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-revision 1.682 by jmc,
Mon Jun 19 01:06:57 2006 UTC
+revision 1.1435 by jmc,
Wed May 18 02:21:49 2011 UTC
 Line 4 
 $Name$
      Notes on tags used in MITgcmUV
      ==============================
+ o obcs and 2d/3d solver norm:
+    use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
+    and outside OB interior region (will allow to place OB further inside the
+    domain). Depending on the domain, can affects cg2d-Norm (previous
+    cancelation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
+    and cg3d-Norm (previous Norm was computed before canceling OB terms),
+    e.g. in tutorial_plume_on_slope.
+   - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
+ o pkg rbcs:
+   - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
+   - add capability to apply relaxation to horizontal velocity uVel & vVel.
+ o pkg/grdchk: add gradient check for control variable xx_shifwflx
+ o pkg/shelfice/shelfice_init_fixed.F
+   fix CPP-flag combinations
+ o pkg/seaice: Merge iceage code of Pierre Rampal
+   * update/change/correct ice age calculations
+   * add age updates for pathological cases
+   Probably needs more testing...
+ checkpoint62x (2011/05/13)
+ o pkg/mom_vecinv:
+    high-order vorticity scheme: use interior masks (maskInW & S)
+    to zero-out (outside OB) gradient of vorticity.
+ o verification exp.:
+    turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
+    hs94.128x64x5 and seaice_obcs ; update results.
+ o pkg/obcs:
+   fix bug in OBeta for YZ sections in obcs_exf_load.F
+ o pkg/ctrl, pkg/shelfice, and optim:
+   - add new control variable xx_shifwflx (fresh water flux underneath ice
+     shelves). This is almost as tedious as obcs-ctrl, because the
+     variables needs its own mask.
+   - add a cost function term that penalizes the deviation of xx_shifwflx
+     from the first guess (zero) in analogy to other control variables
+ o pkg/shelfice:
+   - start basic adjoint
+ o pkg/ctrl:
+   - remove extra 2D field "for good measure" when initializing in
+     ctrl_set_globfld_[xy/xz/yz].F
+   - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
+   - improve error messages in ctrl_set_unpack_*
+ o OBC implementation in momentum:
+    use interior masks (maskInC,W & S) in momentum S/R:
+    - multiply divergence, tension and some del^i.u or del^j.v by maskInC
+    - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
+    - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
+    - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
+    Motivation: fix/clean implementation of OBC with biharmonic-viscosity
+     (and also with Leith/Smagorinsky harmonic-viscosity).
+    Update output of experiment dome and exp4 (+nlfs).
+ o exp4 test-exp:
+   - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
+     and prescribe time-varying OB (without pkg/exf) for zonal-velocity
+     at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
+     time-varying OB at Western-side for wVel (NonHyd); update output.
+   - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
+     and biharmonic-viscosity ; also use prescribed time varying OB.
+ o pkg/obcs:
+   fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
+ o model/src:
+   - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
+   - initialise startTime & nIter0 with unlikely values: allows to set one
+     from the other without ambiguity.
+ o seaice_obcs test-exp.:
+   add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
+ o pkg/obcs:
+   - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
+     no longer needed with maskInC,W,S in pkg/generic_advdiff.
+ o pkg/seaice:
+   - retired SEAICE_SALINITY and SEAICE_salinity in favor of
+     SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
+   - fixed bug in the initialization of sea ice salinity variable HSALT
+     in seaice_init_varia.F  (removed dependence on ICE2WATR)
+ o fizhi-cs test exp.:
+    switch reference output convention for these 2 non-standard test-exp,
+     from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
+       to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
+    reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
+ o model/inc:
+   - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
+     of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
+ o pkg/seaice:
+   - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
+ o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
+   - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
+     and initial HSALT
+ checkpoint62w (2011/04/26)
+ o pkg/mom_fluxform:
+   - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
+   - use parameter "sideDragFactor" in no-slip BC side-drag part.
+   - update output of exp. global_ocean.90x40x15
+ o pkg/mom_vecinv:
+   mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
+ o update seaice exp.:
+   use more consistent parameter values (remove "backward compatability only":
+    ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
+   related to thermodynamics seaice. Update output (fwd+AD) of exp.:
+D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
+ o update test-exp global_ocean.90x40x15:
+   o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
+   o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
+   o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
+   o turn on zStar & viscA4 in standard set-up (dir input/)
+     and update output files: output.txt & output.dwnslp.txt
+ o new AD-test experiment: obcs_ctrl
+   (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
+ o pkg/dic:
+   fix two bugs in handling water vapour pressure in carbonate chemistry
+   and air-sea fluxes. Found by Val Bennington and Galen McKinley
+   (add DIC Option = WATERVAP_BUG to recover old results)
+   update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
+ o adding allowInteriorFreezing option to check for water below freezing point
+   at depth and bring the negative heat anomaly to the surface level
+ o pkgs _fields_load:
+   - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
+   - use new S/R GET_PERIODIC_INTERVAL in pkgs:
+     bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
+     rbcs to get interpolation weights and time reccord number.
+   - fix multi-threading in aim_fields_load.F
+   - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
+ o external_fields_load:
+   new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
+    interpolation weights) to use in a periodic time-series ; do not divide by
+    time-step to convert to integer:
+    - this fixes case where externForcingPeriod is not multiple of time-step
+       (Thanks to Christopher L. Wolfe)
+    - this fixes case where externForcingPeriod is an odd multiple of time-step
+      (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
+   store index of time-record which is currently loaded:
+    - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
+    - needed for the adjoint but not yet used because of extensive recomputations;
+      (to be fixed soon)
+ checkpoint62v (2011/04/02)
+ o verification/1D_ocean_ice_column added to test Ian Fenty's
+   pkg/seaice_growth.F modifications for improving sea ice code differentiability
+ o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
+   (new velocity statistics after changing maskInW & maskInS definition)
+ o pkg/generic_advdiff with OBCS:
+   use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
+   equivalent to assumption of no tracer gradient outside the OB region.
+   This will affect the results if using obcs+biharmonic diffusion.
+   update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
+ o pkg/obcs:
+   change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
+   (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
+   in Interior region. No impact on solution but affects Velocity monitor stats.
+ o pkg/ptracers (adjoint)
+   New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
+   tape file for each tracer
+ o model/inc/src and pkg/autodiff: add parameters that allow to turn
+   of parts of the adjoint code at run time. For now, there are only
+   useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
+   parameters are set in data.pkg.
+   This is the lazy coward's version of doing this, but still useful for
+   debugging. In order to do it right, everything needs to be moved to
+   pkg/autodiff.
+ o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
+   the end; this fixes the adjoint balancing code for open boundaries.
+ 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
+ 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
-Line 18 
 o adjoint store dir. adjusted accordingl
+Line 2847 
 o adjoint store dir. adjusted accordingl
  o genmake2
    replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
- checkpoint58i_post
+ 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
-Line 32 
 o pkg/seaice: added SEAICEuseEVPpickup p
+Line 2861 
 o pkg/seaice: added SEAICEuseEVPpickup p
      non-EVP pickup files when using SEAICEuseEVP
    - fix sign error in diffusion in seaice_calc_rhs
- checkpoint58h_post
+ 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
-Line 42 
 checkpoint58h_post
+Line 2871 
 checkpoint58h_post
    o works for 5x5 box, doesnt work for global_ocean.90x40x15
  * Adding verification for 5x5 box (4-layer) bottom topography control
- checkpoint58g_post
+ 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
-Line 58 
 o couple pkg/thsice to pkg/seaice:
+Line 2887 
 o couple pkg/thsice to pkg/seaice:
  o pkg/seaice
    - make (default) second order advection a bit less confusing?
- checkpoint58f_post
+ 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
-Line 89 
 o fix bug in aim+thsice albedo: snow & i
+Line 2918 
 o fix bug in aim+thsice albedo: snow & i
  o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
    testreport accordingly
- checkpoint58e_post
+ 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/ )
-Line 97 
 o R_STAR adjoint implemented.
+Line 2926 
 o R_STAR adjoint implemented.
  o Make pkg/profile fully independent of ecco,cost, etc. stuff
    to be able to use it in pure forward.
- checkpoint58d_post
+ 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)
-Line 137 
 o new package prifiles:
+Line 2966 
 o new package prifiles:
  o Benign bug fix in initialization (spotted by M. Mazloff) of
    ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
- checkpoint58c_post
+ 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
-Line 171 
 o seaice:
+Line 3000 
 o 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
+ 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:
-Line 234 
 o seaice:
+Line 3063 
 o seaice:
      (turn on with SEAICEuseFluxForm)
    - replace 1 in 3d global fields by kSurface in growth.F
- checkpoint58a_post
+ checkpoint58a_post (2006/02/13)
  o seaice:
    - bug fix in advect.F
  o shelfice:
-Line 287 
 o pkg/bulk_force:
+Line 3116 
 o pkg/bulk_force:
     and parameters (note: calcWindStress replaces .NOT.readwindstress).
   - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
- checkpoint58
+ 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
-Line 300 
 o clean up 3-dim. relaxation codes:
+Line 3129 
 o clean up 3-dim. relaxation codes:
    * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
    * Thanks to Tom Haine for testing!
- checkpoint57z_post
+ 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
-Line 331 
 o Adding Laplacian-type smoothness const
+Line 3160 
 o Adding Laplacian-type smoothness const
    * Absolute scale somewhat unclear so far
    * no area weighting was included since no other cost term does so far
- checkpoint57y_post
+ 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
+ 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)
-Line 346 
 o cfc fixes for final year of integratio
+Line 3175 
 o cfc fixes for final year of integratio
  o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
    be in GCHEM_OPTIONS).
- checkpoint57x_post
+ 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)
-Line 366 
 o adjoint
+Line 3195 
 o adjoint
      (there are a number of extensive recomputations)
    * Initialize certain variables needed for adjoint
- checkpoint57w_post
+ 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.
-Line 383 
 o PTRACERS: added namelist parameter PTR
+Line 3212 
 o PTRACERS: added namelist parameter PTR
    ptracers in a large domain with a constant non-zero value. Also,
    untangle ptracers_init.F a little.
- checkpoint57v_post
+ 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
-Line 424 
 o reduce number of exch calls in shap_fi
+Line 3253 
 o reduce number of exch calls in shap_fi
  o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
    truncation level) 4/5 MLAdjust test results (11&12 digits match).
- checkpoint57t_post
+ 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
-Line 447 
 o Clean, new version of mom_calc_visc.
+Line 3276 
 o Clean, new version of mom_calc_visc.
    Suggested values of viscosity parameters found in mom_calc_visc.
    Many new viscosity diagnostics available.
- checkpoint57s_post
+ 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
-Line 473 
 o various changes to mnc including:
+Line 3302 
 o various changes to mnc including:
        and works with both EXCH1 and EXCH2 (but needs more testing)
    - writing works for all verification test cases w/ g77 on Linux
- checkpoint57r_post
+ 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.
-Line 493 
 o new infrastructure for seaice model vs
+Line 3322 
 o new infrastructure for seaice model vs
  o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
    (see README file)
- checkpoint57q_post
+ 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
-Line 510 
 o Modifications to enable scripted COMMO
+Line 3339 
 o Modifications to enable scripted COMMO
    * verification/OpenAD/code/ has necessary scripts and description;
    * converts, compiles and runs successfully;
- checkpoint57p_post
+ 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)
-Line 524 
 o Dissipation & phiHyd gradient are alwa
+Line 3353 
 o Dissipation & phiHyd gradient are alwa
    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
+ 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
-Line 533 
 o set to #undef CTRL_SET_OLD_MAXCVARS_30
+Line 3362 
 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
+ 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.
-Line 549 
 o enable useSingleCpuIO for mdsio vector
+Line 3378 
 o enable useSingleCpuIO for mdsio vector
    (applies in particular to tapelev I/O)
  o removed inefficient K-loop in all active_file*control*.F
- checkpoint57m_post
+ 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
+ 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)
-Line 567 
 o fix aim_diagnostics_init.F mate number
+Line 3396 
 o fix aim_diagnostics_init.F mate number
  o add mnc output capability to diagnostics/diagstat and update
    our cvsignore files for the ACSII output generated
- checkpoint57k_post
+ checkpoint57k_post (2005/07/02)
  o lab_sea now uses diagnostics package and provides a suite of
    new EXF diagnostics output.
- checkpoint57j_post
+ 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);
-Line 601 
 o fix bug in rStar code (calc_r_star.F)
+Line 3430 
 o fix bug in rStar code (calc_r_star.F)
  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
+ 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 ;
-Line 620 
 o pkg/diagnostics:
+Line 3449 
 o pkg/diagnostics:
    tested against monitor output (including land & thSIce) on various exp.
  o make seaice-pkg I/O type flags (MNC/MDS) more standard.
- checkpoint57h_done
+ checkpoint57h_done (2005/05/19)
    tag after changing user customized files (DIAGNOSTICS_SIZE.h,
    data.diagnostics, data.gchem, data.ptracers) is done.
-Line 629 
 o pkg/diagnostics: prepare for Global/Re
+Line 3458 
 o pkg/diagnostics: prepare for Global/Re
  o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE
    and rename it: DIFFERENT_MULTIPLE
- checkpoint57h_post
+ 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
+ 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
-Line 647 
 o test AB-3 code with 4th.Order advectio
+Line 3476 
 o test AB-3 code with 4th.Order advectio
  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
+ 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
+ checkpoint57g_pre (2005/04/15)
  o make lambda[Theta,Salt]ClimRelax spatially varying
    (default remains spatially uniform constant based on tau)
-Line 661 
 o added new control variables
+Line 3490 
 o added new control variables
  o separate masks used for ctrl_pack/unpack 'from write_grid' output
    (suggested by G. Forget)
- checkpoint57f_post
+ 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
+ checkpoint57f_pre (2005/04/06)
  o mnc-ifying the seaice package
  o introduced an alternative length scale calculation for use in the limiting
-Line 687 
 o adjoint-related modifications
+Line 3516 
 o adjoint-related modifications
    * 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
+ checkpoint57e_post (2005/02/28)
  o Adding eddy stress controls a la Ferreira et al.
  checkpoint57e_pre (actually was tagged: eckpoint57e_pre)
-Line 705 
 o diagnostics: add pickup functionality
+Line 3534 
 o diagnostics: add pickup functionality
  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
+ 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
-Line 727 
 o move state variable diagnostics to the
+Line 3556 
 o move state variable diagnostics to the
    (note: still needs some work specially for snap-shot diagnostics)
    duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z
- checkpoint57c_post
+ 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
+ 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
-Line 763 
 o pkg/mdsio/
+Line 3592 
 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 809 
 o re-arrange diagnostics pkg initialisat
+Line 3638 
 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 836 
 o untangle a few ifdefs related to cost,
+Line 3665 
 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 854 
 o exf:
+Line 3683 
 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 869 
 o testreport previously did a lousy job
+Line 3698 
 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 914 
 o GCHEM:
+Line 3743 
 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 944 
 o mdsio: filename info to both stderr, s
+Line 3773 
 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 955 
 o make all subroutines 30 or less charac
+Line 3784 
 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 970 
 o give MNC the ability to create additio
+Line 3799 
 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 978 
 o allow to set a vertical profile of ver
+Line 3807 
 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 988 
 o Fixing directives for non-ECCO forward
+Line 3817 
 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 999 
 o some delicate re-shuffle of store dire
+Line 3828 
 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 1054 
 o more obcs stuff
+Line 3883 
 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 1068 
 o obcs stuff
+Line 3897 
 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 1079 
 o use a more standard discretization for
+Line 3908 
 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 1087 
 o merged code to
+Line 3916 
 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 1097 
 o up-to-date adjoint of previous breaks
+Line 3926 
 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 1123 
 o overhaul of IO so that we now have fla
+Line 3952 
 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 1153 
 o fix a bug in Flux deriv. vs Ts (pkg/ai
+Line 3982 
 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 1164 
 o define the max number of passive trace
+Line 3993 
 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 1174 
 o staggerTimeStep & NLFS: rescale T & S
+Line 4003 
 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 1195 
 o new parameter "nShapS": allow to treat
+Line 4024 
 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 1208 
 o merged cylindrical coord configuration
+Line 4037 
 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 1227 
 o regenerated output for global_ocean_eb
+Line 4056 
 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 1246 
 o Adjoint of EBM package + verification
+Line 4075 
 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 1264 
 C        Destabilization of the thermoha
+Line 4093 
 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 1272 
 o pkg/land: only liquid water can diffus
+Line 4101 
 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 1285 
 o Fixed verification/natl_box_adjoint ex
+Line 4114 
 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 1295 
 o stable checkpoint with up to date adjo
+Line 4124 
 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 1326 
 o fix in pkg/thsice:
+Line 4155 
 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 1358 
 o test exp. advect_cs: use the standard
+Line 4187 
 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 1369 
 o aim_v23 modification for new land mode
+Line 4198 
 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 1382 
 o fix ini_curvilinear_grid ; test CS exp
+Line 4211 
 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 1395 
 o set all ...Freq to zero after cost_fin
+Line 4224 
 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 1403 
 o Really weird thing!
+Line 4232 
 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 1420 
 o merged mom_vi_calc_relvort3.F, mom_vi_
+Line 4249 
 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 1439 
 o added temporary hack for sea-ice dynam
+Line 4268 
 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 1453 
 o step.1 : rewrite (as in MultiDimAdvec)
+Line 4282 
 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 1464 
 o added exf_offset_atemp for Celsius to
+Line 4293 
 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 1493 
 o check-in the first version of the coup
+Line 4322 
 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 1511 
 o Removed all CPP options for cal packag
+Line 4340 
 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 1519 
 o new version: "thsice" of thermodynamic
+Line 4348 
 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 1529 
 o missing PTRACERS headers in some routi
+Line 4358 
 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 1544 
 o fix problem with ECCO-related divided
+Line 4373 
 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 1565 
 o top level routines the_main_loop, forw
+Line 4394 
 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 1577 
 o pkg/grdchk
+Line 4406 
 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 1598 
 o ctrl package totally restructured
+Line 4427 
 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 1613 
 o create initial cd_code package
+Line 4442 
 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 1634 
 o Correcting initialisations for fVerU,
+Line 4463 
 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 1642 
 o added the [#include "AD_CONFIG.h"] sta
+Line 4471 
 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 1651 
 o modifications to make FREEZE flux visi
+Line 4480 
 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 1659 
 o added [#include "AD_CONFIG.h"] to all
+Line 4488 
 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 1692 
 o added an include barrier to the defaul
+Line 4521 
 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 1706 
 o Moving pkg-specific flow directives to
+Line 4535 
 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 1724 
 o modify gchem pkg to be more versatile
+Line 4553 
 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 1732 
 o update AD-related stuff
+Line 4561 
 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 1749 
 o Bug fix to pkg/ptracers, pkg/generic_a
+Line 4578 
 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 1759 
 o atmospheric geopotential: - include wa
+Line 4588 
 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 1772 
 o Use cluster local disks for purely loc
+Line 4601 
 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 1795 
 o added verification for adjoint with pt
+Line 4624 
 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 1810 
 o merged improved packages from ecco-bra
+Line 4639 
 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 1826 
 o New variable in PARM03 for more flexib
+Line 4655 
 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 1840 
 o exf totally restructured
+Line 4669 
 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 1850 
 checkpoint50f_pre
+Line 4679 
 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 1889 
 o new flag "useCDscheme" (default=F); re
+Line 4718 
 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 1909 
 checkpoint50
+Line 4738 
 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 1947 
 o DIVA:
+Line 4776 
 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 1965 
 o Modif. for DIVA:
+Line 4794 
 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 1985 
 o accurate phiHyd when using interface-W
+Line 4814 
 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 2013 
 o pkg/seaice:
+Line 4842 
 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 2024 
 o following exp works with Olx=Oly=2 (an
+Line 4853 
 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 2032 
 o in preparation for r*:
+Line 4861 
 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 2081 
 o Yet more changes in gmredi:
+Line 4910 
 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 2097 
 o case GM_BOLUS_ADVEC should be cleaned
+Line 4926 
 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 2123 
 Gradient checks OK for
+Line 4952 
 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 2135 
 o modifications for using pkg/exf with p
+Line 4964 
 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 2159 
 o OCEANICP & realFreshWater: include P-E
+Line 4988 
 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 2176 
 o verification/lab_sea
+Line 5005 
 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 2193 
 o bulk_force and therm_seaice
+Line 5022 
 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 2222 
 o Updated verification/carbon/
+Line 5051 
 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 2276 
 o Adding new verification experiment glo
+Line 5105 
 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 2289 
 o introduced flag for controllin non-hyd
+Line 5118 
 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 2302 
 o made convective adjustment work with p
+Line 5131 
 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 2318 
 o S/R aim_initialise.F replace S/R aim_i
+Line 5147 
 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 2341 
 o introduced new parameter rhoConstFresh
+Line 5170 
 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 2365 
 o cleaned up find_rho
+Line 5194 
 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 2375 
 o Enable tangent linear (forward mode) g
+Line 5204 
 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 2384 
 o Added new equation of state -> MDJWF
+Line 5213 
 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 2416 
 o Added UNESCO EOS, but not recommended
+Line 5245 
 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 2453 
 o added hooks for Eliassen Palm fluxes (
+Line 5282 
 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 2467 
 o add new flags:
+Line 5296 
 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 2475 
 o modifications to gradient check packag
+Line 5304 
 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 2487 
 o in initialise_varia, moved call packag
+Line 5316 
 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 2507 
 o errorMessageUnit set non-equal zero in
+Line 5336 
 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 2578 
 o merge of relevant stuff from the ecco-
+Line 5407 
 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 2586 
 o update AIM experiments (NCEP input fil
+Line 5415 
 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 2604 
 o Modified store directives for split of
+Line 5433 
 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 2617 
 o more mods for non-linear free-surface
+Line 5446 
 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 2627 
 o changes to commenting of arguments for
+Line 5456 
 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 2646 
 o TAMC-related update to cope with mom_f
+Line 5475 
 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 2661 
 o corresponding split of calc_diffusivit
+Line 5490 
 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 2675 
 o added new expt "solid-body.cs-32x32x1"
+Line 5504 
 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 2683 
 o extended iMin,jMin range for calc_comm
+Line 5512 
 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 2708 
 checkpoint39
+Line 5537 
 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 2716 
 checkpoint38
+Line 5545 
 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 2733 
 checkpoint37
+Line 5562 
 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 2756 
 checkpoint34
+Line 5585 
 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 2774 
 checkpoint33
+Line 5603 
 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 2785 
 checkpoint32
+Line 5614 
 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 2802 
 checkpoint31
+Line 5631 
 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 2811 
 checkpoint30
+Line 5640 
 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 2827 
 checkpoint28
+Line 5656 
 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 2835 
 checkpoint27
+Line 5664 
 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 2845 
 checkpoint26
+Line 5674 
 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 2856 
 checkpoint25
+Line 5685 
 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 2889 
 checkpoint19
+Line 5718 
 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 2908 
 checkpoint16
+Line 5737 
 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 2917 
 checkpoint15
+Line 5746 
 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 2936 
 branch-point-rdot
+Line 5765 
 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 2966 
 checkpoint7-4degree-ref
+Line 5795 
 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 2974 
 checkpoint7
+Line 5803 
 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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