--- MITgcm/doc/tag-index	2012/07/11 21:51:27	1.1687
+++ MITgcm/doc/tag-index	2013/04/05 21:29:21	1.1851
@@ -1,28 +1,943 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1687 2012/07/11 21:51:27 gforget Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1851 2013/04/05 21:29:21 jmc Exp $
 $Name:  $
 
     Notes on tags used in MITgcmUV
     ==============================
 
+o tools/genmake2:
+  - change default makedepend from the system default to tools/xmakedepend:
+    When no makedepend is specified, select tools/xmakedepend it the test pass,
+    otherwise select the system default (if exist and pass the test) or
+    try to build cyrus-makedepend ; stop if none of the 3 works.
+o pkg/exf & pkg/thsice:
+  - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
+    for energy content of Precip + RunOff & Evap. Assumes:
+   1) Rain has same temp as Air.
+   2) Snow has no heat capacity (consistent with seaice & thsice pkgs)
+   3) Run-Off comes at the temp of surface water (with same Cp)
+   4) Evap over ocean is released to the Atmos @ surf-temp (=SST); should be
+    put directly into Latent Heat flux & should use water-vapor heat capacity.
+   5) Evap over snow/seaice (pkg/thsice) assumes constant Lf+Lv (consistent
+    with snow having no Cp) => water vapor is released to Atmos @ 0^oC (=ERL).
+o pkg/seaice: simplify the use of CPP flags in JFNK-related files
+    (compile when SEAICE_ALLOW_JFNK is defined)
+o pkg/thsice:
+  - fix oceanic flux diagnostics & timeave (left from new sequence of calls
+    implementation): move THSICE_AVE call after the advection (called directly
+    from thsice_do_advect.F).
+o verification/global_ocean.90x40x15 and OpenAD:
+  New experiment for OpenAD is identical to the one in input_ad except that
+    multiDimAdvection=.FALSE.,
+  There is still an issue with this.
+o pkg/thsice:
+  - account for ice velocity (ocean relative velocity) in turbulent heat flux
+    at the base of the ice; update output of global_ocean.cs32x15 (icedyn)
+    and offline_exf_seaice (main test).
+
+checkpoint64f (2013/03/31)
+o verification/OpenAD:
+  - new (smaller, without OAD_DEBUG) output_oadm.txt generated using gfortran.
+o verification/isomip, pkg/shelfice and OpenAD:
+  - add OpenAD setup to this exp and make shelfice package work with OpenAD
+o verification/tutorial_global_oce_biogeo:
+  - update AD and TLM output after turning off ALLOW_FE (in DIC_OPTIONS.h)
+o verification/offline_exf_seaice:
+  - replace adjoint experiment (now similar to fwd input.thermo/ setup).
+o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD:
+  - add OpenAD setup to this exp and make ptracers package work with OpenAD
+o pkg/seaice/seaice_evp.F:
+   mask the asymmetric contribution of the ice-ocean stress (when
+   the turningAngle is non-zero) over open water to avoid stripes
+   in the EVP-solutions after many EVP-substeps. This does not change
+   the verification experiment (because turningAngle=0 in that experiment),
+   but will affect other EVP solutions with turningAngle.ne.0
+o verification, AD & TLM output:
+  - new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple
+    additions and multiplications which affect results at machine truncation
+    level. Update few AD output (1D_ocean_ice_column, bottom_ctrl_5x5,
+    lab_sea.noseaicedyn & offline_exf_seaice) and TLM output
+    (1D_ocean_ice_column & tutorial_tracer_adjsens.som81) which had only 12
+    digits of matching.
+o pkg/seaice:
+   modify lsr-algorithm so that it vectorizes AND converges by using a
+   "zebra" method: split vector loop into two with step size 2; this
+   solves a general convergence problem for the JFNK solver on a vector
+   computer. It has the potential to even improve convergence for
+   non-vector machines, but it does change the results so it is turned
+   off by default. To turn on define CPP-flags SEAICE_VECTORIZE_LSR and
+   SEAICE_VECTORIZE_LSR_ZEBRA in SEAICE_OPTIONS.h
+
+checkpoint64e (2013/03/05)
+o pkg/ecco and several verification experiments:
+   Remove special versions of the_model_main.F, the_main_loop.F, forward_step.F
+   from ecco package, and revert to unified routine in model/src/
+   Adjust verification experiments accordingly, especially gloal_oce_llc90
+   Should conclude long-standing work by Gael to reconsile the_main_loop with
+   ECCO and will enable OpenAD's revolve loop in ECCO setup.
+o pkg/generic_advdiff:
+  - implement compressible flow method for multi-dim advection (similar to
+    gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since
+    TAF generates many recomputations) to use it; no yet coded with implicit
+    vertical advection.
+  - change experiment advect_cs (new output) and advect_xy (same output)
+    to test compressible flow multi-dim advection.
+o pkg/generic_advdiff:
+  - fix SOM advection for unusual cases (linear Free-Surf in r*, other
+    cases where linear Free-Surf is not @ k=1, e.g., useShelfIce)
+o pkg/seaice:
+  - fix bug in the no-slip implementation in seaice_calc_strainrates.F, this
+    bug affects two verification experiments (lab_sea and lab_sea.hb87),
+    recover old (wrong) results by setting noSlipFac = 2. in
+    seaice_calc_strainrates.F;
+  - add another averaging method for etaZ (etaZmethod=3), a mix of 2 and 0
+  - add runtime parameter SEAICE_JFNKepsilon for that finite difference
+    gradient in the Jacobian times vector operation (s/r seaice_jacvec)
+  - fix line search in seaice_jfnk.F (s/r seaice_jfnk_update)
+o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code:
+  - new subroutines seaice_lsr_tridiagu/v
+  - introduce loop bounds i/jmin/max to be able to use a restricted
+    additive Schwarz method, but not used for now.
+  - rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS
+  - use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner
+o OpenAD support
+   Reorganize S/R call for overall time-stepping loop to facilitate
+   OpenAD revolve loop replacement
+   (new S/R main_do_loop.F)
+o model/src:
+  - add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3;
+  - pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R
+    ADAMS_BASHFORTH2.
+o pkg/cheapaml:
+  - add new parameter (default=F, same as before) to disable full domain
+    (including land) periodicity in X & Y dir.
+  - new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of
+    prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer
+    into single S/R CHEAPAML_TIMESTEP.
+
+checkpoint64d (2013/02/17)
+o pkg/monitor (angular momentum):
+  - do not add Eta contribution to the total AM if using rigid-lid;
+  - correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta).
+  - horizontal discretisation: compute Zonal wind contribution separately for
+    each component (instead of from cell centered averaged) and use the 4
+    grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part.
+  - Check that AM is conserved with linear dynamics (momAdvection=F and linear
+    FreeSurf) if using vectorInvariant momentum.
+o model/src (horizontal grid):
+  - move initialisation of all horizontal grid arrays to null value
+    from specific horizontal grid S/R to main S/R INI_GRID;
+  - add 2 new arrays to project model C-grid velocity on to zonal direction
+    (similar to AngleCosC & -AngleSinC but at U and V point location) and
+    compute them in S/R CALC_GRID_ANGLES.
+o pkg/seaice: replace a hard coded parameter by a runtime parameter
+    SEAICE_JFNK_tolIter
+o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in
+    preconditioner for JFNK (run LSR into the overlaps as far as possible,
+    i.e OLx/y-2, but overwrite the solution in the overlaps)
+  - extend loop range in seaice_calc_viscosity
+  - add new parameters SEAICE_OLx/y (default = OLx/y-2)
+  - add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs
+  - slightly modify loops in tridiagonal solver lsr-preconditioner
+  - by default remove the extra exchange in seaice_preconditioner with a
+    replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE
+  - modify offline_exf_seaice so that old results without RAS are reproduced
+    for output.dyn_jfnk.txt
+  in seaice_fgmres.F (unrelated to RAS)
+  - add a cpp-flag option for a re-ordered mapping (potentially more
+    efficient), but because this changes the results, turn it off by
+    default
+  - replace the save statement by local common blocks
+o utils/matlab:
+  - fix tile-offset in rdmnc.m when output was produced using EXCH2.
+  - update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab)
+    instead of local script "load_cs.m".
+o pkg/seaice:
+  - fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected
+    to the scalarProductMetric and the unrolling. By chance this does not
+    change the verification experiment, because of the particular domain
+    decomposition
+o pkg/diagnostics:
+  - change default missing_value from UNSET_RL to -999.
+o pkg/layers: improve vectorization of layers_fluxcalc.F
+  - step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu
+    time spent in this routine by more than a factor of 3 on an NEC-SX8
+  - step 2: replace search algorithm by a bisection algorithm found in
+    Press et al. Numerical Recipes in Fortran. This algorithm can be
+    vectorized and finds the correct bin in approx. log2(Nlayers) steps.
+    For now, use this algorithm only for TARGET_NEC_SX defined.
+  - moved the search algorithm into a separate subroutine, that is kept
+    within the same file for automatic inlining.
+  - modified catching potential errors
+o pkg/ecco:
+  - add compile switches ALLOW_SHALLOW_ALTIMETRY and ALLOW_HIGHLAT_ALTIMETRY.
+o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk :
+  - modifications for ALLOW_GENTIM2D_CONTROL
+  -- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes.
+  -- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid )
+  -- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc
+  -- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F
+o model/src:
+  - account for moist thermodynamics in (dry) potential temperature equation;
+    update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev)
+    and cpl_aim+ocn.
+  - also switch to standard compiler (gfortran, was using ifort previously)
+    for fizhi-cs experiments reference output.
+o pkg/ctrl:
+  - 1st step toward generic time-varying control variable (2D) via CPP option
+    ALLOW_GENTIM2D_CONTROL
+  - note new namelist ctrl_nml_genarr in data.ctrl
+o verification/global_ocean.cs32x15:
+  - switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new
+    thsice calling sequence and update "output.icedyn.txt" output file.
+o pkg/ptracers:
+  - from Ryan A.: code to allow to restart a tracer at regular time interval
+    specifying a reset frequency and a reset-phase (for each tracers).
+o pkg/thsice:
+  - implement new sequence of calls for thsice+seaice:
+      previously:   ice-Dyn,ice-Advect,ice-Thermo(thsice)
+      new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect
+  - allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE"
+    in CPP_OPTIONS.h) to recover old sequence;
+  - update diagnostics for Intermediate State thsice diagnostics: now filled
+    just before advection (instead of just after advection in old sequence);
+  - update output of experiment offline_exf_seaice (standard test);
+  - in global_ocean.cs32x15 exp., postpone output.icedyn.txt update
+    by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h
+o pkg/aim_v23:
+  - use tiled array for aim_CO2 and surface wind speed for export to coupler;
+  - use standard pkg/mdsio routines to read & write CO2 pickup file;
+  - in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F;
+  - Implement new sequence of calls for seaice advection (with thsice and
+    seaice diffusion): do ice advection after ice-Thermodynamic (previously
+    was done before); change aim_do_physics.F (split the bi,bj loops block);
+  - use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence;
+o pkg/thsice:
+  - add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case
+    where just seaice diffusion is used without seaice-dynamics.
+
+checkpoint64c (2013/01/18)
+o pkg/seaice:
+  - add a parameter JFNKres_tFac that can replace JFNKres_t
+    (= JFNKres_tFac*JFNKresidual before JFNK solver)
+  - add a line search option to the JFNK solver
+  - move update of u/vIce and computation of initial residual into a separate
+    routine (same file); makes the code a little easier to read (?)
+  - the line search requires computation of the residual and for some reason
+    I cannot do the update of u/vIce at the beginning of the Newton loop
+    without changing the results, so we move computation of the new residual
+    also to the end of the Newton loop, even without the line search
+o pkg/mdsio:
+  - write missing value (corresponding to undefined array value) to meta files;
+    skip this if missing value is one (UNSET_RL would be a better value for the
+    case of undefined missing value but it's current the default missing-value);
+    Also update mdsio_read_meta.F (reading timeInterval & missing-value).
+o pkg/exf & thsice:
+  - for diagnostics purpose, fill-up and update Qsw array (+ fill the
+    diagnostics) even when SHORTWAVE_HEATING is #undef;
+o verification/cfc_example:
+  - turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to
+    illustrate how to use it).
+o verification/offline_exf_seaice:
+  in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing
+    files to only one time-record.
+  in input.thermo: narrow the 2 bands of low initial ice-concentration near
+    N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for
+    snapshot output; same mcPheePiston value as in thsice with
+    surf-current=0.2m/s.
+  in input.thsice: similar set-up as in input.thermo (channel with same seaice
+    initial conditions).
+o verification/cfc_example:
+  - update file "data" with more standard choice (default rotationPeriod,
+    exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F,
+    set deltaTFreeSurf to deltaTtracer) and update the output.
+o pkg/layers:
+  - fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC;
+  - ensure that "layers_bolus" is switched to False when useGMRedi=False.
+o verification/offline_exf_seaice:
+  - set all {field}period to zero for constant-in-time forcing (not tested
+    anywhere else).
+o verification/offline_exf_seaice:
+  - dyn_lsr  : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice;
+  - dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice.
+o model/src:
+  - implement Finite-Volume method for (hydrostatic) presure gradient
+    from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate.
+o pkg/seaice: implement EVP* by Lemieux et al. (2012).
+  - In order to be compatible with the default EVP code, this requires changing
+    the EVP code around a little; and because any small change immediately
+    breaks the lab_sea.hb87 verification experiment, the reference output is
+    updated two times (each time the remaining aggrement was only 2 digits):
+    - after replacing 1/dt by 1*recip_dt with a precomputed recip_dt
+    - after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt
+    The adjoint test lab_sea.evp also needed to be updated.
+  - Turn on EVP* by setting SEAICE_deltaTevp as before, and setting
+    SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be
+    a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps
+    explicitly with SEAICEnEVPstarSteps (thereby overriding the default of
+    INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately
+    kept obscure, because I need to test it a little more.
+o pkg/cheapaml:
+  - fix few incorrect type (_RL/_RS) in subroutine calls.
+o pkg/seaice:
+  - new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays
+    to _RL vector; this fixes JFNK code when compiling with "-use_r4" option.
+o model/src:
+  - add a warning if using select_rStar=2 with nonlinFreeSurf <> 4;
+    change (in input_ad*/data) select_rStar from 2 to 1 for AD verification
+    experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output)
+o pkg/cheapaml:
+  - replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and
+    update output of experiment cheapAML_box.
+  - store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity,
+    and set them only in one place (cheapaml_readparms.F).
+  - replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI"
+  - remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms)
+    and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia).
+o model/src/the_main_loop.F:
+  - fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION.
+o pkg/seaice:
+  - remove legacy branch code.
+  - retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly.
+o verification/*/code*/SEAICE_OPTIONS.h:
+  - remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY,
+    SEAICE_CAP_HEFF).
+o pkg/cheapaml:
+  - use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time
+    to load new forcing fields.
+  - add missing "_d 0" where it's needed; + some editing (improve indentation).
+  - remove switch to "-r8" compiler option (no longer needed) in verification
+    cheapAML_box, keep same output (small trucation error differences).
+o verification/offline_exf_seaice:
+  - add thermodynamics only test.
+o verification/cheapAML_box:
+  - split the domain in 8 (2x4) tiles; add MPI and multi-threaded test;
+    keep same output (same 14 digits for cg2d).
+  - switch on "-r8" compiler option (some numerical values are missing
+    the "_d 0") and update output (only 6 digits for cg2d were preserved).
+
+checkpoint64b (2012/12/24)
+o pkg/cheapaml:
+  - remove un-used variables (Qnet,EmPmR) from pickup files.
+  - store tendency of advected variables into cheapaml pickup file
+    and fix the AB-2 restart.
+o verification/offline_exf_seaice and lab_sea adjoint:
+  - switch to new code (#undef SEAICE_GROWTH_LEGACY).
+  - switch to 4 time steps in offline, consistent with lab_sea.
+  - match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice.
+  - update results after change of experiment seaice.
+o pkg/seaice:
+  - remove option SEAICE_MULTICATEGORY; has been replaced with run-time
+    parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is
+    still defined since SEAICE_multDim needs to be set to MULTDIM value (from
+    SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default.
+o model/src:
+  - add run-time parameter to select CG2D solver minimum-residual solution
+    (in case of a poor convergence).
+o pkg/seaice/seaice_lsr.F
+  - move calculation of matrix coefficients into new
+    S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same
+    file; the main purpose of this change is to be able to reuse the code
+    in S/R SEAICE_PRECONDITIONER
+  - modify the computation of the residual so that the mass of sea-ice
+    is not used twice; this simplifies the calculations, but since
+    the residual is never used except when LSR_mixIniGuess.ge.4---and this is
+    not tested in testreport---this does not affect the testreport results.
+o verification/seaice_obcs:
+  - disable SEAICE_GROWTH_LEGACY; reset input files to match those of
+    verification/lab_sea/input.salt_plume; changes results/output.txt*
+o model/src:
+  - adapt quasi-hydrostatic formulation to work with p or p* coordinate.
+o pkg/seaice:
+  - improve description of parameters in seaice_fgmres.F and start
+    cleaning up the code
+  - change name of SCALPROD to SEAICE_SCALPROD and modify meaning of
+    second argument
+  - add a metric based on grid cell area to SEAICE_SCALPROD; update
+    results of offline_exf_seaice.dyn_jfnk
+  - compute initial residual norm in seaice_jfnk based on SEAICE_SCALPROD
+o pkg/aim_v23:
+  - fix an other bug in dissipation heating (grid-cell area was missing).
+o model/src + pkg/seaice:
+  - add global (multi-tile) linear solver for pair of tri-diagonal system
+    along X and Y lines, respectively for U and V component.
+    Note: 1) MPI and cube-exchange not yet coded.
+        2) probably not accurate for poorly conditioned / large size problem.
+  - add option for SEAICE_LSR to use global (multi-tile) tri-diagonal solver;
+    default: not compiled and not used.
+o pkg/seaice:
+  - first attempt at a multi-threaded fgmres solver for the JFNK solver:
+    introduce bi/bj loops and use global_sum_tile_rl instead of
+    mpi_allreduce in seaice_fgmres.F
+  - improve diagnostics output for fgmres solver (seaice_fgmres.F)
+  - replace a few unnecessary goto statements by if-blocks  (seaice_fgmres.F)
+  - add a verification experiment for JFNK in offline_exf_seaice
+o verification:
+  - change (for now, only fwd test) offline_exf_seaice experiment:
+    use a re-entrant channel with idealized coastline (trapezoidal shape)
+    at southern boundary to explore seaice dynamics and thermodynamics
+    with simple forcing. Main set-up has dynamics+thermo and SST relaxation;
+    secondary test (input.thsice) use thermodynamics only with SST relaxation.
+  - add seaice-dynamics only secondary test using LSR and pkg/thsice advection.
+o pkg/exf:
+  - disable "sstExtrapol" when Nr=1
+o verification:
+  - add new experiment "cheapAML_box" (simple 1 layer set-up from Bruno Deremble)
+    to test pkg/cheapaml.
+o pkg/aim_v23 & pkg/shap_filt:
+  - fix dissipation heating (erroneous gravity multiplication factor).
+o pkg/seaice:
+  - remove unused field pressPre from jfnk solver
+  - rename two subroutines in seaice_preconditioner.F
+o eesupp/src:
+   - S/R MDSFINDUNIT avoids reserved unit numbers (scrUnit1, eeDataUnit ...)
+o pkg/seaice/seaice_preconditioner.F: fix preconditioner once again
+   - remove wrong parts of the rhs and the lhs (were in there
+     because I did not understand the concept of this preconditioner)
+   - add an exchange between u- and v-sweep. This increases communication
+     by a factor of two but improves the convergence of jfnk. Ideally,
+     one would like the u- and v-sweep to be independent. So far within
+     undocumented ifdefs
+   - reorganize the extra computations for printing the residuals
+o tools/genmake2:
+  - comment out the "mpif.h" include in NetCDF test programm (for MPI built)
+    since it's not necessary (and was preventing to use MNC in some cases).
+
+checkpoint64a (2012/11/16)
+o pkg/autodiff:
+  - improve pkg-internal logical parameter switch (inAd/inFwd mode) so that
+    autodiff_readparms.F no longer depends on calling order (within
+    packages_readparms.F) and no longer requires to include ${PKG}_PARMS.h):
+    rename param turnFreeDriftInAdMode to SEAICEuseFREEDRIFTswitchInAd
+    and change param SEAICEuseDYNAMICSinAdMode to SEAICEuseDYNAMICSswitchInAd.
+o pkg/obcs:
+  - adding tidal velocity forcing capability to obcs
+    for usage example, see verification/seaice_obcs/input.tides
+o pkg/seaice:
+  - turn the LSR-relaxation parameters WFAU/V into runtime parameters
+    SEAICE_LSRrelaxU/V
+  - introduce runtime parameter SEAICEetaZmethod (=0 by default)
+o pkg/aim_v23:
+  - implement heating from friction (bottom friction and stratospheric drag).
+o pkg/shap_filt:
+  - fix diagnostic "SHAP_dKE" (was 2 time smaller); implement heating from
+    dissipation but only for Shap_funct=2, active when addFrictionHeating=T.
+o model/src:
+  - move AddMass common block from DYNVARS.h to FFIELDS.h; allow to read-in
+    time-constant addMass field from file (addMassFile);
+  - support for heating due to friction (and Kinetic Energy dissipation):
+    add option, run-time switch and 3-D field array + support code ; each pkg
+    or S/R can add heating contribution (if there is a sink of KE); the sum is
+    accounted for as a Temperature tendency term (EXTERNAL_FORCING_T).
+o pkg/seaice:
+  - complete merge of ITD code into seaice_growth.F
+    from MITgcm_contrib/torge/itd/code/
+    no verification so far, but Torge Martin tested
+    "1-D test case and Beaufort set up;
+    deliver okay results after 1 model year."
+  - complete merge of SEAICE_SIZE.h into all relevant routines
+  - move computation of eta at Z-points into calc_viscosities
+    + introduce global field etaZ
+    + add different methods for computing etaZ, for now the old
+      method (simple averages of eta to Z-points) is hardwired
+    + replace etaMeanZ by etaZ in seaice_lsr, seaice_calc_residual,
+      seaice_preconditioner
+  - simplify computations for SEAICE_ZETA_SMOOTHREG
+  - seaice_preconditioner:
+    + replace one remaining press by pressLoc (mistake)
+    + adjust printing of residuals
+  - improve I/O of diagnostics of JFNK in seaice_jfnk.F:
+    + add (SEAICE.h) and rename some counters (initiliased in
+      seaice_init_fixed.F)
+    + add _BEGIN/END_MASTER (myThid)  around print statements
+    + print total number of iterations and failures over SEAICE_monFreq
+      interval to STDOUT
+  - move control over output-messages by fgmres to seaice_jfnk to save
+    some operations
+  - move resetting initial guess for fgmres outside of seaice_fgmres_driver
+    in order to make restarts with sol .ne. zero (fgmres with restarts)
+    (seaice_jfnk.F, seaice_fgmres.F)
+  - seaice_calc_l/rhs.F: replace maskW/S by maskInW/S; this fixes
+    a serious convergence problem when open boundaries are involved
+o pkg/ggl90: fix computation of control volumes for the case of
+  ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes
+  up half a grid cell from C-centered to W-centered (pointed out by C. Eden)
+o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC
+o pkg/autodiff
+  - Add inAdMode switch for SEAICEuseDYNAMICS:
+    SEAICEuseDYNAMICSinAdMode
+    (extend logic in ADAUTODIFF_INADMODE_SET)
+o pkg/seaice
+  - Step 1 of merging ice-thickness distribution (ITD) code from
+    MITgcm_contrib/torge/itd/ (author: Torge Martin)
+    The code implements concept laid out in Thorndike et al. (1975);
+    code is enabled via CPP flag SEAICE_ITD
+    nITD (in SEAICE_SIZE.h) defines number of ice thickness categories;
+    code is not complete yet!!
+  - SEAICE_SIZE.h now included in almost all seaice routines
+o verification (using seaice):
+  - switch back seaice-dynamics (+ lower SOLV_MAX_ITERS) in ADM exp.
+    global_ocean.cs32x15.seaice ; update results.
+  - compile B-grid dynamics in FW test exp 1D_ocean_ice_column ;
+  - compile C-grid dynamics with #define SEAICE_ALLOW_JFNK in FW test exp
+    offline_exf_seaice (previously compiling B-grid).
+o pkg/exf:
+  - fix some STOP conditions in exf_check.F (from Aug 28, modifs did not allow
+    to specify neither just 1 comp of wind or wind-stress, nor no surface momentum
+    forcing): just replace CPP option ALLOW_ATM_WIND with run-time param useAtmWind.
+o pkg/layers (adjust changes from Sept 19):
+  - do snap-shot output and fill diagnostics from inside iLa loop (layers_calc.F)
+    this allows to remove "layers_maxNum" dimension from all layers arrays.
+o pkg/layers (adjust changes from Sept 19):
+  - remove ALLOW_LAYERS_OUTPUT ; fix snap-shot and time-ave output ;
+  - snap-shot extended to all type of layers (not just the 1rst type);
+  - remove layers variables when corresponding CPP option is undef.
+o pkg/layers:
+  - rename pkg/layers variable and add new output (layer exist & un-weighted
+    velocity in layer)
+o pkg/seaice:
+  - simplify (?) ocean-drag coefficent computations by using
+    the same routine in all three solvers (saves some code lines)
+  - remove global fields DRAGA and DRAGS from C-grid code and
+    declare them locally in lsr.F (the only place where they are
+    still used)
+  - update AD output of lab_sea.evp (very sensitive anyway).
+o pkg/seaice: add Jacobian-free Newton Krylov solver for ice dynamics
+  (Lemieux et al. 2010, 2012). Turn on with the usual SEAICE_ALLOW_JFNK
+  and SEAICEuseJFNK=.true. A few things to note:
+  - involves a FGMRES, that is parallel but very inefficient,
+    because of many scalar products (global sums) in the Gram-Schmidt
+    orthogonalization method. Needs to be replaced. Original code
+    from J.-F. Lemieux
+  - preconditioner for FGMRES is a stripped down version of LSOR
+  - SOLV_MAX_ITERS is now used for LSOR as a solver and as a
+    preconditioner. For the preconditioner, the default is set to 10.
+  - Jacobian times vector is computed with finite differences
+  - marginally related to JFNK-solver: add a smooth regularization for
+    zeta with tanh that will improve convergence (Lemieux and Tremblay,
+    2009) for any implicit solver (not implemented for EVP because EVP
+    does not need this regularization in the first place). Define
+    SEAICE_ZETA_SMOOTHREG in SEAICE_OPTIONS.h to use.
+o eesupp/src:
+  - check in genmake2 that intrinsic S/R flush is available.
+  - add S/R to flush IO unit (if intrinsic S/R flush is available)
+  - flush standard & error msg unit before MPI termination
+  - if debugMode, flush IO unit after printing msg
+o pkg/ctrl:
+  - ctrl_unpack.F, ALLOW_GENARR3D_CONTROL code: fix missing argument in call
+    to ctrl_set_unpack_xyz.
+
+checkpoint64 (2012/10/09)
+o pkg/shelfice
+  - in mom_fluxform.F, mom_vecinv.F:
+    CALL SHELFICE_V_DRAG(bi,bj,k,vFld,KE,KappaRU,vF,myThid)
+    Bug fix KappaRU -> KappaRV
+    does not change verification/isomip but may change other setups
+    (presumably constant KappaRU=KappaRV)
+  - fix diagnostics SHIU/Vdrag (thanks to Tom Millgate)
+o pkg/obcs:
+  - fixed some indexing bugs in obcs_seaice_sponge.F
+  - added obcs relaxation subroutines for HSALT and HSNOW
+  - changes verification/seaice_obcs/results/obcs_seaice_sponge.F
+o pkg/seaice:
+  - add "multicategory" parameterization for snow in analogy to ice,
+    default is off for now.
+o pkg/obcs:
+  - added obcs_seaice_sponge.F for obcs relaxation of seaice variables;
+    see verification/seaice_obcs/input.seaiceSponge for example application.
+  - remove local commom bloc "OBCS_GLOBAL" in obcs_readparms.F and do all the OB
+    index setting by master-thread. This fix multi-threads Pb in previous modifs.
+o pkg/layers :
+  - add diagnostics to pkg/layers
+  - move the meat of pkg/layers from layers_calc.F to layers_fluxcalc.F
+    (from R.Tulloch). Layers_calc.F now calls layers_fluxcalc.F accordingly.
+o pkg/generic_advdiff/gad_implicit_r.F :
+  - fix ADVr diagnostics in case of both implicit vertical advection and diffusion.
+o pkg/seaice/seaice_growth.F:
+  - fix SItflux diagnostics in virtual salt flux + balanceEmpmr case.
+o pkg/obcs:
+  - change default setting of OBCS_UVICE_OLD from defined to undef;
+  - use new parameter OB_indexNone for null index value (instead of hard-coded 0)
+    in all pkg/obcs code and in other pkgs; remove k loop in obcs_check_depths.F;
+  - pass OB_indexNone as (new) argument to S/R CTRL_MASK_SET_[X,Y]Z;
+  - change OB null index value (OB_indexNone) to -99 ; this fix the problem
+    with Southern & Western OB at a tile edge (at least in a simple set-up).
+o pkg/obcs:
+  - change settings of OB index in case OB coincides with tile edge (shared by
+    2 tiles), so that common OB location is registered by both tiles (instead of
+    only 1). However, for Southern and Western OB, index value = 0 is not
+    recognized as valid OB index (=default null value) and needs to be fixed.
+  - modify accordingly OBCS_BALANCE_FLOW and OBCS_MONITOR (avoid double counting)
+  - new parameter "OB_indexNone" for null index value (for now, still zero)
+    to replace hard-coded null index value of zero.
+o pkg/exch2:
+  - improve W2_USE_E2_SAFEMODE (faster) and W2_E2_DEBUG_ON:
+    always check buffer-size (but outside the loop); move checking for valid
+    index from W2_USE_E2_SAFEMODE to W2_E2_DEBUG_ON; in W2_E2_DEBUG_ON,
+    print each tile and point connection only if |W2_printMsg|>= 2 and 3.
+o pkg/ctrl (pack & unpack):
+  - in ctrl_pack.F & ctrl_unpack.F, use the same local file-name variable
+    (locally defined) for different variables (+ remove the variable-specific
+    file name in CTRL_GENARR.h). For now, only implemented for GENARR2/3D_CONTROL
+    (to be extended to other local file names in ctrl.h).
+o pkg/flt:
+  - add a FLT_Iter0 option (similar to PTRACERS_Iter0).
+o pkg/mdsio:
+  - fix missing STOP in mdsio_readvec_loc.F (case ioUnit=0) when file is missing
+o tools/genmake2:
+  - add similar dependences for target EXE_AD & EXE_FTL as we have for EXECUTABLE
+    (added by Alistair in version 1.51 for building without make depend);
+  - remove Header files list (H_SRC_FILES) from the dependence of targets
+     ad_input_code.f & ftl_input_code.f (not clear why it was added in the first
+    place in version 1.23): this save going through staf when unrelated header
+    file has been modified.
+   Note: for an intermediate target (e.g., ad_input_code.f or adtaf) without
+    "make depend" step, still need to do "make links" before "make adtaf".
+o eesupp/src (+ few pkg src files) & genmake2:
+  - finish to remove ALWAYS_USE_MPI in source code that TAF does not see;
+  - no longer set ALWAYS_USE_MPI in Makefile (was done by genmake2).
+  - improve genmake2 checking for ALLOW_${PKG} in CPP_OPTIONS.h files (distinguish
+     upper/lower case ; account for space between "#" and undef/define)
+o pkg/flt (with exch2):
+  - cleaning: fix so that it compiles; move remaining MPI calls out of flt_exch2.F;
+  - simplify threads synchronisation; fix (many issues) multi-threaded with MPI.
+
+checkpoint63s (2012/09/05)
+o pkg/ecco:
+  - remove #ifdef ALLOW_SMOOTH_CORREL3D brackets.
+  - add more relevant #ifdef ALLOW_SMOOTH ones.
+  - sort out useAtmWind, useSMOOTH, ctrlSmoothCorrel2D.
+o pkg/ctrl:
+  - CTRL_OPTIONS.h : document CPPs related to smoothing; ALLOW_SMOOTH_CORREL2D/3D,
+    ALLOW_CTRL_SMOOTH, ALLOW_SMOOTH_CTRL2D, ALLOW_SMOOTH_CTRL3D.
+  - ctrl.h : document run time params doInitXX, doMainPack, doMainUnpack, doPackDiag,
+    doSinglePrecTapelev (audodiff param!), ctrlSmoothCorrel2D (new) and
+    ctrlSmoothCorrel3D (new).
+    The added ctrlSmoothCorrel2D/3D replace the old ALLOW_SMOOTH_CORREL2D/3D CPP.
+  - ctrl_readparms.F : initialise ctrlSmoothCorrel2D/3D and read from namelist.
+  - ctrl_init.F ctrl_pack.F ctrl_unpack.F : switch off ustress/vstress
+    controls when useAtmWind, and vice versa.
+  - ctrl_map_ini_ecco.F : UVEL0, VVEL0, edtaux, edtauy cannot be smoothed as tracers.
+  - ctrl_get_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL2D with
+      #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel2D, IF useSMOOTH.
+  - ctrl_map_ini_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL3D with
+      #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel3D, IF useSMOOTH.
+  - ctrl_set_pack_xy[z].F, ctrl_set_unpack_xy[z].F:
+    replace ALLOW_SMOOTH_CORREL2D/3D brackets with ctrlSmoothCorrel2D/3D.
+o pkg/smooth:
+  - remove un-necessary includes.
+  - remove ALLOW_SMOOTH*D and ALLOW_SMOOTH_CORREL*D brakets.
+    Those CPP options were never defined, and not necessary.
+o model/src:
+  - fix CPP brackets in ini_mixing.F (GM_background_K belongs to gmredi).
+  - standard treatment of useSMOOTH.
+o pkg/autodiff:
+  - add LOGICAL useGGL90inAdMode, useGGL90inFwdMode, useSALT_PLUMEinAdMode,
+    useSALT_PLUMEInFwdMode allowing to switch off ggl90 and salt_plume adjoint.
+o pkg/exch2:
+  - add "if usingMPI" where it was missing (in exch2_rx?_cube*.template)
+    + start to remove ALWAYS_USE_MPI in source code that TAF does not see.
+  - make new S/R W2_MAP_PROCS out of w2_eeboot.F to setup exch2 CommonFlag
+    and tiles to process mapping.
+  - re-arrange 3 header files (W2_EXCH2_PARAMS.h, _BUFFER.h & _TOPOLOGY.h)
+    moving /EXCH2_FILLVAL_RX/ & /W2_EXCH2_COMMFLAG/ to W2_EXCH2_TOPOLOGY.h;
+    rename "exch2_tProc" to "W2_tileProc" and move seting of e2FillValue_RX
+    from w2_eeboot.F to w2_readparms.F.
+o eesupp/src:
+  - set exchNeedsMemsync & exchUsesBarrier according to "usingMPI" (instead of
+    ALWAYS_USE_MPI) + moved from ini_communication_patterns.F to eeset_parms.F;
+    also move setting of exchCollectStatistics from exch_init.F to eeset_parms.F
+  - in eedie.F and all_proc_die.F, always call MPI_FINALIZE when ALLOW_USE_MPI
+    is defined (remove condition on usingMPI) to match cases where MPI_INIT
+    has been called.
+  - fix bug I put in previous modif of exch_sm_3d_rx.template (not much used);
+  - change default (non-MPI) value of myPid (from 1 to 0) to match MPI settings
+    (so that on 1 proc, get same myPid independently of usingMPI)
+  - add a stop if multi-procs but usingMPI=F ; stop also if usingMPI=T and
+    useCubedSphereExchange with EXCH-1 (safer).
+  - add "if usingMPI" where it was missing (+ start to remove ALWAYS_USE_MPI).
+o pkg/ggl90:
+  - fix bug in filling corner mask array "mskCor" (FILL_CS_CORNER_TR_RL call)
+    used in ALLOW_GGL90_SMOOTH code.
+o pkg/flt:
+  - fix typo in FLT_WITHOUT_Y_PERIODICITY (the effect was to ignore stopping
+    floats at the Southern end of the domain).
+o eesupp/inc:
+  - add a list of CPP-options which can be set by Makefile (DEF_IN_MAKEFILE.h);
+    but not used (and not to be used) anywhere, just for documentation.
+o pkg/autodiff, exf, ptracers & seaice (AD & TL output):
+  - comment out the very nasty "writeBinaryPrec = writeStatePrec" line, since:
+    a) can damage previously written records in any other multi-record files.
+    b) if needed, can easily do it cleanly, by calling S/R WRITE_REC_3D_RL/S.
+o tools/genmake2:
+  - define variable MAKE within Makefile and use it in place of 'make';
+  - update AD_CONFIG.h (if needed) before building any of the executable
+    (forward, adjoint or tangent-lin); this involves a 2nd invocation of make;
+    and add the usual #ifndef/#define AD_CONFIG_H in AD_CONFIG.h;
+  - always print usual warning comment 'this file is automatically generated'
+    from script convert_cpp_cmd2defines (+ remove this warning from genmake2).
+o pkg/cheapaml:
+  - updated to correspond to the code used in accepted paper (Nico Wienders).
+o pkg/exf:
+    added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch.
+    ALLOW_ATM_WIND now just sets the useAtmWind default (see exf_readparms.F)
+    and force defines ALLOW_BULKFORMULAE (EXF_OPTIONS.h).
+o pkg/exf, autodiff, ctrl, ecco and seaice:
+    remove ALLOW_ATM_WIND brackets, or replace them with useAtmWind ones.
+o pkg/ctrl, ecco:
+    allow to compile both ALLOW_U/VSTRESS_CONTROL and ALLOW_U/VWIND_CONTROL.
+    Depending on useAtmWind, one is inactive, and the other is active (see
+    exf_getffields.F/exf_getsurfacefluxes.F).
+o tools/genmake2:
+  - improve error msg when failing in 2nd test of check_for_broken_Ff
+  - fix option '-makefile' short-name (-mf according to genmake2 -help)
+  - source local config file "genmake_local" just after processing the genmake2
+    command arguments (previously done before processing arg).
+o pkg/grdchk:
+  - add a call to TURNOFF_MODEL_IO for Tangent-Linear run (in this case, call
+    to this routine from cost_final has been dropped in g_cost_final)
+  - improve printed information (more explicit msg, no longer using "print *,"
+     fix fcpertminus printed value).
+o model/src:
+  - move call to COST_INIT_VARIA out of packages_init_variables.F directly
+    into initialise_varia.F (just after calling PACKAGES_INIT_VARIABLES):
+    this prevents getting cost-funct reset in adinitialise_varia recomputations.
+o pkg/dic:
+  - move initialisation of "freefe" array from from dic_biotic_forcing.F to
+    fe_chem.F: this prevents TAF from dropping this initialisation in TLM code.
+o pkg/grdchk:
+  - grdchk_main.F : added CALL GLOBAL_SUM_INT( ierr , myThid )
+  - grdchk_getadxx.F etc. : omit I/O if ierr.EQ.0
+o pkg/autodiff/ctrl/grdchk :
+  - attempt to sort out what works and what does not,
+    with regard to I/O, and to warn/stop accordingly.
+o pkg/grdchk:
+  - attempt to fix grdchk in the case of useSingleCpuIO.
+  - "if ( myProcId .EQ. grdchkwhichproc .AND. ierr .EQ. 0 )"
+   statements were moved from grdchk_main.F and into
+   grdchk_getadxx.F grdchk_getxx.F grdchk_setxx.F.
+  - a global sum is applied to record numbers icvrec/layer
+   out of grdchk_loc so that they be passed to I/O routines.
+o pkg/smooth:
+  - fix recomputation that appeared with nlfs : use smooth_recip_hFacC,
+    smooth_hFacW, smooth_hFacS (copied at init_fixed) in 3d case.
+o verification/testreport:
+  - add option '-tlm' for Tangent-Linear test (-adm,-oad,-tlm are all exclusive);
+  - can also use compressed (gzip) reference output file;
+  - change format (in pkg/grdchk) of TLM output (+ add forward gradient)
+    to be easier to collect by testreport.
+  - update existing TLM output (half out-of-date by more than 3 yrs).
+  - report NETCDF & LAPACK settings (from genmake2) in output dir.
+  - report run-time in each individual summary (previously only for AD test);
+    for TLM test, add also TAF version.
+  - add daily TLM test on (old) aces cluster + weekly test on baudelaire.
+
+checkpoint63r (2012/08/15)
+o tools/genmake2:
+  - fix Makefile for target ftlall (+ update files to clean after make ftlall)
+o pkg/ecco/ecco_cost_final.F :
+  - fix fc print statements (to stdout and costfunction0000) so
+    that the printed value is always after the global sum.
+o pkg/seaice/seaice_dynsolver.F :
+  - fix ice strength assymptote at SEAICE_area_max<1
+    (no change for the standard case of SEAICE_area_max=1)
+o some cleaning:
+  - pkg source files: ensure that all *.F files from each pkg included the
+    corresponding ${PKG}_OPTIONS.h file (except stand-alone src file which
+    only includes CPP_EEOPTIONS.h); fix S/R CTRL_SMOOTH ; update AD experiment
+    code_ad/*.F src files; add new option-file in pkg/admtlm + corresponding
+    includes;
+  - model/src: add PACKAGES_CONFIG.h wherever ALLOW_AUTODIFF[_TAMC] is used.
+  - ALLOW_DIFFKR_CONTROL: add a stop in S/R CTRL_CHECK in case ALLOW_3D_DIFFKR
+    is undef; also define /DYNVARS_DIFFKR/ common block in DYNVARS.h when
+    ALLOW_DIFFKR_CONTROL is defined, to allow to compile and reach this stop.
+  - update option-file CPP_OPTIONS.h of all AD experiments:
+    * no longer include PACKAGES_CONFIG.h ;
+    * includes ECCO_CPPOPTIONS.h if PACKAGES_CONFIG.h has been included ;
+    * def/undef ALLOW_3D_DIFFKR independently of ALLOW_DIFFKR_CONTROL (before
+      including ECCO_CPPOPTIONS.h).
+o pkg/cost, pkg/ctrl, pkg/ecco option-file:
+  - clean-up and split content of old pkg/ecco/ECCO_CPPOPTIONS.h file into
+    separated pkg option-file (done according to old doc from ECCO_CPPOPTIONS.h,
+    not necessary accurate).
+  - add a template for option-file ECCO_CPPOPTIONS.h, mostly empty, in
+    pkg/autodiff, i.e., the 1rst pkg to compile for adjoint built, with lines to
+    deliberately break compilation (a remainder that it needs to be customized)
+  - in pkg/ecco, includes ECCO_OPTIONS.h instead of COST_OPTIONS.h
+  - rename COST_CPPOPTIONS.h to COST_OPTIONS.h
+  - rename CTRL_CPPOPTIONS.h to CTRL_OPTIONS.h
+o tools/genamke2:
+  - check for lapack.
+o pkg/cost and pkg/ecco : attempt to sort out some of the limiting intricacies.
+  - pkg/cost.cost_final.F : allow for use of pkg/ecco and pkg/cost cost functions
+    jointly. The exclusive ifdefs were removed, to add costs terms (when defined)
+    from both packages.
+  - the fc global sum in pkg/ecco/ecco_cost_final.F was removed accordingly.
+  - for objf_atl we use either the pkg/ecco or the pkg/cost term depending on CPPs.
+  - pkg/ecco and model/src : add CPP brackets around pkg/cost and pkg/ctrl includes
+    of "CTRL_SIZE.h" "ctrl.h" "ctrl_dummy.h" "optim.h" / "cost.h" accordingly.
+o pkg/cost : add comments to explain special and/or untested setups.
+o pkg/exf:
+  - use EXF_OPTIONS.h to set pkg/exf options except if done in ECCO_CPPOPTIONS.h
+    (previously, ALLOW_AUTODIFF_TAMC was controling this switch).
+o verification/*/code_ad:
+  mimimal cleaning of AD experiments ECCO_CPPOPTIONS.h option-file:
+  - reccord when this file is included (define ECCO_CPPOPTIONS_H)
+  - remove the most obvious obsolete features (e.g., #define ALLOW_COST not
+    allowed since Oct 2003 in any option-file except in PACKAGES_CONFIG.h)
+o pkg/seaice :
+  - added possibility to change ice strength/PRESS0 relationship to
+    HEFF, according to the following run time parameters
+    SEAICEpresPow0 :: HEFF exponent for ice strength below SEAICEpresH0 (integer, >0)
+    SEAICEpresPow1 :: HEFF exponent for ice strength above SEAICEpresH0 (integer, >0)
+    SEAICEpresH0   :: HEFF threshold for ice strength            (m)
+o pkg/ggl90 :
+  - added run time flag mxlSurfFlag to include the code that ensure
+    mixing between first and second level (previously included as a comment)
+o verification/1D_ocean_ice_column/input_ad/data.autodiff :
+  - add test of newly added dumpAdByRec=T option where
+    we write all records to one file per variable.
+o verification/global_ocean.cs32x15/code_ad/CPP_OPTIONS.h :
+  - switch to #define ALLOW_BALANCE_RELAX and ALLOW_BALANCE_FLUXES
+    to check that this code is ok with taf and compiles in adjoint.
+o pkg/autodiff :
+  - added run time param dumpAdByRec : ad dump format switch.
+    If true then write all records to one file per variable.
+    Else write one file per record (remains the default).
+  - revise seaice_ad_dump.F and exf_adjoint_snapshots_ad.F accordingly.
+o pkg/seaice:
+ - Added SEAICEuseTILT run time switch : if set to
+   false then omit the tilt term in seaice dynamics.
+ - Fix free drift calculation.
+o pkg/shelfice:
+  When initializing SHELFICEDragQuadratic, set default to be
+  consistent with shiCdrag in case SHELFICEuseGammaFrict is used,
+  but retain option to set it independently
+  (inconsistenty spotted by Veronique Dansereau)
+o eesupp/inc:
+  - in EEPARAMS.h, add real-type constant for some frequently used simple number
+     (0,1,2,1/2), with name explicitly referring to RS/RL type.
+o model/src:
+  - move balancing of relaxation terms to new S/R balance_relax.F.
+o pkg/autodiff:
+  re-write active I/O high-level (control) S/R:
+  - rename  S/R ACTIVE_READ/WRITE_RL to ACTIVE_READ/WRITE_3D_RL
+  - add 1 more argument (useCurrentDir) to replace the "_LOC" 2nd set of S/R.
+  - use standard pkg/mdsio I/O routines (MDS_READ/WRITE_SEC_XZ/YZ  and
+    MDS_READ/WRITE_FIELD); change loops to multi-threads.
+  - update and merge active_file_control_slice.flow into active_file_control.flow
+  - update the calls in lower level S/R (active_file.F, active_file_g.F and
+    active_file_ad.F) keeping the argument list and function unchanged.
+  - also update lower-level "_LOC" version (call same S/R with "useCurrentDir
+    =.TRUE.") and remove high-level (control) _loc version (not called anymore).
+  - new low-level active I/O routines, one for each type (RL/RS), for active var
+    of various (XY,XZ,YZ) shape and level number (arguments: arrShape, myNr);
+    fix ctrl_init_wet.F & ecco_cost_weights.F by calling the new S/R with the
+    right type.
+o autodiff and RS=real*4:
+  - call the right type (_RS instead of _RL) of S/R in few output S/R (pkg/exf
+    ad-monitor and snapshots); disable arrType='RS' in mdsio_gl*.F ;
+  - change argument type of 3-D mask argument to _RS to match type in the call
+    (in seaice_cost*.F, ctrl_*_gen.F and *ctrl_bound.F); to be continued.
+o pkg/thsice:
+  - re-anable balanceEmPmR when useSEAICE=T with useThSIce=T.
+  - option to correct ocean fresh-water flux for imbalance of Atmos+Land
+    fresh-water flux: uniform correction or proportional to local precip.
+o pkg/ctrl:
+  - new header file CTRL_SIZE.h for parameters maxCtrlArr2D, maxCtrlArr3D
+  - redefine CPP option ALLOW_BOTTOMDRAG_CONTROL to
+                        ALLOW_BOTTOMDRAG_CONTROL_NONGENERIC
+  - verification/hs94.1x64x5/ tests ALLOW_GENARR{2D,3D}_CONTROL
+
+checkpoint63q (2012/07/30)
+o pkg/autodiff:
+  note about monitor and snap-shot of ad-variables:
+  a) need to apply ADEXCH before monitor or output of ad-vars to include
+   overlap contributions (was done for adjDump but missing for monitor).
+  b) since ADEXCH implies adding overlap values to interior array, machine
+   truncation error is expected when adding an ADEXCH call in the middle of
+   the time-stepping (although mathematically identical).
+  modifs:
+  - fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars
+    declaration (adEddyPsiX,adEddyPsiY in adcommon.h).
+  - add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how  to
+    apply ADEXCH before monitor or snap-shot of ad-variables:
+       =0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy.
+  - implement new method (copy+adexch) for snap-shot and monitor of main model
+    ad-vars (initially not used by default -> output unchanged).
+  - change default (set to 2) to use new method and update few output_adm.txt
+    with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo
+    and both tutorial_tracer_adjsens tests).
+  - switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice)
+    and turn off momDissip_In_AB in the 2 other (needed for stable AB-3).
+o pkg/ctrl:
+  enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of
+  generic control variables via
+  #define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL
+  Only required customization should be S/R ctrl_map_ini_genarr.F
+  (routine in repository contains example)
+o pkg/exf:
+  - fix and refine checking of surface-relaxation setting when using EXF
+o verification (adjoint exp):
+  - reduce length of simulation by half for experiment global_ocean.cs32x15
+    (std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output.
+o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag)
+  - replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers
+    of KE that can occur with aggressive optimization
+  + put quadratic bottom drag calculation in separated loops (only done if
+    using bottomDragQuadratic)
+o model/src: CG2D_NSA
+  - clean-up:  stop if cg2dNormaliseRHS=T and AUTODIFF
+     and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE.
+  - in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens),
+     change cg2d residual target to be expressed in Wunits (=> do not normalise
+     RHS ; this fix global_max Pb with TAF); update output.
+o verification/tutorial_tracer_adjsens:
+   improve parameter consistency (and get rid of warnings):
+   - use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf);
+   - switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical)
+   - use staggerTimeStep (for stability) in som81; use default rotation period.
+o pkg/exch2:
+  - with empty facet: fix compact-format (W2_mapIO=1) definition (was previously
+    reset to 0 = 1 long line in X)
+o pkg/mdsio:
+  - fix reading of dimensions from meta file for large-size domain
+o model/src:
+  - fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long);
+  - to refine CS-grid check, add logical flag "hasWetCSCorners": true if using
+    Cubed-Sphere Exch with CS-corners inside the domain;
+    make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate
+    globalArea and to set hasWetCSCorners.
+  - add warning if usingCurvilinearGrid and momAdvection in flux-form (missing
+    metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form.
+  - re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if
+    useCDscheme and useCubedSphereExchange).
+o pkg/seaice/seaice_growth.F :
+  - compute the SEAICE_DISABLE_HEATCONSFIX term accordingly
+    for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0)
+    when the previous code was not correct.
+  - in all cases diagnoze the boundary condition mismatch to SIaaflux
+  - in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add
+    that term to QNET (essentially to set the melt/freeze water to 0degC).
+    when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed.
 o verification/global_ocean.cs32x15/input.seaice :
- - add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget.
- - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces).
- - update results (output.seaice.txt) accordingly.
+  - add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget.
+  - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces).
+  - update results (output.seaice.txt) accordingly.
 o verification/lab_sea/input/data.seaice :
- - remove SEAICEheatConsFix, which is now be tested
-   in global_ocean.cs32x15. The presently coded fix 
-   is only consistent with real fresh water + nlfs.
- - update results (output.txt) accordingly.
+  - remove SEAICEheatConsFix, which is now be tested
+    in global_ocean.cs32x15. The presently coded fix
+    is only consistent with real fresh water + nlfs.
+  - update results (output.txt) accordingly.
 o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd).
 o AD_CONFIG.h file:
- - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;
- - remove #include "AD_CONFIG.h" from all included OPTIONS files and
-   add it explicitly in each fortran src file where it is needed.
-   motivation: header file AD_CONFIG.h is generated/modified after "make depend"
-   thus introducing potentially wrong dependency; therefore, better to include
-   it only where it's really needed, and after any other included OPTIONS file
-   (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN
-   or ALLOW_TANGENTLINEAR_RUN).
+  - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;
+  - remove #include "AD_CONFIG.h" from all included OPTIONS files and
+    add it explicitly in each fortran src file where it is needed.
+    motivation: header file AD_CONFIG.h is generated/modified after "make depend"
+    thus introducing potentially wrong dependency; therefore, better to include
+    it only where it's really needed, and after any other included OPTIONS file
+    (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN
+    or ALLOW_TANGENTLINEAR_RUN).
 
 checkpoint63p (2012/07/06)
 o pkg/autodiff: