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-revision 1.1980 by mlosch,
Wed Apr 23 12:42:19 2014 UTC
+revision 1.2254 by mmazloff,
Thu May 19 20:31:27 2016 UTC
 Line 4 
 $Name$
      Notes on tags used in MITgcmUV
      ==============================
+ o added pkg/bling:
+   - intermediate complexity biogeochemical model
+   - see bling_description.txt for details
+   - verification experiment is global_oce_biogeo_bling
+ o pkg/seaice: fix tensile stength computation
+   - replace global field tensileStrength by tensileStrFac
+   - tensileStrFac can be computed once in S/R seaice_init_varia
+   - fortunately that does not affect any verification results
+ checkpoint65w (2016/05/12)
+ o pkg/ctrl/ctrl.h: fix a comma in common block list, so that code compiles
+      with ECCO_CTRL_DEPRECATED defined
+ o verification/global_ocean.cs32x15:
+   - change secondary test "viscA4" to also test "selectP_inEOS_Zc=3"
+     with "selectNHfreeSurf=1".
+ o model/src (non-hydrostatic free-surface):
+   - More "natural" expression of NH free-surface term (case selectNHfreeSurf=1):
+     was: tmpSurf/(1+tmpSurf); changed to: 1/(1+Gamma) with Gamma=1/tmpSurf.
+   - Calculate surface vertical velocity after 2-D solver adjustment (accounts
+     for EmPmR if RealFreshWaterFlux); used in RHS (cg3d_b) if exactConserv
+     and used to compute dPhiNH (in post_cg3d.F) if selectNHfreeSurf=1.
+     This fixes EmPmR contribution when selectNHfreeSurf=1 & RealFreshWaterFlux.
+   - Update output (changes at machine truncation level) of verification exp:
+     exp4 (11 digits for cg2d), global_ocean.cs32x15.viscA4 (11.d),
+     short_surf_wave (13.d) and tutorial_deep_convection.smag3d (12.d).
+ 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
+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,
+     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_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),
+     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
+     and active_read, making room for gencost_preproc to take effect.
+     Added preproc code ('climmon') to replace GENERIC_BAR_MONTH.
+   - pkg/ecco/cost_generic.F :
+     compute and store misfit maks*(model-data) in localdif that is
+     then used in cost and for output, output misfit if outlev.GT.0
+   - pkg/ecco/cost_averagesfields.F : depend on gencost_barskip
+     rather gencost_barfile for deciding whether to write barfile
+   - pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd
+   - pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from
+     ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip
+   - pkg/ecco/ecco_summary.F : report gencost variables
+   - 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
+     (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,
+     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
+     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
+   - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0
+   - ecco_phys.F : compute etanFull
+   - ecco_readparms.F : rename using_topex as using_tpj, add
+     bpv4-grace to gencost list, initialize added parameters
+   - ecco_summary.F : include SIZE.h needed for augmented ecco.h
+ checkpoint65e (2014/09/28)
+ o pkg/obcs:
+   - replaced the just-added CPP options with run-time variables
+     (see pkg/obcs/OBCS_PARAMS.h for details)
+ o pkg/obcs:
+   - add additional CPP options for sponge boundary layers
+     (see pkg/obcs/OBCS_OPTIONS.h for details)
+ o pkg/atm_phys:
+   - implement simple (obliquity only, assuming circular planet orbit)
+     seasonal cycle for incoming insolation ; used when run-time parameter
+     "select_incSW" is set to 1 ; by default (=0), uses old unchanged formula.
+ o pkg/exf, pkg/ecco, pkg/ctrl:
+   - add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets
+   - activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip
+   - implement gentim2d for xx_tauu, xx_tauv
+ o pkg/ctrl, pkg/ecco :
+   - fix and complement the generic controls implementation
+ o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F,
+     pkg/shelfice/shelfice_thermodynamics.F,
+     verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F,
+     verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F :
+   - add weight in CTRL_GET_GEN calls
+ o pkg/ctrl :
+   - ctrl_get_gen.F : add weight as input parameter, and apply
+     it directly rather than using smooth_correl2Dw (to be retired).
+   - ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call
+ o pkg/ctrl :
+   - introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F,
+     ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F)
+   - re-activate ctrl_summary (call in ctrl_init.F)
+ o pkg/ctrl/ctrl_cost_gen.F :
+   - fix CCP brackets, remove un-necessary myiter, mytime
+ o pkg/ecco, pkg/ctrl :
+   - remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F)
+   - remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F)
+   - add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F)
+   - add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F)
+ checkpoint65d (2014/09/15)
+ o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F :
+   - add xx_genarr2d_bounds,xx_genarr3d_bounds,
+     xx_genarr2d_numsmooth, xx_genarr3d_numsmooth
+ o pkg/ctrl/ctrl_map_ini_genarr.F :
+   - remove compilation failure
+   - replace hard coded example
+   - use ctrl_map_ini_gen2D, 3D
+ o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F :
+   - on/off switch based upon xx_genarr2d_weight,3d
+ o src/packages_init_variables.F :
+   - regroup pkg/estimation calls
+   - remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO
+     (moved to ctrl_init_variables)
+ o cost/cost_init_varia.F :
+   - remove ecco_cost_init_varia
+     (moved to ecco_init_varia)
+ o ctrl/ctrl_init_variables.F :
+   - add CTRL_MAP_INI, CTRL_MAP_INI_ECCO
+   - add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI
+ o ctrl/ctrl_map_ini.F :
+   - remove ctrl_map_ini_genarr, seaice_ctrl_map_ini
+     (moved to ctrl_init_variables)
+ o ctrl/ctrl_map_ini_ecco.F :
+   - remove ECCO_PHYS (mv to ecco_init_varia)
+   - remove seaice_ctrl_map_ini (mv to ctrl_init_variables)
+ o ecco/ecco_ad_diff.list :
+   - add ecco_init_varia.f
+ o ecco/ecco_init_varia.F
+   - new routine
+ o pkg/streamice:
+   - move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F
+     to streamice_init_fixed.F ; fix setting of STREAMICEisOn.
+   - from model/src, only call pkg/streamice routines if useStreamIce is TRUE.
+ o pkg/generic_advdiff:
+   - fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014.
+ o pkg/exf:
+   - exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown,
+      xxg_precip capability
+   - exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch
+ o pkg/ctrl:
+   - ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d
+ o model/src/load_fields_driver.F :
+   - move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING
+     so xx_gentim2d can be applied to e.g. exf fields in a timely manner.
+ o OpenAD verification experiments:
+   - Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h
+     in src files (to enable to skip the ECCO_CPPOPTIONS.h);
+     for now, only in pkgs used in OpenAD verification experiments.
+   - Change all except one (halfpipe_streamice) OpenAD experiments to use pkg
+     specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h)
+     instead of using ECCO_CPPOPTIONS.h (with all relevant options in it).
+     This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests.
+ o OpenAD verification tests:
+   - finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD);
+   - finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for
+     tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp.
+   - leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/)
+     and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC).
+ o model/src & generic_advdiff:
+   - change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S
+     forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model
+     dynamics requires valid tracer forcing only over tile interior but, for
+     some diagnostics, may need to extend it over 1 point in tile halo region.
+   - in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid
+     tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max
+     setting in temp/salt/ptracer_integrate.F
+ o pkg/dic:
+   - multiply tracer tendencies by maskInC (if ussing OBCS) before updating
+     gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER
+     in gchem_forcing_sep.F
+ o pkg/autodiff & obcs:
+   - add storage of current OB values for U & V (was already done for T & S).
+ checkpoint65c (2014/08/30)
+ o pkg/dic:
+   - take out of dic_atmos.F the initialisation part (corresponding to istate=0)
+     and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for
+     AD compilers (but still a Pb with multi-threading and Ajoint dependencies).
+ o verification:
+   - new experiment testing OBCS and DIC pkgs, using params & output from
+     tutorial_global_oce_biogeo but limited to a sub-domain around Drake
+     passage: take OBCS from the last year of a 2 yrs simulation and initial
+     conditions from t=1.yr while keeping the same forcing.
+ o model/src:
+   - when allowFreezing=T, only reset below freezing initial Temp to Tfreezing
+     (at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T).
+ o pkg/diagnostics (Stats-Diags):
+   - re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to:
+     a) refine region where stats are computed, excluding where arrhFac=0 ;
+     b) fix missing interior mask (use with OBCS) in 3-D fields statistics;
+     c) extend regional stats over the region edges (for U or V pt location).
+ o pkg/gchem:
+   - add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since
+     pkg/dic is currently changing/updating ptracers values beyond the OB).
+ o verification (hs94):
+   - convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords
+     bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments
+     hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of
+     apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged.
+ o pkg/ptracers:
+   - implement Adams-Bashforth on pTracers (instead of on tracer tendency),
+     switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs)
+   - change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer
+     with AB-2 code (so that it get tested).
+ o model/src:
+   - allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS)
+     with AB-2 code (previously only available with AB-3 code).
+     Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F
+     to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done
+     there, by calling CYCLE_AB_TRACER).
+ o pkg/generic_advdiff:
+   - change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS,
+     GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R
+     + also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in
+     S/R temp/salt/ptracers_integrate.F
+ o model/src & pkg/ptracers:
+   - remove common block variables gT,gS (in DYNVARS.h), except when
+      USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly.
+   - remove common block variable gPtr.
+ o model/src & pkgs:
+   - change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R
+      ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G,
+      IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT,
+      GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T
+   + change accordingly all calling S/R.
+   - use local temperature/salinity/ptracer tendency array (without bi,bj)
+     in S/R temp/salt/ptracers_integrate.F
+ o pkg/seaice:
+   - move computation of stress contributions to rhsU/V in s/r seaice_lsr
+     to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code
+   - make u/vIceC local variables if SEAICE_CGRID is defined only to be used
+     in seaice_lsr
+   - seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D
+     in s/r seaice_lsr_calc_coeffs
+ o pkg/mdsio:
+   - in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long
+     (e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is
+     too long (e.g., > MAX_LEN_FNAM/2 )
+ checkpoint65b (2014/08/12)
+ o pkg/matrix:
+   - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP
+ o model/src:
+   - fix initialisation of geothermalFile; compile geothermal-flux code in
+     natl_box verification experiment.
+ o model/src & pkg/down_slope:
+   - push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop).
+   - in dwnslp_apply.F, update tracer tendency instead of the future tracer
+     field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects
+     results at machine truncation level: update output of experiments
+     global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD).
+ o pkg/diagnostics (Stats-Diags):
+   - do not cumulate the full volume when DIAGNOSTICS_FILL is
+     called with bibjFlg < 0 (no increment of the counter for 2D/3D diag);
+     This fix the mean statistics when DIAGNOSTICS_FILL is called multiple
+     times (but Min,Max and StD are still wrong).
+ o model/src:
+   - add geothermal flux forcing: read in ini_forcing.F as time-constant
+     field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F)
+ o model/src:
+   - move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer
+     _integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac
+     arrays are already updated while adjustments (filters, conv.adjustment) are
+     still applied later, in S/R TRACERS_CORRECTION_STEP.
+ o model/src:
+   - store in common bloc array "rhoInSitu" the virtual potential temperature
+     anomaly that is used to compute geopotential: this make the atmos code
+     more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F
+ o pkg/seaice/seaice_lsr.F
+   - rename integer variable ilcall to ipass (that's what it is called
+     in the residual diagnostics
+   - change time stepping for NPSEUDOTIMESTEP > 2 (does not change the
+     default) for improved non-linear convergence of the first few steps
+   - adjust a few comments and add new ones to explain some of the store
+     directives
+ o pkg/generic_advdiff (& ptracers):
+   - re-work the code to check for valid advection scheme and for minimum
+     size of overlap (now stored in local common bloc in gad_advscheme.F)
+ o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics
+   - re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1
+   - add an auxilliary variable "bet" and fix store directives and keys in
+     seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or
+     less exact gradients in my tests); but there are still
+     recomputation warning (although gradients are sort of OK), when
+     SEAICE_LSR_VECTORIZE is not defined, so this flag and
+     SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency.
+   - update verification experiments lab_sea.
+   - change some comments in S/R seaice_calc_viscosities
+ o model/src:
+   - if staggerTimeStep=T, always apply exchange to velocity field in
+     do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F
+     (independent of using multi-dim advection or not); no effect on FWD run
+     but affects AD results (at machine truncation level): update output of
+     experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d)
+     and isomip (oad: 12.d).
+ o pkg/generic_advdiff:
+   - stop if doAB_onGtGs is set to FALSE but ignored
+   - refine warning related to stability of tracer time-stepping
+     regarding internal wave dynamics.
+   - setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition
+     on staggerTimeStep & implicitIntGravWave (will now get a warning
+     if potentially unstable).
+ o pkg/kl10:
+   - add new pkg "kl10" for mixing due to internal wave breaking, from
+     http://www.sciencedirect.com/science/article/pii/S1463500310000144
+     (contribution from Jody Klymak), tested in verification experiment
+     verification/internal_wave/input.kl10/
+ o isomip experiment:
+   - test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up
+     (input.htd) and update the output.
+ o cd_code experiments:
+   - use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM &
+     #undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd)
+     global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and
+     update the corresponding output.
+ o pkg/seaice:
+   - reduce the number of include files and store directives in
+     S/R seaice_lsr_tridiagu/v
+   - change the order of loops in one case in S/R seaice_lsr_tridiagv
+     (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to
+     get rid off one store directive (a TAF bug?)
+   - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in
+     S/R seaice_lsr_tridiagv to change the loop range for consistency
+   - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v
+   - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in
+     S/R seaice_lsr_tridiagu/v (requires update of
+     offline_exf_seaice/input.dyn_jfnk)
+ checkpoint65a (2014/07/27)
+ o model/src:
+   - Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than
+     surrounding hFacC=1 @ edge of a step with different kSurfC on either side
+     (topo in p-coords, ice-shelf in z-coords); update output of experiments
+     tutorial_global_oce_in_p and isomip (both AD and OpenAD output).
+ o model/src:
+   - collect momentum forcing tendency into local 2-D array (passed as argument
+     to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE
+     parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default);
+     affects results at machine truncation level (e.g., if using OBCS_SPONGE).
+   - collect T & S forcing tendency into local 2-D array (passed as argument to
+     apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.
+     affects results at machine truncation level (e.g., ocean: if using
+     SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist
+     correction due to vertical advection).
+   - update output of experiments: fizhi-cs-32x32x40 (13 digits),
+     global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
+     seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),
+     obcs_ctrl (ad & fwd grd @ 12 & 7).
+ o pkg/ptracers & diagnostics:
+   - use ptracers (short) name (instead of long one) to make ptracers diagnostics
+     title (to avoid some unexpected truncation); sort out ptracers diags units.
+   - collect ptracer forcing tendency into local 2-D array (passed as argument
+     to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency.
+ checkpoint65 (2014/07/18)
+ o pkg/fizhi:
+   - add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this
+     affects results at machine truncation level. Update output of experiments
+     fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits).
+ o pkg/seaice: more clean up
+   - rename TAF common block tapes to be more consistent and remove
+     unnecessary duplicates
+   - add store directives to remove more recomputations, but use smaller
+     tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined.
+     The idea behind this flag is to reduce the memory footprint when the
+     adjoint of the LSR is not required. As of now, defining the flag
+     SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by
+     a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h).
+     For experiment offline_exf_seaice, this means on a linux box with gfortran
+     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
+     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
+     6695027 1648 1014578664 1021275339 3cdf6ccb
+     6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER)
+   - note: there are still recomputations in global_ocean.cs32x15 and
+     offline_exf_seaice and the gradient agreement changes (gets a
+     little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt)
+   - in general, the AD gradients still are wrong
+ o OpenAD
+   - clean up code_oad/ directories somewhat by moving files
+     dontCompile, dontTransform, keepOriginal to OAD_support/
+ o model/src:
+   - using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F
+     (not currently tested): add dissipation terms before NLFS rescaling of
+     tendencies (previously done after).
+ o pkg/diagnostics:
+   - write stats-diags in ascii file with more digits (same as in monitor).
+ o pkg/down_slope:
+   - drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with
+     NLFS (not tested), use new recip_hFac value in order to conserve tracer.
+ o model/src:
+   - new file "apply_forcing.F" containing all the code previously in
+     external_forcing.F, but with new argument list: pass, as new argument,
+     the current level tendency array to update (instead of a direct update
+     of the common bloc array). Change the corresponding calls.
+   - add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use
+     EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility).
+ o pkg/seaice/seaice_lsr, a little bit of clean up
+   - rearrange some code blocks, so that now all calculations for
+     setting up the right-hand-sides done within one single block
+     (I find that easier to read and understand)
+   - rearrange freedrift-code to reduce the number of ifdefs
+   - adjust some indentations and comments
+ checkpoint64z (2014/07/10)
+ o model/src and several pkgs:
+   - change argument list of all S/R called from external_forcing.F and
+     called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F)
+     to pass, as argument, the current level tendency array to update
+     (instead of a direct update of the common bloc array).
+   - change also (in the same way) argument list of PTRACERS_APPLY_FORCING;
+   - rename taueddy_external_forcing.f to taueddy_tendency_apply.F
+ o pkg/seaice/seaice_lsr.F
+   - always initialize local arrays in seaice_lsr_tridiagu/v
+   - add more local tapes to seaice_lsr_tridiagu/v
+   - move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but
+     keep it in bi/bj loop; this seems to be essential
+   - gradients are still wrong but only by 4-7 orders of magnitude
+     instead of 15 orders of magnitude, lab_sea improves a little
+ o pkg/seaice
+   - (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that
+     generates unnecessary code in seaice_lsr_ad
+   - add more store directives in seaice_lsr to avoid unnecessary code
+     in seaice_lsr_ad
+   - exclude some residual computations in seaice_lsr when
+     ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code
+     in seaice_lsr_ad
+   - add more storing, a new tape (model/src/the_main_loop.F) and
+     another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey
+     and klockey should be checked by a specialist)
+   - modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER )
+     and update lab_sea after previous changes in pkg/seaice below
+ o pkg/autodiff:
+   - introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and
+     viscFacInAd : run time parameters allowing for adjoint switches
+     note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F
+ o pkg/ecco:
+   - introduce cost_gencost_boxmean.F that computes a box mean
+     temperature (for use in adjoint sensitivity studies).
+ o model/src/set_defaults.F : initialize viscFacAdj to 1.
+ o pkg/mom_common/mom_calc_visc.F:
+   - ifdef ALLOW_AUTODIFF then include viscFacAdj factor.
+ o pkg/seaice/seaice_summary.F:
+   - statement for SEAICEadjMODE now in autodiff_readparms.F
+ o pkg/seaice:
+   - remove some store directives and add new ones in an effort to get
+     finally rid off the recomputation warnings. This is successful
+     when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are
+     defined (i.e. no extensive recomputation warnings left), but there
+     are still too many recomputations on the solver iteration level
+   - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h
+   - move definition of MPSEUDOTIMESTEPS into TAMC-block in
+     SEAICE_SIZE.h
+   - add a store directive in S/R seaice_calc_viscosities
+ o pkg/seaice (ITD code):
+   - fix definition of Hlimit for multi-threaded case
+   - use double precision arithmetic to compute Hlimit: this affects results;
+     update output of experiment seaice_itd.
+ o replace content of verification/seaice_itd
+   - instead of a 1D column use the configuration of offline_exf_seaice
+     to test the ice thickness distribution code with ridging
+   - this is a first shot at this experiment
+   - change of some defaults of ridging parameters SEAICEhStar (from
+to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F
+     and lot of new comments.
+ checkpoint64y (2014/06/20)
+ o pkg/seaice/seaice_reg_ridge.F:
+   - modify the regularization of very small volumes of ice; only check
+     total volume HEFF, and do not apply correction to individual ice
+     classes because that leads to funny patterns in the heat and fw-fluxes
+     into the ocean. Adjust seaice_itd/results/output.txt
+   - replace nITD by SEAICE_multDim in loop-ranges
+ o pkg/exf:
+   - add code to process the case field period = -12. with UV interpolation.
+   - move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec
+     into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F)
+ o verification/global_with_exf:
+   - switch all fields period to -12. (was previously untested) in input/data.exf
+     (but keep secondary test ".yearly" unchanged); update the reference output.
+ o pkg/cal:
+   - new calendar type "noLeapYear" for 365 days calendar without any leap year.
+ o pkg/exf:
+   - new integer parameter "exf_debugLev" (default set to main model debugLevel)
+     to replace logical switch "exf_verbose"
+   - report in STDOUT when loading a new record (if exf_debugLev >= 3)
+ o pkg/sbo:
+   - update from Katherine Quinn: evaluate mass directly from density and SSH
+     (budget using Finite Volume method) instead of from bottom pressure.
+   - allow testreport to collect few selected SBO output ; tested in exp.
+     global_ocean.90x40x15 (after updating the results, to include SBO output).
+   - fix some multi-threading issues (in output part).
+ o model/src & most packages:
+   - always call {PKG}_READPARMS even if corresponding use{PKG}=F;
+   - in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R
+     PACKAGES_UNUSED_MSG to print a weak warning when parameter file
+     "data.{pkg}" exist ; and leave the S/R (return) just after.
+   - more standard LAND pkg interface (land_init_fixed.F, land_check.F).
+     + call LAND_READPARMS from packages_readparms.F
+ o pkg/seaice:
+   - remove code that resets useThSice in S/R seaice_readparms and
+     replace it by a warning in S/R seaice_check
+   - remove parameter MULTDIM, replace with nITD and runtime
+     parameter SEAICE_multDim (still hard-wired to nITD if
+     SEAICE_ITD is defined)
+ checkpoint64x (2014/05/24)
+ o verification/lab_sea:
+   - update adjoint and TLM output following changes to pkg/salt_plume
+   - un-do the update after putting back local recip_Cp in few places.
+ o pkg/salt_plume: modifications by An Nguyen:
+   - add capability to do brine rejection (salt-plume) as function of
+     volume+tracers (instead of only salinity tracer).
+   - conserve volume by exchanging volume from each kLev to above to
+     accommodate in-coming brine volume
+   - store surface and klev exchanged fraction + volume in 4 new 3-d arrays
+   - switch KPP surf buoyancy due to brine forcing to 3-d
+     (3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume)
+   - add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t
+   - unrelatedly, also add ad-hoc capability to vary salt_plume scheme
+     in East/West Arctic.
+ o pkg/sbo:
+   - incorporate modifications from Katherine Quinn to enable the use of sbo
+     pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like
+     output for future testreport verification (unfinished).
+ o pkg/atm_phys:
+   - change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R:
+     skip the reseting of t_ref & q_ref to initial t & q ; this preserve the
+     output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics.
+ o pkg/seaice
+   seaice_calc_ice_strength.F: modify expression to avoid divisions
+     (affects truncation)
+   seaice_do_ridging.F: clean up the insectarium
+   - fix a bug that was compensated by areaScaling (-> remove areaScaling code)
+   - added SEAICEsnowFracRidge to redistributed snow (2nd bug)
+   - set closing/openingRate to zero where no extra iteration is need (3rd bug)
+   - add some debugging information and error messages (warnings)
+ o model/src: modifications relatd to atmosphere p*:
+   - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)
+   - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead
+     of vertical profile tRef in geopotential background and anomaly.
+   - Acount for true p* correction in theta <-> T conversion in pkg/aim_v23
+     and pkg/atm_phys.
+   - Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40,
+     fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn.
+ o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt
+ o pkg/ptracers: compute ptracer source/sink due to linear free surface.
+     not used right now, but can be used in BGC packages to fix conservation.
+ o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by
+     other packages too.
+ o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by
+     SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix)
+ o model/src:
+   - since we have several heat capacity (even in model/src), define "recip_Cp"
+     as local variable (no longer in common block) to avoid any confusion.
+   - add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords).
+ o pkg/exf:
+   - from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local
+     air density as function of air Temp, Humidity and atm pressure.
+ checkpoint64w (2014/05/02)
+ o verification:
+   - update output_adm.txt files for experiment global_ocean.cs32x15 (seaice &
+     seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing
+     code from seaice_growth.F & seaice_advdiff.F to new ridging routines
+     seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient
+     (down to 8-7 matching digits for global_ocean and 5-6 for lab_sea).
+ o model/src: for atmosphere in p* coords:
+   - store factor rStarFacC**atm_kappa (= pStarFacK) in common block
+   - implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F),
+     but not yet activated.
+ o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation:
+   - move computation of opnWtrFrac = 1-AREA to before computing ice strength
+   - this changes the results (but not for any verification experiment, because
+     none tests this), but avoids having an extra field in the restart files
+ o pkg/seaice: remove global variable TICE (not needed)
+   - replace by TICES or local variable where necessary (cost_seaice_test,
+     seaice_diagnostics_state)
+   - move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup
+   - use specific read/write routines for reading and writing individual leves
+     of a multilevel field
+ o pkg/ctrl & model/inc:
+   - move additional anomaly fields of control vars (related to options:
+      ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL)
+     from DYNVARS.h into new header file: CTRL_FIELDS.h
+ o pkg/seaice: some small modifications to the ridging code
+   - make fw2ObyRidge a global variable and add the freshwater flux to
+     seaice_growth
+   - pass actual thickness from seaice_prepare_ridging, so that it is
+     computed only in one place and compute it in the same way as in
+     seaice_growth
+   - initialise more fields in seaice_do_ridging that where cause floating
+     point exceptions over land
  o pkg/seaice: preparations for ridging code and first real ridging code
    - move most of "PART 1" of S/R seaice_growth into a new and separate
      S/R seaice_reg_ridge that will both regularize the state variable after
      advection call the actual ridging routine;
    - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,
      d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;
    - remove ridging code from seaice_advdiff
    - clean up remaining part 1 of seaice_growth in an attempt to make it
      more readable (this is probably subjective)
    - call seaice_itd_redist once in the initialisation phase to have the initial
      conditions in the correct category

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Removed from v.1.1980
 


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Removed from v.1.1980
 


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Added in v.1.2254
-Removed from v.1.1980
+Added in v.1.2254

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