--- MITgcm/doc/tag-index	2014/10/06 14:12:28	1.2078
+++ MITgcm/doc/tag-index	2016/04/29 14:29:04	1.2248
@@ -1,22 +1,935 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.2078 2014/10/06 14:12:28 gforget Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.2248 2016/04/29 14:29:04 mlosch Exp $
 $Name:  $
 
     Notes on tags used in MITgcmUV
     ==============================
 
+o pkg/seaice: ITD code
+  - fix picking up from a single category model by initialising 
+    heff/area/hsnowITD = 0. in seaice_itd_pickup.F
+  - split a long warning message in seaice_check_pickup.F into two lines,
+    because NEC SX-ACE cannot deal with the long line.
+o model/src:
+  - fix missing dPhiNH in pressure_for_eos.F (case: selectP_inEOS_Zc=3)
+o pkg/seaice:
+  - add missing checks for SEAICE_ALLOW_KRYLOV and SEAICE_ALLOW_BOTTOMDRAG
+o pkg/seaice:
+  - add basal stress as parameterisation for grounding ice
+    following Lemieux et al. (2015)
+  - turn on by setting new parameter SEAICEbasalDragK2 to a value
+    larger than 0. Lemieux et al. (2015) recommend 15.
+  - The adjoint complains with extra recomputations so there is also a
+    new cpp-flag SEAICE_ALLOW_BOTTOMDRAG that is undefined by default in
+    order to postpone the problem
+  - compile the new code in lab_sea
+o verification/halfpipe_streamice:
+  - update both TAF and OpenAD adm output (machine truncation differences)
+
+checkpoint65v (2016/04/08)
+o verification/advect_xz:
+  - increase overlap size from 3 to 4 and add new secondary test for PQM
+    advection scheme (with mono & wino limiter).
+  - change main exp. to test PPM (with weno limiter) adv.scheme on Temp.
+o model/src:
+  - new parameters "top_Pres" & "seaLev_Z" (replacing Ro_SeaLevel and recently
+    added phi0Ref) to set vertical axis origin and phiRef origin;
+    keep Ro_SeaLevel for backward compatibility (with a warning).
+   According to coordinate and fluid type:
+    OCN in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(1), @ the top)
+    ATM in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(Nr+1) @ bottom)
+    OCN in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(Nr+1)/g, @ the top)
+    ATM in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(1)/g, @ the bottom)
+  - remove Ro_SeaLevel from ATM experiment parameter files;
+  - in tutorial_global_oce_in_p, remove Ro_SeaLevel and set top_Pres to the
+    complement; update output.txt (changes at machine truncation level).
+o pkg/seaice/seaice_evp.F
+  - simplify computation of deltaZ and zetaZ to simple averaging following
+    Bouillon et al. (2013). This removes a lot of code, but also changes
+    verification experiment lab_sea.hb87 -> updated
+
+checkpoint65u (2016/03/14)
+o pkg/generic_advdiff:
+  - from Darren: add PPM and PQM advection schemes (number 40-42 and 50-52)
+    with 2 types of limiter (see: Engwirda & Kelley, submit. to JCP);
+    Note (from Darren): unlimited PPM/PQM scheme (40 & 50) are just for
+    testing and not for actual use.
+o model/src:
+  - add parameter "phi0Ref" to specify reference [pressure/geo] potential at
+    origin r = rF(1);
+  - add options (parameter selectP_inEOS_Zc) to select which pressure to use
+    in EOS for height coordinate: enable to include NH Pressure or to use
+    more accurate pressure vertical profile; options not linked to EOS type
+    (as previously, e.g., JMD95P/JMD95Z) but set default according to EOS type;
+  - start to implement variable gravity (along vertical): for now, only with
+    z-coords (not even z*).
+  - add Ideal Gas equation of state for height coordinate.
+  - update OpenAD output (affected at machine truncation level) of exp:
+    global_ocean.90x40x15, OpenAD (std) and tutorial_global_oce_biogeo.
+o pkg/exf:
+  - add ALLOW_EXF_OUTPUT_INTERP cpp switch to output the result
+    of exf interpolation (before any rescaling, rotation or interpolation
+    to velocity point) for each field that gets loaded from file. This option
+    identically mimics the input file organization (e.g. record numbers in year
+    by year input files) besides the change in horizontal grid.
+  - add rotateStressOnAgrid run-time switch so that wind stress fields
+    can be provided on the A-grid in zonal/meridional direction and
+    rotated on the fly. This only applies to the case when the exf
+    interpolation is off and rotateStressOnAgrid is false by default.
+o model/src:
+  - rename internal parameter "useDynP_inEos_Zc" to "storePhiHyd4Phys" (since
+    it's also used with pkg/atm_phys) and add few more parameters (but still
+    inactive, src code yet to come)
+
+checkpoint65t (2016/02/10)
+o pkg/atm_phys:
+  - from Ruth Geen: add optical depth dependence on CO2 concentration.
+o model/src:
+  - fix vertical inter/extra-polation of density factor rhoFacF (for anelastic)
+    for the case setCenterDr=T (delRc set from "data"); add output of rhoFacC&F.
+    Update output of exp. deep_anelastic (changes at truncation level).
+o tools:
+  - add a hack in "remove_comments_sed" (used only with TAF) for recent
+    version of OpenMPI (shipped with FC.23): comment out the new header
+    file "mpif-sizeof.h" which causes problems to TAF.
+o pkg/seaice:
+  - change the termination criterion so that maxits (SEAICElinearIterMax)
+    has an effect
+  - unify iteration parameters for implicit solvers (JFNK and Picard)
+    SEAICEnonLinIterMax replaces SEAICEnewtonIterMax/NPSEUDOTIMESTEPS
+    SEAICElinearIterMax replaces SEAICEkrylovIterMax/SOLV_MAX_ITER
+    SEAICEpreLinIterMax replaces SOLV_MAX_ITER in preconditioner
+    SEAICEpreNL_IterMax replaces NPSEUDOTIMESTEPS in preconditioner
+    SEAICEnonLinTol     replaces JFNKgamma_nonlin
+  - remove S/R SEAICE_FGMRES_DRIVER and put content into S/R SEAICE_JFKN
+  - add new Picard-Krylov solver, compile with SEAICE_ALLOW_KRYLOV and
+    use with SEAICEuseKrylov
+o pkg/seaice/seaice_lsr.F
+    fix small bug: replace zetaZ by zetaZloc in S/R seaice_lsr_rhsu/v; only
+    relevant if SEAICEuseStrImpCpl=T, and even then it does not seem to have
+    an effect.
+o pkg/seaice: add two new parameters
+  - SEAICEuseLSR to simplify the logic in seaice_dynsolver (this
+    parameter is not in any namelist)
+  - SEAICEusrPicardAsPrecon to allow s/r seaice_lsr to be used as
+    a preconditioner for the non-linear Newton iteration of the JFNK
+    solver
+o pkg/seaice/seaice_lsr.F: replace 1./SEAICE_deltaTdyn with recip_deltaT,
+  affects some experiments at truncation level:
+  - global_ocean.cs32x15.icedyn (11 digits),
+  - global_ocean.cs32x15.seaice (11 digits),
+  - seaice_itd (12 digits), seaice_itd.lipscomb07 (12 digits) -> update
+  - also update global_ocean.cs32x15 adjoint and tangent-linear results
+o pkg/salt_plume & pkg/thsice:
+  - for coupled  set-up with pkg/thsice in ATM and pkg/salt_plume in OCN,
+    connect salt_plume flux to ATM-OCN coupling pkgs interface:
+   a) in ATM: also cumulate salt-plume flux in S/R THSICE_SALT_PLUME (for
+     export to coupler interface) even without compiling pkg/salt_plume ;
+   b) in OCN: apply coupler salt-plume flux to pkg/salt_plume field
+     (saltPlumeFlux) just before exch call, in S/R SALT_PLUME_DO_EXCH.
+o pkg/dic:
+  - use the updated seaice fraction (from seaice pkgs) for DIC forcing
+    instead of the previous time-step value ; done in new S/R DIC_FIELDS_UPDATE
+    called from the top of dic_biotic_forcing.F (instead of in DIC_FIELDS_LOAD);
+  - move also update with values from ATM-OCN Coupler in the same new S/R
+    (previously done in ocn_apply_import.F).
+o tools/adjoint_options:
+  - specify explicitly "-f77" or "-f90" in default ad-optfile since TAF (default)
+    has been changed on Jan 14, 2016.
+o pkg/ggl90:
+  - add alternative discretisation of vertical shear (off by default), to
+    compute the mean (@ grid-cell center) of vertical shear compon instead of
+    vertical shear of mean flow (@ grid-cell center).
+  - add correct parenthesis in ALLOW_GGL90_SMOOTH code to get the same truncated
+    results on adjacent faces of cubed-sphere grids; this fix the restart.
+o pkg/atm_compon_interf:
+  - skip time-ave over cpl_atmSendFrq of Sea-Level Pressure (atmSLPr) and just
+    pass last value, stored directly before export to CPL ;
+    Note: this affects results of Coupled set-up where OCN uses useImportSLP=T
+  - remove atmSLPr from pickup files (no longer needed for restart)
+
+checkpoint65s (2016/01/13)
+o eesupp & genmake2:
+   - first check for Function ETIME and, if it fails, then check for subroutine
+     ETIME and consistent output; use the appropriate version in timers.F
+o model/src:
+  - to check restart test, add option to apply EXCH to U,V earlier, just before
+    integr_continuity; turned off by default.
+o pkg/dic:
+  - remove CPP option USE_ATMOSCO2 (not needed)
+o tools/tst_2+2:
+  - try to ignore difference between +0 and -0 in binary file, causing test
+    to fail for no good reason.
+o eesupp & genmake2:
+  - put back modif from Jinxuan Zhu - change etime fct call to S/R call -
+    but also check (in genmake2) that test runs and returns meaningful results.
+o coupler pkgs:
+  Finish implementation of optionally-exchanged variable switches (started on
+   Nov 12) with addition of few more exchanged fields, including 2-way exchange
+   of pkg/thsice vars to allow to use seaice dynamics (from pkg/seaice) & seaice
+   advection in OCN component; this requires sequential coupling.
+  coupler (pkg/atm_ocn_coupler):
+  - add argument msgUnit and iter number to CPL_SEND/RECV_ATM/OCN_FIELDS
+    routines (useful for debug).
+  - only export/import optionally exchanged fields (RunOff, seaice, Salt-Plume
+     flux, DIC fields) if corresponding switch is ON.
+  - add option to export RunOff to OCN (to use for DIC river input)
+  - add 2-way thSIce vars exchange; check for consistent cpl_sequential setting.
+  components (pkg/atm_ & ocn_compon_interf):
+  - to save memory space in ATM & OCN comp: add some #ifdef ALLOW_${PKG} around
+    optionally exchanged fields; add a check & stop in cpl_readparms.F.
+    ATMCPL.h: ALLOW_LAND for RunOff, ALLOW_THSICE for seaice, ALLOW_AIM for CO2;
+    OCNCPL.h: ALLOW_SALT_PLUME, ALLOW_DIC for DIC, ALLOW_THSICE for 2-W thsice.
+  - rename:   fracIce     -> sIceFrac_cpl (<- match coupler var name)
+    + in ATM: fracIceTime -> sIceFracTime ; seaIceTime -> sIceMassTime.
+  - add 2-way thSIce vars exchange ; add Salt-Plume flux ; add RunOff in OCN.
+  - hold in common block coupler optionally-exchanged variable switch
+    and set default "useImportXXX" accordingly; + check & stop if inconsistent.
+  - add diagnostics for all imported fields from coupler (in both OCN & ATM);
+    this is intended to replace the OCN cplFldtave.* output files (not updated
+    to contain new additional exchanged fields).
+o pkg/dic:
+  - fix an other bug (also from 2014/08/30) in dic_atmos.F, in dic_int1=3 code.
+o pkg/thsice:
+  - when coupled to ATM (useCoupler) with thSIce_skipThermo=T, skip reading
+    and writing of thsice pickup files.
+o pkg/atm_compon_interf:
+  - move all field individual export-call out of cpl_export_import_data.F
+    into new S/R ATM_EXPORT_FIELDS
+o pkg/atm_compon_interf:
+  - store state variables (for now, only thSIce fields) just before beeing
+    exported (in cpl_export_import_data.F, like on ocean side) instead of from
+    atm_store_my_data.F like all exported fluxes.
+  - new version of pickup_cpl: write field names into meta file and read meta
+    file to find field postion in pickup. Also only write/read fields meeded for
+    restart (same logic as main pickup file ; also using pickupStrictlyMatch)
+o pkg/dic:
+  - fix bug (added on 2014/08/30) in dic_atmos.F for the case dic_int1= 2 or 3.
+o pkg/seaice: add new parameter SEAICEpressReplFac to choose between
+    pressure replacement method (=1., default) or original Hibler (1979) (=0.)
+    value can be from domain [0,1] to average between the two methods
+o pkg/atm_phys:
+  - allow to provide 2-d map of albedo and mixed-layer depth from files (but
+    hold fixed in time).
+
+checkpoint65r (2015/12/21)
+o pkg/seaice:
+    fix bug in tridiagonal solvers for SEAICE_OLx/y>0, this affects the JFNK
+    solver (offline.dyn_jfnk) and global_ocean.cs32x15.seaice -> updated
+o pkg/seaice:
+  - fix a bug in computing areaS in (J-J -> J-1) that affects runs
+    when SEAICEscaleSurfStress=.TRUE.,
+  - apply areaW and areaS in S/R seaice_calc_lhs
+o pkg/atm_phys:
+  - add diagnostics for 3-D, Nr+1 levels diagnostics of radiative fluxes
+    (shortwave & longwave, net & downward) and diagnostics of temp. tendency
+    for individual contribution (convection, LSC cond, radiation)
+  - add Ruth Geen etal, GRL 2016, radiation options (see paper supp.
+    information); activated with: solar_exponent=0. and wv_exponent=-1.
+o pkg/ggl90:
+  - within IDEMIX add upper limit for horizontal group velocity to
+    avoid instability problems in the explicit horizontal diffusion term for
+    long time steps or high resolution
+o pkg/diagnostics:
+  - simplify setting of local-array size in diagstats_output.F: uses "numLevels"
+    (from DIAGNOSTICS_SIZE.h) to allow to write out more than Nr levels.
+o testreport:
+  - remove "-v" (verbose option) in default mpirun command.
+o pkg/seaice/seaice_growth:
+  - catch potential division by zero in ITD code, does not change
+    verification results
+o pkg/ecco:
+  - retire old codes to the Attic. The calls to retired functions are
+    left in a commented form in case they ever need to be re-activated.
+  - ecco_check.F: issue warning if any old CPP option is
+    defined that corresponds to retired codes -- then stop.
+o pkg/atm_compon_interf:
+  - change seaice fraction (use for OCN dic surf.flux) stored and sent to
+    coupler: use last time-step value instead of average over cplSendFrq_iter
+    time-step, similar to what is done for seaIceMass.
+    This will affect results (pkg/dic) of coupled ATM-OCN+dic set-up.
+o eesupp & genmake2:
+  - from Jinxuan Zhu: change etime fct call to S/R call (fix gfortran ETIME);
+    <= remove until a fix is found for some ifort version on ia32 machine.
+o pkg/seaice/seaice_evp:
+  - refine residual computation
+
+checkpoint65q (2015/11/18)
+o pkg/seaice/seaice_evp:
+  - fix residual computations so that they no longer affect the actual
+    simulation code
+  - fix seaice_readparams to be able to actually set new parameters
+    SEAICEaEVPcStar and SEAICEaEVPalphaMin, also fix logic a little
+o model/src:
+  - fix wrong truncation (single prec) from "FLOAT" function in expressions
+    like: deltaT*FLOAT(myIter) when myIter is large:
+     a) replaced by DFLOAT (if not seen by TAF);
+     b) remove "FLOAT" and use implicit type conversion (if seen by TAF).
+o pkg/aim_v23:
+  - write/read the expected CO2 pickups (from S/R AIM_DO_CO2): fix reading
+    when pickupSuff is set ; do write rolling pickups + at the end of the run.
+o pkg/atm_ocn_coupler + ocn_compon_interf:
+  - in prep for using pkg/seaice Dyn in coupled set-up, implement sequential
+    coupling option-1: ATM -(cpl)-> OCN and then OCN -(cpl)-> ATM ;
+    add corresponding call in DO_OCEANIC_PHYS.
+o coupler pkgs:
+  Start a new way to set-up optionally-exchanged variables (previously, only
+   there for exchange_DIC): switch on/off from 1 place, at run-time, in coupler
+   data.cpl (new) instead of at compile time in ATMIDS.h & OCNIDS.h ;
+   send switch to ATM & OCN compon before reading their own "data.cpl" (so that
+   compononent param default can be set accordingly).
+  Note: this new switch (cpl_exchange_[xxx]) is not a per variable switch
+   but rather applies to a group a fields (going both ways like for DIC)
+   and corresponds to an option of coupling config.
+  coupler (pkg/atm_ocn_coupler):
+  - change parameter file from "data" to "data.cpl" (in cpl_read_params.F),
+    and read namelist directly (without eessup S/R calls) instead of
+    in the very un-flexible old way, 1 param per line, in fixed order;
+  - add error-counter to track errors (e.g., missing "data.cpl") and to stop
+    cleanly in CPL_CHECK_CPLCONFIG
+  - add new coupling-exchange selectors (some not yet active) including
+    cpl_exchange_DIC (to set to 3 to replace atmCpl_exchange_DIC=T in ATMIDS.h
+                                         and ocnCpl_exchange_DIC=T in OCNIDS.h);
+  - add 2 new S/R (CPL_SEND_ATM/OCN_CPLPARMS) to send coupler-params to each
+    component ; called directly from coupler.F, after comp. registrations;
+  - rename few variable-ID names (in ATMIDS.h & OCNIDS.h):
+     atm/ocnSeaIceName --> atm/ocnSIceMassName ; atm/ocnFCO2Name ->
+      -> atm/ocnCO2FluxName ; atm/ocnWSpdName --> atm/ocnWindSpdName
+  components (pkg/atm_ & ocn_compon_interf):
+  - add ATM/OCN_CPL_OPTIONS.h in component pkgs and include the corresponding
+    CPP header file in all pkg source files.
+  - move checking of comp. configs out of cpl_exch_configs.F into new S/R
+    ATM/OCN_CHECK_CPLCONFIG;
+  - add error-counter to track errors (e.g., in "data.cpl") and to stop
+    cleanly in ATM/OCN_CHECK_CPLCONFIG;
+  - add new S/R CPL_IMPORT_CPLPARMS to import coupling-exchange selectors
+    from coupler ; called from initialise_fixed.F, after PACKAGES_BOOT and
+    before PACKAGES_READPARMS;
+  verification/cpl_aim+ocn/:
+  - update ATMIDS.h & OCNIDS.h (in shared_code) and use new parameter file
+    "data.cpl" for coupler (in input_cpl).
+o eesupp/inc:
+  - change the MPI-global-sum default (in CPP_EEOPTIONS.h) to:
+    #define GLOBAL_SUM_ORDER_TILES (only affects MPI built of global_sum_tile.F)
+    to always cumulate tile local-sum in the same order (still uses
+    MPI_Allreduce like standard code).
+  - in verification experiment code, remove local CPP_EEOPTIONS.h_mpi files
+    that are now identical to standard version (in eesupp/inc).
+o pkg/shelfice:
+  - add SHELFICETransCoeffTFile for initializing spatially varying
+    heat and salt transfer coefficients
+o pkg/atm_compon_interf & ocn_compon_interf:
+  - combine into 1 (new) S/R CPL_EXPORT_IMPORT_DATA the two previous
+    S/R CPL_EXPORT_MY_DATA & CPL_IMPORT_EXTERNAL_DATA
+  - move bi,bj loops inside S/R OCN_STORE_MY_DATA
+o pkg/atm_ocn_coupler:
+  - initialise to zero ATMVARS.h & OCNVARS.h arrays.
+o pkg/rbcs:
+  - select RBCS-mask for Temp & Salt the same way as for pTracer ; this allows
+    to compile with maskLEN=1 when all tracers use the same RBCS-mask.
+  - add a short report (to STDOUT) about RBCS-mask settings.
+
+checkpoint65p (2015/10/23)
+o pkg/seaice/seaice_evp.F: fix store directives and key computations, since
+    there is no adjoint test for EVP, we don't know what it does to the adjoint
+    solution, but at least there are no more recomputation warnings left
+o pkg/seaice/seaice_evp.F: slight modification of averaging so that EVP stands
+    a chance of giving the same results as a fully converged VP (JFNK) solver
+o tools/adjoint_options/adjoint_diva:
+  - fix bug (typo) in Tang-Linear FLAGS setting for MPI + DIVA
+o pkg/streamice:
+  - spotted bug in streamice_driving_stress using dyG where should have been dxG
+o pkg/exf:
+  - remove STOP statement that prevented to use wind or (wind-)stress
+    interpolation for constant-in-time forcing fields (wind/stress period = 0).
+o pkg/seaice:
+  - replace SEAICE_EVP_USE_ADAPTATION by run time parameters, requires
+    5 additionals 2D fields and 6 new store directives
+  - change logic in seaice_readparms.F: EVP code can now be turned on in
+    various ways, setting SEAICE_deltaTev is no longer required,
+    alternatively set SEAICE_evpAlpha/Beta, SEAICEuseEVPstar, SEAICEuseEVPrev,
+    or SEAICEaEVPcoeff
+o pkg/shelfice/shelfice_thermodynamics.F
+  - redefining uLoc/vLoc to u/v, instead of 2u/v
+o pkg/seaice/seaice_evp.F: introduce "adaptive EVP" by Madlen Kimmritz
+  - this is an intermediate state of a truely converging EVP that has
+    the potential of outperforming implicit VP methods, I do not recommend
+    using it yet.
+  - for now, "adaptive EVP" is turned on by setting SEAICE_EVP_USE_ADAPTATION
+    and all parameters are hardwired
+  - for convergence it still requires very smooth regularisations, that means,
+    if SEAICE_DELTA_SMOOTHREG is defined, deltaCreg=deltaC+deltaMin, which is
+    different from the VP case with deltaCreg=sqrt(deltaC**2+deltaMin**2); also
+    specific averaging appears to be required, still subject to tuning
+  - still needs cleaning and I need to turn parameter into runtime parameters
+  - add code to compute and print residuals of iteration, compile with
+    defining ALLOW_SEAICE_EVP_RESIDUAL to enable it
+o pkg/seaice/seaice_evp.F: fix a bug (factor of four in front of e12Csq)
+  that entered with r1.54 on Sep04, 2015, -> update results
+
+checkpoint65o (2015/09/14)
+o pkg/mom_vecinv & mom_common:
+  - add deep-atmosphere geometry factor in mom_calc_visc.F + in routines
+    called from there.
+  - add anelastic and deep-atmosphere geometry factor in pkg/mom_vecinv ; this
+    allows to use Vector-Invariant form in deep atmos and anelastic formulation
+o pkg/seaice: introduce fast ice parameterisation following Itkin et al. (2015)
+  and Koenig-Beatty+Holland (2012)
+  - two new parameters SEAICE_tensilFac and SEAICE_tensilDepth
+  - global 2D field tensileStrength, computed in seaice_calc_ice_strength
+  - requires an extra input argument for S/R seaice_calc_viscosities
+  - tensileStrength's depth dependence is different from Itkin et al. (2015)
+    (to be changed and played with, for now exponential)
+o pkg/seaice: introduce new parameter SEAICEscaleSurfStress (default = .FALSE.)
+  - if TRUE scale ice-ocean and ice-atmosphere stress acting on sea ice
+    by AREA according to Connelly et al. (2004), JPO.
+  - For EVP and the LSR solver, the implicit part of the drag term is
+    the only non-zero term in the denominator when there is no ice (which
+    prevented running the model with zero ice-ocean drag). If
+    SEAICEscaleSurfStress = .TRUE., this results in a division by zero
+    (or zero main diagonals BU/BV) which need to be caught. A practical
+    consequence is that for open water, the momentum equation reduce
+    to trivially 0 = 0 + 0 (for EVP). For LSR, BU/BV are reset to 1, if
+    they happen to be zero, often leading to a non-zero solution over
+    open water.
+o pkg/seaice: revise EVP code (seaice_evp.F) in preparation for a more
+    efficient EVP method.
+  - introduce area-weighted averages for e12 (analogously to
+    seaice_calc_viscosities.F); this totally changes lab_sea.hb87 (2 digits
+    remain, but also changing the order of terms in the previous average
+    changed the results as much) -> update experiment
+  - add SEAICE_DELTA_SMOOTHREG code
+  - disentangle computation of zetaC/deltaC and zetaZ/deltaZ, also for
+    TEM-code
+  - adjust loop bounds so that only required fields are computed
+  - add new averaging code for zetaZ/deltaZ (again similar to
+    seaice_calc_viscosities.F), inactive by default for now (will change
+    results again), but will replace old code eventually
+o eesupp/src:
+  - add an other alternative for multi-proc GLOBAL_SUM (in global_sum_tile.F)
+    to always cumulate tile local-sum in the same order
+    (option #define GLOBAL_SUM_ORDER_TILES in CPP_EEOPTIONS.h).
+    Still uses MPI_Allreduce (like standard code) but on array of tiles
+    and should be faster than GLOBAL_SUM_SEND_RECV code.
+  - switch almost all verification experiments that use GLOBAL_SUM_SEND_RECV
+    (defined in CPP_EEOPTIONS.h_mpi) to GLOBAL_SUM_ORDER_TILES instead.
+  - add CPP_EEOPTIONS.h_mpi with GLOBAL_SUM_ORDER_TILES defined in 14 more exp.:
+     aim.5l_cs, cheapAML_box, deep_anelastic, dome, fizhi-cs-32x32x40,
+     fizhi-cs-aqualev20, fizhi-gridalt-hs, global_ocean_ebm, matrix_example,
+     natl_box, solid-body.cs-32x32x1, tutorial_advection_in_gyre,
+     tutorial_baroclinic_gyre and tutorial_held_suarez_cs.
+
+checkpoint65n (2015/07/29)
+o pkg/thsice:
+  - add a warning when used with pkg/aim but without updating SST
+    (stepFwd_oceMxL=F & useCoupler=F & tauRelax_MxL<>-1 ).
+o pkg/offline:
+  - change where Offline-Fields are loaded, from load_fields_driver.F to
+    directly within FORWARD_STEP, just after updating iter number and time;
+  - move setting of GM and KPP diffusivity out of OFFLINE_FIELDS_LOAD into new
+    S/R OFFLINE_GET_DIFFUS that is called towards the end of DO_OCEANIC_PHYS;
+   These changes allow:
+    a) to recover exactly on-line results using deltaToffline=deltaTClock,
+    tested (using offlineIter0= nIter0 -1 and offlineTimeOffset= -deltaT/2)
+    both with Lin & Non-Lin Free-Surf, both with staggerTimeStep & synchronous
+    time-step, both with GM & KPP files and with recomputing these fields;
+    b) no needs to switch on staggerTimeStep anymore;
+    c) simplify rescaling of offline horiz. velocity with Non-Lin Free-Surf.
+  - update output of experiment tutorial_dic_adjoffline (only 3 digits left).
+o pkg/offline:
+  - change (rarely used) offset-iteration parameter to an offset time (in s):
+    can easily recover previous offset-iter effect by setting offset-time
+    (offlineTimeOffset) to offset-iter x deltaToffline;
+  - do not turn-off Temp & Salinity surface relaxation when using KPP (used
+    in KPP as part of surface buoyancy forcing) in offline run.
+  - fix ptracers KPP non-local term in the case where KPP is re-computed.
+o OpenAD
+  - Adding preliminary ggl90 test to OpenAD verification.
+    Config. with ggl90 currently diverges after 64 time steps
+    so will need more work to become more stable
+  - Adding preliminary kpp test to OpenAD verification.
+    required small tweakes in kpp_routines.F
+  - Merge and update from Krishna Narayanan's contrib area:
+    * Add one variable for preliminary OpenAD DIVA
+    * Add replacement time-stepping for OpenAD DIVA
+    * genmake2 flag -diva (but only for OpenAD; preliminary)
+    * required modifs for OAD_support
+    successful preliminary test for tutorial_global_oce_biogeo/
+o pkg/seaice:
+  - initialise deltaC in seaice_lsr, cosmetic changes in seaice_lsr
+  - add cpp-flag SEAICE_DELTA_SMOOTHREG for option of regularising
+    delta with a smooth function in s/r seaice_calc_viscosity
+    (no effect on EVP)
+  - rename local suffix "sqr" into "sq" for more consistent variable names
+o pkg/seaice:
+    add new parameter SEAICE_deltaMin that is used ***only***
+    for regularizing Delta (and nothing else, like the parameter
+    which is also used for all sorts of things SEAICE_EPS).
+    Defaults to SEAICE_EPS for backward compatibility only.
+o pkg/seaice: replace erroneously storing e12Csqr on the wrong tape with
+    the wrong key by inialising it before use -> fixes a recomputation
+    problem but does not fix the gradient
+o pkg/layers:
+  - move resetting of flux arrays to outside the iLa loop
+    (this caused layers_diapycnal to not work with more than one layer coord.)
+  - fix bug in calculation of layers_recip_delta in layers_init_fixed.F
+o pkg/layers:
+  - remove from common block 3D layers fields (used to diagnose transport
+    in tracer coords) and declare them as local arrays in layers_calc.F
+o pkg/seaice:
+  - Rename SEAICE_VECTORIZE_LSR_ZEBRA to SEAICE_LSR_ZEBRA and define it
+    in lab_sea forward experiment (changes results -> updated)
+  - update adjoint experiment lab_sea after cleaning up seaice_lsr_tridiagu/v
+o pkg/seaice: modify seaice_lsr.F in order to improve the gradient
+   computations; for SEAICE_VECTORIZE_LSR
+  - move the loops over which the tridiagonal solvers (seaice_lsr_tridiagu/v)
+    sweep to the outside,
+  - remove store directives and add "CADJ loop sequential" directives
+    in analogy to model/src/solve_tridiagonal.F
+  - replace many "#ifdef SEAICE_VECTORIZE_LSR_ZEBRA" by variable loop
+    boundaries to yield more readable code. This has also the charming side
+    effect that your can use SEAICE_VECTORIZE_LSR_ZEBRA without
+    SEAICE_VECTORIZE_LSR (i.e. adjoint without recomputations in
+    seaice_lsr_tridiagu/v now requires either of these flags, vectorization
+    still requires SEAICE_VECTORIZE_LSR with SEAICE_VECTORIZE_LSR_ZEBRA as
+    an additional option)
+   The tridiagonal solvers are now completely analoguous to solve_tridiagonal.F
+   but the adjoint gradients (which are affected by this change) still explode.
+o coupler (atm & ocn _compon_interf):
+  - avoid using Exch2 IO mapping if not suitable.
+
+checkpoint65m (2015/06/15)
+o pkg/layers:
+  - clean-up old parameters setting (from Sep 2012):
+    + remove old parameters setting from common block (declared locally);
+    + stop if any old parameter is mixed with new parameters;
+    + check for valid or consistent parameter setting (e.g., layers_name)
+  - check that layers_bounds for Pot.Density are in the right range;
+    this is supposed to catch un-updated setting after recently shifting
+    potential density field "prho" by -1000 (now in "sigma" scale).
+o pkg/layers:
+  - Added missing call to layers_fill for keeping track of tottend in
+    pkg/diagnostics/diagnostics_fill_state.F
+o pkg/layers:
+  - added CPP flux LAYERS_FINEGRID_DIAPYCNAL to disable fine-grid binning
+    of diapycnal fluxes
+o pkg/layers:
+  - reverted changes to interpolation to previous treatment; there
+    was never actually a problem
+o pkg/layers:
+  - fix interpolation of layers tracers in the presence of partial cells
+  - add lots of new functionality to compute water mass transformation
+    (enabled by CPP flag LAYERS_THERMODYNAMICS)
+  - add new calls from main code (diags_oceanic_surf_flux.F,
+    thermodynamics.F, impldiff.F) and gad to save the necessary fields
+    for layers_thermodynamics calculations
+o pkg/ptracers:
+  - add capability of stepping a passive tracer forward without advection
+    by setting PTRACERS_advScheme to 0.
+o pkg/diagnostics:
+  - add few (threads) _BARRIER around any update of "diag_pkgStatus".
+o pkg/layers:
+  - shift potential density field "prho" by -1000 for density layer averaging so
+    that it corresponds to usual "sigma" definition (i.e., rho(p=const)-1000);
+    Note that density bin boundaries (layers_bounds in data.layers) have
+    to be set accordingly (i.e., shifted, in sigma scale).
+o pkg/layers:
+  - fix snap-shot output of layer thickness @ V.pt and output of pot.density
+  - fix calculation of layer non-weighted velocity and layer probability
+  - add diagnostics for pot.density used for layer averaging
+o pkg/seaice:
+  - seaice_calc_viscosity.F: change computation of deltaC**2 to ensure
+    positiveness, modify a few comments and improve variable names,
+  - the changed computation of deltaC affects most seaice-related
+    experiments at the truncation level.
+    seaice_itd.thermo is affected by far the most, with
+    only 7 digits of agreement remaining; update experiments.
+
+checkpoint65l (2015/05/04)
+o pkg/shelfice:
+  - in shelfice_thermodynamics.F, if SHELFICEBoundaryLayer=.true., then set
+    factor drKp1 to zero where it is negative (ie. do not use
+    SHELFICEBoundaryLayer if hFacC>1)
+  - the same for factor drLoc in shelfice_forcing.F
+o tools/genmake2: move FEXTRAFLAGS from FFLAGS to FOPTIM to avoid a problem
+    with modules in ptracers, when using testreport option "-small_f"
+o pkg/seaice/seaice_growth.F (in case of SEAICE_ITD)
+  - replace tmpscal1**1.36 by faster exp(1.36*log(tmpscal1))
+o verification/testreport
+  - add new option -small_f
+    with this option testreport first makes the target small_f (*.f files)
+    before running make (all). This is useful for explicit inlining when
+    all sources need to be full available.
+o pkg/exf/exf_interp.F:
+    remove previous changes related to reverse (decreasing) input grids latitude
+
+checkpoint65k (2015/04/01)
+o pkg/ecco:
+    fix missing cosphi initialization; use eccoiter in place of optimcycle;
+    if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
+    instead of active read/write
+o pkg/ctrl:
+    if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
+    instead of active read/write.
+o pkg/autodiff: make autodiff_readparms.F and autodiff_whtapeio_sync.F
+    return if .NOT.useAUTODIFF
+o pkg/seaice: add CPP brackets (cost function related).
+o model/src:
+    add useAUTODIFF run time switch.
+o pkg/exf/exf_interp.F:
+    add code to allow input grids with latitude starting in the north (i.e. when
+    j=1 corresponds to northern edge of field); modify global_with_exf to test
+    this feature.
+o verification/testreport:
+  - replace "grep -A3" with POSIX conformal sed command, because there are
+    implementations of grep that cannot do contextual searches
+  - replace "cat -n" by "nl" (two occurrences), because not all implementations
+    of "cat" have the option "-n"
+o model/src:
+    add new file gsw_teos10.F that contains 3 functions, more or less a copy
+    of the gsw_toolbox.f90 of the TEOS-10 fortran interface, that are used to
+    convert from conservative to potential temperature. For now they are not
+    called anywhere.
+o pkg/ggl90: make "useIDEMIX" useful
+  - re-organize code in s/r ggl90_calc a little to move computations that
+    are different for idemix into separate loops (changes verification
+    experiment idemix at truncation level, 12 digits remain -> updated)
+  - requires 2 new 2D fields KappaM, verticalShear
+  - make hFacI and recip_hFacI local 3D variables that are passed to
+    s/r ggl90_idemix
+  - fix and improve some comments
+
+checkpoint65j (2015/02/25)
+o pkg/openad
+  - synchronize seawater.F with version in model/src: replace routine
+    body of sw_temp by calling sw_ptmp and fix/add a few comments.
+o pkg/mnc:
+  - change default value of pickup_read/write_mnc params to FALSE
+    (since few features are missing in reading MNC pickup files).
+o model/src:
+  - change default (background) vertical diffusivity for salt to be the
+    temperature (background) vertical diffusivity.
+  - change background vertical diffusivity in vertical mixing pkgs ggl90,
+    kl10, my82 and pp81 from temperature diffusivity to salinity diffusivity.
+    This makes ptracers default diffusivity (that uses salt diffKr) more
+    consistent with vertical mixing schemes.
+o verification/testreport:
+  - fix typo in "-pcls" option ;
+  - put temp files in /tmp (instead of in local dir)
+  - add option "-ncad" to use genmake2 new option "-nocat4ad"
+  - allow to use "-j" option (for multi-procs make) for AD, OAD and TLM.
+o pkg/ggl90 (idemix code):
+  - apply few fixes ; add some missing "_d 0" ; update output of exp.
+    global_ocean.90x40x15.idemix
+o OpenAD
+  - enable active file I/O and begin removal of work-around code
+    for OpenAD for handling control variables (memory vs. active files)
+  - new CPP options file OPENAD_OPTIONS.h
+  - revert to genarr2d gradient check for hs94.1x64x5
+  - (genarr3d tested by tutorial_global_oce_biogeo, tutorial_tracer_adjsens)
+  - gentim2d works for halfpipe_streamice but not yet hs94.1x64x5
+o tools/genmake2:
+  - add option for an alternative Makefile (from Martin) where multiple
+    source files are sent to TAF (instead of all in one file).
+o pkg/ggl90: add IDEMIX (Olbers and Eden, 2013)
+  - code provided by Carsten Eden as an extension of ggl90
+  - so far the code is turned on within ggl90 by setting a CPP-flag at
+    compile time; a runtime flag implementation is not yet complete
+  - tested in new verification experiment global_ocean.90x40x15.idemix
+o verification:
+  - reduce length of the AD test run by half for experiments
+    global_ocean.cs32x15 (std + thsice) and isomip
+  - enable active file I/O for OpenAD, adjust verifications accordingly
+  - halfpipe_streamice: change gradient check from genarr2d to gentim2d
+o verification/testreport:
+  - fix two non-POSIX sed statements so that there are no error messages
+    on Mac OS X
+  - replace hostname -s with hostname | sed 's/\..*$//'
+o model/src/seawater.F:
+  - simplify SW_TEMP to just calling SW_PTMP with P and PR exchanged
+    (following the matlab code), which would have avoided the bug caught
+    by Matt (see below) in the first place
+o pkg/shelfice:
+  - implement alternative discretisation of quadratic drag (selectBotDragQuadr)
+    and true distance in no-slip BC (bottomVisc_pCell) similar to bottom-drag.
+  - fix sign of friction tendency (no-slip BC) and fix u,v drag for thin
+    ice-shelf case (i.e., within surface level).
+  - add config summary in shelfice_check.F
+  - remove global variable recip_SHELFICElatentHeat and replace by a local
+    variable recip_latentHeat
+  - introduce diagnostics for friction velocity uStar (in case of
+    SHELFICEuseGammaFrict)
+  - change verification experiment isomip.htd:
+    + start from pickup (as input_ad at nIter0=8640)
+    + start from SHELFICEmassFile instead of SHELFICEloadAnomaly file
+    + test SHELFICEuseGammaFrict = .TRUE.
+    + test SHELFICEadvDiffHeatFlux = .TRUE.
+o model/src:
+  - fix bug (Thanks to Matt) in function SW_TEMP (to convert Pot.Temp to
+    in-situ Temp) and in routine SW_TEMP (in pkg/openad);
+    update output of experiments global_with_exf.yearly and isomip (all 6).
+o pkg/shelfice:
+  - change setting of kTopC to also be zero where there is no ice-shelf.
+  - zero out surface forcing arrays (for now, for T & S + EmPmR) where
+    ice-shelf is.
+  - first attempt to get RealFreshWaterFlux effects: for now, only without
+    SHELFICEboundaryLayer ; not consistent if using synchronous time-stepping.
+o pkg/seaice: add the option to prescribe a fixed thickness PDF
+  for thermodynamic calculations
+  - because of divisions of the type 7/7 not exactly equal to 1, this change
+    affects results of some verification experiments by up to 4 digits:
+    global_ocean.cs32x15.seaice, lab_sea, lab_sea.fd, lab_sea.salt_plume,
+    seaice_obcs, seaice_obcs.seaiceSponge, seaice_obcs.tides
+    adjoint: lab_sea, lab_sea.noseaicedyn
+    -> updated
+
+checkpoint65i (2015/01/23)
+o model/src:
+  - change units of frictionHeating field from W to W/m^2
+  - fix bug in frictional heating from stratospheric drag in
+    S/R ATM_PHYS_TENDENCY_APPLY_V
+  - with synchronous time-stepping: move resetting to zero of frictionHeating
+    field from load_fields_driver.F to thermodynamics.F ;
+  - add diagnostics for frictional heating.
+o model/src & gmredi K3D:
+  - add frictionHeating field to pickup-files (for synchronous time-stepping)
+  - move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h
+  - rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name
+    and name in pickup file).
+  - fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F
+o model/src:
+  - move (from ini_forcing.F) initialisation of all arrays in header file
+    FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart
+    (since Nov 2012) with option selectAddFluid=1.
+o pkg/shelfice:
+  - change units (+ document) of newly added field "shelfIceMassDynTendency"
+  - upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays.
+o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers
+o pkg/seaice: two new runtime parameters:
+  - SEAICE_cStar replaces the hard wired "20" in the strength formulation,
+    long overdue
+  - SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012)
+    parameterization of tensil stress for fast ice (does not do anything yet)
+o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method
+    for LSR: move checking overlaps out of JFNK-if-block
+o pkg/atm_phys:
+  - move copy of grid and dynamical fields out of atm_phys_driver.F into
+    new S/R ATM_PHYS_DYN2PHYS.
+  - fix level height for Linear Free-Surf case (to be consistent with
+    fixed-in-time pressure levels).
+o pkg/mom_common (bottomdrag):
+  - average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center
+    to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG;
+    update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag.
+o pkg/shelfice (u/v_drag):
+  - add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG;
+  - use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F
+    (now similar to shelfice_u_drag.F)
+  - remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG
+    from mom_vecinv.F (similar to mom_fluxform calls).
+o pkg/mom_common (bottomdrag):
+  - add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG;
+  - add options for alternative discretisation of velocity norm in quadratic
+    bottom drag: averaging of grid-cell-center KE to U.point and V.point
+    (selectBotDragQuadr=0, original code) can produce noisy patterns; this
+    improves when averaging only the other component (e.g. vVel for U bottom
+    drag) using wet-point method (selectBotDragQuadr=2) or not (=1).
+  - add options (bottomVisc_pCell) to account for partial-cell in bottom
+    friction (no-slip BC) thus getting the true distance from the bottom;
+    off by default since this also reduces model stability (explicit bottom
+    friction). Changes produce different machine truncation with linear-drag
+    + no-slip BC: update output of experiments exp4.stevens (10 digits) and
+    front_relax (bvp & mxl, 10 & 11 digits).
+o model/src & mom pkgs:
+  - add one more level to vertical viscosity local arrays (Nr+1, previously Nr)
+    since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k
+  - for now and until vertical mixing scheme are updated to fill up level Nr+1,
+    just copy level Nr value to level Nr+1.
+o doc:
+  - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
+o pkg/streamice:
+  - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
+    SHELFICE.h: move array shelficemass to init_varia, initialise
+    from array shelficemassinit, which is set in init_fixed and
+    has option to be set from file; introduce array
+    shelficeMassDynTend array, set thru file in init_fixed
+  - NEW FILE: shelfice_step_icemass.F: update shelficemass from either
+    shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in
+    pkg/streamice
+  - shelfice_thermodynamics.F: call shelfice_step_icemass if
+    SHELFICEMassStepping = .true.
+  - shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f
+
+checkpoint65h (2014/12/17)
+o verification/global_ocean.90x40x15, global_ocean_ebm:
+  - update to generic controls.
+o pkg/ctrl:
+  - ctrl_map_ini_genarr.F: test for igen>0
+  - ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D.
+  - move gentim2d part of ctrl_map_ini_genarr.F to
+    new separate routine : ctrl_map_ini_gentim2d.F
+  - ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F:
+    add time variable weights and cyclic controls (time mean,
+    seasonal cycle, etc) capabilities to gentim2d
+o pkg/ecco:
+  - move reading of error, conversion to weights from
+    ecco_cost_init_fixed.F to ecco_toolbox.F (ecco_readwei)
+o global_oce_llc90, cs32:
+  - activte sbo.
+  - CTRL_SIZE.h : add maxCtrlProc.
+  - activate the new genctrl capabilities.
+  - update following reorganization of global_oce_input_fields.tar.gz	
+o pkg/ctrl/ctrl_ad_diff.list:
+  - add missing ctrl_init_rec.f
+o tools/OAD_support/keepOriginal:
+  - add ctrl_init_rec.F
+o model/src/the_main_loop.F, pkg/ctrl/ctrl_map_ini_genarr.F:
+  - avoid recomputations of xx_gentim2d_dummy.
+o momentum diagnostics:
+  - move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and
+    mom_vecinv.F to timestep.F (to include Smag-3D contribution).
+o pkg/seaice/seaice_lsr.F:
+  - fix computation of BU/BV, make sure they are non-zero, only necessary
+    for cubed sphere exchanges and SEAICE_OLx/y>0.
+    This makes calling s/r fill_cs_corner_rl obsolete (removed).
+o verification/global_ocean.cs32x15/input.seaice
+  - add test for strong implicit coupling and restricted addtive Schwarz
+    methods for LSR
+  - update results/output.seaice.txt
+o verification/tutorial_global_oce_biogeo:
+  - AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up)
+    and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK);
+    update output_adm,_oadm,_tlm.txt
+o pkg/dic:
+  - change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h
+  - add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn
+    for tracer 1 & 2 is set (to avoid double counting of dilution effect).
+o verification/tutorial_global_oce_biogeo:
+  - AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since
+    dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ;
+    update output_adm,_oadm,_tlm.txt
+o eesupp/src:
+  - add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F)
+    and call it in seaice_lsr when using nonzero SEAICE_OLx/y
+o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing
+  LSR (following Hutchings et al. 2004)
+  - introduce zetaZ as a global variable (requires adjustments in
+    seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ
+    in seaice_calc_viscosities.F
+  - new flag SEAICEuseStrImpCpl (default off)
+  - add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the
+    momentum equations
+  - JFNK-solver (preconditioner) adjusted to allow using this method
+    (where it does not have any positive effect)
+o pkg/seaice
+  - add overlap for restrictive additive Schwartz method also to LSR, but
+    turn it off by default (because it only seems to work for non-cubed
+    sphere/llc topologies)
+o pkg/autodiff
+  - add extra exchanges in addummy_in_steppging also for mnc output
+o pkg/seaice:
+  - add extra exchanges before dumping adjoint fields in seaice_ad_dump.F
+    to avoid stripes in the adjoint output (similar to addummy_in_stepping.F)
+o pkg/obcs:
+  - add option to specify domain-connected piece Id along OB though files
+    (for now, only used to diagnose PhiVel; default =1 -> global correction)
+  - modify obcs_diag_balance.F to process each connected-part separately;
+    exclude OB where Id = 0 but keep the full divergence there (-> constant
+    Psi along this portion of OB and all inflow derived from grad(Phi))
+  - add example of OB-conect files in verification/so_box_biogeo/input.
+o pkg/diagnostics:
+  - improve treatment of Open-Boundaries in Velocity-Potential calculation:
+  a) use non zero matrix element across OB and solve for Phi 1 grid point
+     outside OB (i.e, where tracer OBCS are applied).
+  b) global imbalance of inFlow/outFlow across OB: instead of modifying
+     velocity across OB, spread it uniformly along the OB in the RHS.
+
+checkpoint65g (2014/11/19)
+o pkg/diagnostcis:
+  - add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param
+o pkg/my82,pp81,kl10:
+  - fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D
+    field diffKr as background diffusivity to set minimum diffusivity value.
+o pkg/seaice:
+  - add new parameter SEAICEuseEVPrev (for revisited EVP by
+    Bouillon et al 2013)
+  - add SEAICE_evpAlpha/Beta to namelist
+  - modify seaice_evp code to able to use SEAICEuseEVPrev. These changes
+    involve trivial re-ordering of divisions/multiplications that should not
+    have any effects, but ... they do change the results of lab_sea.hb87 so
+    that only 2 digits of agreement remain, in line with the general
+    instability/fragility of the evp-code. For now, I do not care and just
+    update the verification experiment
+o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc)
+  - remove xx_genarr2d_numsmooth etc
+  - use xx_genarr2d_preproc etc instead
+  - carry out smooth_correl2D at initialization stage rather than during
+    time stepping.
+  - get smoothOpNb from xx_gentim2d_preproc
+o global_oce_cs32 :
+  - add test of generic ecco capabilities.
+o pkg/exf/exf_getsurfacefluxes.F :
+  - add to tmpUE/tmpVN rather than re-initializing them (conventional behavior).
+o pkg/ctrl,ecco :
+  - omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED
+    is defined.
+o pkg/seaice: add diagnostics for Delta (deformation parameter)
+o model/src:
+  - when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical
+    diffusivity (background) is specified but ignored.
+o verification:
+  - in testreport, convert hostname to lower case for default output dir name
+o model, pkg : add useCTRL, useECCO parameters (on/off run time switch).
+o pkg/dic: add modifications from Hajoon:
+  - add iron sedimentation flux function of the flux of PO4 out of bottom layer
+  - light attenuation: add self-shading effect by climatological Chlorophyll
+    (read from file).
+o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also
+    compiles when SEAICE_ALLOW_DYNAMICS is undefined
+o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate
+    AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than
+    ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted,
+    approach where CPP_OPTIONS.h includes an omnipotent
+    ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h').
+o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where
+    ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong.
+o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF
+    to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included
+    (it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...)
+o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl :
+  add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed
+  - ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h
+  - AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h
+  - CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc
+o pkg/ctrl,ecco,exf :
+  - remove variables associated with NON-generic costs,
+    unless ECCO_CTRL_DEPRECATED is defined.
+  - remove NON-generic NON-obcs controls,
+    unless ECCO_CTRL_DEPRECATED is defined.
+o pkg/ctrl : added ctrl_local_params.h
+o pkg/ecco : added ecco_local_params.h
+o verification : added ECCO_CTRL_DEPRECATED to most as and oad
+    experiments, which will progressively be removed once the
+    experiments are revised to use only generic controls/costs.
+
+checkpoint65f (2014/10/13)
+o pkg/ctrl, ecco, seaice : minor changes in headers
+o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic
+    cost function and control capabilities added since checkpoint65c.
+o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h.
 o pkg/ecco: increase modularity and improve logic
-  - ecco_toolbox.F (new) : basic operations that are often used
-     (for now, ecco_toolbox.F simply contains function ecco_zero).
+  - ecco_toolbox.F (new) : basic operations that are often used,
+    including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk,
+    ecco_addcost, ecco_add, ecco_div, ecco_readbar.
   - cost_gencal.F (new) : determine filnames and records.
-  - cost_gendif.F (new) : compute masked model-data difference.
-  - cost_genread.F : use ecco_zero to initialize field to 0s.
+  - cost_genread.F, cost_generic.F : condense code using ecco_toolbox.
   - cost_generic.F : use spzeroloc rather than hard-coded -9999,
     and exploit the above functions leading to more compact code.
+  - cost_genread.F : rm un-necessary arguments, re-arrange args order.
   - ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj,
     using_ers, using_gfo, using_mdt is now only defined within gencost)
 o pkg/ecco: extend generic cost capabilities
   - pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost
-    capabilities via gencost_preproc (+ _c,_i,_r related params), 
+    capabilities via gencost_preproc (+ _c,_i,_r related params),
     gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod,
     gencost_outputlevel arguments to cost_generic
   - pkg/ecco/cost_genread.F (new) : interface between cost_generic
@@ -34,16 +947,16 @@
   - pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs
 o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA
 o pkg/ecco: internal re-organization
-  - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl 
+  - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl
     (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,
-    mv relevant variables definition from ecco_cost.h to ecco.h, 
+    mv relevant variables definition from ecco_cost.h to ecco.h,
     make sure gencost routines only include ecco.h)
   - throughout : add missing CCP switches, rm unused variables,
     and rm un-necessary CPP switches
-  - throughout gencost routines : replace modelstartdate with 
+  - throughout gencost routines : replace modelstartdate with
     gencost_startdate when needed
   - cost_bp_read.F : use arguments, instead of common blocs
-    so that it can be used also by (new) cost_gencost_bpv4.F 
+    so that it can be used also by (new) cost_gencost_bpv4.F
   - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0
   - ecco_phys.F : compute etanFull
   - ecco_readparms.F : rename using_topex as using_tpj, add
@@ -361,8 +1274,8 @@
     nearly a factor of 10 (but keep in mind there is mostly seaice code in
     this experiment):
     > size mitgcmuv_ad
-    text    data        bss     dec 	   hex	
-    5100659 1216  220458952  225560827  d71c8fb	
+    text    data        bss     dec        hex
+    5100659 1216  220458952  225560827  d71c8fb
     5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
     but only a moderate increase of 36% for global_ocean.cs32x15:
     text    data        bss     dec        hex