--- MITgcm/doc/tag-index	2010/04/13 07:00:08	1.1249
+++ MITgcm/doc/tag-index	2011/05/18 02:21:49	1.1435
@@ -1,12 +1,877 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1249 2010/04/13 07:00:08 gforget Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1435 2011/05/18 02:21:49 jmc Exp $
 $Name:  $
 
     Notes on tags used in MITgcmUV
     ==============================
 
-o exf:
+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.:
+   1D_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
+    4th 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
+   1rst 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 
+    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:
@@ -79,8 +944,8 @@
     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
+     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