    first check-in of sigma & hybrid-sigma coordinate code ; also includes
+    non-linear free-surface parts ; but pressure-gradient not yet coded.
+ o pkg/ptracers:
+    option for ptracer to convert Salt Relax into additional EmP.
+     tested in exp. global_ocean.90x40x15.dwnslp (update output)
+ checkpoint62j (2010/08/25)
+ o pkg/ggl90:
+    other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
+ o pkg/dic: car_flux.F, phos_flux.F
+   - reduce number of exp-calls in order to improve performance
+   - clean up a little (replace fields by their macros, etc., fix
+     typo in CPP-flag)
+ o pkg/ggl90: minor changes
+   - GGL90diffKrS was removed --> always use GGL90diffKr
+   - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
+   - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
+     (commented out for now)
+   - change in max/min operations to ensure that smoothing is ok
+   - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
+   - always use diffKrNrT as background profile (i.e. never use diffKr field)
+ o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
+ o pkg/dic:
+   - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
+     vectorization
+   - small bug fix in insol for the unlikely case of a cartesian grid
+   - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
+     + now vectorize, which also removes adjoint recomputations;
+     + replace integer maksp1 by _RL maskp1
+     + replace a**x by exp(x*log(a)) in phos_flux.F for speed
+ checkpoint62i (2010/07/21)
+ o pkg/flt:
+   - with OBCS: stop floats which enter the OB region
+ o model/src:
+   - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
+     for implicit vertical advection.
+ o pkg/seaice:
+  - account for melting in seaice age evolution.
+  - remove double counting of seaice ridging effect on seaice age.
+ checkpoint62h (2010/06/18)
+ o pkg/exch2:
+  - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
+ o tools/genmake2
+   - remove "-pdefault" option: redundant with the use of "packages.conf";
+   - remove file pkg/pkg_default : set the default as a pkg group
+     ("default_pkg_list") defined in pkg/pkg_groups;
+   - fix for case pkg/pkg_depend is missing (was hanging before);
+   - add option "-pgroups" to specify a different pkg_groups than the default.
+ o verification/adjustment.cs-32x32x1:
+    add a "minimal" set-up test (code_min & input_min) which only compiles
+    eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
+ o tools/genmake2
+   - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
+   - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
+ o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
+   files are nearly the same anyway.
+   Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
+    - redefinition of tau(i,i) (by a factor of ustar)
+    - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
+    - replace rhonil by rhoConstFresh in computation of evap (bug fix)
+    - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
+    - replace
+      rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
+      shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
+      by
+      shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
+      (changes results)
+    -> exf_bulkformulae v1.22,
+       update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
+       (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
+                 output.txt 1.63
+        offline_exf_seaice: output.seaicetd.txt 1.7
+        seaice_obcs: output.txt 1.10)
+   Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
+    -> exf_bulkformulae v1.23,
+       unfortunately requires updating lab_sea.salt_plume (6 matching digits),
+       and global_ocean.cs32x15.icedyn (only 11 matching digits)
+   Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
+ o adjoint of exch-1:
+  - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
+    (note: was already like this when using EXCH-2) and remove flow dir
+    and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
+  - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
+  - update pkg/exch2 diff list.
+ checkpoint62g (2010/05/19)
+ o eesupp/src (exch-1):
+  - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
+    and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
+    (renamed to exch1_*rx_cube.F).
+  - change accordingly exch_*_rx.template and AD version in pkg/autodiff
+    to call new exch1 S/R ; update Makefile and .cvsignore.
+  - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
+    exch2_xy_rx later)
+   Note: after updating your code, need to run "make clean" in eesupp/src
+ o test experiment bottom_ctrl_5x5:
+    new output_adm.txt with fewer grdchk & less monitor output.
+ o model/src:
+   remove the call to ini_cori in initialise_varia.F (just keep the usual one
+    in initialise_fixed.F). More consistent with coriolis & horizontal grid
+    beeing treated in the same way (ini_grid is not called a 2nd time).
+ o pkg/exf:
+   - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
+   global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
+   - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
+   - cosmetic changes to exf_bulkformulae.F to make it look more like
+     exf_bulk_largeyeager04.F
+ o eesupp/src (exch-1):
+   - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
+   - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
+     array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
+     (even without using MPI).
+   - Message mode: move RecvAck setting (indicator of buffer being ready)
+     from send_put to recv_get S/R (was useless before, but not sure if
+     it's much more useful now);
+   - Switch the order of sync: MPI-proc 1rst and then threads;
+   - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
+   - fix AD code for communication mode ='get' (but not used).
+ o model/src:
+   initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
+   not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
+ o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
+ o pkg/ctrl: require a specific set of control variables and exf-flags for
+   adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
+ o model/src:
+  a) 1rst version of a new driver S/R to turn-off output freq and flags after the
+rst forward sweep, to avoid over-writing output files during recomputations
+    recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
+  b) 2nd version:
+   - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
+   - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
+      writePickupAtEnd) + seaice & ptracers output;
+   - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
+ o model/src:
+   - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
+ o pkg/exch2:
+   - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
+   - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
+ o pkg/autodiff & exch2:
+   process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
+   (for now, only if ALLOW_EXCH2 is defined).
+ o pkg/autodiff:
+   - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
+     (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
+    + clean-up comments (_RS is not always real*4)
+   - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
+   - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
+     was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
+ o testreport (AD-tests):
+   no longer link files from dir "../input" (1rst link files from
+   "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
+ checkpoint62f (2010/04/29)
+ o model/src/the_main_loop.F:
+   adjust store directives for seaice evp and multicategory according to
+   pkg/ecco/the_main_loop.F
+ o adjoint:
+   global_sum_ad was incomplete (noted many times by many people ;)
+   nice description by Jean U. as follows:
+   * allreduce(var) in global_sum.F can be interpreted as
+     reduce(sum) followed by broadcast of sum.
+   * The adjoint of that is
+     sum(adjoint) followed by broadcast(summed adjoint value)
+     or in other words, allreduce(sum, adjoint vars)
+   We were missing the sum(adjoint)!
+   Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
+   (noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset).
+   The fix should produce 16-digit accuracy between
+   single-CPU multi-tile (e.g. nSx=2, nPx=1) and
+   multi-CPU single-tile (e.g. nSx=1, nPx-2)
+   We'll probably change this yet again shortly
+ o eesupp/src:
+   - fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?)
+ o pkg/icefront
+   - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving
+     specification of addmass array based on a 2D field, which is added
+     at bottommost wet level at each horizontal location.
+ o model/src:
+  horizontal grid initialisation (other than curvilinear): add code for Exch2 IO
+  layout; (not always compatible with delX,delY setting; commented out for now).
+ o pkg/exch2:
+  change tile to processor setting (case nSy*nPy > 1): allows default model mapping
+  (myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config.
+ checkpoint62e (2010/04/15)
+ o pkg/obcs:
+   - fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert).
+ o pkg/dic:
+   -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up;
+     (note: not presently tested in any forward verification exp.)
+    update tutorial_global_oce_biogeo AD output file.
+ o pkg/exf:
+   - account for the variation of albedo as a function of zenith angle
+     by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h
+ o build_options:
+  - rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas"
+ o pkg/dic:
+   change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart:
+   - use binary pickup file for restart;
+   - initialise atmos-CO2 box from dic_pCO2 parameter;
+   - fix multi-threaded.
+ o pkg/rbcs:
+  - clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ;
+    change (+ fix IO calls) type of array RBC_mask from _RL to _RS.
+  - add RBCS to exp4 passive tracer 01 (rbcs was previously untested)
+    and update output.txt
+ o pkg/kpp:
+  - add diagnostics for KPP non-local flux of Temp, Salinity and pTracers;
+  - change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS
+    (= ratio of KPP non-local (salt) flux relative to surface-flux) when
+    using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat ');
+  - change pkg/offline to read-in average KPPghat*KPPdiffKzS from file
+    KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile).
+ o pkg/offline:
+   fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor
+   (bug was added in version 1.10 on 2007-08-23).
+ o pkg/offline:
+   - no need to specify periodicExternalForcing, etc ... to use offline pack
+   - offline input files no longer just single prec --> parameter offlineLoadPrec
+ o verification/lab_sea:
+   change AD test to multi-tile setup and update all 4 AD output.
+   NOTE: while cost function values remain very similar,
+   gradients are very different, although gradient checks are self-consistent
+   Should try to get to the bottom of this (cost function summation order?)
+ o pkg/dic:
+   in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid
+   a weakness of TAF that drops part of double precision in log10 derivative.
+   <= changes removed since problem has been fixed in current TAF version 1.9.71
+   update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo.
+ o pkg/ecco:
+   add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F
+   update all 4 lab_sea AD output.
+ checkpoint62d (2010/03/22)
+ o build_options:
+   remove '-r8' (and '-i4') from linux_*pgf and linux_*ifort optfiles.
+ o remove unbalanced quote (single or double) in commented line of source code
+   (may cause some warning with some preprocessor/makedepend versions).
+ o pkg/seaice:
+   fix seaice_model.F for adjoint (gael) and update AD results of experiments
+    lab_sea (std + evp + noseaicedyn) and offline_exf_seaice.
+ o testreport:
+   add option '-runonly' (short: '-ro') to just do the run part (without make).
+ o eesupp: remove JAM communication code (obsolete).
+ o add option to genmake2 & testreport to switch "_RS" type to "real*4"
+   (if allowed in CPP_EEOPTIONS.h); update default CPP_EEOPTIONS.h and return
+   to default CPP_EEOPTIONS.h for exp. inverted_barometer & solid-body.cs-32x32x1
+   (update also the output).
+ checkpoint62c (2010/03/02)
+ o tools/build_options :
+    move (some) old optfiles from build_options/ to build_options/unsupported/
+ o model/src and pkg/exf
+    surface relaxation -- separating data and data.exf options
+    The point is to ensure that we specify the surface relaxation
+    either in data or in data.exf (but not half and half) and to
+    avoid an accidental relaxation to 0 (which happened if a time
+    scale was specified but the file name was left empty)
+ o model/src model/inc and pkg/mom_common
+    ALLOW_3D_VISCAH/ALLOW_3D_VISCA4 => 3D specification of Viscosity
+    => addition to the viscosity field as computed by others schemes
+ o tools/build_options:
+   - rename "_generic_mpi" -> "+mpi_generic" (like other "+mpi" optfile)
+     but keep the former optfile for few weeks for smooth transition
+ o pkg/ecco
+   - allow user defined cost function contributions
+      CPP: ALLOW_USERCOST_CONTRIBUTION
+      USAGE: compute contributions in cost_usercost_all.F
+   - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
+       the two options are complementary.
+ o pkg/smooth
+   - migration from contrib to the main repository
+ checkpoint62b (2010/01/26)
+ o pkg/monitor:
+   - change back mon_printstats_rl.F & mon_stats_rl.F and add a stop
+     (in case someone forgot to update customized pieces of code)
+ o nonHydrostatic:
+   - add Non-hydrostatic free-surface form (selectNHfreeSurf=1)(not fully tested);
+   - add a simple 2-D experiment (short_surf_wave) to test it.
+ o pkg/icefront:
+    adding the shell of, and the hooks to, a new package that
+    will model melting and freezing of vertical glacier ice fronts
+ o momentum:
+   add diagnostics of momentum tendency from Hydrostatic pressure gradient
+    (without surf.pressure term: would need a 2nd filling since implicit term).
+ o add 3 "_d 0"s so that fizhi compiles with xlf on iblade, and replace
+   two " &end" by " &" (in fizhi-cs-*) because S/R NML_SET_TERMINATOR
+   cannot deal with the former
+ o cleaning:
+   - remove all (except OpenAD) old TLM output from results_ad dirs.
+   - remove unused S/R (MDSWRITEMETA, DIAGNOSTICS_ADD2LIST, old DFILE IO S/R)
+   - comment out maskH definition (replaced by maskInC)
+ o pkg/monitor:
+   - change mon_printstats_rl.F & mon_stats_rl.F (were similar to mon_writestats_rl
+     & mon_calc_stats_rl) to be the RL equivalent of mon_printstats_rs & mon_stats_rs.
+ checkpoint62a (2010/01/15)
+ o model/src:
+   - bottom pressure diagnostic: correct for r* (when nonlinFreeSurf >= 4)
+ o pkg/diagnostics:
+   - add optional level number diagnostics (i.e., level number to be define
+     explictly with S/R DIAGNOSTICS_SETKLEV) with parser-code(10)="X".
+   - strictly check for valid parser-code(10) ;
+   - check if adding diag to the list from the right place.
+ o pkg/longstep:
+   - change parameters and fix tracer conservation with rstar/nonlinear free surface
+ o diagnostics:
+  - in all pkgs, replace remaining calls to old S/R DIAGNOSTICS_ADD2LIST with newer
+    S/R DIAGNOSTICS_ADDTOLIST ; fix seaice VICE diagnostics.
+ o pkg/diagnostics:
+  - Add option for writing vertical integral (sum of selected levels) of an output
+     field instead of writing output field levels. Activate this option on a per
+     output-file basis, by setting the 2nd character of fileflag to 'I'.
+  - Add field-specific information relative to level integral in 3rd postion
+     of parser diagnostics code (gdiag): " "=cumulate levels, "R"=integrate
+     vertically (x level-thickness x hFac), "r"=same but without hFac.
+ o do_the_model_io:
+   - pass end-of-model-run flag as argument, from forward_step to diagnostics_write:
+     in case useSIGREG, will write (averaged) diagnostics (if dumpAtLast) before
+     writing pickups and stopping.
+ o pkg/diagnostics (for now, only with mdsio):
+   - write time information to meta file (and modify accordingly rdmds.m) :
+     time-averaged diagnostics output: write starting and ending time of the
+     time-averaging interval ; snap-shot diagnostics output remains unchanged;
+ o pkg/timeave:
+   - S/R TIMEAVE_NORMALIZ: change size of cumulated-time array (was previously
+     always Nr), now assumed to be equal to number of levels of averaged field;
+     only used for DIC_COST monthly mean arrays: this fixes dic_aver_final.F
+ o pkg/sbo:
+   - fix ocean bottom pressure global-average & 2-D time-ave output (was
+     neither initialised nor filled).
+   - add starting iteration in suffix of global-average output file
+     (to avoid over-writing the file after a restart)
+   - use standard MDSIO pkg S/R instead of SBO_WRITEVECTOR (fix byte-swap Pb).
+ o time-average:
+   - use simple cumulative-time array (no k index) in all pkgs: {PKG}_timeAve(bi,bj)
+     (pkgs: aim_v23, bulk_force, dic, gmredi, kpp, land, ocn_compon_interf,
+      ggl90, my82, opps, pp81, ptracers, sbo, seaice, shelfice, thsice)
+     this fix DIC_COST cumulative-time array (previously: bi,bj,k)
+   - fix 1rst call (nIter0) snap-shot output and accumulation (pkg/shelfice)
+   - fix missing accumulation for pkg/opps.
+   - cumulate fields only if doing time-ave output ({PKG}_taveFreq > 0)
+      (pkgs: ptracers, kpp, ocn_compon_interf, ggl90, my82, pp81);
+   - fix initialisation of time-ave vars and do only full time-step increment
+     (i.e.: no first & last "half time-step") (pkgs: ggl90, my82, opps, pp81);
+ o pkg/layers:
+   - use standard RW pkg S/R to write the output
+     and remove local write_fld version (which had a problem).
+   - use simple cumulative-time array (no level index) to fix time-ave S/R calls.
+   - fix LAYERS_CALC argument list.
+ o pkg/timeave:
+   - store cumulative-time in a simple tiled array (drop the level index)
+   - add new S/R (TIMEAVE_NORMALIZE) which uses simple cumulative-time array.
+ o pkg/ocn,aim_compon_interf
+   - changes for multi-threaded coupled run. (tested with ifort-11 on danton)
+ checkpoint62  (2009/12/23)
+ o switch on useOBCSbalance in tutorial_plume_on_slope exp. and update output.
+     (was not previously tested in any other exp.)
+ o pkg/monitor:
+   - clean-up _RL/_RS version: add specific S/R for statistics with mask & volume:
+     mon_writestats_rl/s,F mon_calc_stats_rl/s.F ; will keep the old one
+     (mon_printstats_rl/s,F mon_stats_rl/s.F) just for bare statistics.
+   - use hFac & 2-D mask (instead of 3-D mask + hFac in previous mon_stats_rl.F).
+   - change del2 calculation.
+   - use interior masks (instead of maskH, <- to be remove).
+   - shorter monitor suffix for forcing stats ("forcing" instead of "extforcing").
+ o mask & obcs:
+   - define 2-D "interior" masks (i.e., zero beyond OB) at 3 locations (C, W & S).
+   - move global area computation from ini_masks_etc.F to ini_linear_phisurf.F
+     (called after packages_init_fixed)
+ o pkg/obcs:
+   - move bi,bj loops into obcs_calc, so obcs_prescribe_read is called only once.
+     Fixes bug in obcs+exf with nSx*nSy.GT.1
+   - fix multi-tile handling in obcs balance code
+ o nonHydrostatic:
+   - Implement AB-3 for non-hydrostatic vertical momentum ;
+     (change ordering of var. stored in pickup file when using NH)
+   - move NH code from solve_for_pressure.F to 2 new S/R: PRE_CG3D & POST_CG3D.
+   - add 2-D field to store Hydrostatic Surface Pressure adjusment from cg3d_x
+     (in prep. for new NH free surface form).
+ o pkg/obcs:
+   add files & OB-variables for wVel (Non-Hydrostatic) with useOBCSprescribe
+ o model/src:
+   fix 2-D solver initialisation for deep-atmosphere (p-coord) with topography
+ checkpoint61z (2009/12/01)
+ o nonHydrostatic:
+   Fix missing vertical flux of vert. momentum near surface (k=1). This fixes
+     a spurious source of energy in simple baroclinic adjusment test case.
+   Update all non-hydrostatic exp output.
+ o model/src (3-d solver):
+   Change again 3-D solver free-surface RHS term when exactConserv=T:
+     simpler, consistent with exactConserv, and works with implicDiv2Dflow < 1
+     (which was not the case with previous formulation).
+   To recover previous version, just reset "oldFreeSurfTerm" to previous value.
+   Affects results of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW.
+ o nonHydrostatic:
+   - compatible with implicDiv2Dflow < 1 ; + implement implicit factor
+     for Non-Hydrostatic pressure gradient (similar to implicSurfPress).
+   - change 3-D solver to work with r* (for now, only with linear free-surf.)
+   - add few debug diagnostics (cg3d_x, residual)
+ o model/src:
+   fix missing EmPmR in 3-D solver RHS (was in cg2d_b but missing in cg3d_b).
+     update output of exp. global_ocean.cs32x15.viscA4
+ o update output of exp. global_ocean.cs32x15.icedyn after removing
+   #define SEAICE_OLD_AND_BAD_DISCRETIZATION from SEAICE_OPTIONS.h
+ o add entry points for Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
+ o mnc: add horizontal grid coordinates (XC,YC) and (XG,YG) to netcdf output
+   for complex grids, for now only to "state", "adstate", "adexf", "adseaice"
+ o model: add Christopher Wolfe's implemetation of the single reduction cg2d
+   (d'Azevedo, Eijkhout, and Romine, 1999) with CPP-flag ALLOW_SRCG and
+   runtime flag useSRCGSolver. Modify verification experiment global_with_exf
+   to test this code
+ o pkg/cd_code:
+   Change defaut D-grid time-stepping to get the same for D-grid momentum as for
+    C-grid momentum. D-grid velocity used to be stepped forward in time with
+    Adams-Bashforth only on surface pressure term. Tests show that using AB on
+    D-grid coriolis term improves stability (as expected from CD-scheme paper).
+   To reproduce old results, add 2 options (in CD_CODE_OPTIONS.h).
+   Update results of exp: global_with_exf (x2), ideal_2D_oce, isomip (x2),
+    lab_sea (3 Fwd +3 AD), natl_box (x2), tutorial_global_oce_biogeo (Fwd+AD),
+    tutorial_global_oce_latlon, tutorial_global_oce_optim & tutorial_tracer_adjsens.
+   Keep old results by adding CD_CODE_OPTIONS.h in exp: cfc_example, exp2,
+        global_ocean.90x40x15(+AD), global_ocean_ebm(+AD) and OpenAD.
+ o pkg/obcs:
+  - fix bug in initialisation (broken since Oct 1rst modification)
+    for useOBCSprescribe without useEXF.
+ checkpoint61y (2009/11/15)
+ o pkg/seaice
+  - change (once again) the discretization for the evp solver: rather than
+    squaring the averages of strain rates, average the squares to give
+    a better approximation to VP behavior (in simple test); this breaks
+    verification experiments that use EVP (lab_sea and lab_sea.hb87)
+     --> update outputs
+ o add CPP-flag (in mom_calc_visc.F) and TAF directive (in gmredi_slope_limit)
+   to improve vectorization of adjoint code on TARGET_NEC_SX
+ o verification/vermix:
+   - change vermix to a more "classical" 1d column with high vertical
+     resolution, seasonal heat flux forcing and constant wind forcing
+     --> update outputs
+ o pkg/seaice
+  - fix diagnostics of principal stress components for EVP
+  - add optional diagnostics of non-linear convergence for LSOR solver
+  - make maximum zeta a runtime parameter
+ o model/src (3-d solver):
+   Undo modif from Dec 12, 2005 (solve_for_pressure.F cvs version v.49),
+    which consisted in removing the Surf. Non-Hydrostatic pressure from the
+    whole column and adding it to Eta (inspired from Casualli, 1999):
+    Only affects 3-D solver initial guess and only if using ExactConserv,
+    but tests did show a degradation of solver convergence. For this reason,
+    decide to disable this piece of code.
+    to recover previous version, just set zeroPsNH = exactConserv (line 78).
+   Update output of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW
+ o pkg/ggl90:
+  - fix previous modif (unfortunatly has not been documented here).
+ o pkg/seaice/autodiff:
+  - add CPP flag to include clipping of zeta in EVP code;
+    although clipping of zeta is not necessary for EVP and not recommended
+    it was done by default, now clipping is disabled by default
+  - modify computation and store zetaC/Z in seaice_evp for TAF
+  - add CPP-flag SEAICE_ALLOW_CLIPVELS (undefined by default)
+  - change seaice_calc_viscosities/strainrates for better
+    vectorization after AD by TAF
+  - rearrange common blocks in SEAICE.h once again for easier dumps of
+    adjoint output, adjust adcommon.h and g_common.h
+  - change flux form of default advection scheme for better vectorization
+    of adjoint code
+  - modify lab_sea/input.lsr to test the flux form of default advection
+    scheme
+ o autodiff: fix seaice fields in g_common.h (left over from 3 to 1 level
+   transition in checkpoint61r)
+ checkpoint61x (2009/10/19)
+ o adjoint: adding two new verification experiments
+   * tutorial_global_biogeo: an online dic sensitivity experiment
+     (work with G. Forget)
+   * tutorial_dic_adjoffline: an offline dic sensitivity experiment
+     (an update of the Dutkiewicz et al., 2006 paper)
+   Both use the same CO2FLUX cost function, but different controls
+   Gradient checks look good, but some recomp. could still be traightened out
+   Should add xx_dic control variable to test at some point
+ o model/src:
+   add run-time parameters to check and/or mask initial Temp & Salt
+ o pkg/ptracers:
+   apply zonal filter (if used) to all passive tracers
+ checkpoint61w (2009/10/12)
+ o adjoint:
+   * update and finish work on adjoint of dic package (G. Forget)
+   * start adjoint of offline package
+   * bug fix for cube-sphere TLM code (active_file_g.F)
+ o tutorial_global_oce_optim:
+   now tested with 4 tiles (change data.grdchk and update output_adm.txt)
+   and add SIZE.h_mpi for MPI testing
+ o pkg autodiff
+  - fix bug in autodiff_restore
+  - make genmake2 remove comments and empty lines from ad_input_code.f in
+    order to reduce file size (new script file remove_comments_sed)
+ o allows to specify vertical profile of vertical viscosity (viscArNr)
+ o pkg autodiff
+   autodiff_ini_model_io: comment out writing of grid information to netcdf
+   files, because at this time the grid fields are a bunch of zeros
+   (this is analogous to ini_mnc_vars.F)
+ o pkg seaice/autodiff:
+  left-over from removing the 3-time-level fields:
+  - small rearrangement of common blocks (SEAICE.h)
+  - fix field declaration in order to get meaningful output in
+    adseaice.*.nc (adcommon.h)
+ o pkg obcs:
+  - go through NH code only if nonHydrostatic=T
+  - fix restart for Orlanski (Hydrostatic; still to fix NH+Orlanski restart)
+  - move call to OBCS_CALC before SEAICE_MODEL which needs seaice-obc fields
+    => Update output of experiment seaice_obcs
+  - useOBCSbalance: code is wrong with multi-tile / proc: add a stop.
+  - fix NH+Orlanski restart (add wvel OBC value in pickup file)
+  - fix restart for useOBCSprescribe + useEXF
+ o pkg ctrl
+  - make obcs as control parameter work also with useSingleCPUio
+  - replace a few sny and snx by Ny and Nx to be consistent with
+    ctrl_set_globfld_x/yz.F
+ o pkg seaice
+  - re-introduce global field frWtrAtm for the case of
+    ALLOW_MEAN_SFLUX_COST_CONTRIBUTION defined (SEAICE.h, seaice_growth.F)
+  - catch the case of an empty filename in seaice_cost_init_fixed.F
+ o pkg ecco:
+  - small bug fixes in the_main_loop
+   . fix order of monitor arguments
+   . change SEAICE_MULTILEVEL to SEAICE_MULTICATEGORY
+   . move include DYNVARS.h up outside the ALLOW_AUTODIFF_TAMC block so
+     that ALLOW_ECCO_FORWARD_RUN works with NONLIN_FRSURF
+  - replace cos(yc*deg2rad) by _rA in cost_mean_heat/saltflux.F, fix the
+    imbalance diagnostics for wmean_h/sflux = 0
+  - add actual values to f_obcsn/s/w/e in ecco_cost_final.F
+  - catch the case of empty filenames in ecco_cost_init_fixed.F
+    and ecco_readparms.F
+  - fix the logic of wsalt=0.and.wsalt2=0 to wsalt=0.or.wsalt2=0 (and theta)
+    to make this statement meaningfull in ecco_cost_weights.F
+ o pkg zonal_filt:
+   - change ZONAL_FILTER S/R interface (allows to filter 2-D fields)
+   - when using rStar, filter uVel*hFacW instead of uVel
+    (tested without topography: fix a Pb of growing instability with NLFS)
+ o pkg/aim/thsice:
+  -Add capacity to read a Q-Flux to be applied in slab-mixed layer thsice_slab_ocean.F
+   (works as SST restoring)
+ o pkg/thsice:
+  -add specific parameter for salt restoring in slab mixed-layer
+    (by default equal to the temperature restoring)
+ checkpoint61v (2009/09/21)
+ o pkg/kpp:
+  -add double diffusive contributions as a hack, turned off by default
+   for now, and the code can be excluded with a CPP-flag
+   EXCLUDE_KPP_DOUBLEDIFF just as EXCLUDE_KPP_SHEAR_MIX
+  -add a verification experiments to "vermix" to test this code
+ o pkg/mom_common:
+   Move computation of length scales to mom_init_fixed.F (avoid recomputation
+   at each time-steps*levels).
+ o pkg/layers:
+   Created a new package for computing volume fluxes in temperature or
+   [not yet implemented] density layers, e.g. for calculating residual
+   overturning circulations.
+ o pkg/diagnostics:
+   implement a RS type version for the set of DIAGNOSTICS-FILL subroutines
+ o fix few RS/RL type mismatch (check with ifort 11.1 "-warn all" option)
+ o pkg/mdsio (& pkg/rw): rework high level S/R interface:
+   To avoid mixing type (RS/RL) of input/output array argument,
+   replace single mixed-type array with a pair from each type (RS/RL).
+ o setting pickupSuff force to start from a pickup (even if nIter0=0): this
+   is now implemented for all pkgs (previously only done for the main pickup)
+ checkpoint61u (2009/08/25)
+ o pkg/obcs:
+   - change OB?eta from _RS to _RL and put them into a separate commen block
+   - add code to read OB?eta from a file via obcs_prescribe_read: the code
+     compiles and does not destroy any other experiments, the data is read
+     properly, but the code is not tested in actual applications
+ o ini_mnc_vars.F: if available (ALLOW_CAL), use startTime_1 and 2 to
+   create a meaningful unit attribute for the time coordinate variable
+ o pkg/ebm: add plenty of missing "_d 0" ;
+    update results of experiment global_ocean_ebm (fwd + adjoint tests)
+   Notes: several pieces of code only works for (very) specific set up
+    (domain size, lat range, etc ...); should be documented & stop if one
+    of those assumptions is not meet.
+ o pkg/seaice: add missing "_d 0" in HSNOW initialisation
+    update results of experiments: lab_sea (3 fwd tests + 2 adjoint tests)
+       and offline_exf_seaice (seaicetd + adjoint).
+ o add missing "_d 0" in ShortWave flux penetration (S/R SWFRAC):
+    update results of experiments: lab_sea (4 fwd tests + 3 adjoint),
+     seaice_obcs, global_ocean.cs32x15 (icedyn & thsice) and natl_box (x2).
+ o few changes to pass when compiling with strick checking of arguments
+    across S/R (allow to find few bugs in S/R calls).
+ o pkg/seaice:
+  - seaice_evp: move if-statement out of loop (TEM) at the cost of 11 new
+d-fields, for slightly better performance
+ checkpoint61t (2009/07/22)
+ o pkg/seaice:
+  - remove unused variables in seaice_evp
+  - reduce number of SQRT in seaice_evp and seaice_calc_viscosities
+ o eeset_parms.F, open_copy_data_file.F & ini_parms.F:
+    named file replacing SCRATCH files (for TARGET_BGL & TARGET_CRAYXT):
+    each processor opens a different file (a fix from Matt).
+ o cg2d:
+    use simple EXCH (overlap size = 1 and ignore corners), like in cg3d.F :
+    this reduces number of EXCH calls by 2 when using exch2.
+    For now, keep previous size array for gc2d_nsa.F to avoid Pb with store
+    directives and missing simple EXCH (exch_s3d_rx) adjoint code.
+ o pkg/thsice:
+    add code for Near Infra-Red albedo (from Jeff)
+    (turned on with run-time flag: thSIce_calc_albNIR, in data.ice).
+ o ini_model_io:
+    move (from packages_readparms.F & initialise_fixed.F) to ini_model_io.F
+    MNC & MONITOR initialisation calls; move MNC calls from {pkg}_readparms.F
+    to {pkg}_init_fixed.F for {pkg}= kpp, seaice & shelfice.
+ checkpoint61s (2009/06/30)
+ o pkg/exch2 (exch2_rxN_cube*):
+    remove last BARRIER (no need to synchronise after getting data from shared
+    buffer (get) as long as any change to buffer (put,recv) is between BARRIER)
+ o change tiling of natl_box (from 2 to 4 tiles) to get it tested with MPI+MTH
+   and generate new output (for the 2 tests) using default rotationPeriod.
+ o pkg/exch2:
+   - always call exch2_*_cube, not exch-1 anymore, if useCubedSphereExchange=F
+     (was already the case with AUTODIFF_EXCH2 defined)
+   - add bj in exch2 arrays and S/R.
+   - can now use pkg/exch2 for regular (non CS) set-up; switch test experiment
+     MLAdjust to exch2 (identical results except with MPI -> truncation diff);
+ o add pkg/longstep for ptracer timestep a multiple of U/V/T/S timestep
+   - adds deltaT argument to the subroutines TIMESTEP_TRACER DWNSLP_APPLY
+     GAD_ADVECTION GAD_CALC_RHS GAD_IMPLICIT_R GAD_SOM_ADVECT
+   - verification experiment natl_box.longstep
+ o build_options: ifort+mpi_aces optfile (following Constantinos advise):
+   allow different versions of ifort (8 or 9) and different versions
+    of mpi (mpich or mpich2) to be used with the same optfile.
+   requires to load a netcdf module and set MPI_INC_DIR (see comments inside
+    optfile). Change testing scripts (example_scripts/ACESgrid) accordingly.
+ o pkg/seaice:
+   fix previous modif (3-level field removed) for old-pickup reading
+ checkpoint61r (2009/06/25)
+ o pkg/seaice:
+  - clean up the 3-time levels of UICE,VICE,HEFF,AREA in three steps:
+. introduce fields for time step (N-1)
+. do not use levels 2 and 3 anymore (but keep them)
+. replace 3D versions of UICE,VICE,HEFF,AREA by 2D versions. This
+      includes changes to pkg/thsice/thsice_get_velocity.F,
+      model/src/external_forcing_surf.F, pkg/obcs/obcs_apply_seaice.F, and
+      pkg/obcs/obcs_apply_uvice.F.
+  - completely remove code for leap-frog time stepping for second order
+    advection
+  - adjusted adjoint accordingly;
+    gradient checks have improved by an order of magnitude!
+ checkpoint61q (2009/06/22)
+ o pkg/seaice: fix bug in free slip boundary conditons for LSOR solver
+  - the boundary conditions along open boundaries are unclear, because the
+    associated masks are set to zero and are thus treated as closed when
+    applying the slip-boundary conditions.
+  - move initialisation of grid variables from seaice_init_varia to _fixed
+ o adding doc/diags_changes.txt
+ o model/src:
+   do_the_model_io: rename few pkg S/R which are called from do_the_model_io,
+    to avoid "_diags" naming if no relation to pkg/diagnostics.
+   ini_theta,ini_salt: fix (at least compile the code) reading from NetCDF
+    file and only call PLOT_FIELD_XYZ if debugMode=T.
+   remove few PLOT_FIELD_XY calls outside initialisation.
+   remove few unnecessary BARRIER.
+ o pkg/salt_plume: add SaltPlumeSouthernOcean to allow disabling
+   of salt_plume package in Southern Ocean
+ o pkg/thsice:
+  - fix hOceMxL in overlap (needed for sea-ice advection);
+    update output of experiment global_ocean.cs32x15.icedyn.
+ o pkg/seaice:
+  - make the (placeholder-)tracer IceAge a little more meaningful
+   by avoiding ridging of age due to convergent ice flow
+  - add diagnostics for surface temperature, atmospheric and oceanic
+    heat flux, and atmospheric and oceanic ice growth
+ checkpoint61p (2009/06/10)
+ o eesupp (global_max & global_sum):
+  - add one more element to buffer (start at index 0) for GL_MAX/SUM output;
+  - remove starting & endding barrier (no longer needed)
+ o pkg/mdsio, writelocal:
+    works also in multi-threaded when LOCBIN_IO_THREAD_SAFE is undefined
+    (remove the STOP): uses shared buffer IO to store data from all threads
+    and then let master-thread write nThreads tiles.
+ o pkg/mdsio (read/write field):
+  - tiled IO done in 1 piece (all levels at a time);
+  - new header file "MDSIO_BUFF_3D.h" with 3-D buffers.
+  - multi-threaded: allow to read/write local (non-shared) array
+    (was already working with singleCpuIO ; now works also without);
+    => no longer needs barrier call after reading a file (added inside
+    mds_read/write field).
+  - move barrier calls outside gather/scatter_2d to mds_read/write_field
+ o pkg/obcs/exf
+   - exf_getffieldrec.F: add a few ". _d 0" and
+                         add code to catch the case fldperiod = 0.
+   - obcs_precribe_read.F: change if statements so that they match
+                           the variable type (_RL)
+   - add a separate exf_iprec_obcs to exf_set_obcs (by default equal to
+     exf_iprec) as part of namelist EXF_NML_01
+ o pkg/mdsio:
+   - read/write tiled (local) files: read/write 1-level tile chunk at a time
+     (instead of segment of length sNx); expected to speed up tiled IO.
+ o pkg/exch2:
+   - take buffer copy from/to array out of S/R exch2_send/recv into new
+     S/R exch2_put/get ; Exch of local variable now works with MPI+MTH
+     (tested by removing commom block statement in SOLVE_FOR_PRESSURE.h).
+   - ad version of send/recv no longer needed (but needs exch2_ad_put/ad_get)
+   - simplify argument list of S/R exch2_get_uv_bounds and exch2_get_scal_bounds
+     (which replaces exch2_get_recv_bounds & exch2_get_send_bounds) by
+     including Topology header file (and common blocks).
+   - implement EXCH_IGNORE_CORNERS in scalar exchange (rx1);
+     remove 2nd exch call in exch2_s3d_rx (no longer needed).
+   - document S/R arg. list (+ update some comments)
+ o pkg/seaice:
+   - added SEAICE_CLIM_AIR code, which permits modulation of surface air
+     temperature and humidity over sea ice based on climatological values.
+   - clean up computation of Hibler+Bryan (1987) stress coupling for the case
+     of LSR (this change is expected to change the results slightly because now
+     it uses slightly difference moduli from the second last LSR solution, but
+     that is more consistent with the stress computations; this part of the code
+     is not tested in the verification experiments)
+   - fix diagnostics for flux of ice in case of B-grid
+   - turn strain rates eij and press into global fields within global
+     common block in SEAICE.h for more straighforward diagnostics
+   - fix diagnostics for principal stress components, press, zeta, eta
+     to give something meaning full
+ o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate
+   new output (all 4 tests) using default rotationPeriod.
+ o pkg KPP:
+   - add flag (LimitHblStable) to avoid limiting BL depth under stable conditions
+   - fix vertical indices in RI_IWMIX (match between KPP grid from 0 to Nr+1
+     and normal grid from 1 to Nr)
+ o Fix computations of L4rdt in mom_calc_visc.F
+ o eesupp:
+   new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg):
+   should be called before a "stop" if we know that all process are going
+   to stop; if one Proc does call this S/R, will hang in MPI_FINALISE.
+ checkpoint61o (2009/05/26)
+ o pkg/exch2: change check_depths to issue just a warning (instead of error+stop)
+ o model/src/ini_curvilinear_grid.F:
+    compute angleSin/CosC when they are not read from a file
+ o pkg/seaice:
+    add pseudo time stepping for LSOR
+ o pkg/exch2:
+    temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW
+ o pkg/seaice:
+    Adding separate sea ice albedo, drag coefficients, and HO in Southern
+    Ocean from those in Arctic Ocean.  See *_south in SEAICE_PARAMS.h
+ o SingleCpuIO:
+    fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used.
+ o pkg/seaice:
+    put exchanged variable in (local) common block for MPI+Multi-Threads
+    to work (necessary with exch1, and for now with exch2 too).
+ o verification: to get more experiments tested with mpi, mth and mpi+mth,
+   change tiling of:
+    aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15,
+    hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope
+   update output of exp:
+    exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5),
+    tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod)
+   + ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU
+                    (note: output.txt generated on faulks using only 1 tile)
+ o eesupp & mdsio (SingleCpuIO):
+  - remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time
+    parameter "W2_useE2ioLayOut" (read from file "data.exch2").
+    Note: was not effective for globalFile & useSingleCpuIO=F; now fixed.
+  - move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc).
+  - fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same
+    gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array).
+ o pkg/exch2:
+  - new code to set-up W2-Exch2 topology (replace matlab-topology-generator):
+    read parameter file "data.exch2" if it exists; otherwise try default regular
+    cube without blank-tile; new header file "W2_EXCH2_SIZE.h";
+  - update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible
+    with new code (not to be used, just as a backup solution).
+  - add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2"
+    in utils/exch2/input.
+ checkpoint61n (2009/05/12)
+ o eesupp & mdsio (SingleCpuIO):
+   - move mapping to global io-buffer inside gather_2d/scater_2d: this save
+     memory (1 less 2D global RL array); skip 1 buffer copy; and only send/
+     receive real*4 array (instead of real*8) to read/write 32.bit files.
+     (new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S
+      and remove new mapping S/R)
+ o pkg/mdsio: in preparation for topology-generator within pkg/exch2:
+   - Change declaration of SingleCpuIO buffer, reduced to only 1 dim.:
+     xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h
+     when using exch2. Add S/R to map global io-buffer to global model array.
+   - uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt.
+ checkpoint61m (2009/04/29)
+ o write_utils : change WRITE_1D_R8 to WRITE_1D_RL
+   and add 3 other S/R for other types (R4,R8,RS).
+   Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument.
+ o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros):
+  - ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ;
+  - reduce number of macro definitions (keep only those which are used);
+    can always call directly the corrresponding S/R if needed.
+  - everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix
+    _R4/_R8 to _RS/_RL when applied to _RS/_RL variable.
+  Fixed wrong type of arg in:
+    atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F
+    ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F
+  To fix: global_sum of var in common block is wrong (multi-threaded) in:
+    dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F
+  To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops)
+ o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd
+   "nlfs" mpi test is going to stop when checking for unconnected tile egdes.
+ o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error
+ o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile
+   edges are closed (zero depth); might happen with "blank tiles";
+   for now, disabled if using OBCS.
+ o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi":
+   link *_mpi files from "MODS" dir) to return to a strait-forward behavior.
+ o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D)
+   to reduce length of 1.D array print in STDOUT.
+ o adjustment.cs-32x32x1: changed to oceanic test with 1 continent
+   + use 48 tiles (16x8): this will allow to test "blank tiles".
+ o start to test MPI + multi-threaded (change testreport to skip tests
+   where number of tiles do not match).
+ o genmake2: add option "-omp" to turn on Open-MP ;
+   passed to testreport (if using -mth) ; merge few (*+mth) optfiles.
+ o pkg/exch2 (+ utils/exch2): ignore blank tiles (instead of removing them)
+   and keep the original tile numbering. Note: compatible with old
+   W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files.
+ checkpoint61l (2009/04/07)
+ o Overlaps had been forgotten in calculating ijk keys : fixed
+ o fix cyrus makedepend for gcc 4.4
+ o experiment fizhi-cs-aqualev20:
+   switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE)
+   and generate new output. Note: new output is much closer to the old
+   one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from
+   the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007.
+ o pkg/fizhi:
+  - change to avoid indices going deliberately over array-bounds
+  - remove unnecessary MPI stuff
+  - perpetual spring equinox with "#define FIZHI_USE_FIXED_DAY"
+  - new version of S/R GETPWHERE available with #define TRY_NEW_GETPWHERE:
+    does not go over array-bounds and therefore returns reliable output.
+  - in fizhi_driver.F & fizhi_turb.F, fix "get_alarm" calls:
+    this S/R has 4 output arguments, which are used inside "get_alarm";
+    when it is called with the same variable "ndum" in place of several
+    output arguments, this produces weird side effect inside "get_alarm"
+   (e.g., datein=dates(n) is overwritten by timein=times(n) since both
+    datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum"
+    address) and produces error.
+ o tools/gemake2: (March 27-29 2009)
+   with option "-mpi": link *_mpi files from "MODS" dir (this is what
+   testreport does).
+ o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output
+ o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F:
+    update lab_sea.lsr & lab_sea.salt_plume results
+ o pkg/seaice:
+   Major overhaul of the LSOR solver: change discretization from original
+   finite differences to finite volume. The old routine is still in the
+   file seaice_lsr.F and can be turned on with the CPP-flag
+   SEAICE_OLD_AND_BAD_DISCRETIZATION
+   Along with this change, the discretization of the strain rates is changed.
+   The same flag turns on the old discretization in seaice_calc_strainrates.F
+   All verification experiments with seaice are affected (except for
+   seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old
+   results by setting the above flag.
+   Further changes involve changes in defaults:
+   - ALLOW_FLOODING is defined and turned on by default
+   - SEAICEadvSnow = .true. is now the default
+   - SEAICEadvSalt = .true. is now the default
+   - SEAICEadvAge  = .true. is now the default
+   - SEAICE_clipVelocities  = .false. is now the default
+                                      (as per J. Zhang's recommendation)
+   - B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE
+     is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS
+   - seaice_growth: replace computation of UG by a simple copy from wspeed
+ checkpoint61k (2009/03/18)
+ o pkg/seaice: a few bug fixes mostly concerning the metric terms:
+   seaice_lsr: fixed a few metric terms,
+               affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs
+               add more debugging diagnostics
+   seaice_evp: removed superfluous many metric terms of FV discretization
+               of stress divergence
+               affects lab_sea, lab_sea.hb87
+   seaice_ocean_stress: removed superfluous many metric terms of FV discretization
+               of stress divergence for non-evp solver
+               (this part is not tested anywhere)
+   seaice_calc_strainrates: fixed a bug in no-slip boundary conditions,
+               they were effectively only half slip
+               affects lab_sea.hb87
+   updated all relevant verification experiments (except lab_sea//output_adm.txt
+     which was left over, but fails at level 7 & 6)
+ checkpoint61j (2009/03/17)
+ o pkg/seaice: turn a few hard wired parameters into run time parameters
+ o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model
+   time in seconds as promised by the usints in seaice_monitor and exf_monitor
+ o pkg/mnc: fix the coordinate variables for multi-tile curvi-linear grids
+   that are not cubed-sphere grids
+ o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR
+ o pkg/ctrl:
+   fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low)
+ o non-hydrostatic (calc_gw.F):
+   fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec
+   update output of exp. global_ocean.cs32x15.viscA4
+ o remove backward compatibility for thetaMin,phiMin
+   (replaced by xgOrigin,ygOrigin on Jan 27, 2009)
+ o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the
+   interpolated wind field not only for curvilineargrid=.true., but also
+   for a rotated grid (rotateGrid=.true.)
+ o pkg/exf: add capability to bypass interpolation for runoff
+   by setting yet another CPP-flag
+ o eesupp/src, B-grid exchange:
+   add simple (6 tiles, non MPI) CS exch + standard interface S/R.
+ o autodiff
+   new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV
+   allows to switch to single-prec common blocks;
+   corresponding switch occurs in tamc.h, integer isbyte
+   TAF store directivs "byte" and "kind" seem equivalent;
+   Most tamc.h have been updated correspondingly.
+ checkpoint61i (2009/02/13)
+ o autodiff:
+   fix autodiff_sore/_restore indices for obcs
+   (spotted by I. Hoteit, M. Mazloff)
+ o pkg/autodiff, pkg/ctrl:
+   Add flag to reduce all tapelev I/O to single-prec.
+   In data.ctrl set
+     doSinglePrecTapelev = .TRUE.
+ o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2:
+   check in hack for SX8 compiler (for dxV, dyU); remove it afterwards.
+ o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for
+   real fresh water flux (not yet)
+ o pkg/mdsio & rw:
+  - add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta)
+  - add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX.
+ o pkg/flt:
+  - replace FLT_INIT by 3-steps standard initialization S/R: readparms,
+    init_fixed & ini_varia.
+  - clean-up & simplify linear interpolation S/R:
+    move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid.
+  - fix some indices (mainly vertical index) ; add IMPLICIT NONE.
+  - more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R.
+  - add vert. coordinate & horiz. indices to output files.
+  - change vertical position in initial condition, from index to depth [m].
+  - store horizontal (decimal) indices i,j in common block (instead of coord. x,y)
+    (easier to get to a curvilinear grid) ; delX,delY no longer used.
+ o pkg/ggl90: a few modifications:
+  - fix bottom boundary condition, and interpolation of KappaE
+    near top and bottom
+  - use same set of viscosity/diffusivity for TKE/momnetum/tracer
+  - add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH)
+  - add a few options for mixing-length upper limit (--> mxlMaxFlag)
+ o rename thetaMin,phiMin -> xgOrigin,ygOrigin
+   (maintain temporary backward compatibility, until next checkpoint)
+ checkpoint61h (2009/01/27)
+ o pkg/diagnostics with "periodic averaging diagnostics":
+   fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output.
+ o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82
+ o pkg/obcs: fix loop ranges for balancing code
+ o pkg/flt:
+  - improve criteria for finding which tile owns a float.
+  - fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case.
+ o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg
+   aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling
+   with ocean biogeo)
+ o pkg/flt:
+  - do some cleaning and fix the restart ;
+  - add output.txt in flt_example/results to get this pkg tested.
+ o genmake2: add an EXTENDED_SRC option and flag.
+    for now, cannot be turned on on command line (only through genmake_local)
+ o pkg/mdsio: read/write vector:
+  - singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS
+  - singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR
+    & MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS.
+  - affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO)
+   (drop to 4 digits matching for grad). But this test does not look very
+   reliable (was already failling on eddy, fc5, at 6.digits). Update output.
+ checkpoint61g (2008/12/29)
+ o pkg/flt:
+   - move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name)
+    + make OPTIONS file more standard.
+   - rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name)
+   - fix _BYTESWAPIO CPP-Flag
+   - standard reading of file-parameter "data.flt"
+   - fix argument list of S/R FLT_RESTART
+   still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F
+ o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell
+ o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to
+   a still unfixed compiler/optimization bug
+ checkpoint61f (2008/11/21)
+ o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ;
+   update results of global_ocean.cs32x15.icedyn test.
+ o move getcon.F from model/src to pkg/fizhi.
+ o pkg/exf: add parameter for extrapolation of temp up to the surface
+    and option to prevent negative evap (in bulk_largeyeager04 only).
+ o Prather Advection scheme: fix tracer conservation for divergent flow
+   (e.g., when using NonLin Free-Surface).
+ o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead
+ o gmredi (Visbeck-variable-K):
+  - add more parameters to Visbeck-variable-K.
+  - use a 5 points average for dSigmaR in Visbeck-K calculation
+    (more "homogenous": same stencil and same weights as in dSigmaH)
+  - update output of ideal_2D_oce experiment.
+ o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4
+   (#undef REAL4_IS_SLOW)
+  - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4
+    coordinate variable
+  - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables
+    (surface forcing fields), removes some of the functionality
+  - model/src/write_grid.F: write _RS variables as RS-netcdf variables
+  - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but
+    probably not all: copy _RS surface flux fields to RL field before
+    calling DIAGNOSTICS_FILL
+  - model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into
+    real*4 (CALL EXCH_*_RS) versions.
+  - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1
+    (generate new output).
+ checkpoint61e (2008/10/23)
+ o gmredi (Visbeck-variable-K):
+   - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
+   - change computation of Visbeck-K where Slope > Smax :
+     now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct)
+     previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output.
+ o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
+   to be the same as with Z-coord. (i.e., m/s & no-units respectively).
+ o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
+ o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
+   does not become too large (to avoid precision problems in implicit-diffusion
+   solver); update ideal_2D_oce output.
+ o pkg ggl90:
+   - in ggl90_cal.F: compute only one set of visc/diff, used to
+     step forward TKE/T/S/momentum
+   - default value of GGL90viscMax/GGL90diffMax larger and equal (to
+     have Prandlt =1)
+ o gmredi (fm07):
+   - add lower limit on Transition layer thickness + lower limit on 1/lambda
+   - allow to set few more params from data.gmredi
+ o pkg ggl90:
+       - add missing sqrt(2) factor in computation of mixing length
+         scale in ggl90_calc.F
+         (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
+ checkpoint61d (2008/09/25)
+ o adjoint modifs
+   - adapt to new field rhoInSitu
+   - allow to revert from StoreDynVars2D, StoreDynVars3D
+     to individual fields
+     (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
+ o store 3-D (in-situ) density in commom block (DYNVARS.h)
+  - save 1 rho computation.
+  - no longer modify T & S inland when using down_slope pkg.
+ o gad_som : allow to switch to SOM advection for T & S without corresponding
+   pickup files (using new S/R: MDS_CHECK4FILE).
+ o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
+   (for useSingleCpuIO to work in multi-threaded)
+ o pkg/shelfice:
+  - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
+    with SHELFICEtopoFile in data.shelfice
+  - move code for reading ice shelf topography and modifying hFacC into separate
+    subroutines of the shelfice package
+  - separate initialisation of "fixed" and "variable" variables
+  - kTopC is not (yet) replaced by kSurfC, although this is possible
+ o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
+ o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
+   and rename:
+   ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
+   ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
+ o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
+ checkpoint61c (2008/08/30)
+ o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
+   to add mass source/sink of fluid in the interior (3-D generalisation
+   of oceanic real-fresh water flux).
+ o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
+ o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
+ o new pkg: down_slope
+   density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
+   - presently, modify T & S inland (dwnslp_calc_rho.F).
+     can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
+   - implementation for ocean in P-coords not tested.
+   - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
+ o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
+   (to facilitate conversion of oceanic pkg to p-coordinate).
+ o change FIND_RHO to FIND_RHO_2D :
+   pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
+ o new pkg: cheapaml
+ checkpoint61b (2008/08/05)
+ o exch2:
+   change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
+   - no longer depend on the order sequence (N,S,E,W).
+   - 3rd exchange no longer needed (tested with 24 tiles).
+   - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
+   - exch_UV_A-grid readily available (but not yet tested).
+   comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
+   (both are no longer needed) in exch_uv: no effect in forward run; but
+    get truncation error differences with adjoint exch.
+ o exch2:
+  - change index-bounds storage (moved from target to local tile,
+    more intuitive this way) ; rename/remove some variables.
+  - change utils/exch2/matlab-topology-generator & code_mods accordingly.
+ checkpoint61a (2008/07/29)
+ o exch2/matlab-topology-generator:
+   fix bug in index bounds for N-S internal exchange (hard to tell if this
+   had any effect on the solution).
+ o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
+   is exceeded
+ o testreport: modify syntax of awk, so that it works also with
+   awk, and not only with nawk and gawk
+ checkpoint61 (2008/06/24)
+ o autodiff
+   Change default for TAF usage by removing argument '-nonew_arg'
+   This changes TAF subroutine argument list (ordering of active var.)
+   Omission of this flag leads to incompatibility w.r.t. TAMC
+   To restore TAMC-compatibility, need following modifs:
+   * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
+   * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
+   Tested TAF version is 1.9.22
+   N.B.: exch2 hand-written adjoint code currently not TAMC compatible
+ checkpoint60 (2008/06/19)
+ --->>> This is the last checkpoint for which generating the adjoint
+ --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
+ --->>> by default.
+ --->>> Future checkpoints will ommit this flag by default.
+ o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
+ o pkg/grdchk: Add gradient check to etan0 perturbations.
+ o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
+ o pkg/autodiff: more flexibility in zeroadj.
+   model/src: modifying do_oceanic_phys.F accordingly.
+ o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
+ o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
+   special setup of gmredi for which the adjoint is stable
+   enough for parameter optimization.
+ o bridging the gap between eddy stress and GM.
+   -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
+       along with a change in CPP option (now ALLOW_EDDYPSI).
+   -> when using GM w/ GM_AdvForm:
+       The total eddy streamfunction (Psi = eddyPsi + K x Slope)
+       is applied either in the tracer Eq. or in momentum Eq.
+       depending on data.gmredi (intro. GM_InMomAsStress).
+   -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
+   The key modifications are in model/src/taueddy_external_forcing.F
+   pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
+ checkpoint59r (2008/05/29)
+ o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
+   from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
+   fix option to read coriolis(@ cell-corner) from files with CS-grid.
+ o pkg/mnc: add some attributes to standard 1D-coordinate variables
+ o pkg/diagnostics: enforce missing_value attribute for scalar variables at
+   mass points, when using mnc for output
+   - add runtime parameter (missing_value, missing_value_int) to override
+     default (which is the value of getcon('UNDEF'))
+ o pkg/mnc: prepare mnc for the actual use of missing values with the
+   diagnostics package: small fix in mnc_cw_readwrite.template and more
+   initialisation of never used fields
+   - replace mnc_common.h and mnc_id_header.h with corresponding upper case
+   versions
+ o pkg/thsice/thsice_ini_vars.F added default initial values so that
+   thermodynamics sea ice solver does not blow up when some initial fields
+   are missing.
+ o move from external_forcing_surf.F to ini_forcing.F
+   the p-coord. hack consisting in using pLoad to set phi0surf ;
+   update output of tutorial_global_oce_in_p (affected @ truncation level).
+ 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 (2008/05/06)
+ 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 (2008/04/10)
+ 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 (2008/03/07)
+ 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
+      COMM="$CC $CFLAGS -c genmake_tc_1.c"
+      echo $COMM >> genmake_warnings
+      $COMM >> genmake_warnings 2>&1
+   to make genmake2 always see the value of CC as specified in the optfile.
+ o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
+   - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
+   - modify verification advect_cs test to test SOM-advection on CS-grid.
+ o pkg/ctrl:
+   - Rewrite of ctrl_map_ini_ecco.F,
+     introducing a generic routine (ctrl_map_ini_gen.F).
+   - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
+ checkpoint59n (2008/02/09)
+ o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
+   number in dedicate array "hdiag":
+   - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
+     with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
+   - many small changes (integer format) for large number of diagnostics
+   - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
+     a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
+ o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
+   usingSphericalGrid, this allows to define the rotated grid coordinates
+   via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
+   geographical coordinates according to the inverse of the rotation defined
+   by the Euler angles, so that Coriolis parameter and online-interpolation by
+   exf works with the geographical coordinates on XC/YC/XG/YG.
+   Naturally, this feature does not work with all packages, so some
+   combinations are prohibited in config_summary (flt, flt_zonal, ecco,
+   profiles), because there the coordinates are assumed to be regular
+   spherical grid coordinates.
+ o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
+   - introduce isopycnal diffusion coefficient control.
+ o tools/adjoint_options:
+   - additional control vector components.
+ o pkg/mnc: have mnc create marginally meaning full coordinate variables
+   (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
+ o pkg/mypackage:
+   - add example of read/write pickup for state-var ;
+   - add entry points to the main code for state-vars diags & write-pickup.
+ o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
+   transitions for useExfYearlyFields
+   - add new subroutine that determines the file to read from for
+     use*YearlyFields = .TRUE. and .FALSE.
+   - add a verification experiment to global_with_exf that tests
+     useExfYearlyFields with USE_EXF_INTERPOLATION defined
+ o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
+   analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
+   subroutines (which could be generated from a template, because they are
+   almost identical), for now they are included in obcs_prescribe_read.F for
+   simplicity
+ o pkg/exf:
+   - add a little more diagnostic to exf_interp_read (in analogy to
+     mds_read_field, can be turned off with debugLevel < debugLevA=1)
+   - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
+     ugly but fast by unrolling short inner loops, inserting a unroll=8
+     directive in routine lagran, and splitting a loop and making do while the
+     outermost loop (the latter requires the intoduction of index arrays)
+ o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
+ o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
+   http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
+ o verification/seaice_obcs: updated for restart test and latest options
+ o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
+   ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
+   for now this is only available for the C-grid code and also within
+   #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
+ checkpoint59m (2008/01/14)
+ o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
+   and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
+ o gad_som : fix flux output (& diagnostics) to have same units as other
+   advection scheme fluxes (was previously multiplied by deltaT).
+ o added verification/seaice_obcs both to test seaice open boundaries
+   and to provide an example matlab scrpt for generating them
+ o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
+ o pkg/salt_plume: clean up salt_plume_frac.F to
+   remove redundancy in PlumeMethod 1 and 4
+ o pkg/kpp: added saltplume diagnostics
+ o pkg/obcs and pkg/seaice:
+   - do not set uice and vice to zero when OB*icefile are unspecified
+   - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
+   - moved seaice tracer obcs after call to seaice_growth
+ o pkg/salt_plume: added various options for salt plume depth
+   criterion and for vertical distribution of the salt
+ checkpoint59l (2007/12/18)
+ o pkg/ptracers: new version of ptracers pickup:
+   read meta file and write only fields which are needed to restart.
+   ( same logic as main pickup file ; also using pickupStrictlyMatch )
+ o pkg/seaice:
+   - add timescale for melting due to warm mixed layer as a means of
+     setting SEAICE_availHeatFrac more conveniently
+   - add a CPP-flag/runtime parameter check for flooding algorithm
+   - reformulated availHeat in seaice_growth.F to be independent of AREA
+ o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
+   unit changes
+ o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
+ o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
+   SX vector computer.
+ o pkg/seaice:
+   - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
+     seaice forcing fields can now be read only through pkg/exf
+   - removed some unused halos
+ o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
+ o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
+   or U/VICE from U/VWIND before computing U/VSTRESS
+ checkpoint59k (2007/11/30)
+ o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
+   dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
+ o fix un-initialised variable problem (in mom_vecinv & shap_filt):
+   all experiments pass when compile with un-initialised var. checking option.
+ o added pkg/salt_plume
+ o script to test restart (for now, in MITgcm_contrib/jmc_script)
+ o pkg/seaice: new read/write pickup version.
+   read meta file and write only fields which are needed to restart.
+   ( same logic as main pickup file ; also using pickupStrictlyMatch )
+ o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
+ o lab_sea.hb87: modify the domain & update output.hb87.txt :
+   lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
+   at j=1 & j=Ny+1 : this case is not treated correctly in the restart
+   process. Fixed here by closing the domain at the Northern boundary.
+ o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
+ o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
+   a set of consecutive levels in/from a 3-D array.
+ o pkg/ptracers:
+   use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
+   to-do: fix pkg/diagnostics when large number of diagnostics are defined.
+ checkpoint59j (2007/11/09)
+ o in pkgs: dic, obcs, offline, rbcs:
+   standard way to compute coeff. for time interpolation between 2 time reccords
+   which retains full precision (& make results less dependent on compiler).
+   update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
+ o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
+   packages instead of reading ice cover and wind speed separately
+ o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
+  (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
+   to allow to compile customized code before the update)
+ o cleaning-up:
+   - fix CPP instruction syntax in pkg/obcs
+   - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
+     add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
+   - fix some threads issue in IO parts.
+ o pkg/dic:
+   - add tons of "_d 0" (--> much better testreports !)
+    and then update outputs of tutorial_global_oce_biogeo
+ o pkg/mom_fluxform:
+   add a special version of momentum advection intended to conserve momentum
+   next to a bathymetry step or a coastline edge. (default = off = #undef)
+ o new read/write pickup version:
+   - for now, only implemented for main (mdsio) pickup file.
+   - write out only what is needed to restart; merge pickup_nh , pickup_ph
+     and main pickup together.
+   - read meta file; read only what is needed to restart; stop if a field
+     is missing (if pickupStrictlyMatch=T, = the default) or try to restart
+     if it make sense (even if the restart is not perfect).
+   - if no meta file, assume that pickup to read corresponds exactly to
+     a pickup that would currently be written.
+   - read pickup written in the old format (until checkpoint59i) if it
+     recognizes an old meta file (no field-list).
+   - add a meta file in exp. which starts from a pickup: 2 cases:
+     a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
+      e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
+     b) a meta file describing the content of the associated pickup file
+      e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
+ o pkg/mdsio & pkg/rw:
+   - new routine to read a meta file ; new set of routine to read
+     Multiple-fields file (with meta file).
+ o added open boundary conditions capability for seaice
+     HSNOW, HSALT, UICE, and VICE
+ checkpoint59i (2007/10/21)
+ o adjoint:
+   * fix multiDimAdvection adjoint
+     (partial recomputation problem by TAF for fVerT(:,:,kDown)
+     and comlev1 size definition (maxpass vs. max. number of tracers)
+   * verification/global_ocean.90x45x15 adjoint now tests
+     NLFS and multiDimAdvection using DST3 (=30)
+   * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
+ o pkg/kpp: add "_d 0" to real constant (if missing);
+   update output of exp: natl_box (10.digits); vermix (std, 7.digits)
+   and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
+ o prepare for "clever pickup" implementation: add new header file "RESTART.h"
+   for internal parameters related to restart process (formerly from PARAMS.h)
+   and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
+ o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
+   as argument. (only atm2d & obcs write_pickup have not yet been updated)
+ o pkg/monitor:
+   - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
+   - fix mon_stats_rs (statistics over the full domain, even where field is zero)
+   - account for deep Atmosphere factor and density factor (anelastic)
+ o added open boundary conditions capability for seaice HEFF and AREA
+ o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
+   thermodynamics
+   - requires a little reorganization, which affects the testreport results
+     of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
+     so that now the conservative form is tested
+   - add a few comments
+ o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
+ o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
+ o add new diagnostics to seaice: advective, diffusive fluxes (only for
+   multidim-advection, for scheme 2 they are not filled) and transports,
+   thermodynamic growth rates
+ o change units of EmPmR (inside the code, + within coupling interface)
+   from m/s to kg/m2/s (mass flux) but leave input file unchanged.
+   Affects results @ truncation level (cg2d match) and update output of
+    experiments: lab_sea(6), global_ocean.90x40x15(10),
+   global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
+   + adjoint results: global_ocean_ebm(11) and lab_sea (12).
+   Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
+   Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
+ checkpoint59h (2007/09/29)
+ o pkg/exf:
+   - improve vectorization by moving if-statement out of loops in
+     exf_mapfields, exf_radiation
+   - exf_bulkformulae.F: introduce 2D fields and vectorize code
+ o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
+ o testreport:
+   - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
+     monitor & update offline_exf_seaice exp. output.
+   - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
+ o pkg/seaice:
+   - bug fix in the evp solver: boundary conditions were affected be
+     masking of zMax/zMin (changes results)
+   - minor bug fix in boundary conditions in seaice_calc_strainrates
+     (changes results for no_slip)
+   - seaice_lsr.F: make interpolation of eta dependent on boundaries
+   - replace hardcoded lower limit for zeta (zMin) by runtime parameter
+   - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
+     stress formulation and no-slip boundary conditions
+ o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
+   in gad_calc_rhs.F ; add few safety stops in initialisation phase.
+ o pkg/seaice: a first HSALT time stepping equation has been checked in
+ o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
+   in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
+   without requiring DO-IF statements
+ o pkg/thsice:
+   use continuous power-law function for partition of energy between lateral
+   melting/freezing and thinning/thickening ; old code using step function
+   still available with #undef THSICE_FRACEN_POWERLAW
+   update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
+ o testreport: change AD testing : check against results/output_adm.txt
+   using same scripts as for forward test.
+ checkpoint59g (2007/09/17)
+ o adjoint testing: in preparation for changing testreport:
+   - output format: cost and grad written on separated lines
+   - ad output results in directory "results" (instead of "results_ad")
+ o pkg/seaice: adding ice salinity HSALT as a prognostic variable
+ o pkg/seaice: changes for using pkg/seaice with pkg/obcs
+ o pkg/ecco: allow user defined cost function contributions
+ o testreport:
+   Allow to choose (per experiment) the list of tested output variables
+    and the main variable (used to issue a pass/FAIL ) ;
+   - for now, done by adding the specific list in file: [exp]/input/tr_checklist
+   - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
+   Also modify printing of summary:
+    a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
+    b) echo the list of tested variables in the individual summary.txt of
+       each experiment.
+ o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
+   threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
+   (but still depend on the tile decompostion of the domain).
+ o pkg/seaice: change a discretization detail to make the B-grid code
+   "more symmetric". This change is likely to remove all "ridges/leads" that
+   where quasi-aligned with the grid in B-grid solutions. It may also be
+   the solution to the stress coupling issues with the B-grid.
+ o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
+   remove .cvsignore from input dir. (since testreport no longer run here).
+ o pkg/thsice:
+  - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
+  - fix reshaping of sea-ice just after advection:
+    melt all the ice only if ice-volume is too small.
+  - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
+    prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
+  and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
+ o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
+   tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
+ o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
+   forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
+   (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
+   and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
+   of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
+   -> update output.txt
+ o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
+  this affects truncation error: -> update output.txt of exp:
+   global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
+   ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
+ checkpoint59f (2007/08/21)
+ o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
+ o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
+   a bounded range (in forward mode)
+ o pkg/ecco, ctrl, autodiff and mom_common:
+  internal parameter controls, completements of implementations
+ o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
+ o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
+   (not seem any difference in testing results).
+ o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
+    at face corners.
+ o pkg/generic_advdiff:
+  - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
+   loop range indices for computing vertical advection tendency
+   and do the calculation in the interior only (no overlap) ;
+   for now, only implemented for SOM advection (to save CPU time).
+  - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
+ o exch2 adjoint
+   First set of changes:
+   - add exch2 hand-written adjoint templates
+   - exch2 hand-written no longer use TAF-flag 'nownew_arg'
+     This will require cleanup in pkg/autodiff/*.F
+     (changed routines currently kept separate in verif. code/)
+   - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
+     that used to hide exch2 or cubed-sphere specific code
+     (commented via 'cph-exch2')
+ o pkg/seaice
+   - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
+ o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
+    output of global_ocean.cs32x15.thsice .
+ checkpoint59e (2007/07/26)
+ o exch2: new S/R that only use the cube-tracer (center-position) exchange:
+   for B-grid vector (not yet tested) and C-grid vector (<- only used
+   when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
+ o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
+   (#ifdef ALLOW_SALT_PLUME)
+ o gather_2d/scatter_2d: removed halo regions
+ o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
+   scheme and the corresponding test case (under front_relax dir). For now,
+   only available with Skew-flux form and not yet tested in realistic set-up.
+   adjoint: store directives updated, but gradient checks deteriorated,
+   so maybe GM/Redi adjoint is now broken.
+ o seaice adjoint
+   * add AREA, HEFF, HSNOW as control variable
+     (should not change lab_sea results)
+   * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
+ o pkg/seaice:
+   * added computation of saltFlux in seaice_growth;
+     For time being, sea ice salinity is assumed constant
+     contribution of snow flooding to freshening of sea ice is neglected.
+     SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
+     defaults to 0.0 in order to maintain backward compatibility.
+     Typical values for SEAICE_salinity are 4 to 10 g/kg.
+   * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
+   * added SEAICE_availHeatFrac, which specifies fraction of surface level
+     heat content used to melt or grow ice
+   * commented out cap of HICE: it helps keep ice thinner
+   * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
+   * applied OBCS T/S mask to HEFFM sea ice mask
+ checkpoint59d (2007/06/21)
+ o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
+  for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
+  (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
+ o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
+  and change default value of parameter "GM_Small_Number";
+  update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
+    global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,
+    tutorial_global_oce_biogeo, tutorial_global_oce_latlon
+ o pkg/ecco: cost function when applying pkg/smooth to controls
+ o pkg/ctrl: add forcingPrecond run time parameter
+ o pkg/seaice:
+  - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
+  - fix bug in metric terms of u-equation in LSR solver (implicit part),
+    changes verification/lab_sea
+  - rearrange implicit part of u-equation in LSR solver to make it easier to
+    read, understand, and debug. This causes changes at the truncation level.
+  - fix (serious) bug in the boundary conditions (sign error in the implicit
+    part) of the LSR solver. Changes all LSR results.
+  - fixed problem with HSNOW initialization to avoid thick snow when AREA
+    is initilized with small values - does not change lab_sea results.
+  - added HsnowFile initialization capability
+ o pkg/smooth: addition to model/src and pkg/ctrl so allow
+  initialization of pkg/smooth and application to control vector
+ o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
+ o dependencies: pkg/profiles requires pkg/cal
+ o pkg/profiles:
+  - added option ALLOW_PROFILES_GENERICGRID
+      -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
+      that interpolation information (grid points and coefficients) is provided
+      within the netcdf input files.
+      -> sample matlab scripts can be found in MITgcm_contrib/gael
+      that allow you to prepare netcdf input files.
+  - also modified: cleaner include statements, cleaner error print statements,
+    cleaner stops when error, and more tests of the netcdf input files consistency.
+ o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
+ o pkg/seaice:
+  - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
+    requires a new routine: seaice_diagnostics_fill.F
+  - make sure that seaice does not move if not forced (pressure replacement
+    method, Hibler and Ip, 1995), changes results
+  - and new damping criterion for EVP solver according to Hunke, JCP, 2001
+  - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
+    It is turned off by default (=-1.), because it changes the results.
+  - make it possible to read AREA from a file, too.
+ checkpoint59c (2007/06/04)
+ o add S/R and diagnostics for oceanic mixed-layer depth
+ o move GMRedi call after all vertical mixing schemes (including KPP)
+ o pkg/thsice:
+  - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
+   (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
+ o pkg/obcs:
+  - bug fix for balance code
+ o pkg/seaice:
+   - allow values of SEAICE_elasticParm > 1
+   - add new parameter SEAICE_evpTauRelax as an alternative
+     to SEAICE_elasticParm
+   - make lsr boundary conditions free slip (by default), changes result
+   - add code for no slip boundary conditions for lsr
+   - set minimum of zeta to zero (and not 4e8) (changes results)
+   - add a cap on AREA after advecting AREA if seaice_growth is not called
+ o change calculation of Visbeck K:
+   - no longer depend on tapering scheme; instead, compute slope (limited
+     by GM_maxSlope). this is equivalent to what was comuted before with
+     clipping or linear tappering.
+   - fix vertical averaging (wrong by 1/2 level)
+   - leave the old version (but will not be maintained) within
+     #ifdef OLD_VISBECK_CALC / #endif
+   - update output of exp. ideal_2D_oce
+ o change error catch in calc_r_star to improve vectorization
+ o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
+   add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
+ o adjoint:
+   Re-organized adjoint checkpointing according to Matt Mazloff
+   (but with modifs/completions/cleanups)
+   Storing is now bundled into large arrays to optimized I/O
+   (and second step in cleanup of the_main_loop)
+ checkpoint59b (2007/05/16)
+ o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
+   - export/import (between ocean & coupler) fields needed for ocean DIC.
+ o pkg/seaice:
+   - get rid of three more exchanges seaice_calc_viscosities (required
+     different loop boundaries in seaice_lsr and seaice_ocean_stress)
+   - bug fix in seaice_ocean_stress (update of lab_sea required)
+   - reduce loop boundaries to necessary minimum also in seaice_evp
+   - go back to the old way of computing deltaC/Z as the adjoint likes that
+     better
+ o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
+   passive tracer to an Age Tracer) + update output.txt
+ o pkg/exf:
+   - implement A-grid / C-grid selection for wind-stress input files.
+   - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
+   for now, in exf_bulk_largeyeager04.F only :
+   - change implementation for case where windspeed + 2. components wind-stress
+     are read-in. AND use rhoConstFresh to convert evap.
+ o pkg/seaice:
+   - use correct EXCH_UV for wind-forcing (on A-grid).
+   - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
+     SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
+ o pkg/exf:
+   - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
+   EXF_INTERPOLATION:
+   - merge global_with_exf/code version of exf_interp_read.F
+     to the main code ;
+   - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
+     reading the file ; Important: This options needs to be defined to recover
+     previous code.
+     otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
+   - no longer loose real*8 precision along the way when using exf_iprec=64.
+ o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
+   - change discretisation of evp-solver in order to avoid another exchange
+     (changes lab_sea) and clean up a little
+   - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
+     help the adjoint (this also changes the results slightly)
+   - add a few "_d 0" where they had been missing in seaice_evp.F
+   - cleaning up: remove unused seaice_calc_rhs.F
+ o pkg/exf: some cleaning-up:
+   - change various "constants" into runtime parameters
+   - cleaned-up Large&Yeager04 routine which should eventually
+     replace exf_bulkformulae.F (changed names of S/R and CPP)
+     and merged various ALLOW_ATM_WIND options
+  only used with thsice pkg (in thsice_get_exf.F):
+   - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
+     which are used when useStabilityFct_overIce=TRUE (= the default)
+   - change default values of ice & snow emissivity and scale downward LW
+     by ice & snow emissivity.
+ o pkg/thsice:
+  fix few little problems, in thsice_calc_thickn.F:
+   - growth vertically (and not laterally) if iceFrac == iceMaskMax
+   - melt only laterally if hIce < hThinIce (as the comments say)
+   and in thsice_extend.F:
+   - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
+   - start to form ice as soon as the minimum ice-volume is reachable.
+  update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
+   and cpl_aim+ocn
+ o pkg/kpp
+  - move computation of surface related input fields to KPP into a new
+    subroutine kpp_forcing_surf.F
+  - remove wrong (within bi,bj loops) EXCH calls.
+  - little cleaning (add argument myThid in last position, cvs header ...)
+  - for now, fix conservation problem by exchanging KPPviscAz (may not
+    be the best fix)
+ o pkg/seaice
+  - check for inconsistent evp parameter/cpp-flag combination
+  - remove leftover errIO flat for obsolete name list error handling
+ o OpenAD
+  - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
+ checkpoint59a (2007/05/01)
+ o pkg/seaice: some parameter clarifications and a little bit of clean up
+ o pkg/thsice: rename run-time parameters:
+    himin       -> hIceMin
+    himin0      -> hThinIce
+    hihig       -> hThickIce
+    i0          -> i0swFrac
+    transCoef   -> bMeltCoef
+    frac_energy -> fracMelting
+   add new parameters: hNewIceMax, fracFreezing, dhSnowLin
+    with default values (for now) that do not change the results.
+   remove old version of thsice vars advection in pkg/seaice.
+ o in FFIELDS.h:
+   - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
+   - make pLoad & sIceLoad always available (but still only used if
+      ATMOSPHERIC_LOADING is #define).
+ o pkg/kpp: replaced _KPP_RL with _RL
+ o bug fixes for vertical diffusivity computations when both KPP and
+D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
+     are no longer updating the vertical diffusivity array
+     (passed as argument) but are (re-) setting those arrays.
+ o pkg/seaice: fix bug in evp solver, while doing that
+   - change (improve?) discretization of stress computations for both
+     cgrid-lsr and evp solver
+   - add a new routine to compute strain rates
+   - the above changes lab_sea results
+   - add no slip conditions for evp solver (off by default), lsr-version
+     may follow
+   - fix exchange for shear at Z-points (does not change lab_sea)
+   - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
+     (to force the user to pick a time step since there is not "safe" way
+     of choosing it)
+   - add principal stress diagnostics
+   - rearrange fields for evp a little to avoid having to call a: too many
+     exchanges and b: exchanges for stress trensor components which we do
+     not have.
+   - modify Hibler+Bryan (1987) stress coupling so that it reuses information
+     of evp, complete rewrite for lsr case (latter is does not yet work
+     in all cases)
+ o pkg/kpp: add code to have mixing in shelf ice caverns
+   - add myThid to all kpp routines (long overdue)
+ checkpoint59 (2007/04/19)
+ o pkg/exf:
+   - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
+     ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
+   - move exf header files from lower_case.h to UPPER_CASE.h ;
+     add missing cvs Header & Name
+   - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
+   - add namelist param. selectStressGridPosition, exf_monFreq
+   - retire many _CLIM routines, and remove data.exf_clim
+     + params moved to data.exf
+     + climsst, climsss now handled by exf_set_gen, i.e.
+       climss?period=0 refers to constant field,
+       climss?period=-12 to monthly forcing
+   - split up namelists in data.exf
+ o pkg/seaice:
+   - remove seaice_exch and seaice_exch_uv
+   - remove superfluous exchange of theta
+   - add myThid to seaice_budget_ocean/ice
+   - add new interface for atmospheric wind forcing (C-grid only)
+     + new routine
+     + two new field (taux, tauy for stress over ice)
+     + removed one global field (DAIRN) for C-grid case only
+ o pkg/thsise
+   - 2nd set of modifs for thsice adjoint in conjunction with exf
+ o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
+ checkpoint58y_post (2007/04/15)
+ o Added capability for latitudinal dependence of Bryan and Lewis, 1979
+   vertical diffusivity, similar to that in MOM4; turned on using
+   #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
+   diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
+ o Added capability for 3D specification of background vertical diffusion
+   coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
+   in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
+   "data" file that contains the 3D vertical diffusivity coefficients.
+ o ice dynamics (pkg/seaice) with thsice thermodynamics:
+   - add code within pkg thsice to advect & diffuse sea-ice fields
+   similar to (and will replace) what has been added in  seaice_advdiff.F,
+   but: - conserving Mass, Heat & Salt.
+        - better when using non-linear advection scheme (not yet fully tested)
+        - can also be used in atmospheric set-up (for now, only the diffusion).
+ checkpoint58x_post (2007/04/04)
+ o IO option for global-file compact format:
+   - add options when generating topology (utils/exch2/matlab-topology-generator)
+   - add I/O capability (pkg/mdsio).
+   - adapt utils/matlab/rdmds.m to read this format.
+   for now long-line format not yet supported by pkg/mdsio (& exch2).
+ o shelfice: add a few diagnostics
+ checkpoint58w_post (2007/03/13)
+ o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
+   rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
+   (and replace horiVertRatio in NH code).
+   Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
+                      and tutorial_plume_on_slope (sensitive to truncation)
+ o seaice: if ALLOW_ATM_WIND is undefined use wind stress
+   directly to drive seaice model (C-grid only)
+ o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
+  - reintroduce computation of wind from stress,
+  - compute tau (in exf_bulkformulae.F) from windstress averaged to
+    mass points to avoid tau = 0
+  - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
+ o rdmnc.m: make it work with "global" files created with gluemnc
+ o rdmnc.m : some improvements in dealing with singleton dimension
+   (tested on all testreport mnc output files).
+ o genmake2: disable pkg/profiles if netcdf test fails.
+ o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
+ o move call to cal_readparms up to make calendar parameters/variable available
+   to all packages
+ checkpoint58v_post (2007/02/08)
+ o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
+   useDynP_inEos_Zc tested.
+ o pkg/exf: changes to properly interpolate/mask/scale initial fields
+ o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
+   and portions thereof.  See read_cs.txt for description and examples.
+ o utils/matlab/cs_grid/bk_line: to compute transport through passages,
+   add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
+   following the great-circle arc between those 2 points.
+ o trap un-initialized variable with pathscale compiler on weddell.mit.edu
+   (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
+ o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
+  - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
+  - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
+  - still needs work (not working with some options ; efficiency to improve)
+    and serious testing.
+  - use this scheme for temperature & salinity in 2 advection test exp.:
+    advect_xy & advect_xz, respectively.
+ checkpoint58u_post (2007/01/12)
+ o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
+ o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
+ o testreport: add option "-skipdir" to skip some test.
+ o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
+   momentum calculation.
+ o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
+ o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
+   remove checkpoint.F and the_correction_step.F (no longer used);
+   do the k loop inside CYCLE_TRACER (supposed to be more efficient).
+ o add option (linFSConserveTr) to correct for tracer source/sink due to
+   Linear Free surface
+ o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
+ o pkg/thsice: fix reading mnc-pickups
+ checkpoint58t_post (2006/12/30)
+ o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
+ o pkg/mdsio:
+  - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
+    move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
+    mdsio_write_field.F (S/R MDS_WRITE_FIELD);
+  - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
+  - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
+    either MDS_READ_FIELD or MDS_WRITE_FIELD )
+  - new S/R (to replace MDSWRITEMETA), which allows to write more
+    informations (variable names, time ...) to meta files.
+  - modify rdmds.m to give back the meta file content.
+ o pkg/diagnostics: change vertical interpolation to be safer, and more
+    flexible (define p-levels to interpolate to in data.diagnostics);
+   add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
+    diagnostic pointer.
+ o pkg/seaice: more cleaning up of seaice_growth, added many comments
+ o pkg/exf: put runoff0 and runoff1 into the appropriate common block
+ o fix multi-category seaice:
+  - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
+    SEAICE_MULTICATEGORY
+  - fix short wave heat flux
+ o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
+    and allow to use EVP solver. Change forward lab_sea: test both EVP
+    solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
+ o Initial check-in of lab_sea adjoint
+   (very similar to natl_box_adjoint/code_seaice)
+   * used C-grid and EVP solver
+   * used KPP, GM/Redi
+   * uses inAdExact=.TRUE.
+   * gradient checks fail for both ADM and TLM
+     due to sensitive snow melt code in seaice_grwoth (look for "JZ")
+     f.d. gradients actually seem more problematic than ADM, TLM gradients;
+     issue is related to forward mismatch between g77 an ifort
+ o pkg/seaice: overhaul of thermodynamics
+  - growth.F and groatb.F are replaced by new routine seaice_growth.F
+  - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
+  - move a few global fields out of SEAICE.h into seaice_growth.F and
+    make them 2D (FICE/QNETO/ ...)
+  - remove FO (it is the same as QNETO)
+  - introduce a few local fields to avoid modifying external fields such
+    as atemp, etc.
+ checkpoint58s_post (2006/12/11)
+ o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
+   changed exf_set_gen.F so that
+     genperiod=0 means input file is one time-constant field and
+     genperiod=-12 means input file contains 12 monthly means
+ o CG2D: use pre-computed solver main-diagonal (stored in common block);
+   this affects truncation error ; generate new output file for exp. which
+   fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
+     global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
+     ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
+     MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
+     tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
+     vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
+ o start implementation of deep-atmosphere and anelastic formulation
+ o verification: remove 2nd copy of input files and use script "prepare_run"
+   to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
+ o mom_common/vecinv/fluxform: fix a few initialisation isssues
+ o profiles: fix for multithreaded case
+ o diagnostics: rename few diags:
+   s/'PRESSURE'/'RCENTER '/g
+   s/'TICE    '/'oceFreez'/g
+   s/'TAUX    '/'oceTAUX '/g
+   s/'TAUY    '/'oceTAUY '/g
+   s/'SWFLUX  '/'oceQsw  '/g
+   s/DIFx/DFxE/g
+   s/DIFy/DFyE/g
+   and add few ocean-forcing diagnostics:
+   atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
+ o modifications to pkg/seaice/growth.F and budget.F, which change results of
+   lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
+   as actual snow thickness.  It now refers everywhere to effective snow
+   thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
+ checkpoint58r_post (2006/11/17)
+ o modifications to pkg/seaice/growth.F, which change results of
+   lab_sea experiment: fixes pertain to melting snow over open water, to
+   masking EVAP under sea ice, and to using the correct AREA variable for
+   computations of EVAP, PRECIP, HSNOW, and GHEFF
+ o add ability to read bathy, salt, and theta using MNC (off by def)
+ o add flooding algorithm and advection of HSNOW for pkg/seaice;
+   both are turned off by default and do no change any results
+ o seaice advection with pkg/thsice: a step toward the use of non-linear
+   advection scheme, but #ifdef or commented out for now (requires more EXCH).
+ o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
+   (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
+   in natl_box (affects results @ truncation level: update output.txt)
+ o multi-threading and IO:
+   - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
+   - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
+     (needed to work with SingleCpuIO): tested in all verif. exp.
+ o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
+   affects the results (but none of the verification test uses this scheme).
+ o Adding some pkg/diagnostics capability to pkg/seaice
+   (will certainly be subject to changes)
+ o ctrl: adding new control variables:
+   lwflux, lwdown, evap, snowprecip, apressure, runoff
+ checkpoint58q_post (2006/10/20)
+ o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
+/6-deg Southern Ocean configuration by 8% on IBM Datastar and
+   high_res_cube configuration by 4% on Columbia.
+ o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
+   add (in global_with_exf/code) a version of EXF_INTERP_READ without
+   dynamical allocation (seems to work in multi-threaded).
+ o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
+   single CPU io) so that TAF does not have to see EESUPPORT.h
+ o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
+ checkpoint58p_post (2006/09/08)
+ o obcs: stop if obcs is used with useCDscheme = .true.
+ o shelfice:
+  - fix a sign error so that no slip at shelfice interface works
+  - remove stop for combination non-hydrostatic code and shelfice. That does
+    not mean, that the results are correct, but at least they are numerically
+    stable
+ o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
+ o added adjoint exch routined for all exch*3d* routines
+   and updated flow directives
+ checkpoint58o_post (2006/08/28)
+ o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
+   remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
+ o change controling S/R for writing pickup file (new S/R do_write_pickup)
+   and clean-up reading/writing of pickup files.
+ o fix local version of read/write pickup (NH part) in rotating_tank/code
+ o simplify EXCH interface:
+  - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
+  - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
+ o added the regrid package
+ o shelfice:
+  - add a simple boundary layer scheme to reduce noise
+  - fix the indexing in shelfice_u/v_drag so that there will be actually drag
+ checkpoint58n_post (2006/08/14)
+ o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
+    local variable (not in common block).
+ o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
+   - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
+   - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
+     to work with SingleCpuIO.
+ o add "_d 0" to real constant of pkg/cfc subroutines ;
+    update exp. cfc_exemple & tutorial_cfc_offline output files.
+ o multi-threading and IO:
+   - all threads call READ_FLD S/R (needed if using SingleCpuIO):
+     (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
+   - barrier before and after reading.
+   - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
+   - avoid using MDS_WRITELOCAL for LAND pkg output.
+   - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
+     common-block variables ; Allows multi-threading with master-thread IO.
+ o change default MAX_NO_THREADS from 32 to 4 ;
+   and stop cleanly when MAX_NO_THREADS is too small.
+ o add S/R BAR_CHECK to check multi-threaded barrier synchronization
+ checkpoint58m_post (2006/07/17)
+ o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
+    and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
+ o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
+    keep global_ocean.90x40x15 (for AD testing) with former secondary test
+    (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
+ o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
+     add MITgcm_tutorials (= code + all the tutorials)
+ o ecco, option to compute cost for total ssh (mean+anom)
+ o consistent with addition of ptracer and ssh in pkg/profiles
+ o profiles: adding ptracer and ssh
+ o testreport: change multi-test output-file name
+   (from output.txt.{name} to output.{name}.txt)
+ o profiles: now ok for mutli-tiles case
+ o seaice: add 4 parameters for different advection schemes for area,
+   (effective) seaice thickness, enthalphy, and snow height. Their default
+   is the standard parameter SEAICEadvScheme
+ o calc_gw:
+  - add cosFacU in zonal viscous flux (harmonic.visc.).
+  - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
+    of tutorial_plume_on_slope.
+ o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
+ o calc_gw: true flux-form, account for horizontal grid spacing.
+   update rotating_tank results, but not plume_on_slope (affected at
+   truncation level, 11 digits).
+ checkpoint58l_post (2006/07/12)
+ o calc_gw:
+  - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
+  - remove side-drag for now (need to fix it); update plume_on_slope results.
+  - fix for partial-cell & non-uniform dz; update plume_on_slope results.
+ o commit code to make SST/SSS weights spatially variable
+   (based on either variable in-situ or variable initial T/S weights)
+ o pkg/ecco:
+   * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
+     now based on horizontally varying weights wthetaLev, wsaltLev
+   * cost_averagesflags now returns year indices in addition to day, month
+   * sflux balance is performed on annual basis
+     (sflxumm, sfluxmm2, bal_sfluxmm)
+   * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
+     including separate counting and multipliers
+ o pkg/rbcs
+   * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
+ checkpoint58k_post (2006/07/06)
+ o testreport:
+  - always build in dir. "build" (if not there, mkdir build instead of building
+    & running in input)
+  - run in dir run (if it exists), in build otherwise.
+  - call prepare_run (if input/prepare_run exists)
+  - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
+ o pkg/exf modifications to interpolation and rotation routines for more
+    reasonable treatment of North Pole singularity: for tracers North Pole
+    value is set to northernmost zonal-mean value, for zonal velocity it is
+    set to zero, and for meridional velocity it is set to northernmost value.
+ o pkg/exf/exf_check_range.F
+  - add tile index to diagnostics and move stop statement to the very
+    end of the routine.
+ o pkg/diagnostics: (diagnostics_main_init.F)
+   define title of isomorphic variables according to the current config.
+ o pkg/thsice with pkg/seaice dynamics:
+ - fix domain of computation (interior only, required for exf) and do exchanges
+ - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
+ o towards a standard way of dealing with multi-threading in MONITOR
+   and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
+ o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
+    to W momentum equation in nonhydrostatic and quasihydrostatic runs.
+ o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
+ o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
+ o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
+    (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
+ o tracer advection:
+  - clean-up and simplify calc_common_factors.F
+  - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
+    advection subroutine (but still not used within DST advection S/R)
+ o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
+ checkpoint58j_post (2006/06/15)
+ o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
+   from file (collects calls previously in FORWARD_STEP)
+ o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
+ o adjoint store dir. adjusted accordingly
+ o genmake2
+   replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
+ checkpoint58i_post (2006/06/14)
+ o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
+   on wind stress (SEAICEstressFactor defaults to 1.)
+ o Total number of Timers is finite (<=40): comment out 2 non-essential one
+   in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
+ o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
+   on CS-grid: no longer loosing mass.
+ o exf & curvilinear-grid: no longer modify longitude xC & xG.
+ o pkg/ggl90: fix sloppy output and fix a bug
+ o pkg/seaice: added SEAICEuseEVPpickup parameter
+   - Set to false in order to start EVP solver with
+     non-EVP pickup files when using SEAICEuseEVP
+   - fix sign error in diffusion in seaice_calc_rhs
+ checkpoint58h_post (2006/06/07)
+ * Modifications for bottom topography control
+   o replace hFacC by _hFacC at various places
+   o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
+   o add non-self-adjoint cg2d_nsa
+   o update autodiff support routines
+   o re-initialise hfac after ctrl_depth_ini
+   o works for 5x5 box, doesnt work for global_ocean.90x40x15
+ * Adding verification for 5x5 box (4-layer) bottom topography control
+ checkpoint58g_post (2006/06/07)
+ o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
+    used for mean seasonal cycle, mean diurnal cycle); add an example
+    in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
+ o pkg/ggl90:
+   - add parameter (minimum surface kinetic energy)
+   - fix bug (avoiding division by zero)
+ o couple pkg/thsice to pkg/seaice:
+   - modify advection in seaice to accomodate new scalar fields to be advected
+   - only muliDimAdection scheme work with seaice/thsice
+   - mapping of thsice-variables to seaice-variables, back and forth
+   - does not break the verification experiments, but does not give the
+     desired results either
+ o pkg/seaice
+   - make (default) second order advection a bit less confusing?
+ checkpoint58f_post (2006/06/05)
+ o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
+   to pkg/seaice):
+   - new routines thsice_map_exf and thsice_get_exf provide the interface
+   - add an additional formal parameter to thsice_solve4temp
+ o pkg/exf:
+   - add new fields wspeed, snowprecip (to be able to couple to thsice)
+   - correct Stefan-Boltzmann constant
+   - new parameter for longwave surface emittance
+   - separate some stuff from exf_bulkformulae into new routines
+     exf_radiation, exf_wind
+   - add new parameters and constants: longwave emissivity for ocean, ice
+     and snow, evaporation parameters over ice
+   - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
+     either wind from stress or stress from wind
+ o pkg/thSIce:
+ - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
+ - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
+    and THSICE_CALC_THICKN
+ - for now, call to THSICE_GET_BULKF remains inside i,j loops.
+ - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
+   to make debugging easier.
+ - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
+ o pkg/bulk_force:
+   - clean-up comments and parameters ;
+   - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
+ o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
+   generate new output for test-experiment: aim.5l_cs.thSI
+ o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
+   testreport accordingly
+ checkpoint58e_post (2006/05/17)
+ o SEAICE_CGRID adjoint done
+ o R_STAR adjoint implemented.
+   * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
+   * need to sort out init. of h0facc, etc.
+ o Make pkg/profile fully independent of ecco,cost, etc. stuff
+   to be able to use it in pure forward.
+ checkpoint58d_post (2006/04/21)
+ o upgrade simple test-experiment to tutorial example:
+  step.1: duplicate the experiment and (step.2) will remove the old copy.
+   tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
+   tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
+   tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
+   tutorial_global_oce_biogeo    <- copy of dic_example
+   tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
+   tutorial_plume_on_slope       <- copy of plume_on_slope
+   tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
+   tutorial_global_oce_optim     <- empty for now (David ?)
+   tutorial_global_oce_in_p      <- copy of global_ocean_pressure
+  some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
+ o correct a sign problem in cost_scat.F
+ o obcs and ptracers: fix boundary conditions for advections schemes
+   with larger stencil
+ o thsice adjoint: start
+ o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
+   completeness
+ o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
+   and COSINEMETH_III, add comments in default CPP_OPTIONS.h
+ o ptracers adjoint:
+   * avoid extensive recomputatations
+   * fix missing re-init. of gptr (missed by TAF)
+ o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
+   me to turn off the excessive output to STDOUT that this package produces
+ o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
+   and add those terms in Vector-Invariant formulation.
+ o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
+   if the control period (xx_hfluxperiod etc) is 0
+ o in profiles pkg, clean routines and fix details
+ o in ecco pkg, reading ssh data:
+   fix problem in case the model does not start at iter0=0
+ o fix mnc-pickup/restart for ptracers
+ o new package prifiles:
+   code to compute profile-based cost by Gael Forget
+   (modifs in ecco, ctrl, autodiff)
+ o Benign bug fix in initialization (spotted by M. Mazloff) of
+   ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
+ checkpoint58c_post (2006/03/23)
+ o adjoint: finish NLFS adjoint and provide reference output in
+   verification/global_ocean.90x40x15/results_ad_nlfs
+ o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
+   documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
+   SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
+   with SEAICE_CGRID defined.
+ o move calendarDumps from "data" to "data.cal" and clean-up the code
+   with a simple call to pkg/cal S/R: CAL_TIME2WRITE
+ o add useEXF & useCAL flags (for now, set in hard-coded way)
+ o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
+   (were missing in NH mode, and wrong in quasihydrostatic mode).
+   waiting for Chris updated version of calc_gw to add those CALLs.
+ o fix bug in quasihydrostatic S/R ;
+   add a test for this option: global_ocean.90x40x15.qshyd
+ o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
+   (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
+ o add on/off flag useOffLine for package OFFLINE
+ o seaice:
+   - modify advection so that it works also on the C-grid
+   - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
+     problem in multi-tile runs with C-grid
+   - add flags for clipping ice velocities and/or masking solver forcing
+   - fix drag (ocean on ice) formulation and a bug that caused noise in the
+     C-grid solver
+   - added a few comments to seaice_diffusion.F
+   - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
+     are now exclusive)
+   - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
+     required re-ordering the code a little:
+    + make DAIRN global variable (defined in SEAICE)
+    + move computation of the viscosities eta and zeta into a new separate
+      routine (because I need to recompute them in seaice_ocean_stress.F)
+ checkpoint58b_post (2006/03/13)
+ o AIM+thSIce: fix sign of Short-Wave through the Ice ;
+   update output.txt of exp. aim.5l_cs.thSI
+ o various mnc cleanups and improvements:
+   + shrink lookup tables by factor of ~4
+   + better error reporting when running out of lookup space
+   + able to handle longer path/file names (up to 500 chars)
+ o adjoint:
+   - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
+   - TBD: "hidden" mom_vecinv recomp. in dynamics
+ o change forcing_In_AB to affects both T,S forcing and Momentum forcing
+  (allow to differentiate between forcing components using new integer flags:
+   momForcingOutAB=1/0 & tracForcingOutAB=1/0)
+  and add new flag to put Dissipation tendency out of Adams-Bashforth.
+ o ecco
+   - enable trend removal from SSH anomaly obs.
+ o adjoint
+   - a fix for PmEpR when #undef EXACT_CONSERV
+   - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
+   - try to fix "hidden" recomp. in forward_step for NLFS
+     (NLFS seems broken sometimes after I checked it in)
+ o seaice:
+  - add c-grid version of the dynamic solver:
+    + three new routines that are the c-grid substitute lsr, dynsolver
+      and ostres
+    + put a few fields that were local to dynsolver into global common
+      blocks, so that I can move the computation of stresses etc into
+      seaice_lsr (saves coding but may break the adjoint).
+  - replace more hardwired parameters by runtime parameters
+  - add ice masks that mask the rhs of the implicit solvers where there
+    is no ice (commented out in seaice_dynsolver, because i am not sure
+    if this works properly), eventually this should replace the clipping
+    of ice velocities in seaice_dynsolver to +/-40cm/s.
+ o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
+   include it only where its needed
+ o move balancing of fluxes before the call of external_forcing_surf
+ o seaice:
+   - correct units of turning angles (now they are really in degrees)
+   - move computation of GWATX/Y out of main routine into dynsolver
+   - initialize GWATX/Y in seaice_init
+ o Apply mask on Fresh-Water flux (needed for SSH forcing).
+   update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
+ o seaice: add runtime flags for turning angles (default to zero)
+ o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
+   and trend from exf forcing and ctrl control adjustments
+ o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
+   (since checkpoint57x_post)
+ o change the default rotation period to 86164.s = the Earth rotation
+ o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
+   and based on a reference stratification. Tested within hs94.cs-32x32x5.
+ o seaice advection: add code for choosing between the default (2nd order
+   central differences) and multiDim advection schemes provided by
+   pkg/generic_advdiff
+ o seaice:
+   - removed all references to SEAICE_GRID.h fields from
+     dynsolver, advect, diffus, lsr, without changing the results of lab_sea
+     (cubed-sphere configuration will change a little)
+   - grid computations in seaice_init are obsolete now.
+   - cleaned up code a little so that is easier to read (hopefully).
+   - added new (better?) discretizations of default advection and diffusion
+     (turn on with SEAICEuseFluxForm)
+   - replace 1 in 3d global fields by kSurface in growth.F
+ checkpoint58a_post (2006/02/13)
+ o seaice:
+   - bug fix in advect.F
+ o shelfice:
+   - separate shelfice load anomaly from pload (breaks with time
+     dependent forcing), => introduce constant field shelficeLoadAnomaly.
+     Its default is 0., but it may be computed more cleverly from (unknown)
+     t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
+     done offline. A good approximation of the pressure load anomaly is
+     necessary to avoid large initial adjustment processes underneath
+     deep-reaching shelfice.
+   - small fix in ISOMIP shelfice_thermodynamics
+   - add more sophisticated thermodynamics of Hellmer (1989), this is
+     now the default
+   - give a few constants more intuitive names
+ o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
+   if bulk formulae are used in long integration (especially EmPmR). Turn
+   on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
+   if balancePrintMean, the imbalance that is substracted is printed to
+   STDOUT.
+ o fix bug (typo) in obcs_apply_eta.F
+ o add a new package shelfice which enables us to model the circulation
+   underneath shelf-ice with draughts of hundreds of meters.
+  - works
+  - to do: + include improved thermodynamics
+           + check whether kSurfC (from model/inc/SURFACE.h) can be used
+             instead of new field kTopC
+           + can we use topoFile, Ro_surf and existing code in ini_depth.F
+             instead of new field R_shelfIce and new code in ini_depth.F
+             and ini_mask_etc.F?
+           + adjust vertical mixing schemes?
+ o seaice pkg:
+  - add a cpp-flag to include a simple formula for a salinity dependent
+    freezing point of sea water at the surface
+  - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
+    meridional stresses are now different (and hopefully correct)
+ o AIM pkg: change threshold on large-scale condensation to conserve Heat.
+    update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
+    and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
+ o pkg/diagnostics: add options and parameters for regional-statistics
+    diagnostics ; define regions by reading a region-mask from a file
+    (might add other options later)
+ o pkg/bulk_force:
+  - add option and parameters to use AIM surface-flux formulae.
+  - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
+    others forcing fields (defined in PARM05, parameter file "data") are loaded
+    from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
+  - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
+  - use the right EXCH call for uwind,vwind (to work on CS-grid).
+  - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
+    and parameters (note: calcWindStress replaces .NOT.readwindstress).
+  - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
+ checkpoint58 (2006/01/12)
+ o add "--embed-source" option to genmake2 which, when the supporting
+   tools can be compiled (as determined by genmake2) will turn on the
+   embed_files package which then embeds the entire MITgcm source code
+   (*.[fFhc] + Makefile) used for the build within the executable
+   - requested by CNH but off by default
+   - adds a paltry <9MB to the mitgcmuv executable in most cases
+   - only writes the output when useEMBEDSRC in eedata is true
+ o clean up 3-dim. relaxation codes:
+   * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
+   * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
+   * Thanks to Tom Haine for testing!
+ checkpoint57z_post (2005/12/31)
+ o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
+   affects output (@ truncation level) of exp. plume_on_slope ; updated.
+ o fix the pickup behavior for obcs in combination with ptracers
+ o fix a bug in ptracers_external_fields_load
+ o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
+   affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
+ o transfered surface NH pressure to eta field (if exactConserv).
+ o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
+      and update lab_sea output.txt file.
+ o completing 3-dim. relaxation code: additional term
+/tau*( theta(i,j,k) - thetaStar(i,j,k) )
+   in S/R EXTERNAL_FORCING_T (file external_forcing.F)
+   * At compile time, in "EXF_OPTIONS.h" set
+       #define  ALLOW_CLIMTEMP_RELAXATION
+       #define  ALLOW_CLIMSALT_RELAXATION
+   * At runtime in "data", under &PARM03 set (e.g., units in seconds)
+       tauThetaClimRelax3Dim = 15552000.0,
+       tauSaltClimRelax3Dim  = 15552000.0,
+   * 3 cases:
+) Use a constant-in-time 3-dim. field
+) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
+) Real-time relax. to time-evolving prescribed field
+ o Adding Laplacian-type smoothness constraint on
+   initial and boundary (forcing) controls (ic, bc)
+   * enable at compile-time via
+     ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
+   * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
+   * Absolute scale somewhat unclear so far
+   * no area weighting was included since no other cost term does so far
+ checkpoint57y_post (2005/12/08)
+ First step for a NLFS adjoint
+ o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
+ o new init. routines for calc_r_star, calc_surf_dr
+ o still need to deal with ini_masks_etc
+ o testreport seemed happy
+ checkpoint57y_pre (2005/12/08)
+ o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
+ o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
+ o add new offset feature to offline pkg (plus minor cleanup)
+ o cfc fixes for final year of integration
+ o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
+   be in GCHEM_OPTIONS).
+ checkpoint57x_post (2005/12/04)
+ o fix testreport Pb in multiple test experiment.
+ o cleanup our namelist syntax in verification:
+   - make it more F95 standards compliant (some work still needed)
+   - allows the vast majority of our tests to work with gfortran
+ o Non-Hydrostatic:
+  - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
+  - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
+ o Allow to apply AB on T,S rather than on AB(gT,gS):
+  - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
+  - use the same arrays (gtNm,gsNm) to hold tracer field at previous
+    time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
+  - need a "clever" read_pickup to restart from the other AB formulation
+ o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
+ o remove some unused variables (reduces number of compiler warnings)
+ o adjoint
+   * Disable useVariableViscosity for adjoint for time being
+     (there are a number of extensive recomputations)
+   * Initialize certain variables needed for adjoint
+ checkpoint57w_post (2005/11/03)
+ o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
+              fix the singleCpuIO RS version of MDSWRITEFIELD
+    and add a WARNING if using globalFiles=T with multi-processors.
+ o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
+   using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
+ o tracer advection scheme:
+   add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
+    those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
+    was not very convenient).
+   add implicit version for DST-3 & DST3_Flux_Limit vertical advection;
+    (further tests needed for the implicit DST & Flux-Limiter schemes).
+ o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
+   and sRef for convenience, handy, when you want to initialize
+   ptracers in a large domain with a constant non-zero value. Also,
+   untangle ptracers_init.F a little.
+ checkpoint57v_post (2005/10/13)
+ o change dome exp. to use variable viscosity in side-drag terms.
+ o remove all the files from the cfc_offline test since they are now
+   incorporated into tutorial_cfc_offline which has been producing
+   identical results for a few days of testing
+ o add new parameter: sideDragFactor to enable half-slip-side BC
+   and change side-drag S/R to use viscosity from mom_calc_visc
+   (can switch back by setting sideDragFactor=0.); affects results at
+   truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
+    global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
+ o vorticity & strain are now computed without masking, to account for
+   no-slip-side BC in variable viscosity calculation ; mask is applied
+   anyway later on, before computing advection/coriolis terms.
+ o modify exp4 to test new obcs support for reading from external files
+   and for passive tracers
+ o fix behavior of ptracers_monitor when monitor output is written to a
+   netcdf-file; still not independent of monitor.F (writes in the same
+   file).
+ o change default value of tRef (put a uniform, meaningful value for ocean
+   & atmos) and initialize sRef (was missing, as Martin mentioned).
+ o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
+   to be proportional to enstrophy dissipation length.  Thus,
+    viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
+   This is now consistent with Smagorinsky and with the manual.
+ checkpoint57u_post
+ o OBCS and PTRACERS: add open boundary support for passive tracers
+   - either use homogenous (pseudo) v.Neumann conditions or prescribe
+     OB-values from file; this is not different from the way theta and salinity
+     are treated
+   - however, Orlanski-radiation conditions are not supported, and the model
+     will stop if you use pTracers and Orlanski at the same time.
+   - beefed up the rountine obcs_external_fields_load: now only those open
+     boundary values are overwritten with values from files for which there
+     are really files, otherwise the OB-fields remain untouched. This makes
+     it possible to use different OBs at different ends of the domain (as
+     with EXF)
+ o reduce number of exch calls in shap_filt (s2).
+ o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
+   truncation level) 4/5 MLAdjust test results (11&12 digits match).
+ checkpoint57t_post (2005/10/03)
+ o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
+ o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
+   same truncation, independent of the face number: affects affects several
+   test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
+ o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
+   note that biharmonic viscosity + no-slip was not tested in any experiment.
+ o fix bug in non-linear free-surf side-drag ; generate new output for
+   global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
+ o make mnc honor the writeBinaryPrec flag for most kinds of output
+ o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
+ o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
+   error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
+ o add brackets in multi-terms sum to get same truncation, independent of
+   the face number (manage to get exactly same value of gU,gV at the cs-edge)
+   affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
+ o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
+   and viscA4Remax, which allow one to limit the minimum viscosity by specifying
+   a maximum grid-scale Reynolds number.  Also, changes all length calculations
+   in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
+   Suggested values of viscosity parameters found in mom_calc_visc.
+   Many new viscosity diagnostics available.
+ checkpoint57s_post (2005/09/20)
+ o Add clearing-house for viscosity calculations, mom_calc_visc and
+   correct numerous bugs in LeithD and Smagorinsky discretizations.
+   mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
+   used simultaneously, and to be used in mom_vecinv and mom_fluxform.
+   Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
+   and with Strain-Tension viscous term calculation (mom_hdissip.F).
+   The Strain-Tension form is now called with useStrainTensonVisc=.true.
+   ViscAhStrain and viscAhTension are now retired.
+ o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
+ o In response to JMC's bug report, genmake2 now ignores any soft-links
+   that it finds in the *current* directory when searching for files.
+   Soft-links found in any other source directories will still work as
+   they did before.
+ o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
+   a C routine to unlimit the stack size
+ o mnc-ify pkg/aim snapshot vars
+ o mnc-ify pkg/land as requested by Daniel
+ o various changes to mnc including:
+   - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
+   - output can now be grouped so that all files within a group
+       change the ITER portion of their names in lock-step together
+   - can now read ("global") PER-FACE (in addition to PER-TILE) files
+       and works with both EXCH1 and EXCH2 (but needs more testing)
+   - writing works for all verification test cases w/ g77 on Linux
+ checkpoint57r_post (2005/09/07)
+ o make MNC variable initialization happen earlier
+ o add diagnostics for (almost) each term of the momentum Eq.
+ o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
+ o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
+ o remove MINIMAL_TAVE_OUTPUT option ;
+   add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
+ o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
+   allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
+ o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
+ o add time-dependent SST, SSS control
+ o cost terms in ecco/ modularized (new cost_generic.F)
+ o cost_averages routines are modularized (new cost_averagesgeneric.F)
+ o new infrastructure for seaice model vs. obs misfits in seaice/
+   * driver from the_main_loop.F is seaice_cost_driver.F
+   * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
+   * gradient check in Exp. 6a of natl_box_adjoint/
+ o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
+   (see README file)
+ checkpoint57q_post (2005/08/19)
+ o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
+ o fix annoying months-old bug in mnc/mdsio output for seaice pkg
+   - bug was reported by Jean-Michel and Ian Fenty
+ o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
+   update exp. cpl_aim+ocn output.
+ o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
+   Needed for high-res. runs with large global files
+   to be able to limit tapelev size
+ o Changed some tests for adjoint:
+   * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
+   * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
+   * global_ocean.90x40x15/ back to default 3-level checkpointing
+ o Modifications to enable scripted COMMON to MODULE conversion
+   * verification/OpenAD/code/ has necessary scripts and description;
+   * converts, compiles and runs successfully;
+ checkpoint57p_post (2005/08/01)
+ o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
+ o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
+   (already the case for some pkgs, including recent MNC_init, e.g. thsice)
+ o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
+ o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
+   (was already the case for dissipation with mom_vecinv,
+    and also the case for grad.PhiHyd when staggered-timeStep)
+   This will allow to put dissipation out-off the AB time-stepping.
+  Unfortunately, affects truncation error. Update output of exp. that "fails"
+   (cg2d matching number) and leave the others for later: front_relax(10),
+   global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
+   matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
+ checkpoint57o_post (2005/07/30)
+ o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
+   (2) its ready to be documented during the 20050801 DocFest
+ o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
+   for ideal_2D_oce and lab_sea on linux_ia32_g77
+ o set to #undef CTRL_SET_OLD_MAXCVARS_30
+   in global1x1_tot/code_seaice_adj to access indices 32, 33
+   (worth another tag)
+ checkpoint57n_post (2005/07/29)
+ o adding precip control xx_precip 32
+ o adding swflux control xx_swflux 33
+ o Replacing 10 forcing penalty cost routines by 1 generic.
+ o Implementing partitioning in time-mean and variable adjustment
+   for atmos. state.
+ o Time-mean constant error is now read in data.ecco (instead of hard-coded)
+ o in natl_box_adjoint:
+   * updated exp 1 to 10
+     (but does not have time-mean vs. variable split results yet)
+ o updated global1x1/*_seaice_adj/
+   to incorporate latest changes
+ o enable useSingleCpuIO for mdsio vector routines
+   (applies in particular to tapelev I/O)
+ o removed inefficient K-loop in all active_file*control*.F
+ checkpoint57m_post (2005/07/28)
+ o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)
+   and advect_cs (use EXCH-2 and standard cs-32 grid files).
+ o pkg/exch2: filling of face-corner halo regions is optional
+   (ifdef W2_FILL_NULL_REGIONS) and is turned off by default.
+ checkpoint57l_post (2005/07/14)
+  tag before updating tutorials (pre-release-2)
+ o add cos & sin of grid-direction orientation angle (curvilinear grid only,
+    for output and interpolation of input fields onto model grid)
+ o fix radius in mom_v_metric_cylinder.F (wrong by dy/2).
+    Affects results of exp. rotating_tank ; update output.txt.
+ o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor
+       and taking the square quantity and/or using a fraction-weight field.
+ o fix aim_diagnostics_init.F mate numbers.
+ o add mnc output capability to diagnostics/diagstat and update
+   our cvsignore files for the ACSII output generated
+ checkpoint57k_post (2005/07/02)
+ o lab_sea now uses diagnostics package and provides a suite of
+   new EXF diagnostics output.
+ checkpoint57j_post (2005/06/30)
+ o exf
+   * bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton):
+     Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982);
+     terms -2*ATAN(x) + pi/2 were added to both stable and unstable case.
+   * extended diagnostics output
+     - now includes all EXF variables
+     - hs, hl moved to common block
+     - separate S/R for diagnostics, called after ctrl vector is added
+     - name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet
+     - EXFqnet contains true Qnet (i.e. includes qsw)
+   * updated verif. lab_sea, global_with_exf
+   * Rearranging hflux (exf_mapfields -> exf_getforcing)
+     to ensure that diagnostics sees a true EXFqnet
+ o add matlab scripts for CS-grid vectors (in utils/cs_grid)
+ o diagnostics pkg: change pointers so that 1 diagnostic can be used
+   several times with different frequencies.
+ o mnc-ify the thsice package as requested by Daniel Enderton
+   - the monitor--MNC output needs work
+   - many attributes need to be added (most are currently blank)
+ o mnc-ify theaim_v23 package as requested by Daniel Enderton
+   - many attributes need to be added (most are currently blank)
+ o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign)
+ o add Sadourny like discretization to the 4th.O vorticity advection scheme
+ o fix bug in rStar code (calc_r_star.F) when used with topo/bathy.
+   update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn,
+      fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice).
+ o fix few little things to avoid floating error with -ftrapuv (ifort v9)
+  (ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F)
+ checkpoint57i_post (2005/06/19)
+ o Diagnostics package was changed: diagnostic allocation is now deactivated
+   by setting an empty file name in the namelist (used to be by setting 0 frequency)
+ o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ;
+   add 1rst Order upwind vertical Shear.
+ o add a quick fix for A/B checkpointing in OFFLINE mode
+ o add IGNORE_TIME define and -ignore_time option to genmake2 as an
+   end-run around the C/Fortran linking horror in eesup/src/timers.F
+ o added pkg/runclock: allows user to terminate run based on wall clock
+ o added non-hydrostatic scaling parameter: nh_am2
+ o pkg/my82: futile attempt to make results compiler-independent by adding
+   some "_d 0", etc. no effect.
+ o for mnc output, fill the 'T' coordinate var with myTime and create a
+   separate 'iter' variable for iteration count
+ o pkg/diagnostics:
+   add new capability: output of Global/Regional & per-level statistics ;
+   tested against monitor output (including land & thSIce) on various exp.
+ o make seaice-pkg I/O type flags (MNC/MDS) more standard.
+ checkpoint57h_done (2005/05/19)
+   tag after changing user customized files (DIAGNOSTICS_SIZE.h,
+   data.diagnostics, data.gchem, data.ptracers) is done.
+ o pkg/diagnostics: prepare for Global/Regional statistics.
+   add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h
+ o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE
+   and rename it: DIFFERENT_MULTIPLE
+ checkpoint57h_post (2005/05/14)
+ o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers
+ o pkg/diagnostics: change output frequency, now in seconds (instead
+   of Nb of iterations). This requires to change data.diagnostics.
+ checkpoint57h_pre (2005/05/12)
+ o in mnc, let the user create the output dir if both mnc_outdir_date
+   and mnc_outdir_num are false
+ o add fflags() to pkg/diagnostics which allows one to specify, on a
+   per-file basis, the file precision [default behavior is unchanged]
+ o added diagnostics to pkg/kpp, including computation of mixed layer
+   depth based on a temperature/density criterion
+ o updated verification/natl_box to test the new pkg/kpp diagnostics
+ o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T)
+ o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4)
+ o fix mnc flags in pkg/seaice so that they are "owned" by seaice,
+   not mnc -- this mistake was found by JMC and is now corrected
+ checkpoint57g_post (2005/04/15)
+ o add Adams-Bashforth 3rd Order time stepping:
+   - default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3)
+   - not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ...
+ checkpoint57g_pre (2005/04/15)
+ o make lambda[Theta,Salt]ClimRelax spatially varying
+   (default remains spatially uniform constant based on tau)
+ o added new control variables
+   * init. uVel, vVel, etanN
+   * lambda[Theta,Salt]ClimRelax
+ o separate masks used for ctrl_pack/unpack 'from write_grid' output
+   (suggested by G. Forget)
+ checkpoint57f_post (2005/04/06)
+ o add parameter "baseTime" = model base time = time at iteration zero
+   new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to
+   account for baseTime shift
+ o move Coriolis arrays from PARAMS.h to GRID.h
+ checkpoint57f_pre (2005/04/06)
+ o mnc-ifying the seaice package
+ o introduced an alternative length scale calculation for use in the limiting
+   maximum viscosity (off by default, see mom_vi_hdissip.F for details)
+ o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S
+ o added modified Leith scheme with viscosity proportional to grad(Hdiv)
+   as well as grad(vort3).  Made it compatible with both approximate form
+   for the cubed sphere and full form of these gradients.  Added flag
+   useFullLeith to select between approximate and full form.
+ o add "d0" in getcon.F to reduce differences between compilers/platforms
+   update output.txt of exp. fizhi-gridalt-hs
+ o change port_rand funtion to allow to set the seed.
+ o fix obscure MNC bug involving conversion between reals and integers
+   - it caused no problems with certain (eg. gcc, ifc) compilers but the
+     new version is now more standards-compliant
+ o adjoint-related modifications
+   * gad_dst3_adv_?: to be able to use advscheme=30 in adjoint
+   * gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33
+   * mom_vi_hdissip: to be able to use Leith scheme in adjoint
+ checkpoint57e_post (2005/02/28)
+ o Adding eddy stress controls a la Ferreira et al.
+ checkpoint57e_pre (actually was tagged: eckpoint57e_pre)
+ o fizhi pkg: fix AtoC and CtoA when called with same input & output array
+   update output.txt of exp. fizhi-gridalt-hs
+ o add more "Z" dimensions and associated coordinate vars to MNC
+ o pkg/exf: added twoDigitYear capability for option useExfYearlyFields
+ o parameter calendarDumps: when set, approximate months (30-31 days) and years
+   (360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq,
+   KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar
+   months and years.  Requires pkg/cal.
+ o diagnostics: add pickup functionality
+   - off by default for backwards compatibility
+   - current version only uses MDSIO -- MNC will be added
+ o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies.
+ o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2)
+ checkpoint57d_post (2005/02/11)
+ o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing
+ o modify verification/ideal_2D_oce so that it tests the creation of mnc
+   output from the diagnostics package
+ o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up
+ o make genmake2 more portable by using ".$FS" instead of ".f" for more
+   of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys)
+ o add coordinate variables to the MNC output from the diagnostics package
+ o change MNC-flags default value: true when useMNC=TRUE
+ o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F
+   the ability (off by default) to read the grid information using MNC
+ o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt
+ o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging
+ o do snap-shot diagnostics at the middle of the time-interval (instead of
+   at the end).
+ o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add
+   new test for AIM with thSIce + slab-ocean
+ o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h)
+ o move state variable diagnostics to the beginning of the time step ;
+   (note: still needs some work specially for snap-shot diagnostics)
+   duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z
+ checkpoint57c_post (2005/01/27)
+ o Change testing option (-ieee) to get closer agreement between g77 & ifort
+ o generate new output.txt files on faulks with g77 & the new -ieee option
+ checkpoint57c_pre (2005/01/27)
+ o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF);
+   update output.txt of exp. global_ocean.90x40x15
+ o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer
+   results; update global_ocean_pressure & global_ocean.cs32x15 output.txt
  o add saltFlux(+File) forcing capability with periodicExternalForcing
  o allow to use pkg diagnostics for GM-Redi & ThSIce output
  o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc.
-Line 20 
 o exf_getffields interpolation defaults
+Line 3422 
 o exf_getffields interpolation defaults
    fields (remains bicubic for wind velocity and stress).  This avoids, e.g.,
    spurious negative numbers for precipitation and humidity.  Will cause
    some small numerical differences for integrations using pkg/exf/exf_interp.F.
- o Add ctrlvec diagnostics in pack/unpack for nondimensional I/O
+ o pkg/ctrl/
-   May be enabled via doPackDiag
+   * Add ctrlvec diagnostics in pack/unpack for nondimensional I/O
+     May be enabled via doPackDiag
+   *  introduce z-scaling of
+      + gradient (doZscalePack) and
+      + control (doZscaleUnpack)
+ o pkg/mdsio/
+   * enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F
+   * N.B.: leave tiled I/O for tapelev (i.e. mds...vector)
- checkpoint57b_post
+ checkpoint57b_post (2004/12/20)
  o simplify options in diagnostics_fill arguments (remove weird combinations)
  o fix MNC coordinate variables so that they now contain per-face index
    values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in
-Line 69 
 o re-arrange diagnostics pkg initialisat
+Line 3478 
 o re-arrange diagnostics pkg initialisat
     look through the short list of active diag. (instead of the long list)
     create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active
- checkpoint57a_post
+ checkpoint57a_post (2004/12/10)
  o this set of changes restores TAMC compatibility
    tested for global_ocean.90x40x15 adjoint on trough
    (what a pain)
- checkpoint57a_pre
+ checkpoint57a_pre (2004/12/10)
  o some modifs in tools/build_options for sunos
  o call ctrl_pack for ctrl at end for optimcycle=0
- checkpoint57
+ checkpoint57 (2004/12/09)
  o add horizontal bi-harmonic viscosity for vertical velocity
    - new parameter viscA4W (defaults to viscA4)
    - affects only non-hydrostatic code
-Line 96 
 o untangle a few ifdefs related to cost,
+Line 3505 
 o untangle a few ifdefs related to cost,
  o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)
    (theta2, salt2 in ecco_cost_weights)
- checkpoint56c_post
+ checkpoint56c_post (2004/12/03)
  o OBCS as control variables
    - update ctrl_ad_diff.list, obcs_ad_diff.list
    - remove balance of obcs controls from default
-Line 114 
 o exf:
+Line 3523 
 o exf:
  o mdsio:
    - i/o-vector change debugLevel from debLevA to debLevB
- checkpoint56b_post
+ checkpoint56b_post (2004/12/01)
  o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that
    is called from DO_THE_MODEL_IO
    - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE
-Line 129 
 o testreport previously did a lousy job
+Line 3538 
 o testreport previously did a lousy job
    testreport.
  o ptracers_monitor: bug fix for MPI
- checkpoint56a_post
+ checkpoint56a_post (2004/11/28)
  o GCHEM: finish reorganizating the package
    - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency
      (introduces another 3D-array for each passive tracer, but only if
-Line 174 
 o GCHEM:
+Line 3583 
 o GCHEM:
    - cleaning up
  o small cleaning of exch2: remove files that are also in eesupp/src
- checkpoint56
+ checkpoint56 (2004/11/17)
  o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0
  o mnc: cleanup "full" files--fixes out-of-memory problem
  o ECCO-GODAE
-Line 204 
 o mdsio: filename info to both stderr, s
+Line 3613 
 o mdsio: filename info to both stderr, s
  o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec]
    from sign change
- checkpoint55j_post
+ checkpoint55j_post (2004/11/10)
  o isolate dissipation tendency (allow to keep it out off AB) in V.I form.
    affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
  o add consistent build directories and .cvsignore files to verification
-Line 215 
 o make all subroutines 30 or less charac
+Line 3624 
 o make all subroutines 30 or less charac
  o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity;
    affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
- checkpoint55i_post
+ checkpoint55i_post (2004/10/28)
  o change arrays for total vertical diffusivity (2.D if explicit,
 .D if implicit) ; each ptracer uses its own background value.
  o added mnc/NetCDF output capability to ocn_compon_interf
-Line 230 
 o give MNC the ability to create additio
+Line 3639 
 o give MNC the ability to create additio
  o Compute the non-local term using either KPP vertical diffusivity (=default)
     or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T)
- checkpoint55h_post
+ checkpoint55h_post (2004/10/20)
  o add verification test "vermix"
  o remove all the *_ioinc flags and replace with the single global
    outputTypesInclusive flag
-Line 238 
 o allow to set a vertical profile of ver
+Line 3647 
 o allow to set a vertical profile of ver
  o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS
  o useMNC moved from data.mnc to data.pkg
- checkpoint55g_post
+ checkpoint55g_post (2004/10/14)
  o Renaming carbon AD experiments to comply with testreport conventions
  o Updating adjoint of Held-Suarez hs94.1x64x5
  o Fixing directives for non-ECCO forward_step, after ECCO directives
-Line 248 
 o Fixing directives for non-ECCO forward
+Line 3657 
 o Fixing directives for non-ECCO forward
  o Updating adjoint output for natl_box_adjoint after
    pkg/ecco has been modified (see taga c55d_post)
- checkpoint55f_post
+ checkpoint55f_post (2004/10/13)
  o rename to timeave_init_fixed
- checkpoint55e_post
+ checkpoint55e_post (2004/10/13)
  o some delicate re-shuffle of store directives to avoid one
    extra call of do_oceanic_physics
    affects ecco_the_main_loop.F, do_oceanic_physics.F
-Line 259 
 o some delicate re-shuffle of store dire
+Line 3668 
 o some delicate re-shuffle of store dire
  o NB: this may break global_ocean adjoint temporarily,
    but it is clear how to fix it. Will do later, need this now.
- checkpoint55d_post
+ checkpoint55d_post (2004/10/11)
  o ECCO specific cost function terms (up-to-date with 1x1 runs)
  o ecco_cost_weights is modified to 1x1 runs
  o modifs to allow observations to be read in as
    single file or yearly files
  o enable to read exf forcing fields as either
    single file or yearly files (flag useExfYearlyFields)
- checkpoint55d_pre
+ checkpoint55d_pre (2004/10/08)
  o switch between 2-level and 3-level checkpointing
  o add ability of MNC to write local and "partial" (eg. 2D slices where
-Line 314 
 o more obcs stuff
+Line 3723 
 o more obcs stuff
    - changed argument list of OBCS_CALC to myTime+deltaTclock
    - fixed about 35 bugs in obcs_external_fields_load
- checkpoint55c_post
+ checkpoint55c_post (2004/09/23)
  o obcs stuff
    - new runtime flags useOBCSprescribe, useOBCSbalance
    - re-arranged obcs_calc
-Line 328 
 o obcs stuff
+Line 3737 
 o obcs stuff
  o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments
    which simplifies the calls and passes the ifc check-bounds test
- checkpoint55b_post
+ checkpoint55b_post (2004/09/22)
  o add a 2D scalar, Z location, exchange_2 routine.
  o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows
    to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]
-Line 339 
 o use a more standard discretization for
+Line 3748 
 o use a more standard discretization for
  o fix gad_advection.F (CubedSphere part), back to version 1.23
  o fix bug in mom_vi_del2uv.F (CubedSphere part).
- checkpoint55a_post
+ checkpoint55a_post (2004/09/20)
  o merged code to
    * prescribe/read time-dependent open boundaries
      (works in conjunction with exf, cal)
-Line 347 
 o merged code to
+Line 3756 
 o merged code to
    * each boundary N/S/E/W now has its own CPP option
      (healthy for the adjoint)
- checkpoint55
+ checkpoint55 (2004/09/17)
  o up-to-date adjoint of previous breaks
    - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix
    - global_ocean_ebm: adjoint still needs fix (TLM ok)
-Line 357 
 o up-to-date adjoint of previous breaks
+Line 3766 
 o up-to-date adjoint of previous breaks
  o remove all tr1-related code (ALLOW_PASSIVE_TRACER)
    (adjoint stuff still has some tr1 'names', but all use ptracer arrays)
- checkpoint54f_post
+ checkpoint54f_post (2004/09/16)
  o in verification/carbin/ remove experiment related to
    ALLOW_PASSIVE_TRACER (array tr1 etc)
    code_ad/ input_ad/ results_ad
-Line 383 
 o overhaul of IO so that we now have fla
+Line 3792 
 o overhaul of IO so that we now have fla
    - numerous small formatting cleanups for ProTeX
  o add version info (via BUILD_INFO.h) to MNC and stdout
- checkpoint54e_post
+ checkpoint54e_post (2004/09/02)
  o add two new packages
    - pp81 (Packanowski and Philander, 1981), Richardson number and
      stratification dependent mixing
    - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
    - these scheme operate in a similar manner as KPP (without ghat, of
      course), however there is only one diffusivity that is used for both
-     temperature and salinity (and passive tracers)�
+     temperature and salinity (and passive tracers)
  o add offline package
  o add "verification/dic_example" which contains a dic-gchem-ptracer setup
    provided by Stephanie Dutkiewicz
  o genmake2: add ability to search for C compilers and cleanup test output
    - fixes recent SX-6 problems and should help with others (eg. HP-UX)
- checkpoint54d_post
+ checkpoint54d_post (2004/07/27)
  o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed
  o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,
    leading to additional shift by 5 days each year of integration
-Line 413 
 o fix a bug in Flux deriv. vs Ts (pkg/ai
+Line 3822 
 o fix a bug in Flux deriv. vs Ts (pkg/ai
  o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")
  o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)
- checkpoint54c_post
+ checkpoint54c_post (2004/07/18)
  o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr
    this affects (truncation error) output.txt of test-exp:
     global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box
-Line 424 
 o define the max number of passive trace
+Line 3833 
 o define the max number of passive trace
  o start to test mnc routinely in exp0
  o add sea-ice loading (sIceLoad) as a new forcing field.
- checkpoint54b_post
+ checkpoint54b_post (2004/07/08)
  o add testreport "-j JOBS" option for parallel builds (tested and pretty
     impressive on Altix and Opteron systems)
  o diagnostics can now write NetCDF files through the mnc package
-Line 434 
 o staggerTimeStep & NLFS: rescale T & S
+Line 3843 
 o staggerTimeStep & NLFS: rescale T & S
    affects (truncation error) output of lab_sea & natl_box exp.: updated
  o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
- checkpoint54a_post
+ checkpoint54a_post (2004/07/06)
  o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).
  o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)
  o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)
  o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)
    + internal_wave (shift in writing cg2d_ini_res)
- checkpoint54a_pre
+ checkpoint54a_pre (2004/07/05)
  o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice
    - modified verification/lab_sea and natl_box_adjoint accordingly
- checkpoint54
+ checkpoint54 (2004/07/02)
- checkpoint53g_post
+ checkpoint53g_post (2004/07/02)
  o prepare splitting of thermodynamics: store convect.counter in common block
  o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)
    output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave
-Line 455 
 o new parameter "nShapS": allow to treat
+Line 3864 
 o new parameter "nShapS": allow to treat
  o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)
  o restore adjointability
- checkpoint53f_post
+ checkpoint53f_post (2004/06/25)
  o modifications that affect AIM experiment results (update output.txt):
    - no advection of S at top interface Nr (pkg/generic_advdiff)
    - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)
-Line 468 
 o merged cylindrical coord configuration
+Line 3877 
 o merged cylindrical coord configuration
  o added rotating_tank experiment
  checkpoint53e_pre
- checkpoint53d_post
+ checkpoint53d_post (2004/06/14)
  o faulks upgraded: re-generate output.txt that have changed:
     global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box
  o Added Bryan and Lewis, 1979, vertical diffusivity profile
-Line 487 
 o regenerated output for global_ocean_eb
+Line 3896 
 o regenerated output for global_ocean_eb
  o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation
    of mom_common/
    - simple re-arrangement of instructions within computing loop
- checkpoint53d_pre
+ checkpoint53d_pre (2004/05/21)
- checkpoint53c_post
+ checkpoint53c_post (2004/05/21)
  o new version of coupler for AIM+thSIce and Ocean models
   - new fields (SSS,h_MixLayer ...) are exchanged through the coupler
   - land: change Evaporation of snow
-Line 506 
 o Adjoint of EBM package + verification
+Line 3915 
 o Adjoint of EBM package + verification
    * TLM OK
    * ADM not sufficient accuracy yet (needs further testing)
- checkpoint53b_post
+ checkpoint53b_post (2004/05/14)
  o Commiting new energy balance model to repository
    * package is pkg/ebm
    * verif. is verification/global_ocean_ebm
-Line 524 
 C        Destabilization of the thermoha
+Line 3933 
 C        Destabilization of the thermoha
  C        by atmospheric eddy transports.
  C        J. Climate 7(12), 1870-1882
  o Will need long integration testing.
- checkpoint53b_pre
+ checkpoint53b_pre (2004/05/14)
  o created pkg/mom_common in preparation for variable viscosity code
  o renamed and split ini_mnc_io
-Line 532 
 o pkg/land: only liquid water can diffus
+Line 3941 
 o pkg/land: only liquid water can diffus
  o AIM using land: soil wetness availability account for snow
  o added printMapIncludesZeros to EEPARMS namelist
- checkpoint53a_post
+ checkpoint53a_post (2004/05/11)
  o restore TAMC compatiility for exf_constants.h
    (no usage of _d in .h)
  o Additional storing in KPP in an attempt to fix
-Line 545 
 o Fixed verification/natl_box_adjoint ex
+Line 3954 
 o Fixed verification/natl_box_adjoint ex
    and hence gives results closer to that of Experiment 2.
    Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.
- checkpoint53
+ checkpoint53 (2004/05/06)
  o stable checkpoint with up to date adjoint
    TLM tests only run for 1st grdchk at the moment. Its unclear if
    this is a code problem or a problem with resetting code for g_
-Line 555 
 o stable checkpoint with up to date adjo
+Line 3964 
 o stable checkpoint with up to date adjo
     o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ)
       are both still in chaos following their security messes.
- checkpoint52n_post
+ checkpoint52n_post (2004/05/06)
  o various build (mostly genmake2) changes including:
    - ability to build/run more easily within Cygwin and MacOS X
    - more complicated Makefiles with a stronger dependence on Gnu Make
-Line 586 
 o fix in pkg/thsice:
+Line 3995 
 o fix in pkg/thsice:
    - maintain snow precipitation unchanged (even if Tsf >=0).
   both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice
- checkpoint52m_post
+ checkpoint52m_post (2004/04/18)
  o commented out call to cal_GetMonthsRec in swfrac.F and added some comments;
    this does not change any of the results, because myIter=0 in swfrac always
    lead to jwtype=2 (the default anyway), but the call makes little sense
-Line 618 
 o test exp. advect_cs: use the standard
+Line 4027 
 o test exp. advect_cs: use the standard
  o Added functionality to grdchk:
    pick global i,j,k position (or nearest wet) where to perform check.
- checkpoint52l_post
+ checkpoint52l_post (2004/03/11)
  o new land formulation:
    a) use ground enthalpy as prognostic variable to ensure exact
       energy conservation.
-Line 629 
 o aim_v23 modification for new land mode
+Line 4038 
 o aim_v23 modification for new land mode
    a) Treat separately land / ocean / sea-ice surface fluxes
       to allow implicit computation of land & sea-ice surface temp.
    b) add snow precipitation.
- checkpoint52l_pre
+ checkpoint52l_pre (2004/03/11)
  o fix problem (when 1 tile is empty) in min/max monitor.
  o fix bug in timeAve (u,vZetatave in common block)
-Line 642 
 o fix ini_curvilinear_grid ; test CS exp
+Line 4051 
 o fix ini_curvilinear_grid ; test CS exp
  o aim.5l_cs: modify sea-ice fraction input file ; update output
  o exf: Adding simple range check routine for exf fields after read
- checkpoint52k_post
+ checkpoint52k_post (2004/02/23)
  o removed top-level directory "diags"
    - we migrated these functions to pkg/timeave a long time ago
  o fixed bug introduced in pkg/monitor
-Line 655 
 o set all ...Freq to zero after cost_fin
+Line 4064 
 o set all ...Freq to zero after cost_fin
    taveFreq, dumpFreq, pChkptFreq
  o MAIN and ECCO differentiability restored
- checkpoint52j_post
+ checkpoint52j_post (2004/02/18)
  o fix nchklev in tamc.h for global_ocean...
  o Bringing flow and store directives up-to-date
  o Really weird thing!
-Line 663 
 o Really weird thing!
+Line 4072 
 o Really weird thing!
    starttime, niter0, instead of mytime, myiter, screws up the adjoint:
    TAF places a faulty re-call of initialise_varia
    after cost_final call which should not be there!
- checkpoint52j_pre
+ checkpoint52j_pre (2004/02/03)
  o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and
    error messages
-Line 680 
 o merged mom_vi_calc_relvort3.F, mom_vi_
+Line 4089 
 o merged mom_vi_calc_relvort3.F, mom_vi_
    mon_vort3.F to make exch2 friendly with >1 tile per cube face
  o limit timeave output for hi-res integrations
- checkpoint52i_post
+ checkpoint52i_post (2004/01/21)
  o removed CPP_EEOPTIONS.h from verification/*/code
  o updated the tiling for global_ocean_pressure
- checkpoint52i_pre
+ checkpoint52i_pre (2004/01/20)
  o update aim.5l_LatLon using the standard aim_v23 pkg (instead of
    the old pkg/aim).
- checkpoint52h_pre
+ checkpoint52h_pre (2004/01/20)
  o shortened offending lines in exch2_send_rx?.template
  o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator
  o genmake2: add build & execute test for NetCDF code
-Line 699 
 o added temporary hack for sea-ice dynam
+Line 4108 
 o added temporary hack for sea-ice dynam
    metric terms are ignored and it is assumed that
    there is no sea-ice on cube faces 1, 2, 4, and 5.
- checkpoint52f_post
+ checkpoint52f_post (2004/01/09)
  o added exch2 cube routines to pkg/exch2
  o modified hs94.cs-32x32x5 to use it
  o added new grid files to hs94.cs-32x32x5
- checkpoint52f_pre
+ checkpoint52f_pre (2004/01/07)
- checkpoint52e_post
+ checkpoint52e_post (2004/01/07)
  o first attempt to solve vertical advection (momemtum & T,S) Implicitly
    for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom)
  o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F)
-Line 713 
 o step.1 : rewrite (as in MultiDimAdvec)
+Line 4122 
 o step.1 : rewrite (as in MultiDimAdvec)
  o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme.
  o update output (gad_calc_rhs.F changes affect truncation error) of exp:
   front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box
- checkpoint52e_pre
+ checkpoint52e_pre (2004/01/02)
  o fix bug in impldiff when Nr=1 or Nr=2.
  o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt
-Line 724 
 o added exf_offset_atemp for Celsius to
+Line 4133 
 o added exf_offset_atemp for Celsius to
  o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024
  o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations
- checkpoint52d_post
+ checkpoint52d_post (2003/12/16)
  o re-tiled many expts to allow comparison in multi-processor mode
    - updated output accordingly
    - changed hs94.128x64x5 to use intial T from file rather than use the
-Line 753 
 o check-in the first version of the coup
+Line 4162 
 o check-in the first version of the coup
  o new verification experiment, cpl_aim+ocn:
     coupled ocean - AIM atmosphere on cs32 grid.
- checkpoint52d_pre
+ checkpoint52d_pre (2003/12/06)
  o surface flux time-av diagnostic modified for NLFS & RealFreshWater
  o add call to AIM pendant S/R in external_forcing & external_fields_load.F
- checkpoint52c_post
+ checkpoint52c_post (2003/11/25)
  o Fixing OPTIONS files for use of exf:
    - ALLOW_ECCO not needed
    - ECCO_CPPOPTIONS.h should not be included from
-Line 771 
 o Removed all CPP options for cal packag
+Line 4180 
 o Removed all CPP options for cal packag
  o modified STOREs in GAD_ADVECTION
  o corrected key comp. for passkey
- checkpoint52b_post
+ checkpoint52b_post (2003/11/23)
  o new version: "thsice" of thermodynamic sea-ice pkg:
   - only 1 call from "forward_step"; conserve energy, fresh-water & salt.
   - modify fluxes but do not change theta directly;
-Line 779 
 o new version: "thsice" of thermodynamic
+Line 4188 
 o new version: "thsice" of thermodynamic
   - add forcing fields + data files in global_ocean.cs32x15/inp_thsice
     + output_thsice.txt to test thsice & bulk_force pkgs.
  o put back grid & coriolis monitor output.
- checkpoint52b_pre
+ checkpoint52b_pre (2003/11/23)
  o call "do_the_model_io" at the beginning (=> dump initial state)
  o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P)
-Line 789 
 o missing PTRACERS headers in some routi
+Line 4198 
 o missing PTRACERS headers in some routi
  o default tamc.h in pkg/autodiff supposed to crash
    to ensure proper customization
- checkpoint52a_post
+ checkpoint52a_post (2003/11/17)
  o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp
    - moved surfaceTendencyTice from pkg/seaice to main code
    - subroutine FREEZE_SURFACE now limits only surface temperature
-Line 804 
 o fix problem with ECCO-related divided
+Line 4213 
 o fix problem with ECCO-related divided
    snapshot file was missing some ad-variables,
    but no warning issued by TAF
- checkpoint52a_pre
+ checkpoint52a_pre (2003/11/12)
  o some bug fixes for #undef REAL4_IS_SLOW
  checkpoint52 = ecco_c52_e35
  o after testing adjoints of checkpoint51u_post
- checkpoint51u_post
+ checkpoint51u_post (2003/11/06)
  o this is the post-merge tag of the ecco-branch
    (needs another clean checkout and re-testing)
  o various natl_box_adjoint configs and results
-Line 825 
 o top level routines the_main_loop, forw
+Line 4234 
 o top level routines the_main_loop, forw
    (new namelist ecco_cost_nml)
  o in ctrl/ cleaned some cross-dependencies and updated CPP options
- checkpoint51t_post
+ checkpoint51t_post (2003/11/04)
  o this is the pre-merge tag of the ecco-branch
- checkpoint51s_post
+ checkpoint51s_post (2003/11/04)
  o cleanup: removed various obsolete #define-s
  o pkg/grdchk
    - renamed 'ph-grd 3' to 'grad-res'
-Line 837 
 o pkg/grdchk
+Line 4246 
 o pkg/grdchk
    - additional high-precision output for testreport
      (grep for 'precision_grdchk_result')
- checkpoint51r_post
+ checkpoint51r_post (2003/11/03)
  o cleaned up or removed CPP_OPTIONS.h files
  o updated results for some of the tests to reflect the new
    optfiles (-ieee: -O0 instead of -O3)
- checkpoint51q_post
+ checkpoint51q_post (2003/10/30)
  o cd_code:
    - moved cd_scheme.F -> cd_code_scheme.F
    - separate read_checkpoint from cd_code_ini_vars.F
-Line 858 
 o ctrl package totally restructured
+Line 4267 
 o ctrl package totally restructured
    - confined inclusion of AD_CONFIG.h to where necessary.
  o genmake2: changed AD dependencies from SRCFILES to AD_FILES
- checkpoint51p_post
+ checkpoint51p_post (2003/10/30)
  o create initial cd_code package
    - WARNING: the initialization of fields within packages
      is broken because INI_FIELDS (where READ_CHECKPOINT is
-Line 873 
 o create initial cd_code package
+Line 4282 
 o create initial cd_code package
  o cleanup verification/*/code/GMREDI_OPTIONS.h
  o cleanup testreport
- checkpoint51o_post
+ checkpoint51o_post (2003/10/27)
  o bringing AD-related verif's up to date with genmake2
    - carbon/
    - global_ocean.90x40x15/
-Line 894 
 o Correcting initialisations for fVerU,
+Line 4303 
 o Correcting initialisations for fVerU,
  o helping TAF to recognize dependency on kUp for
    fVerU, fVerV
  o Replacing delZ by delR in pkg/ctrl/
- checkpoint51o_pre
+ checkpoint51o_pre (2003/10/24)
  o undid all of cp51 pending some cleanups and discussion
  o added the [#include "AD_CONFIG.h"] statement to all files that need
-Line 902 
 o added the [#include "AD_CONFIG.h"] sta
+Line 4311 
 o added the [#include "AD_CONFIG.h"] sta
   o re-worked the build logic in genmake2 to support AD_CONFIG.h
   o removed tools/genmake since it no longer works
- checkpoint51n_post
+ checkpoint51n_post (2003/10/23)
  o modifications to make FREEZE flux visible to pkg/kpp
    - moved surfaceTendencyTice from pkg/seaice to main code
    - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP
-Line 911 
 o modifications to make FREEZE flux visi
+Line 4320 
 o modifications to make FREEZE flux visi
       global_ocean.cs32x15, and global_with_exf)
  o added surface flux output variables to TIMEAVE_STATVARS
- checkpoint51n_pre
+ checkpoint51n_pre (2003/10/23)
  o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F
  o added [#include "AD_CONFIG.h"] to all files that use the following
    defines:
-Line 919 
 o added [#include "AD_CONFIG.h"] to all
+Line 4328 
 o added [#include "AD_CONFIG.h"] to all
    - ALLOW_TANGENTLINEAR_RUN
    - ALLOW_ECCO_OPTIMIZATION
- checkpoint51m_post
+ checkpoint51m_post (2003/10/21)
  o incorporating changes to get TAMC/TAF working in genmake2
    - added new TAMC/TAF targets to the Makefile
    - various cleanups related to package handling
    - these changes should have no impact on the forward model
- checkpoint51l_post
+ checkpoint51l_post (2003/10/20)
  o changes to pkg/cal and pkg/exf that allow and speed-up long integrations
   - faster algorithm for cal_addtime.F
   - higher precision arithmetic, where needed
   - pkg/exf *startdate variables changed from calendar date to
     model integration time
- checkpoint51l_pre
+ checkpoint51l_pre (2003/10/17)
  o add salt flux to forcing fields (used when salty sea-ice forms or melts)
  o enable to apply restoring on S & T only in a latitude band.
  o update output (external_forcing_surf modif. change truncation errors)
     global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box
- checkpoint51k_post
+ checkpoint51k_post (2003/10/16)
  o change default to: useNHMTerms=.FALSE.
   - new output.txt for atmos. exp (NHMTerms were wrong but now turned off):
     adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5
-Line 952 
 o added an include barrier to the defaul
+Line 4361 
 o added an include barrier to the defaul
    removed the #include "PACKAGES_CONFIG.h" from it
  o fix a bug in mom_fluxform (from chk51j_post)
- checkpoint51j_post
+ checkpoint51j_post (2003/10/10)
  o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/
  o adjusted some flow directives (dynamics, thermodynamics)
  o added cubed-sphere case to test cost function
-Line 966 
 o Moving pkg-specific flow directives to
+Line 4375 
 o Moving pkg-specific flow directives to
         - pkg_ad_diff.list
         - pkg_ad_check_lev?_dir.h
- checkpoint51i_post
+ checkpoint51i_post (2003/10/09)
  o merge of the branch-genmake2
    - knowingly breaks the older genmake
    - automatic generation of all ALLOW_${PKG_NAME} defines
    - new testreport supersedes older testscript
  o large number of package inclusion and header cleanups
- checkpoint51i_pre
+ checkpoint51i_pre (2003/10/08)
  o new output for adjoin of global ocean vector invariant
  o fix for checkpoint of thermodynamic seaice and bulk_force
-Line 984 
 o modify gchem pkg to be more versatile
+Line 4393 
 o modify gchem pkg to be more versatile
  o modifications to clean up dic pkg
  o add pkg/cfc
- checkpoint51g_post
+ checkpoint51g_post (2003/10/02)
  o provide links for ARPACK and ADM*TLM
  o start removing verification/vero/
  o update AD-related stuff
-Line 992 
 o update AD-related stuff
+Line 4401 
 o update AD-related stuff
  o adding to verification/global_ocean.90x40x15/ adjoint of
    vector invariant setup
- checkpoint51f_post
+ checkpoint51f_post (2003/10/02)
  o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif)
  o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation
    of tracer Green's fucntions for ocean inversion project.
- checkpoint51f_pre
+ checkpoint51f_pre (2003/08/07)
  o Added on-the-fly spatial interpolation capability
      "USE_EXF_INTERPOLATION" to pkg/exf.
    - This is a temporary Cartesian-grid hack until
-Line 1009 
 o Bug fix to pkg/ptracers, pkg/generic_a
+Line 4418 
 o Bug fix to pkg/ptracers, pkg/generic_a
      and pkg/kpp/kpp_transport_ptr.F for dealing with tracer
      non-local transport term.
- checkpoint51e_post
+ checkpoint51e_post (2003/08/03)
  o pkg/mom_vecinv:
    - changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec)
    - add time-ave diagnostic of vorticity advection.
-Line 1019 
 o atmospheric geopotential: - include wa
+Line 4428 
 o atmospheric geopotential: - include wa
  o land pkg: read initial state from files.
  o AIM : add stratospheric drag in the upper level
- checkpoint51d_post
+ checkpoint51d_post (2003/07/18)
  o change function ILNBLNK (=> last non-blank char.) to return zero
    (instead of the string length) when the string. char is empty
  o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid)
-Line 1032 
 o Use cluster local disks for purely loc
+Line 4441 
 o Use cluster local disks for purely loc
    - new active_file_loc... and mdsio_..._loc routines
    - affected packages: autodiff, ctrl, grdchk, mdsio
- checkpoint51c_post
+ checkpoint51c_post (2003/07/08)
  o introducing integer flag debugLevel
    - debLevZero: suppress all output
    - debLevA: standard
-Line 1055 
 o added verification for adjoint with pt
+Line 4464 
 o added verification for adjoint with pt
    - checked tapelev/comlev recomputations: OK
  <<<checkpoint51b_pre
- checkpoint51a_post
+ checkpoint51a_post (2003/06/25)
  o added code for biogeochemistry package
    - new pkgs: dic, gchem
    - new subroutine in ptracers
  o modify code for biogeo packages
    - in model/src and pkg/ptracers
- checkpoint51
+ checkpoint51 (2003/06/24)
  o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN
    - autodiff, ctrl, exf, grdchk, seaice
    kept separate packages
-Line 1070 
 o merged improved packages from ecco-bra
+Line 4479 
 o merged improved packages from ecco-bra
  o updating verification/internal_wave, verification/lab_sea
    (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)
- checkpoint50i_post
+ checkpoint50i_post (2003/06/23)
  o Preparing next differentiable checkpoint and sync
    of MAIN vs. ecco-branch
    - 1st step: this one is differentiable
    - 2nd step: next(! not this) checkpoint will have updated packages
                from ecco-branch)
- checkpoint50h_post
+ checkpoint50h_post (2003/06/20)
  o new package "land": provide surface BC for AIM.
  o pkg/ptracers: apply exchange to all tracers after reading a pickup.
  o AIM: use true log-P extrapolation for near surface temp (= as in
-Line 1086 
 o New variable in PARM03 for more flexib
+Line 4495 
 o New variable in PARM03 for more flexib
  o somewhat cleaned package initialisation sequence for
    ctrl/ cost/ ecco/ in packages_... routines
- checkpoint50g_post
+ checkpoint50g_post (2003/05/23)
  o merged with release1_p17 (pkg/seaice and verification/lab_sea)
    - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics
    - LSR sea-ice dynamic solver moved to SouthWest B-grid location and
      made the default because of faster convergence than ADI
- checkpoint50f_post
+ checkpoint50f_post (2003/05/23)
  o exf totally restructured
    - replaced all exf_set_ routines by one generic exf_set_gen.F
      and made sure it's still differentiable
-Line 1100 
 o exf totally restructured
+Line 4509 
 o exf totally restructured
    - exf_inscal_/exf_outscal_ suffixes consistent with field names
    - updated adjoint/makefile and relevant verif. accordingly
- checkpoint50f_pre
+ checkpoint50f_pre (2003/05/23)
   o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ;
        + change Evap over land. (update aim.5l_cs output)
   o added missing .cvsignores and made uniform across expts
-Line 1110 
 checkpoint50f_pre
+Line 4519 
 checkpoint50f_pre
   o new fn in pkg/monitor to stop model if solution grows too big
   o removed lots of single quotes from comments
- checkpoint50e_post
+ checkpoint50e_post (2003/05/14)
  o make KPP work with PTRACERS
   - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is
     nearly a copy of kpp_transport_s
   - there is no analogue to SurfaceTendencyS, so I have to use
     gPtr(of the surface layer) instead
  o add a new platform SunFire+mpi (SunFire 15000) to genmake
- checkpoint50e_pre
+ checkpoint50e_pre (2003/05/13)
- checkpoint50d_post
+ checkpoint50d_post (2003/05/13)
  o change kpp output from multiple-record state files to single-record state
    files analogous to write_state.F
  o reduce the output frequency of cg3d-related stuff to the monitor frequency,
    analogous to the cg2d-related output.
  o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512,
    so that writing to internal file fn (with length 512) fails.
- checkpoint50d_pre
+ checkpoint50d_pre (2003/05/12)
- checkpoint50c_post
+ checkpoint50c_post (2003/05/12)
  o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)
  o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.
  o add time-average diagnostic of U*V and vertical diffusive flux for theta.
  o bug fixed in convective adjustment diagnostic (multi-tile set-up).
  o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.
- checkpoint50c_pre
+ checkpoint50c_pre (2003/04/30)
  Merging from release1_p13:
  o bug fix for pkg/seaice dynamic solver
  o Added SEAICE_initialHEFF to pkg/seaice
- checkpoint50b_post
+ checkpoint50b_post (2003/04/17)
  o store u*,v* in gU,V instead of in guNm1,gvNm1
  o in order to put the momForcing out of the Adams-Bashforth:
    move forcing & CD-scheme calls from mom_fluxform & mom_vecinv
-Line 1149 
 o new flag "useCDscheme" (default=F); re
+Line 4558 
 o new flag "useCDscheme" (default=F); re
  o re-generate output for highly sensitive test-exp:
     global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box
- checkpoint50b_pre
+ checkpoint50b_pre (2003/04/17)
  o restore the use of momAdvection & useCoriolis flags (mom_vecinv)
  o corrected CPP option mismatch in exf_Bulk... functions for case
    #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP
- checkpoint50a_post
+ checkpoint50a_post (2003/03/21)
  o Bug fix for merging between c50 and KPP.
    ikey was passed from thermodynamics to kpp_calc via
    common block rather than being recomputed in kpp_calc,
    in contradiction with new key itdkey.
    New key ikppkey created, and tamc.h headers updated.
- checkpoint50
+ checkpoint50 (2003/03/08)
  - 2nd step of merge with ecco-branch:
    merge changes in ecco-branch back into main trunk
  - bug fix in find_alpha
-Line 1169 
 checkpoint50
+Line 4578 
 checkpoint50
  - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC
  - merged some sliced AD support routines
- checkpoint49
+ checkpoint49 (2003/03/06)
  merged from ecco-branch:
  o exf:
    - Enable initialisation of forcing fields to constant
-Line 1207 
 o DIVA:
+Line 4616 
 o DIVA:
    (see MITgcm manual).
  o cal: synchronized between MAIN and ecco-branch
- checkpoint48i_post
+ checkpoint48i_post (2003/03/05)
  o Changes to restore differentiability of code w.r.t. previous tag
    (mostly adding new routines to make list and replacing
    pressure by totPhiHyd).
-Line 1225 
 o Modif. for DIVA:
+Line 4634 
 o Modif. for DIVA:
    tbar, sbar, psbar, which should not be reinitialised;
    only relevant for ecco-branch)
- checkpoint48h_post
+ checkpoint48h_post (2003/02/28)
  o improve "ini_p_ground" when using finite difference form for calc_phi_hyd
  o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F
  o Added SEAICE_initialHEFF to pkg/seaice
  o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT
- checkpoint48g_post
+ checkpoint48g_post (2003/02/18)
  --- EOS:
  o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF
    store total Potential in totPhyHyd for diagnostics & EOS.
-Line 1245 
 o accurate phiHyd when using interface-W
+Line 4654 
 o accurate phiHyd when using interface-W
   ( changes results of ideal_2D_oce )
  o includes r* 2nd term in potential gradient.
- checkpoint48f_post
+ checkpoint48f_post (2003/02/18)
  Merging from release1_p12:
  o Modifications for using pkg/exf with pkg/seaice
    - improved description of the various forcing configurations
-Line 1273 
 o pkg/seaice:
+Line 4682 
 o pkg/seaice:
    - adjoint-friendly modifications
    - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
- checkpoint48e_post
+ checkpoint48e_post (2003/02/12)
  o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post)
  o dynamics: change definition of computational domain & adapt mom_fluxform
    accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2.
-Line 1284 
 o following exp works with Olx=Oly=2 (an
+Line 4693 
 o following exp works with Olx=Oly=2 (an
      inverted_barometer solid-body.cs-32x32x1
    (high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure)
- checkpoint48d_post
+ checkpoint48d_post (2003/02/09)
  o in preparation for r*:
   a) use pre-computed gradient of hydrostatic potential:
      changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce
-Line 1292 
 o in preparation for r*:
+Line 4701 
 o in preparation for r*:
      => affects results of glob_oce_pressure (different truncation error)
    update output.txt of ideal_2D_oce & global_ocean_pressure
- checkpoint48d_pre
+ checkpoint48d_pre (2003/02/08)
  o in preparation for r*:
    new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient.
    pass the 2 comp. of the grad. as arguments to momentum S/R.
    but for the moment, only used if it does not change the results.
  o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP
- checkpoint48c_post
+ checkpoint48c_post (2003/02/06)
  Modifications in treatment of initial flux forcing controls
  to avoid extra storing of flux fields.
- checkpoint48c_pre
+ checkpoint48c_pre (2003/01/21)
  o Added tidal_basin_2d experiment (currently 1D!)
  o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented)
- checkpoint48b_post
+ checkpoint48b_post (2003/01/27)
  o r* coordinate added in #ifdef NONLIN_FRSURF block.
   (modification to pressure gradient not yet implemented)
  o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports
    (for U & V) that are used for vertical advection of momentum.
- checkpoint48a_post
+ checkpoint48a_post (2003/01/24)
  o In preparation for r*, use temp. array to compute vertical transport
     in flux-form momentum pkg. => change results of few test-exp.
    Update output of: exp4, exp5, front_relax, global_ocean_pressure,
                      lab_sea, natl_box & plume_on_slope
- checkpoint48
+ checkpoint48 (2003/01/23)
  o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D')
- checkpoint47j_post
+ checkpoint47j_post (2003/01/21)
  o add new exp. (ideal_2D_oce) to test "exotic" parameters and options.
  o moved adexch from forward_step to addummy_in_stepping
  o added exch in ctrl_map_...
-Line 1341 
 o Yet more changes in gmredi:
+Line 4750 
 o Yet more changes in gmredi:
      re-activated full calculation of taperfct for case 'ac02'
  o updating verification/ adjoints of carbon, global_ocean.90x40x15
- checkpoint47i_post
+ checkpoint47i_post (2003/01/13)
  o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled.
  o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi)
    default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post)
-Line 1357 
 o case GM_BOLUS_ADVEC should be cleaned
+Line 4766 
 o case GM_BOLUS_ADVEC should be cleaned
    S/R gmredi_slope_psi should be cleaned
  o verification/carbon now has exactConserv=.TRUE.
- checkpoint47g_post
+ checkpoint47g_post (2003/01/10)
  o time-average AIM output: becomes independent from statvars time-average
    (can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH)
  o After TAF bug fix:
-Line 1383 
 Gradient checks OK for
+Line 4792 
 Gradient checks OK for
  in conjunction with data.gmredi parameters to be checked in
  in a few minutes under verification/carbon/code/
- checkpoint47f_post
+ checkpoint47f_post (2002/12/28)
  Merging from release1_p10:
  o modifications for using pkg/exf with pkg/seaice
    - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING
-Line 1395 
 o modifications for using pkg/exf with p
+Line 4804 
 o modifications for using pkg/exf with p
    - verification/lab_sea default experiment now uses
      pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf
- checkpoint47e_post
+ checkpoint47e_post (2002/12/27)
  o created a tag prior to creating a branch
- checkpoint47d_post
+ checkpoint47d_post (2002/12/16)
  o fixed bug in the oceanic pressure coordinates code: vertical viscosity
    at the bottom boundary had an erroneous half slip boundary condition
  o added bottom drag and no slip boundary condition capabilities to
    oceanic pressure coordinates code
  o added new verification experiment global_ocean_pressure, this experiment is
    also described in the tutorial section of the manual
- checkpoint47d_pre
+ checkpoint47d_pre (2002/12/16)
- checkpoint47c_post
+ checkpoint47c_post (2002/12/16)
  o Added a verification experiment for a global cubed-sphere ocean run
    -  verification/global_ocean.cubed32x32x30
    -  uses pkg/therm_seaice and pkg/bulk_forcing
-Line 1419 
 o OCEANICP & realFreshWater: include P-E
+Line 4828 
 o OCEANICP & realFreshWater: include P-E
    NOTES: requires option NONLIN_FRSURF to be "#define".
  o update advect_xz/results/output.txt (left from checkpoint44g_post)
- checkpoint47b_post
+ checkpoint47b_post (2002/12/05)
  Merging from release1_p9:
  o pkg/seaice
    - removed GOTO's and added taf directives
-Line 1436 
 o verification/lab_sea
+Line 4845 
 o verification/lab_sea
    - added missing matlab routines
    - added test of thermodynamics parallelization
- checkpoint47a_post
+ checkpoint47a_post (2002/11/23)
  o new pkg: aim_v23
   = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.
     for now, keep the same surface forcing as before.
-Line 1453 
 o bulk_force and therm_seaice
+Line 4862 
 o bulk_force and therm_seaice
  - Two ifdef statements for compile time,
     ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE
- checkpoint47
+ checkpoint47 (2002/11/15)
  differentiable version of checkpoint46n_post
  o bug fix in quasihydrostaticterms
  o * "clean" adjoint code (in terms of extensive recomputations)
-Line 1482 
 o Updated verification/carbon/
+Line 4891 
 o Updated verification/carbon/
    - #define GM_VISBECK_VARIABLE_K
    - GM_taper_scheme    = 'ldd97'
- checkpoint46n_post
+ checkpoint46n_post (2002/11/12)
  Merging from release1_p8:
  o verification/natl_box:
    updating new external_fields_load routine
-Line 1536 
 o Adding new verification experiment glo
+Line 4945 
 o Adding new verification experiment glo
    the exf (and cal) package instead of the
    external_fields_load routine (cf README file).
- checkpoint46m_post
+ checkpoint46m_post (2002/11/07)
  o modified testscript to return -- when there are no lines of "%MON" output
  o added new flag "quasiHydrostatic" for QH mode
    and new routine quasihydrostaticterms()
-Line 1549 
 o introduced flag for controllin non-hyd
+Line 4958 
 o introduced flag for controllin non-hyd
  o removed gravitySign from PARM04
  o switched to g77/ifc from pgf77 in aim experiments
- checkpoint46l_post
+ checkpoint46l_post (2002/11/01)
  o made convective adjustment work with pressure coordinates:
   - changed the direction of k-loop in convective_adjustment.F for the
     case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)
-Line 1562 
 o made convective adjustment work with p
+Line 4971 
 o made convective adjustment work with p
     at the beginning of find_rho, find_alpha, and find_beta, does a
     check of the entire slice, if CPP-option
     CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined
- checkpoint46l_pre
+ checkpoint46l_pre (2002/10/23)
- checkpoint46k_post
+ checkpoint46k_post (2002/10/23)
  o fixed the verification/global_ocean.90x40x15 experiment:
   - new bathymetry (the world according to A., JMC, and M.)
   - new initial fields and forcing fields (*.bin files)
-Line 1578 
 o S/R aim_initialise.F replace S/R aim_i
+Line 4987 
 o S/R aim_initialise.F replace S/R aim_i
   - read AIM physics parameters from a file (data.aimphys)
   - set defaults values = F.Molteni paper (Clim.Dyn., 2002)
- checkpoint46j_post
+ checkpoint46j_post (2002/10/07)
  o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH
  o move wVel computation at the end of the time step, in S/R integr_continuity
  o create specific S/R to exchange T,S before DYNAMICS (for stagger time step)
  o update timeave pkg for wVel diagnostic.
- checkpoint46j_pre
+ checkpoint46j_pre (2002/09/27)
- checkpoint46i_post
+ checkpoint46i_post (2002/09/25)
  o Clean up AIM package (and keep the results unchanged):
    include CPP_OPTION and use IMPLICT NONE in all routines ;
    declare all the variables _RL ; use _d 0 for all numerical constants.
    use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 !
- checkpoint46h_post
+ checkpoint46h_post (2002/09/25)
  o cleaned up the use of rhoNil and rhoConst.
    - rhoNil should only appear in the LINEAR equation of state, everywhere
      else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst
-Line 1601 
 o introduced new parameter rhoConstFresh
+Line 5010 
 o introduced new parameter rhoConstFresh
    value is 999.8 kg/m^3
  o cleanup up external_forcing.F and external_forcing_surf.F
    - can now be used by both OCEANIC and OCEANICP
- checkpoint46h_pre
+ checkpoint46h_pre (2002/09/18)
   Added code to convert surface volume flux (fresh water) into
   a mass flux when using P coordinates in the ocean (OCEANICP).
   Note: It assumes you have set rho0=rhoConst=density of fresh water.
- checkpoint46g_post
+ checkpoint46g_post (2002/09/18)
  o Include a new diagnostic variable phiHydLow for the ocean model
    - in z-coordinates, it is the bottom pressure anomaly
    - in p-coordinates, it is the sea surface elevation
-Line 1625 
 o cleaned up find_rho
+Line 5034 
 o cleaned up find_rho
    - removed obsolete 'eqn' from the parameter list.
  o added two new verification experiments: gop and goz
    (4x4 degree global ocean, 15 layers in pressure and height coordinates)
- checkpoint46g_pre
+ checkpoint46g_pre (2002/09/16)
- checkpoint46f_post
+ checkpoint46f_post (2002/09/16)
  o Enable tangent linear (forward mode) gradient checks:
    - extended active file handling to g_... files
    - added TANGENT_SIMULATION to theSimulationMode
-Line 1635 
 o Enable tangent linear (forward mode) g
+Line 5044 
 o Enable tangent linear (forward mode) g
  o added tangent linear setup in verification/carbon/code_ftl
  o added adjoint setup in verification/front_relax/code_ad
- checkpoint46e_post
+ checkpoint46e_post (2002/09/05)
  o Added new equation of state -> MDJWF
    - EOS of McDougall et al., 2002, JAOT, submitted
    - caveat: the equation of state is only valid for a smaller (more
-Line 1644 
 o Added new equation of state -> MDJWF
+Line 5053 
 o Added new equation of state -> MDJWF
    - added more check values for density in check_eos (ini_eos.F), some of
      the old check values are out of the range of the MDJWF-eos, so don't
      expect perfect matches for those
- checkpoint46e_pre
+ checkpoint46e_pre (2002/08/19)
- checkpoint46d_post
+ checkpoint46d_post (2002/08/19)
  o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and
    'OCEANICP', also initialised field pressure correctly in ini_eos in the
    case of pressure coordinates. eosType='JMD95Z' in
    combination with buoyancyRelation='OCEANICP' now causes an error.
  o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)
    in find_alpha/beta.
- checkpoint46d_pre
+ checkpoint46d_pre (2002/08/15)
  o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)
    so that JMD95Z and JMD95P give approptiate static stability in find_rho.
- checkpoint46c_post
+ checkpoint46c_post (2002/08/15)
  o Changes necessary for ocean in p-coordinates
   -  Added new buoyancy relation = 'OCEANICP'
   -  Added new parameters = gravitySign (this used to be contained inside
      the factor dRdZ which I added when we first switched to R coordinates).
   X GM/Redi is not compatible (yet)
   X bottom drag and no-slip need to be debugged.
- checkpoint46c_pre
+ checkpoint46c_pre (2002/08/07)
- checkpoint46b_post
+ checkpoint46b_post (2002/08/07)
  o Added new equation of state -> JMD95Z and JMD95P
    - EOS of Jackett and McDougall, 1995, JAOT
    - moved all EOS parameters into EOS.h
-Line 1676 
 o Added UNESCO EOS, but not recommended
+Line 5085 
 o Added UNESCO EOS, but not recommended
    in-situ temperature (see JMD95)
  o Modified formatting for knudsen2.f in utils/knudsen2 and added
    unesco.f to be used with POLY3
- checkpoint46b_pre
+ checkpoint46b_pre (2002/07/31)
- checkpoint46a_post
+ checkpoint46a_post (2002/07/31)
  o Added (atmospheric) pressure loading
    - new field in FFIELDS.h, etc...
    - new cpp flag ATMOSPHERIC_LOADING
  o Changed hFacC to _hFacC in calc_phi_hyd.F
  o Added SHORTWAVE_HEATING to some files for consistency
- checkpoint46a_pre
+ checkpoint46a_pre (2002/07/13)
- checkpoint46
+ checkpoint46 (2002/07/13)
  further merges from release1_p5
  o new ctrl package
    - adopted from ECCO environment to enable optimization
-Line 1713 
 o added hooks for Eliassen Palm fluxes (
+Line 5122 
 o added hooks for Eliassen Palm fluxes (
  o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)
  o incorporated hooks for sponge layer code (external_forcing.F)
- checkpoint45d_post
+ checkpoint45d_post (2002/07/12)
  o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)
  o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S
    (affects plume_on_slope "cg2d" output)
-Line 1727 
 o add new flags:
+Line 5136 
 o add new flags:
   - for each tracer, define internal flag for multiDimAdvection & A-B
  o monitor: change definition of KE to check conservation of Energy
- checkpoint45c_post
+ checkpoint45c_post (2002/05/30)
  o Removed f90 comments ("!")
  o Modified initialisations to enable exf package for MITgcm
    (without invoking ECCO_PACKAGE).
-Line 1735 
 o modifications to gradient check packag
+Line 5144 
 o modifications to gradient check packag
    - enable centered differences
    - modified format of standard output
- checkpoint45b_post
+ checkpoint45b_post (2002/05/30)
  o cleaned exchange calls in cg2d
  o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step
  o included CPP option SINGLE_LAYER_MODE in thermodynamics
-Line 1747 
 o in initialise_varia, moved call packag
+Line 5156 
 o in initialise_varia, moved call packag
    (corresponding adjustment of TAF tape initialisation).
  o in calc_diffusivity/calc_viscosity extended domain to full overlap.
- checkpoint45a_post
+ checkpoint45a_post (2002/05/01)
  o compute Rho over the whole domain (extend iMin,jMin indices)
  o specific exchange for X-slice domain (case Ny=1)
  o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code
-Line 1767 
 o errorMessageUnit set non-equal zero in
+Line 5176 
 o errorMessageUnit set non-equal zero in
    (conflict on some platforms, e.g. IBM SP3)
  o modified carbon verif.
- checkpoint44h_pre
+ checkpoint44h_pre (2002/03/14)
  o vertical grid option: allow to put the Interface at the middle between
 cell-centers ; replace delZ in pkg/kpp by drF.
  o GM Advective form: Tracers are advected using the residual transport (=
    Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.
- checkpoint44g_post
+ checkpoint44g_post (2002/03/05)
  o fix surface correction term in multiDimAdvection (affects plume_on_slope
    results) ; ifdef missing in thermodynamics.F
-Line 1838 
 o merge of relevant stuff from the ecco-
+Line 5247 
 o merge of relevant stuff from the ecco-
  o check parameters & config (chkpt44a_pre,post)
  o OBC and NonLin_FrSurf.
- checkpoint44
+ checkpoint44 (2002/01/18)
  o fix bug in mom_vi_del2uv
  o select when filters are applied ; add options to zonal_filter (data.zonfilt)
  o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
-Line 1846 
 o update AIM experiments (NCEP input fil
+Line 5255 
 o update AIM experiments (NCEP input fil
  o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
  o added some stuff for AD
- checkpoint43
+ checkpoint43 (2001/09/28)
  o added two new advection tests
  o added global 4x4 degree ocean test
  o added test of H&S94 with free surface on cube
  o some final mods for gradient check, adjoint,...
- checkpoint42
+ checkpoint42 (2001/09/27)
    Fixed AD-related problems:
  o Store directives up-to-date with re-arranged Adams-Bashforth
    (mainly thermodynamics.F)
-Line 1864 
 o Modified store directives for split of
+Line 5273 
 o Modified store directives for split of
    for the case ALLOW_KPP
  o Cleaned argument list for timestep_tracer.F
- checkpoint41
+ checkpoint41 (2001/09/27)
  o re-formatted/added comments in prologues of key subroutines
    to work with protex
- checkpoint40
+ checkpoint40 (2001/09/27)
  o moved calc_gs, calc_gt and calc_tr1 back to model/src
  o added FLT (floats) package from Arne along with demo. experiment
  o re-arranged Adams-Bashforth scheme for tracers to allow easier
-Line 1877 
 o more mods for non-linear free-surface
+Line 5286 
 o more mods for non-linear free-surface
  o modified multi-dim method to work on cube
  o bug fix in KPP (from DM)
- checkpoint40pre9
+ checkpoint40pre9 (2001/09/27)
  o added DST advection schemes
  o fix MPI bug on SGI's
  o modifications for non-linear free-surface
-Line 1887 
 o changes to commenting of arguments for
+Line 5296 
 o changes to commenting of arguments for
  o added/updated many matlab scripts
  o added multi-dimensional advection method for tracers
- checkpoint40pre8
+ checkpoint40pre8 (2001/09/05)
  o new package rw/
    Added method for dumping intermediate local arrays:
    mdsio_writetile - same as mdsio_writefield except works from inside
-Line 1906 
 o TAMC-related update to cope with mom_f
+Line 5315 
 o TAMC-related update to cope with mom_f
    currently nothing implemented to switch this storing off
    in case fluxform is used since no CPP flag available).
- checkpoint40pre7
+ checkpoint40pre7 (2001/08/14)
  o bug fix in dynamics.F
    calc_viscosity called before k=1,Nr loop.
  o added some #ifdef's ALLOW_PASSIVE_TRACER
  o cleaned initialisations in ctrl_map_ini
    related to TAF
- checkpoint40pre6
+ checkpoint40pre6 (2001/08/13)
  o split dynamics into thermodynamics & dynamics
  o corresponding split of calc_diffusivity into
    calc_diffusivity, calc_viscosity
-Line 1921 
 o corresponding split of calc_diffusivit
+Line 5330 
 o corresponding split of calc_diffusivit
  o Added diffkr, kapgm to control variables
  o bug fix in gmredi_slope_limit for ldd97
- checkpoint40pre5
+ checkpoint40pre5 (2001/07/31)
  o proper initialization of Adams-Bashforth time stepping
    + uses forward step for very first step of model (iter=0)
  o re-generated *all* output since almost all output is modified by this
-Line 1935 
 o added new expt "solid-body.cs-32x32x1"
+Line 5344 
 o added new expt "solid-body.cs-32x32x1"
    + this uses an alternative form of ini_curvilinear_grid.F which
      is not necessarily any better than the current one...
- checkpoint40pre4
+ checkpoint40pre4 (2001/07/30)
  o added re-initialisations of utrans,vtrans,rtrans in
    calc_common_factors which are crucial for TAF.
  o extended iMin,jMin range for calc_common_factors,
-Line 1943 
 o extended iMin,jMin range for calc_comm
+Line 5352 
 o extended iMin,jMin range for calc_comm
  o added option ALLOW_PASSIVE_TRACER
  o a few minor updates and fixes
- checkpoint40pre3
+ checkpoint40pre3 (2001/07/13)
  o created calc_gtr1.F for gad package
  o split the_main_loop and re-introduced forward_step
  o some recomputations of nIter0 for TAMC
- checkpoint40pre2
+ checkpoint40pre2 (2001/07/13)
  o Updated to latest branch of AJA, JMC
  o Added gradient check package
  o Added routines for passive tracer handling
  o Added carbon sequestration sensitivity experiment
- checkpoint39
+ checkpoint39 (2001/05/14)
   o Modifications and fixes to support TAMC
     (mainly missing or wrong directives)
   o Corrected common blocks when fooling TAMC to produce adjoint I/O
-Line 1968 
 checkpoint39
+Line 5377 
 checkpoint39
           (NB: this is not the full ECCO environment)
   o disabled some packages by default in genmake
- checkpoint38
+ checkpoint38 (2001/04/10)
   o see notes_c37_adj.txt
   o corrected wrong layer index in external_forcing_t
   o replaced the_main_loop/forward_step by the_main_loop
-Line 1976 
 checkpoint38
+Line 5385 
 checkpoint38
     (replaced criteria for initial/final state)
   o added runtime flag for pre-C35 pickups: usePickupBeforeC35
- checkpoint37
+ checkpoint37 (2001/03/13)
   o mdsio.F routine split and packaged in pkg/mdsio
     (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
      used unless genmake -disable=mdsio)
-Line 1993 
 checkpoint37
+Line 5402 
 checkpoint37
   o Non-Hydrostatic pickup file Pb fixed.
   o bug with Rigid-lid version (since c35) fixed.
- checkpoint36
+ checkpoint36 (2001/02/20)
   o implement Crank-Nickelson barotropic time-stepping
   o recover Time-Average diagnostics
   o fix Pb in checkpoint (PR#19)
   o AIM become a standard package ; clean unused CPP_kees
- checkpoint35
+ checkpoint35 (2001/02/08)
   o subtantial rewrite of dynamics.f
   o allows staggered time-stepping
   o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
   o added bottom drag (linear + quadratic)
- checkpoint34
+ checkpoint34 (2001/01/30)
   o Modified exchange routines for correct reverse simulation.
   o Added verification output to comply with bug fix in impldiff.F
     as of c33 (exp2, natl_box).
-Line 2016 
 checkpoint34
+Line 5425 
 checkpoint34
   o Added routine GLOBAL_SUM_INT to global_sum.F
   o Added mdsio_gl.F for ECCO purposes.
- checkpoint33
+ checkpoint33 (2000/11/30)
   o Fixed bug in lower BC in impldiff.F
   o Fixed confusion about units of forcing arrays in FFIELDS.h
     namely Fu,Fv,Qnet,Qsw,EmPmR:
-Line 2034 
 checkpoint33
+Line 5443 
 checkpoint33
       possibly use them.
   o Corrected genmake to delete a temporary file during configuration
- checkpoint32
+ checkpoint32 (2000/11/13)
   o Scaling of forcing fields moved from external_forcing.F to
     external_fields_scale.F, called directly after loading fields.
   o Surface relaxation terms added to surface tendency fields in
-Line 2045 
 checkpoint32
+Line 5454 
 checkpoint32
   o Modifications and bug fixes in KPP package.
   o Verification experiment for KPP added (verification/nat_box/)
- checkpoint31
+ checkpoint31 (2000/09/11)
   o Packages interface brought in line with defined standard
     -> new routines packages_...F
     -> changes in initialise_fixed.F, initialise_varia.F
-Line 2062 
 checkpoint31
+Line 5471 
 checkpoint31
     - not yet tested for GMRedi.
     - not yet tested for KPP.
- checkpoint30
+ checkpoint30 (2000/07/13)
   o Updates for OBCs
   o New experiment for test OBCs (internal_wave)
   o New output.txt in verification/exp4/results/
-Line 2071 
 checkpoint30
+Line 5480 
 checkpoint30
   o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)
     and entry for T90 in genmake
- checkpoint29
+ checkpoint29 (2000/06/21)
   o packaged KPP and GM/Redi
- checkpoint28
+ checkpoint28 (2000/06/09)
   o Corrected initialization of hFacMin for difference vertical coordinates
   o Modified calculation of partial cell thickness to more robust algorithm
   o config_summary.F: replaced write_1D_... by write_0D_...
-Line 2087 
 checkpoint28
+Line 5496 
 checkpoint28
     included store directives and tape key computations required for TAMC.
   o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
- checkpoint27
+ checkpoint27 (2000/04/10)
   o fixed calc_isoslopes() to so that cancellation of terms in tensor
     formulation works properly with variable resolution.
   o restructured the calling tree between the_model_main() and dynamics()
-Line 2095 
 checkpoint27
+Line 5504 
 checkpoint27
   o introduced initialization file pSurfInitFile for free surface (cg2d_x)
     in new routine ini_psurf()
- checkpoint26
+ checkpoint26 (2000/04/05)
   o moved some #ifdef in optional routines to encompass everything
     except the argument declarations. This was using up some memory.
   o fixed macros like _ADT to work with both versions of Linux cpp
-Line 2105 
 checkpoint26
+Line 5514 
 checkpoint26
     (macros are now in eesupp/inc/CPP_EEMACROS.h)
   o patch for 2 processor JAM mode
- checkpoint25
+ checkpoint25 (2000/03/15)
   o updates for OBCs and NH
   o dramatically reduced memory usage
   o added "JAM" routines for use on Artic network
-Line 2116 
 checkpoint25
+Line 5525 
 checkpoint25
      an explicit free-surface option)
   o initial state input files for U and V
- checkpoint24
+ checkpoint24 (1999/08/02)
   o Removed some spurious "REAL"s
   o Updated KPP to latest version from JPL
   o Added a COS(latitude) in horizontal viscosity
- checkpoint23
+ checkpoint23 (1999/05/26)
   o Added del^4 diffusion for salt and temperature
   o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
- checkpoint22
+ checkpoint22 (1999/05/18)
   o Made many small changes: implicit none, format(i5), etc...
   o Introduced KPP mixing scheme (compiles and runs but *not* tested)
- checkpoint21
+ checkpoint21 (1999/05/18)
   o Introduced new I/O package that supports direct-access records (mdsio.F)
   o Split-up mid-level I/O routines
   o Updated input data for experiments 0,1,2,4 and 5
   o Finally removed the genmake.* scripts (everyone seems happy with genmake)
- checkpoint20
+ checkpoint20 (1999/03/22)
   o Tidied up open-boundaries some more
   o Added non-hydrostatic code
   o Fixed some input data
   o Modified MPI start-up to work in "coupled" context.
- checkpoint19
+ checkpoint19 (1998/12/15)
   o Tidied up directory structure for verification experiments.
   o Added new code for open boundaries.
   o Corrected advective terms near boundaries.
-Line 2149 
 checkpoint19
+Line 5558 
 checkpoint19
   o Implemented free-slip/no-slip BCs and del^4 dissipation.
   o Split default parameters out of ini_parms.F into set_defaults.F.
- checkpoint18
+ checkpoint18 (1998/11/30)
   o Further changes for optional code generation with
     CPP - ugh!
- checkpoint17
+ checkpoint17 (1998/11/03)
   o Beginning to incorporating modularity
     for supporting atmos. and ocean configs.
   o Small changes for TAMC complinace
   o New ultra simple test case. Barotropic box
     configuration "exp0".
- checkpoint16
+ checkpoint16 (1998/10/28)
   o Minor changes to exchange routines to support
     accumulation in reverse mode. Adjoint of an
     assignment is an addition.
-Line 2168 
 checkpoint16
+Line 5577 
 checkpoint16
     syntax) and by g77 under Linux ( 72 character
     limit ).
- checkpoint15
+ checkpoint15 (1998/09/29)
   Rewrote exchange routines to allow
   o General tile <-> tile connectivity.
   o TAMC reverse mode flag ( is this really needed? )
-Line 2177 
 checkpoint15
+Line 5586 
 checkpoint15
     shmput/shmget, VIA, SYSV shmem and every other cool
     communication method.
- checkpoint14
+ checkpoint14 (1998/09/09)
   Consistent isomorphism chages made. These allow dynamical core
   to support both pressure and meters as a vertical coordinate.
- checkpoint13
+ checkpoint13 (1998/07/17)
   Release which corrects global_max problem and a couple
   of KGM time-averaging diagnostic errors. Also contains
   a double-gyre experiment setup as well as the baseline
-Line 2196 
 branch-point-rdot
+Line 5605 
 branch-point-rdot
   I don't want to commit the rDot to the main-trunk until
   we've actually tested it...
- checkpoint12
+ checkpoint12 (1998/07/08)
   Tidy up and added generic genmake script (formerly
   configure script).
   Released to testers.
- checkpoint11
+ checkpoint11 (1998/07/02)
   Re-arranged initialise() and introduced ini_vertical_grid()
   and ini_masks_etc().
- checkpoint10
+ checkpoint10 (1998/07/01)
   Introduced the configure script.
   Separated out the diags package.
   Added template for writing time-averages of tile/intermediate quantities.
   Updated SIZE.h in exp2 and made the data big-endian.
- checkpoint9
+ checkpoint9 (1998/06/22)
   MPI fix. Filename changes (meta/data). salbin*y stuff.
   General tidy-up.
   SST.bin SSS.bin added to verification/exp2
- checkpoint8
+ checkpoint8 (1998/06/22)
   Inludes time-dependant forcing and time-averaging.
   Works at 4x4 and 2.8125x2.8125 global
-Line 2226 
 checkpoint7-4degree-ref
+Line 5635 
 checkpoint7-4degree-ref
   model etc..
   Configured for verification/exp2 - 4 degree global, two process.
- checkpoint7
+ checkpoint7 (1998/06/15)
   Created by cnh
   Simple 4 degree global simulation
   configuration.
-Line 2234 
 checkpoint7
+Line 5643 
 checkpoint7
   hydrography, bathymetry etc
   Does not include Heat Flux and E-P
- checkpoint6
+ checkpoint6 (1998/06/08)
   Created by cnh
   merged checkpoint5 with CD and
   spherical polar code.
   Still some problems with GM Redi
   abd full topography.
- checkpoint5
+ checkpoint5 (1998/06/08)
   Created by AJA
   contains updates to GM Redi
   and reordered timestepping loop
   for Implicit Diffusion.
- checkpoint4
+ checkpoint4 (1998/05/30)
   Created by cnh
   Contains memory saving macros ( _rdxc etc..) for when
   grid variations are limited.
   Contains polynomial coeffs for EOS and knudsen program
   for generation.
- checkpoint3
+ checkpoint3 (1998/05/26)
   Created by cnh
   Added extra flags for runtime options
   Added this file

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