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-revision 1.1230 by gforget,
Wed Feb 17 00:54:35 2010 UTC
+revision 1.1543 by mmazloff,
Tue Dec  6 04:19:24 2011 UTC
 Line 4 
 $Name$
      Notes on tags used in MITgcmUV
      ==============================
+ o pkg/ecco
+   - added IES cost term
+ o verification/advect_xz
+   - scale down the depth by 1/100 (from 200 km to just 2.km)
+   - add secondary test using divergent flow, r-star and implicit vertical advection.
+ o pkg/rbcs:
+   - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
+ o pkg/obcs (Stevens BCs):
+   - fix various problems in the phase speed computations of the Stevens
+     boundary conditions:
+     - sign error for western and southern boundaries,
+     - time tendencies were underestimated by factor of dTracerLev and some just
+       zero (for multidim advection schemes) -> now estimate time tendencies
+       from difference between previous (n) time level and the one before (n-1);
+       this requires storing a field per tracer per boundary, also in the pickup
+       files.
+     - replace deltaTmom in cflMer/Zon computation with dTracerLev
+     - set default phase velocity to cflMer/Zon
+   - update verification experiment exp4.stevens
+ o pkg/generic_advdiff (implicit_r):
+   - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
+     (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
+   - fix implicit vertical diffusion or advection with NonLin FreeSurf
+     (was using current recip_hFacC instead of future recip_hFacC): set future
+     recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
+     solver S/R ;
+   - fill diagnostics of vertical advective fluxes (computed from tendency)
+     when using implicit vert. advection;
+   - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
+      global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
+      tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
+      and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
+ o pkg/diagnostics:
+   - add diags for T & S tendency which goes through Adams-Bashforth.
+ checkpoint63f (2011/11/30)
+ o pkg/obcs/obcs_calc_stevens.F:
+   - join some loops to reduce number of if-statements
+   - fix a bug in code for northern and southern boundaries.
+ o pkg/seaice/seaice_init_varia.F
+   - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
+     caused zero ice-velocities for the B-grid code
+ o pkg/seaice/seaice_init_fixed.F
+   - fix a bug in the initialisation of the second metric terms
+     k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
+   - this affects all seaice configurations with useCurviLinearGrid = .true.
+     and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
+     = .true. (default)
+   - the only verification experiment affected is global_ocean.cs32x15:
+     icedyn, seaice, and seaice_dynmix (AD)
+ o pkg/thsice/thsice_diagnostics_state.F
+   - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
+     not contain garbage that can lead to surprises in diagstats_calc.F
+ o model/src:
+   - move bi,bj loops inside INTEGR_CONTINUITY ;
+   - call INTEGR_CONTINUITY directly from forward_step.F
+     (previously called from momentum_correction_step.F)
+   - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
+     forward_step.F and pkg/ecco/the_main_loop.F
+ o model/src/do_oceanic_phys.F:
+   - reset addMass to zero only if useICEFRONT ;
+   - separated k-loop for rhoInSitu calculation ;
+   - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
+     and at constant T,S (= WdRHOdP);
+   NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
+     of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
+     transport of locally-referenced potential density);
+     to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
+ o gluemnc:
+   - replace ncrcat with ncks when adding variables to *.glob.nc
+   - change the way variables without record dimensions are handled so that
+     files that have variables with and without record variables can be glued:
+     add a record dimension with a new unique name to be able to differentiate
+     between variable with and without a-prior record dimensions. Remove
+     this record dimension before adding the variable to the *.glob.nc file.
+     This procedure automatically works also for grid.*.nc files that do not
+     have any record dimension.
+ o verification/cpl_aim+ocn:
+   - generate new reference output on baudelaire (gfortran, mpich2) (previously
+     from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
+ o pkg/obcs/obcs_calc_stevens.F:
+   - add code for northern and southern boundaries.
+   - reorder some loops to save some operations and so that drFBar can be scalar
+ o model/src:
+   - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
+     truncation) and add diagnostics for Adams-Bashforth tendency increment.
+   - update test-exp. AD output:
+D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
+   and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
+     front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
+     global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
+     matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
+     tutorial_global_oce_in_p, tutorial_global_oce_latlon and
+     tutorial_plume_on_slope.
+ o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
+   that vectorises. This code uses 3 extra 2D fields, F90 array assignments
+   and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
+   does not even come with an F77 compiler anymore, this should not be
+   a limitation
+ checkpoint63e (2011/11/06)
+ o pkg/seaice adjoint of LSR:
+   - substantially rework STORE dirs.
+   - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
+     this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
+     and only perform SOLV_MAX_FIXED adjoint iters.
+     If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
+     always goes to same record, meaning that the last forward field will be
+     the one used in the adjoint - an approximation.
+   - now produces non-zero LSR-related gradients, and acceptable gradients for
+     An's zonal (x-z) test case (to be checked in)
+   - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
+     (but these are screwed up by the thermodynamics in the first place);
+     reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
+     output_adm.txt also reflects changes to seaice_lsr
+   - global_ocean.cs32x15:
+     * the "default" input_ad.seaice has been re-defined to always exclude dynamics
+       (output_adm.seaice.txt was updated)
+     * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
+       (output_adm.seaice_dynmix.txt)
+ o test-exp. exp4+stevens:
+   - switch off pTracers and nonHydrostatic (restart problems with NH); update output
+ o pkg/seaice (lsr solver):
+   - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
+     update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
+   - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
+   - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
+     into initial guess for linearised solver; use weight ~ (1/err)^2,4.
+   - compute (with new S/R) and print initial (+ free-driff sol. if available)
+     and final residual of linearised system.
+ o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
+   (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
+ o pkg/obcs: Stevens BCs (still only for east and west)
+   - fix Stevens BCs by using intermediate velocities of previous
+     time step as "baroclinic" contribution rather velocity of one grid cell
+     inside the boundaries; more consistent but makes the entire treatment
+     more complicated, requires new pickup files and two new S/Rs:
+     obcs_copy_uv_n and obcs_save_uv_n
+     keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
+     (undefined by default)
+   - silently move computation of some grid factors into separate loops to
+     save some recomputations
+   - add a hack for non-linear free surface
+   - add a verification experiment to exp4 that tests this code
+ o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
+ checkpoint63d (2011/10/25)
+ o pkg/obcs + seaice-dynamics:
+   - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
+     solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
+     values (consistent with an implicit method).
+   - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
+     return to older implementation (same results as before); note that none of
+     the "experimental" OBCS_SEAICE options are implemented in the new version.
+   - switch test exp. seaice_obcs to use new version (update output).
+ o pkg/seaice:
+   - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
+   - add parenthesis in Water-Ice drag calculations (evp & lsr);
+   - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
+     and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
+   - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
+     and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
+ o pkg/layers:
+   - Include potential density as new coordinate (Thanks to David Munday)
+ o pkg/dic:
+   - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
+     carbonate computation/output to CALC_PCO2_APPROX
+ o pkg/generic_advdiff
+   - make TAF generate code that vectorizes:
+     gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
+ o model/src:
+   - improve vectorization also for adjoint code of
+     solve_tridiagonal and solve_pentadiagonal. As this requires up to
+new 3D-fields, this code is only turned on for the combination of
+     ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
+     for singular matrix check (only for TARGET_NEC_SX).
+   - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
+     ALLOW_AUTODIFF. This flag now needs to be set outside of
+     solve_tri/pentadiagonal.F
+ o pkg/exf:
+   - fix previous modif in exf_readparms.F (revision 1.66: treatment of
+     optional namelist EXF_NML_OBCS).
+   - add many debug-print (to trace down where pkg/cal error msg comes from)
+ o pkg/mom_vecinv/mom_vi_hdissip.F
+   - rearrange loops so that vectorization is improved and in particular
+     the adjoint routine vectorizes. The code is a little longer now, but I
+     think easier to read.
+     Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
+ o pkg/seaice:
+   - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
+ o pkg/exch2:
+   - alternative code (without tile x tile matrix) for cumulated (global) sum;
+     used as default; keep using matrix version in adjustment.cs-32x32x1.
+ o tools/build_options:
+   - after merging some MPI and/or multi-threads specific optfiles so that
+     the modified default optfile support both built (using genmake2 -mpi
+     for the MPI built, using genmake2 -omp for OpenMP built),
+     move now obsolete optfiles to tools/build_options/unsupported/
+    (add copy of email sent to support list in doc/optfiles_changes.txt)
+ checkpoint63c (2011/09/28)
+ o pkg/ebm:
+   - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
+     test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
+ o pkg/seaice (SItracer pickup)
+ * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
+   To be done:
+   - thorough testing of missing fields in S/R seaice_read_pickup
+   - thorough matching between generic tracers and specific fields used
+     (e.g. volume-weighted age, area-weighted age, salinity, ...)
+ o pkg/grdchk:
+   - all procs calculate and print finite-difference gradient (for testreport)
+   - change description output used by testreport;
+   - AD testing: also compare and report Finite-difference gradient;
+     => update all output_adm*.txt
+ o test exp. global_ocean_ebm:
+   - switch back useRealFreshWaterFlux (no problem anymore with run-off);
+     and turn on exactConserve; update (fwd) output.
+ o pkg/seaice (LSR):
+   - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
+   - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
+     * identical results with non-CS topology (but save up to half of EXCH calls)
+     * no much changes in cs-32 verification tests since no ice at face edges
+      (differences due to convergence criteria, since nb of iterations changed)
+     * expect some differences on lat-lon-cap grid.
+     update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
+ o pkg/exch2:
+   - add new CPP option to disable Cumul-Sum matrix (to save storage when using
+     many tiles); until alternative coding is added, just add a stop.
+ o pkg/kpp:
+   - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
+     to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
+ o optfiles:
+   - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
+     into corresponding standard one, which now support different build:
+     (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
+   - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
+ o pkg/obcs (seaice):
+   - add missing EXCH for uIce,vIce after applying OBCS;
+   - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
+     argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
+     EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
+   - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
+   - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
+     and eedata.mth for MPI and mutlti-threaded testing.
+ o pkg/flt:
+   - make FLT EXCH working with multi-threads (and MPI + multi-threads);
+   - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
+   - fix pickup and trajectories + profiles output with multi-threads;
+   - add parameter to select group of fields to write along trajectory and
+     profile (default unchanged);
+   - only call PORT_RAND* function when flt_noise <> 0;
+   - add multi-threaded test for verification exp. flt_example.
+ o eesupp/src:
+   - fix S/R ALL_PROC_DIE for MPI+multi-threads.
+   - USE_OMP_THREADING: check that number of threads (from eedata) matches
+     actual number (from env.var. setting).
+ o pkg/ebm:
+   - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
+   - add multi-threaded test for verification exp. global_ocean_ebm
+ checkpoint63b (2011/08/29)
+ o pkg/ebm:
+   - fix sign of runoff;
+   - update directly forcing fields (Qnet,EmPmR) to use standard
+     external_forcing_surf.F (remove ebm_forcing_surf.F);
+   - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
+   - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
+     and apply relaxation towards corresponding SST field (2-D map or ZonAver).
+   - update global_ocean_ebm parameters file data and update output (fwd+ad).
+ o verification/matrix_example:
+   - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
+     MPI and mutlti-threaded testing.
+ o pkg/matrix:
+   - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
+   - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
+   - fix for multi-threaded (remove DATA statement);
+   - use standard DIFFERENT_MULTIPLE function;
+   - add MATRIX_OPTIONS.h
+ o verification/matrix_example:
+    To allow to split the domain in several tiles, change the domain size
+     from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
+     Western side) of land points.
+ o (*_)write_pickup:
+   - fix few bugs in mypackage_read/write_pickup.F
+   - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
+     array of length 1 (was caught by compiler syntax-check).
+ o pkg/diagnostics (velocity potential solver):
+   - fix initialisation of main diagonal matrix (for overlap values)
+ o tools/build_options:
+   - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
+     into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
+   - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
+     * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
+     * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
+     and use "-devel" testreport option for standard testing on baudelaire.
+ o pkg/grdchk:
+   - Assume that all gradient-check position are within the same tile
+     corresponding to global indices (iGloTile,jGloTile) and that
+     positions (i,j indices or nbeg) are local to this tile;
+   - set tile local-indices and proc. number according to tile global-indices;
+   - remove grdchkwhichproc from namelist (retired param);
+   - send adjoint gradient to all procs so that all procs print it to STDOUT;
+   - switch on MPI test for global_ocean.90x40x15 AD test experiment.
+ o adding package bbl (Bottom Boundary Layer)
+   description in MITgcm/pkg/bbl/bbl_description.tex
+   example/test experiment in MITgcm_contrib/bbl
+ o adjoint verifications
+   - changed 5 experiments to multi-tiles
+     * global_ocean.90x40x15
+     * obcs_ctrl
+     * offline_exf_seaice
+     * tutorial_dic_adjoffline
+     * tutorial_tracer_adjsens
+     changed reference output for those that crossed tile boundaries
+     (changed choices of gradient check positions)
+   - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
+   - temporary bug fix in grdchk_loc.F for obcs
+ o genmake2 & testreport
+   - add target "obj" (just for OBJFILES files) to Makefile;
+   - add option to specify FEXTRAFLAGS on command line.
+ o pkg/mypackage:
+   - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
+ checkpoint63a (2011/08/02)
+ o pkg/diagnostics (velocity potential):
+   - fix velocity-potential calculation when using OBCS: balance net inflow
+     at each level (new S/R OBCS_DIAG_BALANCE).
+   - fix some of the problems with OBCS in stream-function calculation.
+ o pkg/exf/exf_readparms.F
+   - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
+     EXF_NML_OBCS) more consistent, so that you need not have these lists
+     in data.exf when they are not used.
+ o optim/optim_readdata.F:
+   - add some output about obcs variables that might help debugging
+   - add a check about nvarlength
+ o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
+ o pkg/diagnostics (velocity potential):
+   - fix mask for OBCS (still problems in stream-function with OBCS);
+   - add specific parameter (default = main code CG2D params) for solver;
+   - in case of poor convergence, use solution corresponding to lowest residual.
+ o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
+   adjoint code. In general statements like tmpscal=fld(i,j) are problematic
+   and should be avoided where possible.
+ o model/src (rStar):
+   - include r* effect on reference-state (PhiRef) in totPhiHyd
+     (so that it's really the potential anomaly at the cell center);
+     affect solution only if z* with full pressure in EOS.
+   - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
+     update output (because of z* in totPhiHyd and viscA4 changes);
+   - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
+     @ constant r) until interpolation at constant r is implemented.
+ o pkg/diagnostics
+   - fix RCENTER diagnostics in case cell center is not at interface middle
+ o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
+   this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
+   that THETA and SALT are "conservative temperature" and "absolute
+   salinity"
+ o pkg/ctrl
+   - fix computation of endrec in s/r ctrl_init_rec
+   - ctrl_pack/unpack_*: remove unused variables and some obsolete code
+ o pkg/seaice/seaice_growth.F
+   - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
+     remove then obsolete STORE directives
+   - fix STORE directives for tice and tices, so that only the
+     appropriate part of the fields are stored (and not the entire
+     field); update global_ocean.cs32x15.seaice AD output.
+   - cosmetic changes: adjust CPP flags and indentation for better
+     legibilty
+ o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
+   Chris Wilson)
+ o pkg/gmredi:
+    Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
+    and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
+ checkpoint63  (2011/07/11)
+ o pkg/exch2:
+  - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
+  - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
+    (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
+    increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
+ o pkg/diagnostics:
+  - deal with pairs of post-processed diags which are computed together; in
+    particular, re-order list of diags within 1 file to save 2nd computation.
+  - add S/R to compute velocity stream-function (called after velocity-potential
+    calculation) from divergence free transport -> new diagnostics "PsiVEL".
+  - add parameter to select grid-point location where PsiVEL == 0.
+ o eesupp/src:
+    new S/R to calculate cumulated sum on tiled array, corner grid-cell location
+    (specific S/R needed with exch2 topology - for now, just print an error msg)
+ o pkg/shelfice
+  - Implement friction velocity-dependent transfer coefficients following
+    Holland and Jenkins, JPO, 1999
+    Original code by M. Losch with small modifs.
+    Enable with CPP option SHI_ALLOW_GAMMAFRICT
+    and runtime flag SHELFICEuseGammaFrict
+ o verification lab_sea & global_ocean.cs32x15:
+  - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
+    does not miss some dependencies (but is slower) and also works with many files
+    (default makedepend limitation for AD built).
+  - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
+ o pkg/diagnostics:
+  - add run-time parameter "useMissingValue" (def=False) to fill land-point
+     (i.e., where mask=0) with MissingValue ; used only in MNC output file.
+    This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
+  - Extend the use of "missing_value" setting from data.diagnostics for the case
+    of counter-diagnostics (where fraction-weight is zero). This applies both to
+    MNC and MDS output files.
+ o pkg/seaice/seaice_growth.F:
+   - add 'a priori' cap of latent heat flux based on actual mass considerations
+     when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
+     non-legacy seaice_solve4temp.
+   - add diagnostic of the residual sublimation freshwater flux (the freshwater
+     flux taken from the ocean if the total actual latent heat fluxes exceed
+     the maximum)
+   - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
+    fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
+   - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
+    SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
+   - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
+   - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
+ o verification 1D_ocean_ice_column:
+    made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
+    update results
+ o pkg/diagnostics:
+  - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
+    which are not filled-up but computed from other diags ; In this case, the mate
+    diag points to the primary (filled-up) diag to used for post processing.
+  - Update Velocity-potential computation using post-processed diag framework.
+  ==> Change the ordering of fields and time-periods in MDS output file
+    when using periodic averaging: now writes one time record with the full set
+    of fields for this time period, then the next time reccord (it used to be
+    one field with the full set of time records then the next field).
+      Note: this is now similar to NetCDF (MNC) output file. <==
+ checkpoint62z (2011/06/21)
+ o adjoint monitor:
+  - Add adjoint monitor output for packages exf, seaice
+    and update relevant testreport output
+ o pkg/seaice:
+  - re-order diags inits so that they appear in order in available_diagnostics.log
+  - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
+    area/heff/hsnow preceeding thermodynamic growth/melt.
+  - modified diag: SIdA; output actual effect, as the description states.
+  - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
+  - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
+    (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
+     and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
+  - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
+  - added diagnostics for seaice generic tracers (SItr*).
+  - added SItrUnit and SItrNameLong run time param (for SItr* diags).
+  - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
+  I. Fenty: 18-Jun-2011:
+  Minor changes to seaice package:
+) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
+     added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
+    - Differentiated "regularization variables" from "floor variables"
+     * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
+     * hiceMin became SEAICE_hice_reg (old hiceMin)
+       (with _reg meaning regularization variable)
+    - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
+     so as to ensure energy conservation when going between phases
+   - A22 was not used anywhere
+) Changed regularization procedure for heffActual and hsnowActual to ensure
+     well-boundedness and smooth adjoint in seaice_growth.F
+) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
+     because the old regularization always set heffActual >= 0.05 cm
+) Changed the model so that the default behavior is to put a small (10^-5) "floor"
+     on AREA when HEFF > 0.
+   - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
+     requiring that DISABLE_AREA_FLOOR *not* be defined
+  Affected verifications:
+   - 1D_ocean_ice_column (output.txt output_adm.txt)
+   - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
+ o pkg/diagnostics:
+   - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
+   - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
+     (was _RL, now integer) with option = 0 to retrieve all levels.
+   - add pieces of code to compute velocity potential at each level (new diagnostics
+     PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
+     for now, using same params as CG2D (target-resisual, max Nb of iter ...).
+   - fix few issues with counter diagnostics in diagnostics_setdiag.F &
+     diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
+     and in diagnostics_fract_fill.F (do not need a valid pointer for the
+     diagnostics counter-mate); check that definition of counter-diagnostic
+     includes a valid counter-mate (in diagnostics_set_levels.F).
+ o model/src (rStar):
+   - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
+     affect solution only if z* with full pressure in EOS;
+     update output of test-exp global_ocean.90x40x15.
+ o pkg/seaice:
+   - introduce siEps=1e-5 parameter
+   - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
+   - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
+   - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
+     For now it covers, and was tested for, ice salinity and age (attached to HEFF),
+     as well as ice cover age and ridging index (attached to AREA).
+     For now the run time parameters (in data.seaice/SEAICE_PARM03) are
+     SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
+     Up to SItrMaxNum=3 tracers can be used simultaneously.
+ o pkg/salt_plume:
+   -introduce SPsalFRAC run time parameter that sets the fraction of the
+    salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
+    that gets vertically redistributed (fluxed down) by pkg/salt_plume.
+ o model debug options:
+   - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
+     in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
+   - Refine debug-msg printing selection (3 new levels):
+     debugMode  : controls printing of debug messages (sequence of S/R calls).
+     debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
+      debLevZero =  0 ; /* level of disabled aux. msg printing */
+      debLevA =  1 ; /* level of minimum  aux. msg printing */
+      debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
+      debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
+      debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
+      debLevE =  5 ; /* level of extensive debug printing */
+     New debugLevel default: with default debugMode value (=F),
+       = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
+       and if debugMode=T, default debugLevel = 4 (debLevD).
+     Relation with previous settings:
+      debLevB (=2) corresponds to former debLevA (=1)
+      debLevD (=4) corresponds to former debLevB (=2)
+     Note:
+      a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
+      b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
+         to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
+   - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
+     detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
+ o pkg/obcs:
+   - change OBCSfixTopo default from True to False (should not change the results);
+     keep OBCSfixTopo=T in verification-exp. seaice_obcs.
+ o pkg/thsice:
+   - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
+nd layer seaice sublimation (unlikely to happen)
+   - use Interior mask for OBCS in thsice_advection.F (similar to what is
+     done in gad_advection & seaice_advection).
+ o adjoint:
+   bug fix spotted by Gael Forget:
+   seaice_advection and thsice_advection still had
+   legacy CPP options to avoid CS corner updates for adjoint
+ o pkg/seaice:
+   => Change some of the defaults (2011/05/29):
+      - change SEAICEuseFluxForm default (from False to True)
+      - change DIFF1 default (from 0.004 m/s to 0. m/s)
+      And print warnings if DIFF1 is not set in data.seaice and centered
+       avection scheme is used without any diffusion.
+   also:
+   - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
+   - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
+   - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
+     other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
+     #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
+   update results of test exp.:
+      lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
+          output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
+          output_adm.noseaicedyn (SEAICEuseFluxForm=T)
+      offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
+      seaice_obcs: output (SEAICEuseFluxForm=T)
+   and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
+       for standard fwd & AD lab_sea tests (to keep the same output).
+ o pkg/seaice/seaice_growth.F:
+   - use Ian Fenty's capping formulas for actual ice
+   thickness thoughout EVOLUTION branch.
+   - put treatment pathological case #2) in CPP brackets
+   (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
+   - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
+ o pkg/seaice:
+   - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
+   pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
+   also pass fac as a param, which can be 1. (to update the tendency
+   field) or the time step (to update the field itself).
+   - seaice_advdiff.F: for multidim, call seaice_diffusion with
+   e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
+   seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
+   - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
+   hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
+ o pkg/seaice:
+   diffusion with centered advection scheme (diffus.F & advect.F):
+   - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
+     to just compute the laplacian of input-field.
+   - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
+   - fix flux-form version in diffus.F to conserve tracer.
+   update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
+    machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
+ checkpoint62y (2011/05/26)
+ o pkg/seaice:
+  - seaice_growth.F : in EVOLUTION branch, always include
+    a_QSWbyATM_cover in qnet (as it should be).
+  - verification/global_ocean.cs32x15 : update results accordingly
+    (output.seaice.txt output_adm.seaice.txt).
+ o pkg/seaice + obcs:
+  - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
+    equivalent of assuming no tracer gradient outside the OB region.
+    update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
+  - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
+    after changes above);
+  - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
+    only at OB location (instead of over a band of OLx width).
+ o pkg/seaice:
+  - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
+    (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
+ o pkg/obcs:
+   - split header file "OBCS.h" into 4 separated files:
+     OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
+    Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
+      (contain no conditional statement which depends on OBCS options).
+   - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
+     to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
+ o ctrl, cost, grdchk & autodiff pkgs:
+   - make options file more standard (like other {PKG}_OPTIONS.h file but
+     with AD_CONFIG.h); clean-up some of the included header files.
+ o pkg/obcs:
+   - do not mask tracer when applying OB (tracer == 0 could generate problems)
+   - apply tracer OB values to tracer field only at OB location (instead of
+     over a band of OLx width)
+   - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
+   - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
+     obcs_apply_tloc.F & obcs_apply_sloc.F
+ o obcs in model/src:
+   - call OBCS_APPLY_W only if NonHydrostatic.
+   - call OBCS_APPLY_ETA only if NonLinFreeSurf.
+   - reset dEtaHdt and wVel to zero outside OB interior region ;
+   - leave tracer unchanged outside OB interior region: This has no effect
+     on the solution but just to prevent unrealistic tracer value outside OB.
+   - zero out velocity outside OB interior region: This has no effect on
+     the solution but just to prevent unrealistic velocity outside OB.
+ o obcs and non-lin free-surf:
+    move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
+    and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
+    + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
+    this fixes missing EXCH + get consistent eta OB value (+ fix restart).
+    update results of test-exp. exp4(nlfs).
+ o exp4 (nlfs) test-exp:
+    use OBC for Eta at Western & Eastern OB (to test prescribing Eta
+    with NonLin-FreeSurf); update output.nlfs.txt
+ 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
+    cancellation 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
-Line 12 
 o tools/build_options:
+Line 1580 
 o tools/build_options:
      but keep the former optfile for few weeks for smooth transition
  o pkg/ecco
    - allow user defined cost function contributions
-         CPP: ALLOW_USERCOST_CONTRIBUTION
+      CPP: ALLOW_USERCOST_CONTRIBUTION
-         USAGE: compute contributions in cost_usercost_all.F
+      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

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