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-revision 1.1303 by gforget,
Fri Sep 24 23:25:45 2010 UTC
+revision 1.2087 by jmc,
Tue Nov  4 18:24:46 2014 UTC
 Line 4 
 $Name$
      Notes on tags used in MITgcmUV
      ==============================
+ 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
+   - finally: add new ridging routine for ITD code
+ checkpoint64v (2014/04/11)
+ o pkg/ecco:
+   - add runtime parameters mdt[start,end]date[1,2]
+   - rename variable "tpmean" as "mdt" and "topexmeanfile" as "mdtdatfile"
+ o pkg/seaice:
+   - make deltaC a global variable, so that it can be used in ridging code
+   - first step towards ridging: introduce new routines that compute
+     ice strength based on ridging parameters
+   - add diagnostic for HSNOWITD
+   - add opnWtrFrac as a global variable (required for ridging scheme)
+ o pkg/salt_plume + pkg/seaice/seaice_growth.F
+   - add SALT_PLUME_IN_LEADS flag to activate pkg/salt_plume only when ice
+     AREA exceeds a threshold (code contributed by I.Fenty in 2011)
+ o verification/hs94.1x64x5:
+   - leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h
+   - do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests.
+ o autodiff:
+   - Start to 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 verification/hs94.1x64x5.
+   - Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage
+     which are specific to TAF/TAMC).
+   - Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD:
+     since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad
+     is compiled), this simplifies/reduces which *_OPTIONS.h file to include.
+   - OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when
+     building mitgcmuv_ad (make adAll).
+ o pkg/ecco:
+   - cost_gencost_seaicev4.F:
+      reformulate proxy cost as function of sst and local param SEAICE_freeze
+      change cost names from siv4-[sst,vol] to siv4-[deconc,exconc]
+   - add stop statement if old names siv4-[sst,vol] are used
+   - add snapshots + cost reports for atmospheric longwave
+   - remove factor 0.1 in front of wtau[u,v]
+   - replace never used flag ALLOW_TMI_COST_CONTRIBUTION with
+      ALLOW_TMI_SST_COST_CONTRIBUTION
+ o pkg/atm_phys:
+   - add some diagnostics for Short-wave and for convection S/R.
+ o pkg/seaice/seaice_growth:
+   - fix a bug in the lateral melt parameterization for SEAICE_ITD
+     in seaice_growth; tempFrz needs to be computed inside the i/j-loop
+   - rearrange loop order for better vector code in the same code block
+   - rewrite the floeDiameter formula to have fewer divisions
+   -  (miraculously) none of this changes the results of seaice_itd
+ o pkg/smooth:
+   - move param smooth2Ddiffnbt to pkg/ecco
+ o pkg/salt_plume:
+   - salt_plume_frac.F:
+      clean up local param names
+      reformulate (1-frac) to frac; original 1-frac was based on swfrac code
+ o pkg/rw:
+   - add RS version of S/R READ_MFLDS_LEV.
+ o pkg/streamice:
+   - fix the restart test by writing/reading pickup_streamice files.
+ o pkg/seaice:
+   - refine checks for jfnk-related parameters
+   - comment out if statement with SEAICEuseIMEX parameter as long as there
+     is no IMEX code to avoid confusion and surprises
+ checkpoint64u (2014/03/07)
+ o verification/MLAdjust:
+   - rename secondary test suffix:
+.leith  -> A4FlxF  + switch to flux-form & add side-drag
+.leithD -> AhFlxF  + switch to flux-form
+.smag   -> AhVrDv  (use Vorticity-Div. visc form) + add side-drag
+.leith  -> AhStTn  (use Strain-Tension visc form) + add side-drag
+ o pkg/mom_vecinv:
+   - remove unused arguments from S/R MOM_VI_HDISSIP & MOM_HDISSIP (as it used
+     to be before mom_calc_visc.F)
+   - skip the call to MOM_CALC_TENSION & MOM_CALC_STRAIN if not needed.
+   - add 2nd copy of vort3 & strain that knows about lateral BC (free/no slip):
+     this is simpler for the adjoint and for diagnostics.
+ o model/src + pkg/momentum:
+   - add input files for  2-D additional Western and Southern cell-edge wall
+      (e.g., to add "thin-wall" where it is =1).
+   - fix sideDrag option for thin-walls with Non-Lin Free-Surf
+     using 2nd hFacZ that is computed from initial (fix domain) hFac
+   - known limitations of thin wall implementation: not yet coded for sigma
+     coords; not working with CD-scheme neither.
+ o pkg/seaice:
+   - rename recently introduced parameters from (wrong name) AB to
+     BDF (backward difference time discretisation)
+   - retire runtime parameters SEAICEuseAB2, SEAICE_abEps
+ o tools/adjoint_options:
+   - remove setting of "OPENAD=true" (now set by command line "genmake2 -oad")
+ checkpoint64t (2014/02/01)
+ o pkg/ecco
+   - add compile flag ALLOW_GENCOST_TIMEVARY_WEIGHT in ECCO_OPTIONS.h and
+     runtime logical flag gencost_timevaryweight to read daily sea-ice sigma
+   - replace hard-coded record number and period which only work for monthly
+     with read-in runtime param that works for other periods (month,day,year)
+ o pkg/thsice
+   - corrected store directive fixes thsice adjoint gradient checks
+ o genmake2 & testreport:
+   - add genmake2 option "-oad" to generate a Makefile for OpenAD built and
+     in this case, use tools/adjoint_options/adjoint_oad as default AD optfile.
+     Update testreport accordingly. No need to set "export OPENAD=true"
+     in adjoint_options/adjoint_oad anymore (will be removed later).
+ o pkg/shelfice:
+   - put T & S shelfice forcing into model surfaceForcing_T,_S (for now,
+     only if SHELFICEboundaryLayer=F); Change model/src/external_forcing.F
+     so that surface forcing applies to k=kSurf if using pkg/shelfice.
+ o pkg/ctrl, pkg/grdchk, pkg/ecco:
+   - Changes to make GENARR more modular (i.e. invisible if not used)
+ o model/src/temp_integrate.F and salt_integrate.F
+   - re-include store directives that were removed on Dec 27th.
+ o model/src/external_forcing_surf.F
+   - add storage directives for EmPmR and PmEpR to avoid recomputation of
+     seaice_model in the adjoint that is problematic when seaice_model is
+     turned off in the adjoint. The resolved issue dated back to July when
+     EXTERNAL_FORCING_SURF call was moved.
+     Update global_ocean.cs32x15/*/output_adm.seaice_dynmix.txt accordingly.
+ o pkg/exf/exf_check.F
+   - fix a small bug again (originally found by Wentao Liu, now found again)
+   - streamline error output
+ o pkg/streamice and aim_v23:
+   - replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that
+     Apple's /usr/bin/cpp knows what to do:
+     Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
+     Target: x86_64-apple-darwin13.0.0
+ checkpoint64s (2014/01/05)
+ o tools/adjoint_options:
+   - switch to fastopt.net TAF server (instead of default fastopt.de) for
+     AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default).
+ o model/src:
+   - remove some unnecessary TAF storage directives in forward_step.F and
+     in dynamics.F (note: not always removed by TAF, e.g., double storage
+     of kappaRU,kappaRV in former version of dynamics.F).
+ o model/src & pkg/ptracers:
+   - call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F
+     salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F)
+     and remove ptracers_dwnslp_apply.F & ptracers_implicit.F
+   - call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F)
+   - add fZon & fMer as output argument of S/R GAD_CALC_RHS.
+   - update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad).
+ o useSingleCpuInput separates single-CPU input from single-CPU output;
+     for now only implemented for in exf_interp_read.F
+ o verification/advect_xy:
+   - fix missing EXCH call in local version of ini_salt.F and update output.
+ o momentum diagnostics:
+   - fix which deltaT is used in Total-Tendency diagnostics.
+   - fix typo in diagnostics for momentum tendency from AB.
+ o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the
+     SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8
+ checkpoint64r (2013/12/08)
+ o verification/*/results:
+   - Update reference output of experiments that were passing with just 13 digits
+      (make it easier to detect future changes in results)
+ o model/src & pkg/ptracers:
+   - move calls to GAD_ADVECTION (Multi-Dim advection) from thermodynamics.F to
+     inside temp_integrate.F and salt_integrate.F and from ptracers_advection.F
+     to inside ptracers_integrate.F ; remove ptracers_advection.F
+ o coupling interface pkgs:
+     [atm_compon_interf, ocn_compon_interf & atm_ocn_coupler]
+   - change the config check to test the agreement of Ocean Depth
+     with ATM land/sea mask (instead of ATM orography);
+   - send to coupler the number of coupler time-steps to do for this run:
+     this allows to check for consistency and don't need anymore to be
+     specified in parameter file "data";
+   in coupler:
+   - check consistency of RunOff map versus Ocean Depth and ATM land/sea mask.
+   - improve report to log-file of config setting (pass log-file unit to few S/R)
+ o pkg/compon_communic:
+   - add coupling send/receive for non-tiled integer vector;
+   - add S/R to check and stop if any proc has an error (similar to
+     eesupp/src/stop_if_error.F but single thread and across Comm_World).
+ o pkg/exch2:
+   - in exch2*_get_rx[1,2]: use new list "W2_tileIndex" to replace search
+     through list of all tiles my proc owns.
+ o model/src:
+   - AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying
+     from rTrans) to simplify dependencies (no need to store rTrans anymore in
+     calling S/R); this affects AD results at machine truncation level:
+     update AD-output (TAF) of experiments: 1D_ocean_ice_column,
+     bottom_ctrl_5x5 & obcs_ctrl (12 digits for AD grad, same FWD grad).
+ o tools/build_options:
+   - simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran
+ o coupling interface pkgs:
+     [compon_communic, atm_compon_interf & ocn_compon_interf]
+   - move declaration of local array "ibuf" out of header file "CPLR_SIG.h"
+     to each S/R that needs it; remove un-used variables.
+   - change component tile registration (cpl_register.F in both compon_interf
+     and mitcomponent_tile_register.F) to pass the full list of tiles
+     information (including bi,bj) in 1 vector (instead of in a bi,bj matrix).
+   - with pkg/exch2: adopt the same convention used for I/O to define mapping
+     towards coupler global array (unless W2_useE2ioLayOut=F):
+      a) can now use different tiling between atm & ocn comp.
+      b) no needs to modify the run-Off map when changing tiling (was needed
+         even if using the same tiling between atm & ocn).
+      c) will allow to run with blank-tiles in 1 component (e.g., for ocean
+         full land tiles); not yet tested.
+   - check for valid mapping from comp. tile to coupler global array
+   - improve report of tile registration results to log file.
+ o pkg/exch2:
+   - in eesupp/src/eeboot.F: move call to W2_EEBOOT before Coupler
+     tile-registration (CPL_REGISTER);
+   - activate (un-comment) definition and setting of "W2_tileIndex" list to
+     store the local bi,bj indices of each tile;
+   - also print bi,bj in local report to log file;
+   - fix pkg/debug/debug_cs_corner_uv.F for the case nSy > 1 (left from
+     Jun 2009 modif of pkg/exch2).
+ o testing on baudelaire:
+   - run 2 tests at a time: no significant slow down (since enough cpu) and
+     get the full set of test done earlier
+   - switch the ifort test to "-devel" ; run the OpenAD test everyday.
+ o model/src/thermodynamics.F and routines called from it:
+   - pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F &
+     gmredi_calc_wflow.F) to update eulerian velocity (input) into residual
+     velocity (outp) by adding bolus velocity.
+   - model/src: calc_adv_flow.F (replacing calc_common_factors.F) to compute
+     mass transport from velocity + lateral grid cell area
+   - rename calc_gt.F to temp_integrate.F (includes call to TIMESTEP_TRACER)
+   - rename calc_gs.F to salt_integrate.F (includes call to TIMESTEP_TRACER)
+  in thermodynamics.F
+   - remove k from thermodynamics.F and move it to temp_integrate.F
+     salt_integrate.F and ptracers_integrate.F (now done inside the tracer
+     loop).
+   - compute locally (in thermodynamics.F) 3-D velocity field that is used to
+     advect tracers; pass it as argument to GAD_ADVECTION, GAD_SOM_ADVECT,
+     PTRACERS_ADVECTION, TEMP_INTEGRATE, SALT_INTEGRATE, PTRACERS_INTEGRATE,
+     GAD_IMPLICIT_R and PTRACERS_IMPLICIT
+   - update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column,
+     global_ocean.90x40x15, tutorial_global_oce_biogeo and
+     tutorial_tracer_adjsens (+ TLM output).
+ o tools/OAD_support and (verification/*/) code_oad:
+   - OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to
+     module conversion ; remove unneeded CPP_EEOPTIONS.h.
+   - code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard
+     version (closer to model/inc/CPP_OPTIONS.h).
+ o model/src:
+   - remove parameter "useOldFreezing" from PARAMS.h and push it to the
+     retired list of parameters (routine FREEZE has been replace by surface
+     freezing (10.yrs ago) and by pkg/frazil (interior freezing).
+ o pkg/gmredi:
+   - add option (GM_CALC_TRANSP_FROM_VEL) to compute transport directly from
+     velocity (same scheme but affects machine truncation) for GM_AdvForm.
+   - update output of FWD experiments: front_relax.bvp,
+     global_ocean.90x40x15.dwnslp, global_ocean.cs32x15 and ideal_2D_oce.
+ checkpoint64q (2013/11/17)
+ o verification:
+   - generate new output on baudelaire (gfortran, -ieee) for OpenAD experiments
+     tutorial_global_oce_biogeo and global_ocean.90x40x15.
+   - generate new output (growth & melt) for seaice_itd experiment after
+     updating the input pickup_seaice files (previously wrong).
+ o pkg/cost:
+   - define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL
+     (instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads:
+     o this fixes global-sum value if multi-threads (since GLOBAL_SUM_RL
+       cannot be applied to var in common block).
+     o allows to get results independent of tile-per-proc setting (if using
+       slower GLOBAL_SUM_SEND_RECV option).
+   - update accordingly: seaice_cost_final.F, shelfice_cost_final.F,
+     thsice_cost_final.F and ecco_cost_final.F (this one affects lab_sea
+     forward gradients: update output).
+   - update */code_oad/externalDummies.F by adding dummy GLOBAL_SUM_TILE_RL
+     S/R and, for most exp., also comment out GLOBAL_SUM_R8.
+ o pkg/mom_common:
+   - move to pkg/mom_common and model/src (previously in tutorial_deep_convection
+     code) 2nd version of isotropic 3-D Smagorinsky code interface: strain and
+     viscosity are locally declared in dynmics.F and pass as argument to CALC_GW;
+     ensure that all field value that are used are set.
+ o tutorial_deep_convection (smag3d):
+   - add missing scaling in mom_calc_smag_3d.F;
+   - set smag3D_coeff in input.smag3d such that results do not change.
+ o pkg/dic:
+   - change dic_cost.F to compute cost on each tile first and then apply
+     GLOBAL_SUM_TILE_RL: this affects forward gradient of AD experiments
+     tutorial_dic_adjoffline & tutorial_global_oce_biogeo; update output.
+   - remove kLev argument and use GLOBAL_SUM_TILE_RL in tracer_meanarea.
+ o eesupp/src & pkg/mdsio:
+   - remove gather/scatter_vector.F (from eesupp) and mdsio_read/writevector.F
+     (from pkg/mdsio) since they are no longer used for tape IO.
+   - move simple C subroutine "setdir.c" from pkg/compon_communic to eesupp/src
+     (+ keep a copy in pkg/atm_ocn_coupler).
+ o verification/isomip:
+   - split domain in 8 squared tiles (instead of just 2) for FWD, AD & OAD tests.
+ o tools/build_options:
+   - optfile linux_amd64_ifort11, fast (no ieee) case:
+     to get a working restart for all experiments, add "-fp-model source"
+     to FOPTIM (also remove "-opt-streaming-stores auto" <- this is the default).
+ checkpoint64p (2013/10/20)
+ o pkg/autodiff:
+   - adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO
+     criteria, return to simple (default) tape IO format.
+ o pkg/mdsio (+ eesupp/src):
+   - rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace
+     previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8);
+   - fix globalFile and singleCpuIO options using simpler global mapping.
+   - new pairs of scatter/gather vector S/R (one for each type, generated from
+     template) corresponding to simpler global mapping.
+   - adread_write.F: switch to new S/R (but leave old calls commented) and write
+     to globalFile when parameter globalFiles is set to True.
+   - switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip.
+ o pkg/autodiff:
+   - adread_adwrite.F: add a hack for RS arrays (when RS=real*4);
+     with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is
+     missing, just add a STOP if array type do not match.
+ o pkg/exf:
+   - to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice:
+      rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION
+      and rename array obsSIce to exf_iceFraction.
+ o tutorial_deep_convection:
+   - add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe),
+     for now all in this exp. code dir.
+   - add secondary test using Smag-3D viscosity (keep very low backgroud visc for
+     testing) and flux-limter advection scheme for Temp. (no explicit diffusion).
+ o eesupp/src:
+   - added SINGLE_DISK_IO option because reading of parameter files on
+     very large number of processors did not work with existing set-up
+ checkpoint64o (2013/09/25)
+ o pkg/atm_phys & atm_compon_interf:
+   - allows for coupling of gray-atmosphere (atm_phys) with ocean.
+ o tools/build_options:
+   - switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran
+     & linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also
+     remove CPP setting (was identical to genmake2 default).
+ o pkg/gmredi & model/src: Some updating and work done on the residual model.
+   - created new file model/src/calc_eddy_stress.F to calculate the eddy stress.
+   - fixed up the calculation of the eddy stress and how it is added to the
+     external forcing via taueddy_external_forcing.F
+   - at the moment, it is very experimental and only works with the variable eddy
+     diffusivity calculated in gmredi_k3d.F
+ o pkg/seaice/seaice_check.F: add a check to catch the case of specifying
+     lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice
+ o testreport (& tools/do_tst_2+2):
+   - for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}'
+ o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11:
+   - remove CPP='cpp -traditional -P' (this is genmake2 default)
+   - add switch (for big setups) to use 'medium' memory-model (but leave it
+     commented out for now). Note: needed with FC 19 to compile big setups.
+ o pkg/atm_compon_interf:
+   - regroup per field origin (model & pkgs) the coupling storage routines
+      (which accumalate in time each coupling field)
+   - move bi,bj loops inside atm_store_my_data.F and store also wind-stress;
+     update accordingly + simplify aim_do_physics.F
+ checkpoint64n (2013/08/26)
+ o pkg/bbl:
+   - update formulation to reduce dispersion of tracer properties in bbl
+   - replaced horizontal and vertical transport parameters with velocities
+   - changes results for verification/global_with_exf.yearly
+ o verification/halfpipe_streamice:
+   - change to matrix construction; update both Fwd & AD output.
+ o verification/tutorial_tracer_adjsens:
+   - OpenAD test: switch to vector-invariant momentum since fluxform with
+     rStar causes problems with OpenAD; update output.
+ o tools:
+   - genmake2: define a common prefix for all temp-file names ; move them
+     to local /tmp disk (but would be easy to move them back);
+   - xmakedepend: apply the same switch for temp-files.
+ o pkg/offline:
+   - changes for use with rStar (NLFS): assume that we continue to provide
+     UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid
+     output files) and apply r* scaling at each time-step (function of the time
+     varying Eta field); use normal pickup files (needed for restart with NLFS).
+ o adjoint with OpenAD:
+   - move OpenAD-specific files from verification/OpenAD/code_oad_all to a new
+     package openad.  This package has to be compiled for all runs with OpenAD
+     instead of specifying code_oad_all as a modification directory.
+   - link the fortran templates from tools/OAD_support to the build directory
+     for preprocessing to avoid conflicts between different setups compiled
+     simultaneously and simplify cleanup.
+ o pkg/exf:
+   - in exf_getforcing.F: comment out most of the EXCH calls (fields used by
+     main model or other pkgs are exchanged in EXF_MAPFIELDS).
+ o model/src:
+   - do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline
+     (similar to do_fields_blocking_exchanges.F).
+ o tools/genmake2:
+   - remove TAF output src code just before calling staf (when not doing a fresh
+     built, will stop if things go wrong with staf).
+   - fix target "adobj" (left from TAF version-2 transition)
+ o pkg/diagnostics:
+   - add a parameter to track the status of pkg/diagnostics activation;
+     this replace/extend the use of logical param "settingDiags" (to check
+     when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call.
+     New S/R to print error message and stop when pkgStatus is not right.
+   - to try: add a warning when "data.diagnostics" exist but useDiagnostics=F.
+ checkpoint64m (2013/08/13)
+ o model/inc:
+   - move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from
+yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h)
+ o pkg/kpp & aim_v23:
+   - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
+ o pkg/seaice:
+   - restore (last time on 2011/12/24) ability to compile pkg/seaice with
+     undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options.
+   - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
+ o eesupp/src:
+   - fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH)
+     in exch1_rx[_ad].template (thanks to Francois Lefeuvre report).
+ o switch to TAF version-2:
+   - add flow directives to "freeze" naming convention for ad-routines that
+     are used in I/O routines of adjoint state and associated common blocks
+     that are used in adcommon.h (backward compatible with version-1)
+   - update all ad-optfiles (in tools/adjoint_options + few local to some
+     verification exp) to switch to latest TAF version (currently 2.5.5);
+     merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented
+     out except for diva).
+   - the major change with TAF version-2 is that both the differentiated
+     routines and the forward routines (new) are returned as part of the TAF
+     output source code. Update genmake2 accordingly.
+   - new output for AD experiment tutorial_global_oce_biogeo (better AD gradient
+     with version-2 when compared to TLM or FWD gradient); other experiments
+     output show minor changes (machine truncation level); update the few AD &
+     TLM output with 12 matching digits only (some prior to version-2 switch).
+ checkpoint64l (2013/08/05)
+ o model/src:
+   - in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F
+   - main_do_loop.F: no longer includes additional (AUTODIFF) header files
+     when using TAF but only if using OpenAD.
+ o pkg/mom_common+fluxform+vecinv:
+   - always set horiz. viscosity arrays to background value before calling
+     MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC
+     only when using variable horiz. viscosity (useVariableVisc=T);
+   - simplify mom_vecinv.F (only 1 block for momViscosity).
+ o pkg/mom_common: variable horiz. viscosity in NH code
+   - move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F)
+     from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h
+   - store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc,
+     useBiharmonicVisc & useVariableVisc.
+   - fix old bug (already in 1rst implementation of variable horizontal viscosity
+     in calc_gw.F, version 1.27, 2006/06/20):
+     horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0
+     even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero.
+   - change background horiz viscosity in vertical momentum (gW) to always be
+     viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using
+     any type of variable viscosity, e.g., viscAh/4Grid)
+   - change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of
+     viscAh,viscA4) which default to viscAh,viscA4 :  this avoid missing
+     horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since
+     default viscAh,viscA4 is zero).
+ o model/src:
+   - extend length of drC & recip_drC from Nr to Nr+1.
+ o Divided Adjoint (DIVA) with MPI:
+   - genmake2: do not create local ./mpi_headers dir when no file to copy into.
+   - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT
+     and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h.
+ checkpoint64k (2013/07/23)
+ o tools/OAD_support:
+   - avoid the need for file "oadtempflile" in insertTemplateDir.bash
+     and remove it from genmake2.
+ o tools/build_options:
+   - remove MPI_HEADER_FILES_INC setting (no longer used) and comment out
+     MPI_HEADER_FILES list (let genmake2 find the missing headers)
+ o verification/halfpipe_streamice:
+   - change to driving stress formulation; update both Fwd & AD output.
+ o tools/genmake2 and Divided Adjoint with MPI:
+   - remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken);
+   - only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set;
+   - add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in
+     Makefile, which is set by genmake2, and check which mpi-headers are needed.
+     Note: need to update adjoint_options/adjoint_diva_mpi accordingly.
+   - update target "CLEAN" (to also remove ./mpi_headers/ dir).
+ o testreport:
+   - changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present,
+     perform additional runs (number of additional runs is "add_DIVA_runs" taken
+     from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h").
+ o verification/lab_sea (AD test):
+   - change to test Divided Adjoint Run in this set-up (both standard AD test
+     and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test.
+ o pkg atm_ & ocn_compon_interf:
+   - remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old
+     staggerTimeStep implementation) and disable (retired) corresponding
+     parameter.
+ o pkg/offline:
+   - comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01];
+   - add S/R OFFLINE_CHECK to print offline parameter summary
+     and stop if loading a file that is not used;
+   - enable to calculate GMRedi tensor, KPP mixing and convective index
+     when the corresponding file(s) is/are not specified (but pkg is used).
+   - comment out resetting of monitorFreq (to endTime) since it still useful
+     for monitoring CFL numbers and checking offline fields.
+ o OpenAD:
+   - do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get
+     smaller standard output) and generate new (smaller) output (on baudelaire
+     using gfortran with -ieee) for exp. tutorial_tracer_adjsens
+ o model/src:
+   - call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F),
+     (where external_forcing_adjust was called) and change list of arguments;
+   - merge external_forcing_adjust.F into external_forcing_surf.F
+   - put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F)
+     which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX,
+     previously in file "balance_relax.F", now removed); remove corresponding
+     arrays in FFIELDS.h.
+   - EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement
+     a hack for getting back surfaceForcingS (loaded from file) when using
+     ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up.
+   - update output of AD test experiment global_ocean.cs32x15.seaice_dynmix
+     (was getting only 11 digits for AD-grad, due to different truncation
+      error in AD code).
+ checkpoint64j (2013/07/04)
+ o pkg/offline:
+   - to enable the use of other features with pkg offline (e.g., obcs),
+     also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come.
+   - comment out "allowFreezing" (now active) in 2 offline testing exp.
+ o pkg/exf ALLOW_RUNOFTEMP
+   - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL
+   - ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice
+   - changes verification/global_ocean.cs32x15/results/output.seaice.txt
+ o pkg/atm_phys:
+   - allows to add some damping on uVel,vVel (strength only function of k).
+ o verification, ad-tests:
+   - reduce length of the simulation for AD test: global_ocean.cs32x15.seaice,
+     global_ocean_ebm and offline_exf_seaice.thsice.
+ o verification/halfpipe_streamice:
+   - found a bug in s/r pkg/streamice/streamice_advect_thickness which caused
+     flux input boundary conditions to be ignored; a fix for this bug changed
+     verification results for forward test.
+   - add adjoint test.
+ o pkg/ptracers:
+   - allow to restart without SOM pickup (resetting SOM to zero).
+ o pkg/gmredi:
+   - New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added.
+   - It uses mixing length theory and suppression by steering level effects to
+     calculate a diffusivity used in the Redi tensor (see Bates et al., submitted
+     to JPO, for more details).
+   - It also uses the diffusivity to calculate an eddy induced streamfunction
+     based on a PV closure (rather than a buoyancy closure as in GM).
+   - New files added to pkg/gmredi:
+     gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy
+       induced overturning streamfunction (called from gmredi_calc_tensor)
+     gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required
+       for use in gmredi_k3d
+     gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate
+       the eddy diffusivity
+ checkpoint64i (2013/06/18)
+ o pkg/cheapaml:
+   - take src files from MITgcm_contrib/verification_other/offline_cheapaml/code
+     that enable the use of seaice (pkg/thsice thermo & pkg/seaice dynamics)
+     with pkg/cheapaml.
+ o utils/python: add subpackage for cubed sphere function, first example is
+     simple cs.pcol to plot 2D fields on a map
+ o pkg/streamice:
+   - This is a new package in MITgcm, which solves dynamic equations for ice
+      sheets and ice streams
+   - At the moment it is independent of atmosphere/ocean dynamics, or any
+     other physical packages in MITgcm, even ShelfIce (although it is anticipat-
+     ed that this will change)
+   - There is a new verification exercise that tests it, halfpipe_streamice,
+     evolves a 40x80 km ice stream/ice shelf (at coarse resolution) in a
+     rectangular embayment
+   - halfpipe_streamice is forward-only for now, will have TAF test soon
+   - for questions, email dgoldber@mit.edu
+ o pkg/thsice:
+   - fix filling of snow-precip diagnostic (SIsnwPrc) (left from the removing
+     of snowPrc from common bloc, on May 2nd, thsice_step_fwd.F revision 1.40);
+   - remove diagnostics 'SI_FrcFx' ( now identical to 'SI_Fract' with new
+      call sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect );
+   - allow precip from pkg/cheapaml to make snow over seaice.
+ o pkg/cfc:
+   - move in separated header file (CFC_ATMOS.h) time-serie arrays of Atmos CFC
+   - remove atmos CFC 2-D arrays from common bloc (now local variables)
+   - change some hard-coded constant to run time parameter for reading and
+     and interpolating atmospheric CFC ; keep same default as previously.
+   - more flexible reading of Atmos CFC (number of records no longer hard-coded)
+   - put arguments in standard order: myTime, myIter, myThid
+   - use standard S/R GET_PERIODIC_INTERVAL for time interpolation of
+     atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.
+   - fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf
+   - new routine to print summary of CFC params and check for consistency.
+ o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff,
+   similar to thsice_advdiff.
+   Note that for the B-grid case the routine parameters uc/vc are overwritten.
+ o pkg/cfc:
+   - change time interpolation for atmospheric CFC-11 (now same as for CFC-12);
+     update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline.
+   - fix interpolation of atmphspheric CFC between Sorthern and Northern
+     hemisphere value.
+ o pkg/seaice:
+   - allow to use seaice dynamics without pkg/exf (e.g., using pkg/cheapaml)
+ o pkg/seaice: add Adams-Bashforth2 time discretization for ice dynamics;
+               so far only for JFNK-solver, turn on with SEAICEuseAB2 = .TRUE.
+   - requires an additional time level that is stored in the pickup
+   - you can start with AB2 from a pickup without this time level with
+     pickupStrictlyMatch = .false.
+ checkpoint64h (2013/05/26)
+ o pkg/cheapaml:
+   - replace one ()**.5 with SQRT + use temp var "cdu = tau/Du" (coare3_flux);
+     affect machine truncation (but exp cheapAML_box still pass with 13 digits).
+   - consistent treatment of uWind,vWind location: assume everywhere in
+     pkg/cheapaml that they are on C-grid (@ uVel,vVel location)
+     (Note: was already the case for Tair,Qair advection);
+     add option (INCONSISTENT_WIND_LOCATION) to recover old results.
+   - compute diabatic forcing only in the interior (excluding overlap regions)
+   - fill in array "Qsw" (for short-wave heating);
+   - add diagnostic for precip ; fill-in diagnostics for cheapAML state vars
+     before any update (consistent with MITgcm state var diagnostics);
+   - cheapaml_fields_load.F & cheapaml_init_varia.F : only fill outer edges if
+     non periodic ; + adjusted for uWind,vWind (C-grid).
+ o pkg/seaice:
+   - remove dependence of pkg/seaice versus pkg/exf (file: pkg/pkg_depend) and
+     add explicitly pkg/exf in experiments that currently use pkg/seaice.
+   - allows to compile pkg/seaice without pkg/exf.
+ o tools/OAD_support:
+   - use a local copy (ourRWCPinBd) to ensure index ourRWCP stays within bounds
+     of array "ourStepOf" in function rvNextAction (revolve.F90).
+ o pkg/aim_compon_interf renamed to pkg/atm_compon_interf
+   - change pkg name (to be used with other atmospheric physics pkg)
+     but by-pass CVS when making the new pkg so that we keep the CVS history.
+ o pkg/offline:
+   - call OFFLINE_FIELDS_LOAD from pkg/offline/offline_init_varia.F
+     (previously called from pkg/dic_surfforcing_init.F)
+ o model/src:
+   - re-order sequence of calls within packages_init_variables.F, using
+     standard order, except for:
+      DIAGNOSTICS_INIT_VARIA and OFFLINE_INIT_VARIA (called @ the top),
+      CTRL_MAP_INI and OBCS_INIT_VARIABLES (called @ the bottom)
+ o new pkg: atm_phys
+   - add entry point and source code (previously in contrib
+       verification_other/atm_gray/code_gray/) for new pkg "atm_phys"
+     (atmospheric physics pkg from P. O'Gorman and T. Schneider, JCl, 2008).
+   - re-order sequence of calls within packages_readparms.F,
+      packages_init_fixed.F and packages_write_pickup.F
+     (but skip packages_init_variables.F because of TAF issues).
+   - update contrib/*/atm_gray/ experiment.
+ o pkg/seaice (ITD code):
+   - simplify and fix the writing of pickup-files for ITD case
+ o pkg/seaice (ITD code):
+   - introduce floe size dependent lateral melt for ITD case;
+   - cleaning (avoid division by zero, change to f77 syntax, remove tabs)
+   - update seaice_itd experiment main output.
+ o pkg/thsice:
+   - remove snowPrc from common block THSICE_FLUX, in THSICE_VARS.h and
+     declared it locally (without bi,bj) in thsice_main.F & aim_do_physics.F;
+     changed accordingly pkg/atm2d.
+ checkpoint64g (2013/05/01)
+ o pkg/exf ALLOW_RUNOFTEMP
+   - if defined,  river and glacier runoff temperature can be read-in from
+     runoftempfile; runoftempfile needs to have same format as runofffile
+ o pkg/thsice (& pkg/bulk_force):
+   - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
+     for energy content of Precip + RunOff & Evap (like with pkg/exf).
+   - change computation domain to always be the interior (without overlap).
+   - fix bug (wrong overlap) when using EXF and stressReduction > 0.
+ o verification/tutorial_global_oce_biogeo:
+   - add preliminary OpenAD setup (still has problems)
+ o pkg/seaice:
+   - turn some parameters for choosing the convergence criterion of
+     the inexact Newton method (JFNK) into runtime parameters for convenience
+   - clean up seaice_calc_viscosities.F: remove/retire two options for
+     SEAICetaZmethod (1,2), introduce area weighting for method 3; this changes
+     the results of lab_sea/input because a division has been replaced by
+     a multiplication with the reciprocal (sumNorm)
+   - modify offline_exf_seaice/input.dyn_jfnk/data.seaice to improve
+     convergence of solver (changes results, of course), and to test some
+     new features
+ o model/src:
+   - remove unused (since Aug 2006) S/R SET_WRITE_GLOBAL_PICKUP and its call.
+   - remove unused forcing field "dQdT" and associated parameter "dQdTFile".
+   - move forcing adjustment (balancing surface forcing) in specific S/R
+     where might also be applied exchanges (if needed) to forcing arrays.
+ o pkg/shelfice:
+   - allow to specify the Ice-Shelf mass per unit area (instead of
+     shelficeLoadAnomaly) and do the conversion from one to the other
+   - move loading from file of shelficeLoadAnomaly from SHELFICE_INIT_VARIA
+     to SHELFICE_INIT_FIXED: (a) avoid some TAF recompution issues and
+     (b) will be loaded in time (before calling INI_PRESSURE) in case it is
+     needed in phi0surf for initial pressure calculation when useDynP_inEos_Zc
+   - update isomip experiment forward output (get machine truncation error
+     from conversion shelficeLoadAnomaly -> shelficeMass -> shelficeLoadAnomaly)
+ o verification/offline_exf_seaice:
+   revise data.seaice in input.thermo and input_ad and update results accordingly
+     HO = 0.2, SEAICE_areaLossFormula = 2,
+     SEAICE_growMeltByConv = .TRUE.,
+     SEAICE_doOpenWaterMelt = .TRUE.,
+   Improve consistency with input.thsice and fix the spurious 500m ice corners
+ o verification/global_ocean.cs32x15:
+   - set Energy Reference Level to liq. water @ 0 degC: temp_EvPrRn=0.,
+     in icedyn (thsice+seaice-dyn) test and update output.
+ o verification/offline_exf_seaice:
+   - adjust list of tested variables (with testreport) and update
+     standard test output with better slection of monitored fields.
+ o pkg/cd_code:
+   - swtich off Adams-Bashforth on the 1rst iteration. Update output of
+     experiment lab_sea.hb87
+ o tools/genmake2:
+   - change default makedepend from the system default to tools/xmakedepend:
+     When no makedepend is specified, select tools/xmakedepend it the test pass,
+     otherwise select the system default (if exist and pass the test) or
+     try to build cyrus-makedepend ; stop if none of the 3 works.
+ o pkg/exf & pkg/thsice:
+   - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
+     for energy content of Precip + RunOff & Evap. Assumes:
+) Rain has same temp as Air.
+) Snow has no heat capacity (consistent with seaice & thsice pkgs)
+) Run-Off comes at the temp of surface water (with same Cp)
+) Evap over ocean is released to the Atmos @ surf-temp (=SST); should be
+     put directly into Latent Heat flux & should use water-vapor heat capacity.
+) Evap over snow/seaice (pkg/thsice) assumes constant Lf+Lv (consistent
+     with snow having no Cp) => water vapor is released to Atmos @ 0^oC (=ERL).
+ o pkg/seaice: simplify the use of CPP flags in JFNK-related files
+     (compile when SEAICE_ALLOW_JFNK is defined)
+ o pkg/thsice:
+   - fix oceanic flux diagnostics & timeave (left from new sequence of calls
+     implementation): move THSICE_AVE call after the advection (called directly
+     from thsice_do_advect.F).
+ o verification/global_ocean.90x40x15 and OpenAD:
+   New experiment for OpenAD is identical to the one in input_ad except that
+     multiDimAdvection=.FALSE.,
+   There is still an issue with this.
+ o pkg/thsice:
+   - account for ice velocity (ocean relative velocity) in turbulent heat flux
+     at the base of the ice; update output of global_ocean.cs32x15 (icedyn)
+     and offline_exf_seaice (main test).
+ checkpoint64f (2013/03/31)
+ o verification/OpenAD:
+   - new (smaller, without OAD_DEBUG) output_oadm.txt generated using gfortran.
+ o verification/isomip, pkg/shelfice and OpenAD:
+   - add OpenAD setup to this exp and make shelfice package work with OpenAD
+ o verification/tutorial_global_oce_biogeo:
+   - update AD and TLM output after turning off ALLOW_FE (in DIC_OPTIONS.h)
+ o verification/offline_exf_seaice:
+   - replace adjoint experiment (now similar to fwd input.thermo/ setup).
+ o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD:
+   - add OpenAD setup to this exp and make ptracers package work with OpenAD
+ o pkg/seaice/seaice_evp.F:
+    mask the asymmetric contribution of the ice-ocean stress (when
+    the turningAngle is non-zero) over open water to avoid stripes
+    in the EVP-solutions after many EVP-substeps. This does not change
+    the verification experiment (because turningAngle=0 in that experiment),
+    but will affect other EVP solutions with turningAngle.ne.0
+ o verification, AD & TLM output:
+   - new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple
+     additions and multiplications which affect results at machine truncation
+     level. Update few AD output (1D_ocean_ice_column, bottom_ctrl_5x5,
+     lab_sea.noseaicedyn & offline_exf_seaice) and TLM output
+     (1D_ocean_ice_column & tutorial_tracer_adjsens.som81) which had only 12
+     digits of matching.
+ o pkg/seaice:
+    modify lsr-algorithm so that it vectorizes AND converges by using a
+    "zebra" method: split vector loop into two with step size 2; this
+    solves a general convergence problem for the JFNK solver on a vector
+    computer. It has the potential to even improve convergence for
+    non-vector machines, but it does change the results so it is turned
+    off by default. To turn on define CPP-flags SEAICE_VECTORIZE_LSR and
+    SEAICE_VECTORIZE_LSR_ZEBRA in SEAICE_OPTIONS.h
+ checkpoint64e (2013/03/05)
+ o pkg/ecco and several verification experiments:
+    Remove special versions of the_model_main.F, the_main_loop.F, forward_step.F
+    from ecco package, and revert to unified routine in model/src/
+    Adjust verification experiments accordingly, especially gloal_oce_llc90
+    Should conclude long-standing work by Gael to reconsile the_main_loop with
+    ECCO and will enable OpenAD's revolve loop in ECCO setup.
+ o pkg/generic_advdiff:
+   - implement compressible flow method for multi-dim advection (similar to
+     gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since
+     TAF generates many recomputations) to use it; no yet coded with implicit
+     vertical advection.
+   - change experiment advect_cs (new output) and advect_xy (same output)
+     to test compressible flow multi-dim advection.
+ o pkg/generic_advdiff:
+   - fix SOM advection for unusual cases (linear Free-Surf in r*, other
+     cases where linear Free-Surf is not @ k=1, e.g., useShelfIce)
+ o pkg/seaice:
+   - fix bug in the no-slip implementation in seaice_calc_strainrates.F, this
+     bug affects two verification experiments (lab_sea and lab_sea.hb87),
+     recover old (wrong) results by setting noSlipFac = 2. in
+     seaice_calc_strainrates.F;
+   - add another averaging method for etaZ (etaZmethod=3), a mix of 2 and 0
+   - add runtime parameter SEAICE_JFNKepsilon for that finite difference
+     gradient in the Jacobian times vector operation (s/r seaice_jacvec)
+   - fix line search in seaice_jfnk.F (s/r seaice_jfnk_update)
+ o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code:
+   - new subroutines seaice_lsr_tridiagu/v
+   - introduce loop bounds i/jmin/max to be able to use a restricted
+     additive Schwarz method, but not used for now.
+   - rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS
+   - use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner
+ o OpenAD support
+    Reorganize S/R call for overall time-stepping loop to facilitate
+    OpenAD revolve loop replacement
+    (new S/R main_do_loop.F)
+ o model/src:
+   - add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3;
+   - pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R
+     ADAMS_BASHFORTH2.
+ o pkg/cheapaml:
+   - add new parameter (default=F, same as before) to disable full domain
+     (including land) periodicity in X & Y dir.
+   - new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of
+     prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer
+     into single S/R CHEAPAML_TIMESTEP.
+ checkpoint64d (2013/02/17)
+ o pkg/monitor (angular momentum):
+   - do not add Eta contribution to the total AM if using rigid-lid;
+   - correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta).
+   - horizontal discretisation: compute Zonal wind contribution separately for
+     each component (instead of from cell centered averaged) and use the 4
+     grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part.
+   - Check that AM is conserved with linear dynamics (momAdvection=F and linear
+     FreeSurf) if using vectorInvariant momentum.
+ o model/src (horizontal grid):
+   - move initialisation of all horizontal grid arrays to null value
+     from specific horizontal grid S/R to main S/R INI_GRID;
+   - add 2 new arrays to project model C-grid velocity on to zonal direction
+     (similar to AngleCosC & -AngleSinC but at U and V point location) and
+     compute them in S/R CALC_GRID_ANGLES.
+ o pkg/seaice: replace a hard coded parameter by a runtime parameter
+     SEAICE_JFNK_tolIter
+ o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in
+     preconditioner for JFNK (run LSR into the overlaps as far as possible,
+     i.e OLx/y-2, but overwrite the solution in the overlaps)
+   - extend loop range in seaice_calc_viscosity
+   - add new parameters SEAICE_OLx/y (default = OLx/y-2)
+   - add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs
+   - slightly modify loops in tridiagonal solver lsr-preconditioner
+   - by default remove the extra exchange in seaice_preconditioner with a
+     replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE
+   - modify offline_exf_seaice so that old results without RAS are reproduced
+     for output.dyn_jfnk.txt
+   in seaice_fgmres.F (unrelated to RAS)
+   - add a cpp-flag option for a re-ordered mapping (potentially more
+     efficient), but because this changes the results, turn it off by
+     default
+   - replace the save statement by local common blocks
+ o utils/matlab:
+   - fix tile-offset in rdmnc.m when output was produced using EXCH2.
+   - update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab)
+     instead of local script "load_cs.m".
+ o pkg/seaice:
+   - fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected
+     to the scalarProductMetric and the unrolling. By chance this does not
+     change the verification experiment, because of the particular domain
+     decomposition
+ o pkg/diagnostics:
+   - change default missing_value from UNSET_RL to -999.
+ o pkg/layers: improve vectorization of layers_fluxcalc.F
+   - step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu
+     time spent in this routine by more than a factor of 3 on an NEC-SX8
+   - step 2: replace search algorithm by a bisection algorithm found in
+     Press et al. Numerical Recipes in Fortran. This algorithm can be
+     vectorized and finds the correct bin in approx. log2(Nlayers) steps.
+     For now, use this algorithm only for TARGET_NEC_SX defined.
+   - moved the search algorithm into a separate subroutine, that is kept
+     within the same file for automatic inlining.
+   - modified catching potential errors
+ o pkg/ecco:
+   - add compile switches ALLOW_SHALLOW_ALTIMETRY and ALLOW_HIGHLAT_ALTIMETRY.
+ o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk :
+   - modifications for ALLOW_GENTIM2D_CONTROL
+   -- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes.
+   -- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid )
+   -- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc
+   -- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F
+ o model/src:
+   - account for moist thermodynamics in (dry) potential temperature equation;
+     update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev)
+     and cpl_aim+ocn.
+   - also switch to standard compiler (gfortran, was using ifort previously)
+     for fizhi-cs experiments reference output.
+ o pkg/ctrl:
+   - 1st step toward generic time-varying control variable (2D) via CPP option
+     ALLOW_GENTIM2D_CONTROL
+   - note new namelist ctrl_nml_genarr in data.ctrl
+ o verification/global_ocean.cs32x15:
+   - switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new
+     thsice calling sequence and update "output.icedyn.txt" output file.
+ o pkg/ptracers:
+   - from Ryan A.: code to allow to restart a tracer at regular time interval
+     specifying a reset frequency and a reset-phase (for each tracers).
+ o pkg/thsice:
+   - implement new sequence of calls for thsice+seaice:
+       previously:   ice-Dyn,ice-Advect,ice-Thermo(thsice)
+       new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect
+   - allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE"
+     in CPP_OPTIONS.h) to recover old sequence;
+   - update diagnostics for Intermediate State thsice diagnostics: now filled
+     just before advection (instead of just after advection in old sequence);
+   - update output of experiment offline_exf_seaice (standard test);
+   - in global_ocean.cs32x15 exp., postpone output.icedyn.txt update
+     by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h
+ o pkg/aim_v23:
+   - use tiled array for aim_CO2 and surface wind speed for export to coupler;
+   - use standard pkg/mdsio routines to read & write CO2 pickup file;
+   - in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F;
+   - Implement new sequence of calls for seaice advection (with thsice and
+     seaice diffusion): do ice advection after ice-Thermodynamic (previously
+     was done before); change aim_do_physics.F (split the bi,bj loops block);
+   - use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence;
+ o pkg/thsice:
+   - add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case
+     where just seaice diffusion is used without seaice-dynamics.
+ checkpoint64c (2013/01/18)
+ o pkg/seaice:
+   - add a parameter JFNKres_tFac that can replace JFNKres_t
+     (= JFNKres_tFac*JFNKresidual before JFNK solver)
+   - add a line search option to the JFNK solver
+   - move update of u/vIce and computation of initial residual into a separate
+     routine (same file); makes the code a little easier to read (?)
+   - the line search requires computation of the residual and for some reason
+     I cannot do the update of u/vIce at the beginning of the Newton loop
+     without changing the results, so we move computation of the new residual
+     also to the end of the Newton loop, even without the line search
+ o pkg/mdsio:
+   - write missing value (corresponding to undefined array value) to meta files;
+     skip this if missing value is one (UNSET_RL would be a better value for the
+     case of undefined missing value but it's current the default missing-value);
+     Also update mdsio_read_meta.F (reading timeInterval & missing-value).
+ o pkg/exf & thsice:
+   - for diagnostics purpose, fill-up and update Qsw array (+ fill the
+     diagnostics) even when SHORTWAVE_HEATING is #undef;
+ o verification/cfc_example:
+   - turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to
+     illustrate how to use it).
+ o verification/offline_exf_seaice:
+   in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing
+     files to only one time-record.
+   in input.thermo: narrow the 2 bands of low initial ice-concentration near
+     N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for
+     snapshot output; same mcPheePiston value as in thsice with
+     surf-current=0.2m/s.
+   in input.thsice: similar set-up as in input.thermo (channel with same seaice
+     initial conditions).
+ o verification/cfc_example:
+   - update file "data" with more standard choice (default rotationPeriod,
+     exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F,
+     set deltaTFreeSurf to deltaTtracer) and update the output.
+ o pkg/layers:
+   - fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC;
+   - ensure that "layers_bolus" is switched to False when useGMRedi=False.
+ o verification/offline_exf_seaice:
+   - set all {field}period to zero for constant-in-time forcing (not tested
+     anywhere else).
+ o verification/offline_exf_seaice:
+   - dyn_lsr  : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice;
+   - dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice.
+ o model/src:
+   - implement Finite-Volume method for (hydrostatic) presure gradient
+     from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate.
+ o pkg/seaice: implement EVP* by Lemieux et al. (2012).
+   - In order to be compatible with the default EVP code, this requires changing
+     the EVP code around a little; and because any small change immediately
+     breaks the lab_sea.hb87 verification experiment, the reference output is
+     updated two times (each time the remaining aggrement was only 2 digits):
+     - after replacing 1/dt by 1*recip_dt with a precomputed recip_dt
+     - after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt
+     The adjoint test lab_sea.evp also needed to be updated.
+   - Turn on EVP* by setting SEAICE_deltaTevp as before, and setting
+     SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be
+     a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps
+     explicitly with SEAICEnEVPstarSteps (thereby overriding the default of
+     INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately
+     kept obscure, because I need to test it a little more.
+ o pkg/cheapaml:
+   - fix few incorrect type (_RL/_RS) in subroutine calls.
+ o pkg/seaice:
+   - new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays
+     to _RL vector; this fixes JFNK code when compiling with "-use_r4" option.
+ o model/src:
+   - add a warning if using select_rStar=2 with nonlinFreeSurf <> 4;
+     change (in input_ad*/data) select_rStar from 2 to 1 for AD verification
+     experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output)
+ o pkg/cheapaml:
+   - replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and
+     update output of experiment cheapAML_box.
+   - store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity,
+     and set them only in one place (cheapaml_readparms.F).
+   - replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI"
+   - remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms)
+     and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia).
+ o model/src/the_main_loop.F:
+   - fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION.
+ o pkg/seaice:
+   - remove legacy branch code.
+   - retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly.
+ o verification/*/code*/SEAICE_OPTIONS.h:
+   - remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY,
+     SEAICE_CAP_HEFF).
+ o pkg/cheapaml:
+   - use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time
+     to load new forcing fields.
+   - add missing "_d 0" where it's needed; + some editing (improve indentation).
+   - remove switch to "-r8" compiler option (no longer needed) in verification
+     cheapAML_box, keep same output (small trucation error differences).
+ o verification/offline_exf_seaice:
+   - add thermodynamics only test.
+ o verification/cheapAML_box:
+   - split the domain in 8 (2x4) tiles; add MPI and multi-threaded test;
+     keep same output (same 14 digits for cg2d).
+   - switch on "-r8" compiler option (some numerical values are missing
+     the "_d 0") and update output (only 6 digits for cg2d were preserved).
+ checkpoint64b (2012/12/24)
+ o pkg/cheapaml:
+   - remove un-used variables (Qnet,EmPmR) from pickup files.
+   - store tendency of advected variables into cheapaml pickup file
+     and fix the AB-2 restart.
+ o verification/offline_exf_seaice and lab_sea adjoint:
+   - switch to new code (#undef SEAICE_GROWTH_LEGACY).
+   - switch to 4 time steps in offline, consistent with lab_sea.
+   - match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice.
+   - update results after change of experiment seaice.
+ o pkg/seaice:
+   - remove option SEAICE_MULTICATEGORY; has been replaced with run-time
+     parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is
+     still defined since SEAICE_multDim needs to be set to MULTDIM value (from
+     SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default.
+ o model/src:
+   - add run-time parameter to select CG2D solver minimum-residual solution
+     (in case of a poor convergence).
+ o pkg/seaice/seaice_lsr.F
+   - move calculation of matrix coefficients into new
+     S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same
+     file; the main purpose of this change is to be able to reuse the code
+     in S/R SEAICE_PRECONDITIONER
+   - modify the computation of the residual so that the mass of sea-ice
+     is not used twice; this simplifies the calculations, but since
+     the residual is never used except when LSR_mixIniGuess.ge.4---and this is
+     not tested in testreport---this does not affect the testreport results.
+ o verification/seaice_obcs:
+   - disable SEAICE_GROWTH_LEGACY; reset input files to match those of
+     verification/lab_sea/input.salt_plume; changes results/output.txt*
+ o model/src:
+   - adapt quasi-hydrostatic formulation to work with p or p* coordinate.
+ o pkg/seaice:
+   - improve description of parameters in seaice_fgmres.F and start
+     cleaning up the code
+   - change name of SCALPROD to SEAICE_SCALPROD and modify meaning of
+     second argument
+   - add a metric based on grid cell area to SEAICE_SCALPROD; update
+     results of offline_exf_seaice.dyn_jfnk
+   - compute initial residual norm in seaice_jfnk based on SEAICE_SCALPROD
+ o pkg/aim_v23:
+   - fix an other bug in dissipation heating (grid-cell area was missing).
+ o model/src + pkg/seaice:
+   - add global (multi-tile) linear solver for pair of tri-diagonal system
+     along X and Y lines, respectively for U and V component.
+     Note: 1) MPI and cube-exchange not yet coded.
+) probably not accurate for poorly conditioned / large size problem.
+   - add option for SEAICE_LSR to use global (multi-tile) tri-diagonal solver;
+     default: not compiled and not used.
+ o pkg/seaice:
+   - first attempt at a multi-threaded fgmres solver for the JFNK solver:
+     introduce bi/bj loops and use global_sum_tile_rl instead of
+     mpi_allreduce in seaice_fgmres.F
+   - improve diagnostics output for fgmres solver (seaice_fgmres.F)
+   - replace a few unnecessary goto statements by if-blocks  (seaice_fgmres.F)
+   - add a verification experiment for JFNK in offline_exf_seaice
+ o verification:
+   - change (for now, only fwd test) offline_exf_seaice experiment:
+     use a re-entrant channel with idealized coastline (trapezoidal shape)
+     at southern boundary to explore seaice dynamics and thermodynamics
+     with simple forcing. Main set-up has dynamics+thermo and SST relaxation;
+     secondary test (input.thsice) use thermodynamics only with SST relaxation.
+   - add seaice-dynamics only secondary test using LSR and pkg/thsice advection.
+ o pkg/exf:
+   - disable "sstExtrapol" when Nr=1
+ o verification:
+   - add new experiment "cheapAML_box" (simple 1 layer set-up from Bruno Deremble)
+     to test pkg/cheapaml.
+ o pkg/aim_v23 & pkg/shap_filt:
+   - fix dissipation heating (erroneous gravity multiplication factor).
+ o pkg/seaice:
+   - remove unused field pressPre from jfnk solver
+   - rename two subroutines in seaice_preconditioner.F
+ o eesupp/src:
+    - S/R MDSFINDUNIT avoids reserved unit numbers (scrUnit1, eeDataUnit ...)
+ o pkg/seaice/seaice_preconditioner.F: fix preconditioner once again
+    - remove wrong parts of the rhs and the lhs (were in there
+      because I did not understand the concept of this preconditioner)
+    - add an exchange between u- and v-sweep. This increases communication
+      by a factor of two but improves the convergence of jfnk. Ideally,
+      one would like the u- and v-sweep to be independent. So far within
+      undocumented ifdefs
+    - reorganize the extra computations for printing the residuals
+ o tools/genmake2:
+   - comment out the "mpif.h" include in NetCDF test programm (for MPI built)
+     since it's not necessary (and was preventing to use MNC in some cases).
+ checkpoint64a (2012/11/16)
+ o pkg/autodiff:
+   - improve pkg-internal logical parameter switch (inAd/inFwd mode) so that
+     autodiff_readparms.F no longer depends on calling order (within
+     packages_readparms.F) and no longer requires to include ${PKG}_PARMS.h):
+     rename param turnFreeDriftInAdMode to SEAICEuseFREEDRIFTswitchInAd
+     and change param SEAICEuseDYNAMICSinAdMode to SEAICEuseDYNAMICSswitchInAd.
+ o pkg/obcs:
+   - adding tidal velocity forcing capability to obcs
+     for usage example, see verification/seaice_obcs/input.tides
+ o pkg/seaice:
+   - turn the LSR-relaxation parameters WFAU/V into runtime parameters
+     SEAICE_LSRrelaxU/V
+   - introduce runtime parameter SEAICEetaZmethod (=0 by default)
+ o pkg/aim_v23:
+   - implement heating from friction (bottom friction and stratospheric drag).
+ o pkg/shap_filt:
+   - fix diagnostic "SHAP_dKE" (was 2 time smaller); implement heating from
+     dissipation but only for Shap_funct=2, active when addFrictionHeating=T.
+ o model/src:
+   - move AddMass common block from DYNVARS.h to FFIELDS.h; allow to read-in
+     time-constant addMass field from file (addMassFile);
+   - support for heating due to friction (and Kinetic Energy dissipation):
+     add option, run-time switch and 3-D field array + support code ; each pkg
+     or S/R can add heating contribution (if there is a sink of KE); the sum is
+     accounted for as a Temperature tendency term (EXTERNAL_FORCING_T).
+ o pkg/seaice:
+   - complete merge of ITD code into seaice_growth.F
+     from MITgcm_contrib/torge/itd/code/
+     no verification so far, but Torge Martin tested
+     "1-D test case and Beaufort set up;
+     deliver okay results after 1 model year."
+   - complete merge of SEAICE_SIZE.h into all relevant routines
+   - move computation of eta at Z-points into calc_viscosities
+     + introduce global field etaZ
+     + add different methods for computing etaZ, for now the old
+       method (simple averages of eta to Z-points) is hardwired
+     + replace etaMeanZ by etaZ in seaice_lsr, seaice_calc_residual,
+       seaice_preconditioner
+   - simplify computations for SEAICE_ZETA_SMOOTHREG
+   - seaice_preconditioner:
+     + replace one remaining press by pressLoc (mistake)
+     + adjust printing of residuals
+   - improve I/O of diagnostics of JFNK in seaice_jfnk.F:
+     + add (SEAICE.h) and rename some counters (initiliased in
+       seaice_init_fixed.F)
+     + add _BEGIN/END_MASTER (myThid)  around print statements
+     + print total number of iterations and failures over SEAICE_monFreq
+       interval to STDOUT
+   - move control over output-messages by fgmres to seaice_jfnk to save
+     some operations
+   - move resetting initial guess for fgmres outside of seaice_fgmres_driver
+     in order to make restarts with sol .ne. zero (fgmres with restarts)
+     (seaice_jfnk.F, seaice_fgmres.F)
+   - seaice_calc_l/rhs.F: replace maskW/S by maskInW/S; this fixes
+     a serious convergence problem when open boundaries are involved
+ o pkg/ggl90: fix computation of control volumes for the case of
+   ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes
+   up half a grid cell from C-centered to W-centered (pointed out by C. Eden)
+ o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC
+ o pkg/autodiff
+   - Add inAdMode switch for SEAICEuseDYNAMICS:
+     SEAICEuseDYNAMICSinAdMode
+     (extend logic in ADAUTODIFF_INADMODE_SET)
+ o pkg/seaice
+   - Step 1 of merging ice-thickness distribution (ITD) code from
+     MITgcm_contrib/torge/itd/ (author: Torge Martin)
+     The code implements concept laid out in Thorndike et al. (1975);
+     code is enabled via CPP flag SEAICE_ITD
+     nITD (in SEAICE_SIZE.h) defines number of ice thickness categories;
+     code is not complete yet!!
+   - SEAICE_SIZE.h now included in almost all seaice routines
+ o verification (using seaice):
+   - switch back seaice-dynamics (+ lower SOLV_MAX_ITERS) in ADM exp.
+     global_ocean.cs32x15.seaice ; update results.
+   - compile B-grid dynamics in FW test exp 1D_ocean_ice_column ;
+   - compile C-grid dynamics with #define SEAICE_ALLOW_JFNK in FW test exp
+     offline_exf_seaice (previously compiling B-grid).
+ o pkg/exf:
+   - fix some STOP conditions in exf_check.F (from Aug 28, modifs did not allow
+     to specify neither just 1 comp of wind or wind-stress, nor no surface momentum
+     forcing): just replace CPP option ALLOW_ATM_WIND with run-time param useAtmWind.
+ o pkg/layers (adjust changes from Sept 19):
+   - do snap-shot output and fill diagnostics from inside iLa loop (layers_calc.F)
+     this allows to remove "layers_maxNum" dimension from all layers arrays.
+ o pkg/layers (adjust changes from Sept 19):
+   - remove ALLOW_LAYERS_OUTPUT ; fix snap-shot and time-ave output ;
+   - snap-shot extended to all type of layers (not just the 1rst type);
+   - remove layers variables when corresponding CPP option is undef.
+ o pkg/layers:
+   - rename pkg/layers variable and add new output (layer exist & un-weighted
+     velocity in layer)
+ o pkg/seaice:
+   - simplify (?) ocean-drag coefficent computations by using
+     the same routine in all three solvers (saves some code lines)
+   - remove global fields DRAGA and DRAGS from C-grid code and
+     declare them locally in lsr.F (the only place where they are
+     still used)
+   - update AD output of lab_sea.evp (very sensitive anyway).
+ o pkg/seaice: add Jacobian-free Newton Krylov solver for ice dynamics
+   (Lemieux et al. 2010, 2012). Turn on with the usual SEAICE_ALLOW_JFNK
+   and SEAICEuseJFNK=.true. A few things to note:
+   - involves a FGMRES, that is parallel but very inefficient,
+     because of many scalar products (global sums) in the Gram-Schmidt
+     orthogonalization method. Needs to be replaced. Original code
+     from J.-F. Lemieux
+   - preconditioner for FGMRES is a stripped down version of LSOR
+   - SOLV_MAX_ITERS is now used for LSOR as a solver and as a
+     preconditioner. For the preconditioner, the default is set to 10.
+   - Jacobian times vector is computed with finite differences
+   - marginally related to JFNK-solver: add a smooth regularization for
+     zeta with tanh that will improve convergence (Lemieux and Tremblay,
+) for any implicit solver (not implemented for EVP because EVP
+     does not need this regularization in the first place). Define
+     SEAICE_ZETA_SMOOTHREG in SEAICE_OPTIONS.h to use.
+ o eesupp/src:
+   - check in genmake2 that intrinsic S/R flush is available.
+   - add S/R to flush IO unit (if intrinsic S/R flush is available)
+   - flush standard & error msg unit before MPI termination
+   - if debugMode, flush IO unit after printing msg
+ o pkg/ctrl:
+   - ctrl_unpack.F, ALLOW_GENARR3D_CONTROL code: fix missing argument in call
+     to ctrl_set_unpack_xyz.
+ checkpoint64 (2012/10/09)
+ o pkg/shelfice
+   - in mom_fluxform.F, mom_vecinv.F:
+     CALL SHELFICE_V_DRAG(bi,bj,k,vFld,KE,KappaRU,vF,myThid)
+     Bug fix KappaRU -> KappaRV
+     does not change verification/isomip but may change other setups
+     (presumably constant KappaRU=KappaRV)
+   - fix diagnostics SHIU/Vdrag (thanks to Tom Millgate)
+ o pkg/obcs:
+   - fixed some indexing bugs in obcs_seaice_sponge.F
+   - added obcs relaxation subroutines for HSALT and HSNOW
+   - changes verification/seaice_obcs/results/obcs_seaice_sponge.F
+ o pkg/seaice:
+   - add "multicategory" parameterization for snow in analogy to ice,
+     default is off for now.
+ o pkg/obcs:
+   - added obcs_seaice_sponge.F for obcs relaxation of seaice variables;
+     see verification/seaice_obcs/input.seaiceSponge for example application.
+   - remove local commom bloc "OBCS_GLOBAL" in obcs_readparms.F and do all the OB
+     index setting by master-thread. This fix multi-threads Pb in previous modifs.
+ o pkg/layers :
+   - add diagnostics to pkg/layers
+   - move the meat of pkg/layers from layers_calc.F to layers_fluxcalc.F
+     (from R.Tulloch). Layers_calc.F now calls layers_fluxcalc.F accordingly.
+ o pkg/generic_advdiff/gad_implicit_r.F :
+   - fix ADVr diagnostics in case of both implicit vertical advection and diffusion.
+ o pkg/seaice/seaice_growth.F:
+   - fix SItflux diagnostics in virtual salt flux + balanceEmpmr case.
+ o pkg/obcs:
+   - change default setting of OBCS_UVICE_OLD from defined to undef;
+   - use new parameter OB_indexNone for null index value (instead of hard-coded 0)
+     in all pkg/obcs code and in other pkgs; remove k loop in obcs_check_depths.F;
+   - pass OB_indexNone as (new) argument to S/R CTRL_MASK_SET_[X,Y]Z;
+   - change OB null index value (OB_indexNone) to -99 ; this fix the problem
+     with Southern & Western OB at a tile edge (at least in a simple set-up).
+ o pkg/obcs:
+   - change settings of OB index in case OB coincides with tile edge (shared by
+tiles), so that common OB location is registered by both tiles (instead of
+     only 1). However, for Southern and Western OB, index value = 0 is not
+     recognized as valid OB index (=default null value) and needs to be fixed.
+   - modify accordingly OBCS_BALANCE_FLOW and OBCS_MONITOR (avoid double counting)
+   - new parameter "OB_indexNone" for null index value (for now, still zero)
+     to replace hard-coded null index value of zero.
+ o pkg/exch2:
+   - improve W2_USE_E2_SAFEMODE (faster) and W2_E2_DEBUG_ON:
+     always check buffer-size (but outside the loop); move checking for valid
+     index from W2_USE_E2_SAFEMODE to W2_E2_DEBUG_ON; in W2_E2_DEBUG_ON,
+     print each tile and point connection only if |W2_printMsg|>= 2 and 3.
+ o pkg/ctrl (pack & unpack):
+   - in ctrl_pack.F & ctrl_unpack.F, use the same local file-name variable
+     (locally defined) for different variables (+ remove the variable-specific
+     file name in CTRL_GENARR.h). For now, only implemented for GENARR2/3D_CONTROL
+     (to be extended to other local file names in ctrl.h).
+ o pkg/flt:
+   - add a FLT_Iter0 option (similar to PTRACERS_Iter0).
+ o pkg/mdsio:
+   - fix missing STOP in mdsio_readvec_loc.F (case ioUnit=0) when file is missing
+ o tools/genmake2:
+   - add similar dependences for target EXE_AD & EXE_FTL as we have for EXECUTABLE
+     (added by Alistair in version 1.51 for building without make depend);
+   - remove Header files list (H_SRC_FILES) from the dependence of targets
+      ad_input_code.f & ftl_input_code.f (not clear why it was added in the first
+     place in version 1.23): this save going through staf when unrelated header
+     file has been modified.
+    Note: for an intermediate target (e.g., ad_input_code.f or adtaf) without
+     "make depend" step, still need to do "make links" before "make adtaf".
+ o eesupp/src (+ few pkg src files) & genmake2:
+   - finish to remove ALWAYS_USE_MPI in source code that TAF does not see;
+   - no longer set ALWAYS_USE_MPI in Makefile (was done by genmake2).
+   - improve genmake2 checking for ALLOW_${PKG} in CPP_OPTIONS.h files (distinguish
+      upper/lower case ; account for space between "#" and undef/define)
+ o pkg/flt (with exch2):
+   - cleaning: fix so that it compiles; move remaining MPI calls out of flt_exch2.F;
+   - simplify threads synchronisation; fix (many issues) multi-threaded with MPI.
+ checkpoint63s (2012/09/05)
+ o pkg/ecco:
+   - remove #ifdef ALLOW_SMOOTH_CORREL3D brackets.
+   - add more relevant #ifdef ALLOW_SMOOTH ones.
+   - sort out useAtmWind, useSMOOTH, ctrlSmoothCorrel2D.
+ o pkg/ctrl:
+   - CTRL_OPTIONS.h : document CPPs related to smoothing; ALLOW_SMOOTH_CORREL2D/3D,
+     ALLOW_CTRL_SMOOTH, ALLOW_SMOOTH_CTRL2D, ALLOW_SMOOTH_CTRL3D.
+   - ctrl.h : document run time params doInitXX, doMainPack, doMainUnpack, doPackDiag,
+     doSinglePrecTapelev (audodiff param!), ctrlSmoothCorrel2D (new) and
+     ctrlSmoothCorrel3D (new).
+     The added ctrlSmoothCorrel2D/3D replace the old ALLOW_SMOOTH_CORREL2D/3D CPP.
+   - ctrl_readparms.F : initialise ctrlSmoothCorrel2D/3D and read from namelist.
+   - ctrl_init.F ctrl_pack.F ctrl_unpack.F : switch off ustress/vstress
+     controls when useAtmWind, and vice versa.
+   - ctrl_map_ini_ecco.F : UVEL0, VVEL0, edtaux, edtauy cannot be smoothed as tracers.
+   - ctrl_get_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL2D with
+       #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel2D, IF useSMOOTH.
+   - ctrl_map_ini_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL3D with
+       #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel3D, IF useSMOOTH.
+   - ctrl_set_pack_xy[z].F, ctrl_set_unpack_xy[z].F:
+     replace ALLOW_SMOOTH_CORREL2D/3D brackets with ctrlSmoothCorrel2D/3D.
+ o pkg/smooth:
+   - remove un-necessary includes.
+   - remove ALLOW_SMOOTH*D and ALLOW_SMOOTH_CORREL*D brakets.
+     Those CPP options were never defined, and not necessary.
+ o model/src:
+   - fix CPP brackets in ini_mixing.F (GM_background_K belongs to gmredi).
+   - standard treatment of useSMOOTH.
+ o pkg/autodiff:
+   - add LOGICAL useGGL90inAdMode, useGGL90inFwdMode, useSALT_PLUMEinAdMode,
+     useSALT_PLUMEInFwdMode allowing to switch off ggl90 and salt_plume adjoint.
+ o pkg/exch2:
+   - add "if usingMPI" where it was missing (in exch2_rx?_cube*.template)
+     + start to remove ALWAYS_USE_MPI in source code that TAF does not see.
+   - make new S/R W2_MAP_PROCS out of w2_eeboot.F to setup exch2 CommonFlag
+     and tiles to process mapping.
+   - re-arrange 3 header files (W2_EXCH2_PARAMS.h, _BUFFER.h & _TOPOLOGY.h)
+     moving /EXCH2_FILLVAL_RX/ & /W2_EXCH2_COMMFLAG/ to W2_EXCH2_TOPOLOGY.h;
+     rename "exch2_tProc" to "W2_tileProc" and move seting of e2FillValue_RX
+     from w2_eeboot.F to w2_readparms.F.
+ o eesupp/src:
+   - set exchNeedsMemsync & exchUsesBarrier according to "usingMPI" (instead of
+     ALWAYS_USE_MPI) + moved from ini_communication_patterns.F to eeset_parms.F;
+     also move setting of exchCollectStatistics from exch_init.F to eeset_parms.F
+   - in eedie.F and all_proc_die.F, always call MPI_FINALIZE when ALLOW_USE_MPI
+     is defined (remove condition on usingMPI) to match cases where MPI_INIT
+     has been called.
+   - fix bug I put in previous modif of exch_sm_3d_rx.template (not much used);
+   - change default (non-MPI) value of myPid (from 1 to 0) to match MPI settings
+     (so that on 1 proc, get same myPid independently of usingMPI)
+   - add a stop if multi-procs but usingMPI=F ; stop also if usingMPI=T and
+     useCubedSphereExchange with EXCH-1 (safer).
+   - add "if usingMPI" where it was missing (+ start to remove ALWAYS_USE_MPI).
+ o pkg/ggl90:
+   - fix bug in filling corner mask array "mskCor" (FILL_CS_CORNER_TR_RL call)
+     used in ALLOW_GGL90_SMOOTH code.
+ o pkg/flt:
+   - fix typo in FLT_WITHOUT_Y_PERIODICITY (the effect was to ignore stopping
+     floats at the Southern end of the domain).
+ o eesupp/inc:
+   - add a list of CPP-options which can be set by Makefile (DEF_IN_MAKEFILE.h);
+     but not used (and not to be used) anywhere, just for documentation.
+ o pkg/autodiff, exf, ptracers & seaice (AD & TL output):
+   - comment out the very nasty "writeBinaryPrec = writeStatePrec" line, since:
+     a) can damage previously written records in any other multi-record files.
+     b) if needed, can easily do it cleanly, by calling S/R WRITE_REC_3D_RL/S.
+ o tools/genmake2:
+   - define variable MAKE within Makefile and use it in place of 'make';
+   - update AD_CONFIG.h (if needed) before building any of the executable
+     (forward, adjoint or tangent-lin); this involves a 2nd invocation of make;
+     and add the usual #ifndef/#define AD_CONFIG_H in AD_CONFIG.h;
+   - always print usual warning comment 'this file is automatically generated'
+     from script convert_cpp_cmd2defines (+ remove this warning from genmake2).
+ o pkg/cheapaml:
+   - updated to correspond to the code used in accepted paper (Nico Wienders).
+ o pkg/exf:
+     added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch.
+     ALLOW_ATM_WIND now just sets the useAtmWind default (see exf_readparms.F)
+     and force defines ALLOW_BULKFORMULAE (EXF_OPTIONS.h).
+ o pkg/exf, autodiff, ctrl, ecco and seaice:
+     remove ALLOW_ATM_WIND brackets, or replace them with useAtmWind ones.
+ o pkg/ctrl, ecco:
+     allow to compile both ALLOW_U/VSTRESS_CONTROL and ALLOW_U/VWIND_CONTROL.
+     Depending on useAtmWind, one is inactive, and the other is active (see
+     exf_getffields.F/exf_getsurfacefluxes.F).
+ o tools/genmake2:
+   - improve error msg when failing in 2nd test of check_for_broken_Ff
+   - fix option '-makefile' short-name (-mf according to genmake2 -help)
+   - source local config file "genmake_local" just after processing the genmake2
+     command arguments (previously done before processing arg).
+ o pkg/grdchk:
+   - add a call to TURNOFF_MODEL_IO for Tangent-Linear run (in this case, call
+     to this routine from cost_final has been dropped in g_cost_final)
+   - improve printed information (more explicit msg, no longer using "print *,"
+      fix fcpertminus printed value).
+ o model/src:
+   - move call to COST_INIT_VARIA out of packages_init_variables.F directly
+     into initialise_varia.F (just after calling PACKAGES_INIT_VARIABLES):
+     this prevents getting cost-funct reset in adinitialise_varia recomputations.
+ o pkg/dic:
+   - move initialisation of "freefe" array from from dic_biotic_forcing.F to
+     fe_chem.F: this prevents TAF from dropping this initialisation in TLM code.
+ o pkg/grdchk:
+   - grdchk_main.F : added CALL GLOBAL_SUM_INT( ierr , myThid )
+   - grdchk_getadxx.F etc. : omit I/O if ierr.EQ.0
+ o pkg/autodiff/ctrl/grdchk :
+   - attempt to sort out what works and what does not,
+     with regard to I/O, and to warn/stop accordingly.
+ o pkg/grdchk:
+   - attempt to fix grdchk in the case of useSingleCpuIO.
+   - "if ( myProcId .EQ. grdchkwhichproc .AND. ierr .EQ. 0 )"
+    statements were moved from grdchk_main.F and into
+    grdchk_getadxx.F grdchk_getxx.F grdchk_setxx.F.
+   - a global sum is applied to record numbers icvrec/layer
+    out of grdchk_loc so that they be passed to I/O routines.
+ o pkg/smooth:
+   - fix recomputation that appeared with nlfs : use smooth_recip_hFacC,
+     smooth_hFacW, smooth_hFacS (copied at init_fixed) in 3d case.
+ o verification/testreport:
+   - add option '-tlm' for Tangent-Linear test (-adm,-oad,-tlm are all exclusive);
+   - can also use compressed (gzip) reference output file;
+   - change format (in pkg/grdchk) of TLM output (+ add forward gradient)
+     to be easier to collect by testreport.
+   - update existing TLM output (half out-of-date by more than 3 yrs).
+   - report NETCDF & LAPACK settings (from genmake2) in output dir.
+   - report run-time in each individual summary (previously only for AD test);
+     for TLM test, add also TAF version.
+   - add daily TLM test on (old) aces cluster + weekly test on baudelaire.
+ checkpoint63r (2012/08/15)
+ o tools/genmake2:
+   - fix Makefile for target ftlall (+ update files to clean after make ftlall)
+ o pkg/ecco/ecco_cost_final.F :
+   - fix fc print statements (to stdout and costfunction0000) so
+     that the printed value is always after the global sum.
+ o pkg/seaice/seaice_dynsolver.F :
+   - fix ice strength assymptote at SEAICE_area_max<1
+     (no change for the standard case of SEAICE_area_max=1)
+ o some cleaning:
+   - pkg source files: ensure that all *.F files from each pkg included the
+     corresponding ${PKG}_OPTIONS.h file (except stand-alone src file which
+     only includes CPP_EEOPTIONS.h); fix S/R CTRL_SMOOTH ; update AD experiment
+     code_ad/*.F src files; add new option-file in pkg/admtlm + corresponding
+     includes;
+   - model/src: add PACKAGES_CONFIG.h wherever ALLOW_AUTODIFF[_TAMC] is used.
+   - ALLOW_DIFFKR_CONTROL: add a stop in S/R CTRL_CHECK in case ALLOW_3D_DIFFKR
+     is undef; also define /DYNVARS_DIFFKR/ common block in DYNVARS.h when
+     ALLOW_DIFFKR_CONTROL is defined, to allow to compile and reach this stop.
+   - update option-file CPP_OPTIONS.h of all AD experiments:
+     * no longer include PACKAGES_CONFIG.h ;
+     * includes ECCO_CPPOPTIONS.h if PACKAGES_CONFIG.h has been included ;
+     * def/undef ALLOW_3D_DIFFKR independently of ALLOW_DIFFKR_CONTROL (before
+       including ECCO_CPPOPTIONS.h).
+ o pkg/cost, pkg/ctrl, pkg/ecco option-file:
+   - clean-up and split content of old pkg/ecco/ECCO_CPPOPTIONS.h file into
+     separated pkg option-file (done according to old doc from ECCO_CPPOPTIONS.h,
+     not necessary accurate).
+   - add a template for option-file ECCO_CPPOPTIONS.h, mostly empty, in
+     pkg/autodiff, i.e., the 1rst pkg to compile for adjoint built, with lines to
+     deliberately break compilation (a remainder that it needs to be customized)
+   - in pkg/ecco, includes ECCO_OPTIONS.h instead of COST_OPTIONS.h
+   - rename COST_CPPOPTIONS.h to COST_OPTIONS.h
+   - rename CTRL_CPPOPTIONS.h to CTRL_OPTIONS.h
+ o tools/genamke2:
+   - check for lapack.
+ o pkg/cost and pkg/ecco : attempt to sort out some of the limiting intricacies.
+   - pkg/cost.cost_final.F : allow for use of pkg/ecco and pkg/cost cost functions
+     jointly. The exclusive ifdefs were removed, to add costs terms (when defined)
+     from both packages.
+   - the fc global sum in pkg/ecco/ecco_cost_final.F was removed accordingly.
+   - for objf_atl we use either the pkg/ecco or the pkg/cost term depending on CPPs.
+   - pkg/ecco and model/src : add CPP brackets around pkg/cost and pkg/ctrl includes
+     of "CTRL_SIZE.h" "ctrl.h" "ctrl_dummy.h" "optim.h" / "cost.h" accordingly.
+ o pkg/cost : add comments to explain special and/or untested setups.
+ o pkg/exf:
+   - use EXF_OPTIONS.h to set pkg/exf options except if done in ECCO_CPPOPTIONS.h
+     (previously, ALLOW_AUTODIFF_TAMC was controling this switch).
+ o verification/*/code_ad:
+   mimimal cleaning of AD experiments ECCO_CPPOPTIONS.h option-file:
+   - reccord when this file is included (define ECCO_CPPOPTIONS_H)
+   - remove the most obvious obsolete features (e.g., #define ALLOW_COST not
+     allowed since Oct 2003 in any option-file except in PACKAGES_CONFIG.h)
+ o pkg/seaice :
+   - added possibility to change ice strength/PRESS0 relationship to
+     HEFF, according to the following run time parameters
+     SEAICEpresPow0 :: HEFF exponent for ice strength below SEAICEpresH0 (integer, >0)
+     SEAICEpresPow1 :: HEFF exponent for ice strength above SEAICEpresH0 (integer, >0)
+     SEAICEpresH0   :: HEFF threshold for ice strength            (m)
+ o pkg/ggl90 :
+   - added run time flag mxlSurfFlag to include the code that ensure
+     mixing between first and second level (previously included as a comment)
+ o verification/1D_ocean_ice_column/input_ad/data.autodiff :
+   - add test of newly added dumpAdByRec=T option where
+     we write all records to one file per variable.
+ o verification/global_ocean.cs32x15/code_ad/CPP_OPTIONS.h :
+   - switch to #define ALLOW_BALANCE_RELAX and ALLOW_BALANCE_FLUXES
+     to check that this code is ok with taf and compiles in adjoint.
+ o pkg/autodiff :
+   - added run time param dumpAdByRec : ad dump format switch.
+     If true then write all records to one file per variable.
+     Else write one file per record (remains the default).
+   - revise seaice_ad_dump.F and exf_adjoint_snapshots_ad.F accordingly.
+ o pkg/seaice:
+  - Added SEAICEuseTILT run time switch : if set to
+    false then omit the tilt term in seaice dynamics.
+  - Fix free drift calculation.
+ o pkg/shelfice:
+   When initializing SHELFICEDragQuadratic, set default to be
+   consistent with shiCdrag in case SHELFICEuseGammaFrict is used,
+   but retain option to set it independently
+   (inconsistenty spotted by Veronique Dansereau)
+ o eesupp/inc:
+   - in EEPARAMS.h, add real-type constant for some frequently used simple number
+      (0,1,2,1/2), with name explicitly referring to RS/RL type.
+ o model/src:
+   - move balancing of relaxation terms to new S/R balance_relax.F.
+ o pkg/autodiff:
+   re-write active I/O high-level (control) S/R:
+   - rename  S/R ACTIVE_READ/WRITE_RL to ACTIVE_READ/WRITE_3D_RL
+   - add 1 more argument (useCurrentDir) to replace the "_LOC" 2nd set of S/R.
+   - use standard pkg/mdsio I/O routines (MDS_READ/WRITE_SEC_XZ/YZ  and
+     MDS_READ/WRITE_FIELD); change loops to multi-threads.
+   - update and merge active_file_control_slice.flow into active_file_control.flow
+   - update the calls in lower level S/R (active_file.F, active_file_g.F and
+     active_file_ad.F) keeping the argument list and function unchanged.
+   - also update lower-level "_LOC" version (call same S/R with "useCurrentDir
+     =.TRUE.") and remove high-level (control) _loc version (not called anymore).
+   - new low-level active I/O routines, one for each type (RL/RS), for active var
+     of various (XY,XZ,YZ) shape and level number (arguments: arrShape, myNr);
+     fix ctrl_init_wet.F & ecco_cost_weights.F by calling the new S/R with the
+     right type.
+ o autodiff and RS=real*4:
+   - call the right type (_RS instead of _RL) of S/R in few output S/R (pkg/exf
+     ad-monitor and snapshots); disable arrType='RS' in mdsio_gl*.F ;
+   - change argument type of 3-D mask argument to _RS to match type in the call
+     (in seaice_cost*.F, ctrl_*_gen.F and *ctrl_bound.F); to be continued.
+ o pkg/thsice:
+   - re-anable balanceEmPmR when useSEAICE=T with useThSIce=T.
+   - option to correct ocean fresh-water flux for imbalance of Atmos+Land
+     fresh-water flux: uniform correction or proportional to local precip.
+ o pkg/ctrl:
+   - new header file CTRL_SIZE.h for parameters maxCtrlArr2D, maxCtrlArr3D
+   - redefine CPP option ALLOW_BOTTOMDRAG_CONTROL to
+                         ALLOW_BOTTOMDRAG_CONTROL_NONGENERIC
+   - verification/hs94.1x64x5/ tests ALLOW_GENARR{2D,3D}_CONTROL
+ checkpoint63q (2012/07/30)
+ o pkg/autodiff:
+   note about monitor and snap-shot of ad-variables:
+   a) need to apply ADEXCH before monitor or output of ad-vars to include
+    overlap contributions (was done for adjDump but missing for monitor).
+   b) since ADEXCH implies adding overlap values to interior array, machine
+    truncation error is expected when adding an ADEXCH call in the middle of
+    the time-stepping (although mathematically identical).
+   modifs:
+   - fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars
+     declaration (adEddyPsiX,adEddyPsiY in adcommon.h).
+   - add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how  to
+     apply ADEXCH before monitor or snap-shot of ad-variables:
+        =0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy.
+   - implement new method (copy+adexch) for snap-shot and monitor of main model
+     ad-vars (initially not used by default -> output unchanged).
+   - change default (set to 2) to use new method and update few output_adm.txt
+     with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo
+     and both tutorial_tracer_adjsens tests).
+   - switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice)
+     and turn off momDissip_In_AB in the 2 other (needed for stable AB-3).
+ o pkg/ctrl:
+   enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of
+   generic control variables via
+   #define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL
+   Only required customization should be S/R ctrl_map_ini_genarr.F
+   (routine in repository contains example)
+ o pkg/exf:
+   - fix and refine checking of surface-relaxation setting when using EXF
+ o verification (adjoint exp):
+   - reduce length of simulation by half for experiment global_ocean.cs32x15
+     (std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output.
+ o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag)
+   - replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers
+     of KE that can occur with aggressive optimization
+   + put quadratic bottom drag calculation in separated loops (only done if
+     using bottomDragQuadratic)
+ o model/src: CG2D_NSA
+   - clean-up:  stop if cg2dNormaliseRHS=T and AUTODIFF
+      and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE.
+   - in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens),
+      change cg2d residual target to be expressed in Wunits (=> do not normalise
+      RHS ; this fix global_max Pb with TAF); update output.
+ o verification/tutorial_tracer_adjsens:
+    improve parameter consistency (and get rid of warnings):
+    - use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf);
+    - switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical)
+    - use staggerTimeStep (for stability) in som81; use default rotation period.
+ o pkg/exch2:
+   - with empty facet: fix compact-format (W2_mapIO=1) definition (was previously
+     reset to 0 = 1 long line in X)
+ o pkg/mdsio:
+   - fix reading of dimensions from meta file for large-size domain
+ o model/src:
+   - fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long);
+   - to refine CS-grid check, add logical flag "hasWetCSCorners": true if using
+     Cubed-Sphere Exch with CS-corners inside the domain;
+     make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate
+     globalArea and to set hasWetCSCorners.
+   - add warning if usingCurvilinearGrid and momAdvection in flux-form (missing
+     metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form.
+   - re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if
+     useCDscheme and useCubedSphereExchange).
+ o pkg/seaice/seaice_growth.F :
+   - compute the SEAICE_DISABLE_HEATCONSFIX term accordingly
+     for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0)
+     when the previous code was not correct.
+   - in all cases diagnoze the boundary condition mismatch to SIaaflux
+   - in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add
+     that term to QNET (essentially to set the melt/freeze water to 0degC).
+     when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed.
+ o verification/global_ocean.cs32x15/input.seaice :
+   - add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget.
+   - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces).
+   - update results (output.seaice.txt) accordingly.
+ o verification/lab_sea/input/data.seaice :
+   - remove SEAICEheatConsFix, which is now be tested
+     in global_ocean.cs32x15. The presently coded fix
+     is only consistent with real fresh water + nlfs.
+   - update results (output.txt) accordingly.
+ o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd).
+ o AD_CONFIG.h file:
+   - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;
+   - remove #include "AD_CONFIG.h" from all included OPTIONS files and
+     add it explicitly in each fortran src file where it is needed.
+     motivation: header file AD_CONFIG.h is generated/modified after "make depend"
+     thus introducing potentially wrong dependency; therefore, better to include
+     it only where it's really needed, and after any other included OPTIONS file
+     (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN
+     or ALLOW_TANGENTLINEAR_RUN).
+ checkpoint63p (2012/07/06)
+ o pkg/autodiff:
+   - rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ;
+   - create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters
+     which are now read from new parameter file "data.autodiff" (inAdExact
+     previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg)
+   - add file "data.autodiff" in all verification/*/input_ad/ directories.
+   - add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward
+     mode (used in global_ocean.cs32x15.seaice_dynmix test exp.)
+ o verification/tutorial_tracer_adjsens/
+   - add extra sub-verification which uses "SOM" advection scheme
+     (2nd Order-Moment Advection Scheme, Prather Limiter) with
+       #define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h
+     and in data:
+       multiDimAdvection=.TRUE.,
+       tempAdvScheme=81,
+       saltAdvScheme=81,
+ o model/src:
+   - introduce ALLOW_BALANCE_RELAX which allow the removal
+    of the global mean of relaxation terms by setting
+    balanceThetaClimRelax and balanceSaltClimRelax
+   - disable balanceEmPmR and balanceQnet in the case when useSeaice.
+    This case is now treated appropriately in seaice_growth.F
+ o pkg/seaice:
+   - do balanceEmPmR and balanceQnet based on the net fluxes
+     (SItflux) that enter the ocean+ice system rather than QNET
+     and EMPMR. Works best in real fresh water.
+   - SIatmFW, SIatmQnet, and SItflux computations had to be moved
+     out of the diagnotics bloc, and stored in global arrays.
+ checkpoint63o (2012/06/29)
+ o vertical mixing schemes:
+   - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging)
+   - replace computation of density (in Function STATE1, opps_calc.F) by a call
+     to S/R FIND_RHO_SCALAR
+   - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC
+     and use it for N^2 calculation in ggl90_calc.F (save 2 density computations);
+     affects output (vermix.ggl90) at truncation level.
+ o testreport:
+   - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles
+     (nSx,nSy) for the number of threads (from eedata.mth)
+ o model/src:
+   - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part)
+     related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary).
+ o verification/tutorial_tracer_adjsens/
+   - compile with ALLOW_CG2D_NSA
+   - run with nonlinFreeSurf=3
+   - update reference output_adm.txt
+ o tools/genmake2:
+   - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
+     refine usePROFILES switching off (only when NetCDF is not available).
+ o verification (atmospheric set-up):
+   - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
+ o pkg/profiles : refine profiles and files handling.
+ o model/src and pkg/ecco : introduce run-time switch usePROFILES.
+ o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
+   - changes to use model/src/the_main_loop.F rather than the ecco version
+     in ecco type adjoint runs.
+ o model/src:
+   - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
+   - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
+   - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
+ o model/src:
+   - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
+     update output of test experiment bottom_ctrl_5x5.
+ o pkg/generic_advdiff:
+   - implement vertical bi-harmonic diffusion (for now, only for T & S and
+     only explicitly).
+ o verification/bottom_ctrl_5x5/
+   update reference output (results changed quite some time ago,
+   not sure when; but new reference results look ok in terms of grdchk)
+ o verification/1D_ocean_ice_column/
+   For verification purposes, the exact adjoint rather than an approx.
+   should be used (e.g., to comare against F.D. or TLM).
+   removed autodiff_inadmode*_ad.F routines in code_ad/
+   Update results/ accordingly.
+ o pkg/cal:
+   - change cal_getdate.F so that output date is function of input time only
+     (less ambiguous, not mixed up with input iteration number).
+   - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
+ o pkg/diagnostics:
+   - implement calendarDumps also for stats-diags
+   - implement calendarDumps also for snap-shot output (negative freq)
+   - for now, ignores calendarDumps if non-zero phase-lag.
+ checkpoint63n (2012/06/04)
+ o model/src:
+   - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
+     between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
+   - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
+     similar to calc_r_star.F); update results of experiment internal_wave and
+     tutorial_global_oce_in_p (affected @ truncation level).
+ o pkg/shelfice:
+   - add parameterisation of advective-diffusive flux into the ice shelf
+     according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
+   - simply eps3/3a computation
+ o eesupp:
+  - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
+    between tiles, just fill-in edges assuming locally periodic subdomain) and
+    add corresponding exchange subroutines (EXCH0);
+  - new CG-solver version (_EX0) for disconnected-tiles special case.
+ o model/src (CG-solvers):
+  - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
+    (similar final residual output and max-Iter number as with standard version);
+  - allows to store and use lowest-residual solution (standard & _SR versions);
+  - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
+  - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
+ o eesup/src:
+  - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
+    ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
+ o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
+ checkpoint63m (2012/04/27)
+ o pkg/shelfice:
+  - account for partical cells in surface level below ice-shelf for hydrostatic
+    pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
+ o ad test experiments:
+  - update and rename to "ad_optfile.local" local AD-optfile specific to a
+    particular adjoint verification experiment (in verification/*/code_ad/)
+ o pkg/seaice & pkg/exf:
+  - Part two of ECCO-CLIVAR code merges.
+    Completes merge of seaice area relax. code.
+    Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
+    to be set in EXF_OPTIONS.h since this pkg controls its I/O
+    (and avoids second CPP option in SEAICE_OPTIONS.h)
+  - change default value of costIceStart & costIceEnd to a valid date.
+  - add snowPrecip to HSNOW in seaice_growth
+ o pkg/ptracers:
+  - move ptracers summary and setup check into separated S/R ; add a check for
+    valid PTRACERS_Iter0 value (error+stop or just warning).
+ o pkg/cal (+ pkg/ecco):
+  - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
+    as input; and for AD, unless both are not differentiable (e.g., k index)).
+ o model/src:
+  - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
+    is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
+    temporary set to usingZCoords value (to be changed to F when using shelfice).
+  - hydrostatic pressure: implement partial cell near the surface also for
+    Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
+    usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
+ o pkg/ctrl/ctrl_init.F:
+  - add a formal parameter to s/r ctrl_init_rec to print
+    xx_$(ctrl_valiable)_file for easier debugging
+  - move call of cal_* routines into the if-block where they are really
+    needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
+    to specify a startdate
+ o pkg/seaice:
+  - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
+    global_ocean.cs32x15/code versions).
+  - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
+    verification experiment global_ocean.cs32x15.seaice and update results.
+ o pkg/exf:
+  - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
+    (according to useExfYearlyFields).
+ o pkg/cal:
+  - move calendar setting & summary (previously in cal_readparams.F) into new
+    S/R CAL_INIT_FIXED to be called later in the initialisation process, once
+    length of the simulation is set (after SET_PARMS call); This is an attempt
+    to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
+  - For safety: keep a record of pkg/cal parameter settings status
+            to allow to STOP if one pkg/cal S/R is called too early.
+  - add a stop in all basic pkg/cal subroutines if called before setting is done.
+  - modify cal_getdate.F: stop when nothing was returned;
+    if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
+    this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
+ checkpoint63l (2012/04/04)
+ o pkg/bbl:
+   - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
+     update global_with_exf output.yearly.txt file.
+ o pkg/cal:
+   - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
+   - remove 2 unsused and very short (1 line only) functions ;
+   - remove unsused subroutines from AD-Diff list.
+ o model/src:
+   - start to implement clean wait to stop in initialization S/R (config_check.F,
+      packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
+ o folowing PRINT_MESSAGE changes:
+   - remove reminder multiple print to the same file (STDOUT) when multi-threads.
+ o pkg/bbl:
+   - modification so it can work with z*
+   - replace deltaT with dTtracerLev(k) for asynchronous time stepping
+   - global_with_exf/input.yearly verification; changes output.yearly.txt
+ o eesupp/src:
+   - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
+     writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
+   - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
+     # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
+   - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
+   - when using MPI, always set usingMPI=T ; set default accordingly and stop
+     if not consistent.
+   - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
+     argument is zero (in case called within single-thread section).
+ o pkg/fizhi:
+     clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
+     in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
+ o pkg/exch2:
+   - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
+     activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
+   - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
+     but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
+     with bad ones coming from a not-yet-updated halo.
+     This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
+ o pkg/frazil:
+     move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
+     http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
+ o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
+ o verification/lab_sea
+   * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
+   * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
+   * nTimeSteps 3 -> 4
+   * changed reference output accordingly
+ o pkg/ctrl:
+   * fix ctrl_get_gen for xx_sst, xx_sss
+ o pkg/fizhi:
+   - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
+     update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
+   - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
+     fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
+     clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
+ o pkg/gmredi:
+   - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
+ o pkg/fizhi:
+   - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
+     (old)aces open64 tuv test.
+ o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
+ o pkg/mom_vecinv:
+   - fix 1 loop range in mom_vecinv.F to be like all the other loops which
+     set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
+     with non-lin free-surf).
+ o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
+   in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
+   some compilers (gfortran 4.6.0 on MacOS)
+ o momentum:
+   - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
+     & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
+     fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
+ checkpoint63k (2012/03/17)
+ o model/src:
+    - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
+      flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
+    - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
+      (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
+ o model/src: solve_*diagonal.F
+    - replace division with multiplication by inverse (similar to original version)
+      update output of AD exp. global_ocean.90x40x15.
+    - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
+      to enable the use of the vectorized & differentiable solve_tridiagonal.F
+    - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
+      vertical advection (to get solve_tridiagonal tested in AD mode).
+ o pkg/seaice: ECCO-CLIVAR merge:
+. seaice AREA relaxation
+      * CPP option: SEAICE_ALLOW_AREA_RELAXATION
+      * runtime flag: SEAICE_tauAreaObsRelax
+. modified global mean cost imbalance code: CPP option
+       ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
+ o another iteration on solve_*diagonal.F
+    Make choices independent of AUTODIFF
+    Default will be the adjoinable vectorized version.
+    Alternative choices are:
+    * non-adjoinable original version with low memory footprint:
+      #define SOLVE_DIAGONAL_LOWMEMORY
+    * still adjoinable but does not vectorize (k as inner-most loop):
+      #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
+ o testreport
+  - add option to use a home made wrapper around "make"
+  - remove MITGCM_IEEE env. variable (no longer active)
+ o pkg/shelfice
+  - improve computation of friction velocity for velocity dependent
+    exchange coefficients: include velocities into SHELFICEBoundaryLayer
+    block to average velocities vertically
+  - add TAF store directives for SHI_ALLOW_GAMMAFRICT
+ o Modify diagonal solvers, now three versions (upon request):
+   #ifndef SOLVE_DIAGONAL_AUTODIFF
+. default version (dating back a while ago)
+   #else /* def SOLVE_DIAGONAL_AUTODIFF */
+   # ifdef SOLVE_DIAGONAL_KINNER
+. adjoinable version with k-innermost loop (G. Forget)
+   # else
+. adjoinable vectorized version of 2.
+   # endif
+   #endif /* SOLVE_DIAGONAL_AUTODIFF */
+   All flags are currently set within routines, but could/should be moved to CPP-options.
+   Array bounds for 1. are as before, for 2.,3. cover the entire domain
+   (could be changed for 1. too).
+ o verification/lab_sea (fwd):
+   - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
+     use 7 categories (except hb87), new solve4temp params (except salt_plume),
+     constant salinity (=4) or variable salinity (salt_plume) done through
+     SItracer.
+ o pkg/seaice:
+   - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
+   - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
+      SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
+     from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
+     SEAICE_freeze got retired) but already better than previously with
+     SEAICE_freeze=123456.7 deg.C;
+   - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
+     (safer multi-threaded setting); always set SEAICEuseEVP;
+   - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
+     SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
+     stop if multiple specifications for the same coeff; make sure default
+     SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
+ o pkg/obcs:
+   - allow to switch to upwind 1rst order advection scheme for the advective
+     flux computation at the open-boundary; disabled for adjoint built.
+ o pkg/ptracers:
+   - rename PTRACERS_RESTART.h -> PTRACERS_START.h
+   - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
+   - add parameter to decide when to start a tracer; use internal flag to
+     know which tracer to step-forward; switch this internal flag at the top
+     of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
+     for adjoint built.
+ o pkg/seaice:
+   - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
+   - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
+   - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
+ o pkg/ecco:
+   - fix writing of output file DiagnosCost_ClimSalt/Theta
+     and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
+ o pkg/seaice:
+   - add missing initialisation of COR_ICE array in dynsolver.F
+   - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
+     compiled either way, and is tested in all exps (multidim was only tested
+     in lab_sea ad before).
+   - cosmetic change to prepare for future addition of ITD. no change to results.
+     no defaults change.
+   - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
+   - by lack of adequate verification experiments, I further used custom versions
+     of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
+     should be correct.
+   - avoid recomputations in ad.
+ o array initialisation in adjoint mode:
+) pkg/mom_common/mom_calc_ke.F:
+     add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
+     The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
+     part this initialisation is gone, resulting in Floating Point Exception
+     (caught by open64 compiler with debug option).
+) model/src/convective_weights.F
+     set output convectCount over the full array range (instead of doing
+     an update): this fix a similar issue when called within recomputation (adjoint)
+     which could by-pass the initialisation (normally done in the caller S/R).
+ o pkg/seaice:
+   - final version of turbulent flux params, as agreed at MIT ice meet:
+        SEAICE_mcPheePiston (default is ~ 0.000875)
+        SEAICE_mcPheeTaper (default is 0.)
+        SEAICE_frazilFrac (defualt is 1.)
+        SEAICE_mcPheeStepFunc (default is false)
+   - changes results at trunction error level
+   - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
+ o added pkg/frazil:
+   - see frazil_description.tex for details
+   - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
+ o pkg/shelfice/shelfice_thermodynamics.F
+   - fix exponents for velocity dependent exchange coefficients: change
+     from 2/3(=0) to 0.66666666666666667
+   - move computation of velocity dependent exchange coefficients into
+     separate loop, so that it applies to both thermodynamics
+   - move some divisions by constants out of loops
+ checkpoint63j (2012/02/16)
+ o pkg/seaice:
+   - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
+   - SItracer:  added run time params, and allow coupling to ocn salinity.
+ o pkg/seaice: remove (almost) all divisions by constants within loops
+   in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
+   results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
+   those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
+   output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
+ o pkg/seaice :
+   - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
+     = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
+   - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
+   - add permanent SItflux diag that corresponds to TFLUX but includes
+     ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
+   - allow activation/testing of a fix for suspected missing term in
+     ocn-ice heat budget (to be confirmed). To test this, you want to
+     undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
+     SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
+   - no change in results, fwd or ad.
+ o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
+   - switch to variable freezing point.
+        Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
+   - bug fix : the sublimation term that was missing is now activated.
+        Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
+   - bug fix : flooding sign term for SIsal0.NE.0.
+        Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
+ o pkg/seaice:
+   - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
+     is now the default, and the old default constant freezing point is recovered
+     with SEAICE_tempFrz0    = -1.96,
+          SEAICE_dTempFrz_dS = 0.,
+   - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
+   - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
+   - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
+     activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
+   - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
+     was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
+   - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
+     seaice_growth r149 for legacy branch (no results change).
+   - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
+     from I. Fenty).
+   - results did not change except for global_ocean.cs32x15, mostly due to the
+     switch to variable freezing point (see above item for detail).
+ o pkg/thsice:
+   - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
+     seawater freezing in thsice_calc_thickn (not used).
+ o pkg/seaice: turbulent flux term specification via run time params.
+   - replace CPP switches with run time switches to facilitate testing
+   - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
+                    GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
+   - added runtime parameter : SEAICEturbFluxFormula
+   - move Mcphee constants to SEAICE_PARAMS.h
+   - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
+              SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
+              remove seaice_summary call (moved to seaice_init_fixed)
+   - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
+     SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
+   - seaice_summary.F : add missing report of read turbulent flux term set up
+                        and SITRACER.
+   - seaice_check.F : check range; inform and stop if retired CPPs are used
+                      (incl. SEAICE_AGE).
+   - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
+          CPP switch, same computation as before for the different options.
+   - change results at the truncation level.
+ o pkg/seaice:
+   - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
+     useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
+     SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
+   - update verification/*/input*/data.seaice:
+     to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
+     code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
+     and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
+     set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
+ o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
+   - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
+     algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
+     difference in results only due to machine truncation.
+   - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
+     MaykutPolySatVap; keep MIN_LWDOWN.
+   - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
+   - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
+     + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
+ o pkg/salt_plume:
+   - isolate saltPlumeFlux array exch into a specific S/R called from
+     do_oceanic_phys.F
+   - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
+ o verification:
+   - move untested set-up to MITgcm_contrib/verification_other.
+ o pkg/seaice:
+   - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
+ o pkg/seaice:
+   - seaice_solve4temp.F (keeping results unchanged):
+     * add 2 future run-time params to select which saturation vapor pressure
+       formula is used and how post-iteration fluxes are set.
+       Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
+     * New piece of code (not used) to update surf. atmos. heat flux F_ia using
+       the linearized expression to stay consistent with tsurf finding.
+   - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
+     can be < 0.
+ o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
+   - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
+     conductive heat flux F_c , and add it explicitly when updating tsurf as
+     solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
+     so that now F_ia has a consistent meaning through the entire routine.
+     This causes differences at truncation level: update output of fwd exp.
+     global_ocean.cs32x15.seaice.
+ o pkg/seaice:
+   - lots of editing/cleaning in seaice_solve4temp.F + better documentation
+     of arrays, sign/direction of fluxes; no effect on results.
+   - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
+     in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
+     note: this should have been done before changing celsius2K default.
+   - to keep results unchanged, add back old value of celsius2K in verification
+     exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
+   - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
+     SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
+     value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
+     freezing temp is consistent with value in seaice_growth.F ; this causes
+     differences at machine truncation level: update lab_sea AD output (3/4).
+ o pkg/seaice:
+   - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
+     and climsst/sss even when using seaice (to prevent calculation that might
+     use SST on land); does not affect any verification exp.
+   - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
+     of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
+ o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
+   over land (non-legacy code)
+ o vectorize salt_plume package:
+   - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
+   - this code computes plumebk everywhere (also over land), thus requires
+     code to avoid divisions by zero and catch the case of kLev=Nr.
+   - efficiency of salt_plume_frac is still sub-optimal
+ o tools (genmake2):
+   - fix makefile NAME specification (option: -makefile NAME) by adding
+     "-f $MAKEFILE" in few places where it was missing including makedepend
+     command (contribution from Paul).
+ checkpoint63i (2012/01/24)
+ o model/src:
+   - add factorized versions of some EOS code to find_rho.F,
+     define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
+ o model/src:
+   - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
+   - change default celsius2K from 273.16 to 273.15
+   - to keep results unchanged, add back old value of celsius2K in verification
+     exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
+      global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
+ o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
+   to make TAF generate vectorizable code
+ o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
+    Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
+    have flags that do this more efficiently.
+ o pkg/diagnostics/diagstats_calc.F
+   - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
+ o pkg/obcs (with exch2):
+   - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
+     and remove code (in obcs_readparms.F) which was based on EXCH of indices
+     (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
+ o pkg/exf and seaice exp:
+   - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
+     so that switching off area & heff advection flags does not affect results.
+   - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
+   - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
+     EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
+     results of verification experiments: 1D_ocean_ice_column(fwd),
+     global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
+     and offline_exf_seaice (all 4).
+ o pkg/seaice:
+   - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
+     remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
+   - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
+     but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
+     not multi-dim advection;
+   - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
+     SHORTWAVE_HEATING #undef.
+ o optim: make Makefile more robust (?)
+ o pkg/obcs:
+   * fix treatment of obcs_read_pickup for TAF
+ o pkg/shelfice:
+   * add missing initialisation of num_shifwflx
+   * new adjoint verification exp. for isomip
+   * change Prandtl and Schmidt numbers from generic formulations
+     (in terms of model diffus. and visc.) to separate runtime
+     parameters, with Holland and Jenkins (1999) default values.
+ o pkg/exf (interpolation):
+   - extended input field (2 rows) near the N & S poles:
+     * fill in with the symetric value (when even Nb of data in longitude)
+     * add average value at the poles only for scalar quantities ; for vector
+       component interpolation, skip the averaging and keep duplicated values,
+       unless the 2 components have same location (uvInterp=T) in which case
+       interpolate the 2 components together using S/R EXF_INTERP_UV.
+   - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
+     together: this allows to account properly for local orientation when
+     averaging at N & S pole.
+   - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
+     exf-interpolation near N & S poles. Undef by default.
+   - add debug check/print on 1rst iter if debugLevel >=2.
+ o pkg/exf:
+   - change masking flags definition (no longer "parameter"), put them in
+     common block and set them in S/R EXF_INIT_FIXED.
+   - change recognized masking flag from s,u,v to c,w,s since the mask
+     to use (maskC,W,S) depends on position on model grid and has little to
+     do with scalar/vector difference; fix masking if using P-coordinates.
+   - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
+     and update results of exp. global_with_exf (x2).
+   - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
+ o pkg/obcs
+   - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
+ o pkg/exf (interpolation):
+   - assume periodicity in X only if input field cover full longitude range.
+   - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
+     and should vectorise).
+   - fix input lat of the 2 added row (in case we provide N.pole data).
+ checkpoint63h (2011/12/30)
+ o pkg/seaice:
+   - change declaration of UVM from _RL to _RS in order to get B-grid
+     uIce,vIce monitor when _RS = real*4
+ o pkg/offline:
+   - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
+   - compute vertical velocity if not read from file (switch on exactConserv
+     & staggerTimeStep);
+   - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
+ o verification:
+   - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
+     with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
+     fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
+   - update output of exp. global_ocean.cs32x15.viscA4 after changing
+     grid-file angles (used here for coriolis-3d);
+   - remove (or gzip) few files not needed to run fizhi-cs experiments.
+ o pkg/exf (vector interpolation):
+   - rotate vector component toward local grid-axis orientation using grid-angles
+     (stored in GRID.h) instead of locally computed rotation angle; keep old code
+     available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
+ o pkg/seaice:
+   - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
+     undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
+ o pkg/PKG_OPTIONS.h files:
+   - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
+     outside of the #ifdef ALLOW_THISPKG / #endif block.
+   - update verification/*/code/PKG_OPTIONS.h files.
+ o add a verification experiment (offline_exf_seaice/input.seaice) that test
+   the B-grid LSOR solver
+ o pkg/seaice: sort out emissivity and long wave radiation step 2:
+   - add emissivity for snow and ice as new run-time parameters
+     (unfortunately) that default to the corresponding exf values; this
+     changes results in most verification experiments so that for backward
+     compatibility these parameter have to be set explicitly to inconsistent
+     values (ugly);
+   - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
+     emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
+     until we agree how to handle this bug properly
+ o pkg/exf (interpolation):
+   - add a set of run-time param ({inputfield}_interpMethod), one for
+     each interpolated input field, to select the interpolation method
+     with a value of zero switching off the interpolation;
+   - print interpolation parameters to standard output;
+   - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
+     (to use instead runoff_interpMethod=0 in data.exf).
+   - simplify default setting of interpolation parameters (for all fields,
+     set position to match model grid cell-center position, leading to trivial
+     interpolation in case of regular Lat-Lon grid) and fix for the case of
+     non-uniform delY.
+ o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
+    within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
+    this factor is absolutely required, because the lw exitance (= out-going
+    long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
+    where the reflectivity rho = 1-emissivity for conservation reasons. Once
+    this is established, we can remove the CPP-Flag (if we want to).
+ o pkg/seaice:
+   - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
+     ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
+   - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
+     what the name implies (and not emissivity*BoltzmannConstant), this means
+     the old default value of 5.5e-8 now means
+.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
+     S/R exf_readparms
+   - FV-discretization of the B-grid LSOR solver, turn on with
+     SEAICE_LSRBNEW. This new solver also involves a slight re-organization
+     of the calling routine dynsolver, so that B and C-grid code look a
+     little more alike.
+   - fix index bugs in ostres.F (B-grid code)
+ o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
+ o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
+   default for SEAICE_emissivity, if useEXF; requires setting a wrong
+   parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
+   backward compatiblity
+ o model/src: use sigmaR in calc_ivdc
+ checkpoint63g (2011/12/16)
+ o pkg/seaice/seaice_growth.F:
+   fix heat conservation of the coupled ocean-seaice system.
+   when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
+   solid vs liquid water treatment is resolved via QNET.
+ o pkg/seaice/seaice_growth.F:
+   add missing term for sublimation in saltFlux, which was breaking conservation.
+ o pkg/seaice/seaice_model.F:
+   Remove this patholigical case treatment in evolution branch,
+   where it is un-necessary and breaks conservation.
+   Update global_ocean.cs32x15/results accordingly for
+   output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
+ o model/src:
+   useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
+   external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
+ o pkg/obcs:
+   modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
+   tendency for temperature and salinity that is then applied to update
+   theta and salt in S/R obcs_apply_ts; this requires proper masking of all
+   horizontal advection and diffusion contributions on the boundary (in
+   S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
+   removing the mask in S/R timestep_tracer. The advantage of this approach is
+   that the updated tracer values include contributions from the surface
+   forcing and vertical diffusion.
+   This modification changes exp4.stevens because of vertical diffusion.
+ o model/src:
+   change non-curvilinear grid setting to also work with exch2 + blank tiles:
+   - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
+     face dimensions.
+   - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
+     as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
+     and INI_SPHERICAL_POLAR_GRID.
+   change test-experiment global_ocean.90x40x15:
+   - split the domain in many more tiles (9x4 tiles of 10x10 each);
+   - switch to exch2 and remove 1 blank-tile (but only for MPI test).
+   - update results of both test (std & dwnslp).
+ o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
+    tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
+ o model/src:
+   - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
+     and fix initialisation when using sigma-coords.
+ o model/src:
+  - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
+    to their current value at the beginning of forward_step.F": add a new run-time
+    switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
+  - set doResetHFactors=T in the following test exp:
+     global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
+     global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
+     and tutorial_global_oce_in_p (nonLinFS in p)
+ o pkg/ecco
+   - added IES cost term
+ o verification/advect_xz
+   - scale down the depth by 1/100 (from 200 km to just 2.km)
+   - add secondary test using divergent flow, r-star and implicit vertical advection.
+   - add note (check_conserve_TS.txt) and matlab script to check global
+     conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
+ o pkg/rbcs:
+   - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
+ o pkg/obcs (Stevens BCs):
+   - fix various problems in the phase speed computations of the Stevens
+     boundary conditions:
+     - sign error for western and southern boundaries,
+     - time tendencies were underestimated by factor of dTracerLev and some just
+       zero (for multidim advection schemes) -> now estimate time tendencies
+       from difference between previous (n) time level and the one before (n-1);
+       this requires storing a field per tracer per boundary, also in the pickup
+       files.
+     - replace deltaTmom in cflMer/Zon computation with dTracerLev
+     - set default phase velocity to cflMer/Zon
+   - update verification experiment exp4.stevens
+ o pkg/generic_advdiff (implicit_r):
+   - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
+     (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
+   - fix implicit vertical diffusion or advection with NonLin FreeSurf
+     (was using current recip_hFacC instead of future recip_hFacC): set future
+     recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
+     solver S/R ;
+   - fill diagnostics of vertical advective fluxes (computed from tendency)
+     when using implicit vert. advection;
+   - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
+      global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
+      tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
+      and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
+ o pkg/diagnostics:
+   - add diags for T & S tendency which goes through Adams-Bashforth.
+ checkpoint63f (2011/11/30)
+ o pkg/obcs/obcs_calc_stevens.F:
+   - join some loops to reduce number of if-statements
+   - fix a bug in code for northern and southern boundaries.
+ o pkg/seaice/seaice_init_varia.F
+   - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
+     caused zero ice-velocities for the B-grid code
+ o pkg/seaice/seaice_init_fixed.F
+   - fix a bug in the initialisation of the second metric terms
+     k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
+   - this affects all seaice configurations with useCurviLinearGrid = .true.
+     and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
+     = .true. (default)
+   - the only verification experiment affected is global_ocean.cs32x15:
+     icedyn, seaice, and seaice_dynmix (AD)
+ o pkg/thsice/thsice_diagnostics_state.F
+   - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
+     not contain garbage that can lead to surprises in diagstats_calc.F
+ o model/src:
+   - move bi,bj loops inside INTEGR_CONTINUITY ;
+   - call INTEGR_CONTINUITY directly from forward_step.F
+     (previously called from momentum_correction_step.F)
+   - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
+     forward_step.F and pkg/ecco/the_main_loop.F
+ o model/src/do_oceanic_phys.F:
+   - reset addMass to zero only if useICEFRONT ;
+   - separated k-loop for rhoInSitu calculation ;
+   - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
+     and at constant T,S (= WdRHOdP);
+   NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
+     of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
+     transport of locally-referenced potential density);
+     to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
+ o gluemnc:
+   - replace ncrcat with ncks when adding variables to *.glob.nc
+   - change the way variables without record dimensions are handled so that
+     files that have variables with and without record variables can be glued:
+     add a record dimension with a new unique name to be able to differentiate
+     between variable with and without a-prior record dimensions. Remove
+     this record dimension before adding the variable to the *.glob.nc file.
+     This procedure automatically works also for grid.*.nc files that do not
+     have any record dimension.
+ o verification/cpl_aim+ocn:
+   - generate new reference output on baudelaire (gfortran, mpich2) (previously
+     from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
+ o pkg/obcs/obcs_calc_stevens.F:
+   - add code for northern and southern boundaries.
+   - reorder some loops to save some operations and so that drFBar can be scalar
+ o model/src:
+   - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
+     truncation) and add diagnostics for Adams-Bashforth tendency increment.
+   - update test-exp. AD output:
+D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
+   and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
+     front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
+     global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
+     matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
+     tutorial_global_oce_in_p, tutorial_global_oce_latlon and
+     tutorial_plume_on_slope.
+ o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
+   that vectorises. This code uses 3 extra 2D fields, F90 array assignments
+   and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
+   does not even come with an F77 compiler anymore, this should not be
+   a limitation
+ checkpoint63e (2011/11/06)
+ o pkg/seaice adjoint of LSR:
+   - substantially rework STORE dirs.
+   - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
+     this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
+     and only perform SOLV_MAX_FIXED adjoint iters.
+     If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
+     always goes to same record, meaning that the last forward field will be
+     the one used in the adjoint - an approximation.
+   - now produces non-zero LSR-related gradients, and acceptable gradients for
+     An's zonal (x-z) test case (to be checked in)
+   - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
+     (but these are screwed up by the thermodynamics in the first place);
+     reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
+     output_adm.txt also reflects changes to seaice_lsr
+   - global_ocean.cs32x15:
+     * the "default" input_ad.seaice has been re-defined to always exclude dynamics
+       (output_adm.seaice.txt was updated)
+     * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
+       (output_adm.seaice_dynmix.txt)
+ o test-exp. exp4+stevens:
+   - switch off pTracers and nonHydrostatic (restart problems with NH); update output
+ o pkg/seaice (lsr solver):
+   - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
+     update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
+   - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
+   - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
+     into initial guess for linearised solver; use weight ~ (1/err)^2,4.
+   - compute (with new S/R) and print initial (+ free-driff sol. if available)
+     and final residual of linearised system.
+ o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
+   (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
+ o pkg/obcs: Stevens BCs (still only for east and west)
+   - fix Stevens BCs by using intermediate velocities of previous
+     time step as "baroclinic" contribution rather velocity of one grid cell
+     inside the boundaries; more consistent but makes the entire treatment
+     more complicated, requires new pickup files and two new S/Rs:
+     obcs_copy_uv_n and obcs_save_uv_n
+     keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
+     (undefined by default)
+   - silently move computation of some grid factors into separate loops to
+     save some recomputations
+   - add a hack for non-linear free surface
+   - add a verification experiment to exp4 that tests this code
+ o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
+ checkpoint63d (2011/10/25)
+ o pkg/obcs + seaice-dynamics:
+   - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
+     solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
+     values (consistent with an implicit method).
+   - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
+     return to older implementation (same results as before); note that none of
+     the "experimental" OBCS_SEAICE options are implemented in the new version.
+   - switch test exp. seaice_obcs to use new version (update output).
+ o pkg/seaice:
+   - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
+   - add parenthesis in Water-Ice drag calculations (evp & lsr);
+   - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
+     and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
+   - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
+     and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
+ o pkg/layers:
+   - Include potential density as new coordinate (Thanks to David Munday)
+ o pkg/dic:
+   - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
+     carbonate computation/output to CALC_PCO2_APPROX
+ o pkg/generic_advdiff
+   - make TAF generate code that vectorizes:
+     gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
+ o model/src:
+   - improve vectorization also for adjoint code of
+     solve_tridiagonal and solve_pentadiagonal. As this requires up to
+new 3D-fields, this code is only turned on for the combination of
+     ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
+     for singular matrix check (only for TARGET_NEC_SX).
+   - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
+     ALLOW_AUTODIFF. This flag now needs to be set outside of
+     solve_tri/pentadiagonal.F
+ o pkg/exf:
+   - fix previous modif in exf_readparms.F (revision 1.66: treatment of
+     optional namelist EXF_NML_OBCS).
+   - add many debug-print (to trace down where pkg/cal error msg comes from)
+ o pkg/mom_vecinv/mom_vi_hdissip.F
+   - rearrange loops so that vectorization is improved and in particular
+     the adjoint routine vectorizes. The code is a little longer now, but I
+     think easier to read.
+     Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
+ o pkg/seaice:
+   - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
+ o pkg/exch2:
+   - alternative code (without tile x tile matrix) for cumulated (global) sum;
+     used as default; keep using matrix version in adjustment.cs-32x32x1.
+ o tools/build_options:
+   - after merging some MPI and/or multi-threads specific optfiles so that
+     the modified default optfile support both built (using genmake2 -mpi
+     for the MPI built, using genmake2 -omp for OpenMP built),
+     move now obsolete optfiles to tools/build_options/unsupported/
+    (add copy of email sent to support list in doc/optfiles_changes.txt)
+ checkpoint63c (2011/09/28)
+ o pkg/ebm:
+   - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
+     test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
+ o pkg/seaice (SItracer pickup)
+ * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
+   To be done:
+   - thorough testing of missing fields in S/R seaice_read_pickup
+   - thorough matching between generic tracers and specific fields used
+     (e.g. volume-weighted age, area-weighted age, salinity, ...)
+ o pkg/grdchk:
+   - all procs calculate and print finite-difference gradient (for testreport)
+   - change description output used by testreport;
+   - AD testing: also compare and report Finite-difference gradient;
+     => update all output_adm*.txt
+ o test exp. global_ocean_ebm:
+   - switch back useRealFreshWaterFlux (no problem anymore with run-off);
+     and turn on exactConserve; update (fwd) output.
+ o pkg/seaice (LSR):
+   - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
+   - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
+     * identical results with non-CS topology (but save up to half of EXCH calls)
+     * no much changes in cs-32 verification tests since no ice at face edges
+      (differences due to convergence criteria, since nb of iterations changed)
+     * expect some differences on lat-lon-cap grid.
+     update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
+ o pkg/exch2:
+   - add new CPP option to disable Cumul-Sum matrix (to save storage when using
+     many tiles); until alternative coding is added, just add a stop.
+ o pkg/kpp:
+   - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
+     to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
+ o optfiles:
+   - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
+     into corresponding standard one, which now support different build:
+     (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
+   - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
+ o pkg/obcs (seaice):
+   - add missing EXCH for uIce,vIce after applying OBCS;
+   - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
+     argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
+     EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
+   - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
+   - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
+     and eedata.mth for MPI and mutlti-threaded testing.
+ o pkg/flt:
+   - make FLT EXCH working with multi-threads (and MPI + multi-threads);
+   - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
+   - fix pickup and trajectories + profiles output with multi-threads;
+   - add parameter to select group of fields to write along trajectory and
+     profile (default unchanged);
+   - only call PORT_RAND* function when flt_noise <> 0;
+   - add multi-threaded test for verification exp. flt_example.
+ o eesupp/src:
+   - fix S/R ALL_PROC_DIE for MPI+multi-threads.
+   - USE_OMP_THREADING: check that number of threads (from eedata) matches
+     actual number (from env.var. setting).
+ o pkg/ebm:
+   - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
+   - add multi-threaded test for verification exp. global_ocean_ebm
+ checkpoint63b (2011/08/29)
+ o pkg/ebm:
+   - fix sign of runoff;
+   - update directly forcing fields (Qnet,EmPmR) to use standard
+     external_forcing_surf.F (remove ebm_forcing_surf.F);
+   - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
+   - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
+     and apply relaxation towards corresponding SST field (2-D map or ZonAver).
+   - update global_ocean_ebm parameters file data and update output (fwd+ad).
+ o verification/matrix_example:
+   - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
+     MPI and mutlti-threaded testing.
+ o pkg/matrix:
+   - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
+   - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
+   - fix for multi-threaded (remove DATA statement);
+   - use standard DIFFERENT_MULTIPLE function;
+   - add MATRIX_OPTIONS.h
+ o verification/matrix_example:
+    To allow to split the domain in several tiles, change the domain size
+     from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
+     Western side) of land points.
+ o (*_)write_pickup:
+   - fix few bugs in mypackage_read/write_pickup.F
+   - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
+     array of length 1 (was caught by compiler syntax-check).
+ o pkg/diagnostics (velocity potential solver):
+   - fix initialisation of main diagonal matrix (for overlap values)
+ o tools/build_options:
+   - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
+     into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
+   - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
+     * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
+     * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
+     and use "-devel" testreport option for standard testing on baudelaire.
+ o pkg/grdchk:
+   - Assume that all gradient-check position are within the same tile
+     corresponding to global indices (iGloTile,jGloTile) and that
+     positions (i,j indices or nbeg) are local to this tile;
+   - set tile local-indices and proc. number according to tile global-indices;
+   - remove grdchkwhichproc from namelist (retired param);
+   - send adjoint gradient to all procs so that all procs print it to STDOUT;
+   - switch on MPI test for global_ocean.90x40x15 AD test experiment.
+ o adding package bbl (Bottom Boundary Layer)
+   description in MITgcm/pkg/bbl/bbl_description.tex
+   example/test experiment in MITgcm_contrib/bbl
+ o adjoint verifications
+   - changed 5 experiments to multi-tiles
+     * global_ocean.90x40x15
+     * obcs_ctrl
+     * offline_exf_seaice
+     * tutorial_dic_adjoffline
+     * tutorial_tracer_adjsens
+     changed reference output for those that crossed tile boundaries
+     (changed choices of gradient check positions)
+   - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
+   - temporary bug fix in grdchk_loc.F for obcs
+ o genmake2 & testreport
+   - add target "obj" (just for OBJFILES files) to Makefile;
+   - add option to specify FEXTRAFLAGS on command line.
+ o pkg/mypackage:
+   - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
+ checkpoint63a (2011/08/02)
+ o pkg/diagnostics (velocity potential):
+   - fix velocity-potential calculation when using OBCS: balance net inflow
+     at each level (new S/R OBCS_DIAG_BALANCE).
+   - fix some of the problems with OBCS in stream-function calculation.
+ o pkg/exf/exf_readparms.F
+   - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
+     EXF_NML_OBCS) more consistent, so that you need not have these lists
+     in data.exf when they are not used.
+ o optim/optim_readdata.F:
+   - add some output about obcs variables that might help debugging
+   - add a check about nvarlength
+ o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
+ o pkg/diagnostics (velocity potential):
+   - fix mask for OBCS (still problems in stream-function with OBCS);
+   - add specific parameter (default = main code CG2D params) for solver;
+   - in case of poor convergence, use solution corresponding to lowest residual.
+ o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
+   adjoint code. In general statements like tmpscal=fld(i,j) are problematic
+   and should be avoided where possible.
+ o model/src (rStar):
+   - include r* effect on reference-state (PhiRef) in totPhiHyd
+     (so that it's really the potential anomaly at the cell center);
+     affect solution only if z* with full pressure in EOS.
+   - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
+     update output (because of z* in totPhiHyd and viscA4 changes);
+   - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
+     @ constant r) until interpolation at constant r is implemented.
+ o pkg/diagnostics
+   - fix RCENTER diagnostics in case cell center is not at interface middle
+ o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
+   this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
+   that THETA and SALT are "conservative temperature" and "absolute
+   salinity"
+ o pkg/ctrl
+   - fix computation of endrec in s/r ctrl_init_rec
+   - ctrl_pack/unpack_*: remove unused variables and some obsolete code
+ o pkg/seaice/seaice_growth.F
+   - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
+     remove then obsolete STORE directives
+   - fix STORE directives for tice and tices, so that only the
+     appropriate part of the fields are stored (and not the entire
+     field); update global_ocean.cs32x15.seaice AD output.
+   - cosmetic changes: adjust CPP flags and indentation for better
+     legibilty
+ o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
+   Chris Wilson)
+ o pkg/gmredi:
+    Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
+    and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
+ checkpoint63  (2011/07/11)
+ o pkg/exch2:
+  - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
+  - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
+    (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
+    increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
+ o pkg/diagnostics:
+  - deal with pairs of post-processed diags which are computed together; in
+    particular, re-order list of diags within 1 file to save 2nd computation.
+  - add S/R to compute velocity stream-function (called after velocity-potential
+    calculation) from divergence free transport -> new diagnostics "PsiVEL".
+  - add parameter to select grid-point location where PsiVEL == 0.
+ o eesupp/src:
+    new S/R to calculate cumulated sum on tiled array, corner grid-cell location
+    (specific S/R needed with exch2 topology - for now, just print an error msg)
+ o pkg/shelfice
+  - Implement friction velocity-dependent transfer coefficients following
+    Holland and Jenkins, JPO, 1999
+    Original code by M. Losch with small modifs.
+    Enable with CPP option SHI_ALLOW_GAMMAFRICT
+    and runtime flag SHELFICEuseGammaFrict
+ o verification lab_sea & global_ocean.cs32x15:
+  - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
+    does not miss some dependencies (but is slower) and also works with many files
+    (default makedepend limitation for AD built).
+  - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
+ o pkg/diagnostics:
+  - add run-time parameter "useMissingValue" (def=False) to fill land-point
+     (i.e., where mask=0) with MissingValue ; used only in MNC output file.
+    This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
+  - Extend the use of "missing_value" setting from data.diagnostics for the case
+    of counter-diagnostics (where fraction-weight is zero). This applies both to
+    MNC and MDS output files.
+ o pkg/seaice/seaice_growth.F:
+   - add 'a priori' cap of latent heat flux based on actual mass considerations
+     when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
+     non-legacy seaice_solve4temp.
+   - add diagnostic of the residual sublimation freshwater flux (the freshwater
+     flux taken from the ocean if the total actual latent heat fluxes exceed
+     the maximum)
+   - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
+    fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
+   - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
+    SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
+   - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
+   - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
+ o verification 1D_ocean_ice_column:
+    made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
+    update results
+ o pkg/diagnostics:
+  - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
+    which are not filled-up but computed from other diags ; In this case, the mate
+    diag points to the primary (filled-up) diag to used for post processing.
+  - Update Velocity-potential computation using post-processed diag framework.
+  ==> Change the ordering of fields and time-periods in MDS output file
+    when using periodic averaging: now writes one time record with the full set
+    of fields for this time period, then the next time reccord (it used to be
+    one field with the full set of time records then the next field).
+      Note: this is now similar to NetCDF (MNC) output file. <==
+ checkpoint62z (2011/06/21)
+ o adjoint monitor:
+  - Add adjoint monitor output for packages exf, seaice
+    and update relevant testreport output
+ o pkg/seaice:
+  - re-order diags inits so that they appear in order in available_diagnostics.log
+  - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
+    area/heff/hsnow preceeding thermodynamic growth/melt.
+  - modified diag: SIdA; output actual effect, as the description states.
+  - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
+  - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
+    (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
+     and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
+  - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
+  - added diagnostics for seaice generic tracers (SItr*).
+  - added SItrUnit and SItrNameLong run time param (for SItr* diags).
+  - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
+  I. Fenty: 18-Jun-2011:
+  Minor changes to seaice package:
+) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
+     added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
+    - Differentiated "regularization variables" from "floor variables"
+     * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
+     * hiceMin became SEAICE_hice_reg (old hiceMin)
+       (with _reg meaning regularization variable)
+    - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
+     so as to ensure energy conservation when going between phases
+   - A22 was not used anywhere
+) Changed regularization procedure for heffActual and hsnowActual to ensure
+     well-boundedness and smooth adjoint in seaice_growth.F
+) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
+     because the old regularization always set heffActual >= 0.05 cm
+) Changed the model so that the default behavior is to put a small (10^-5) "floor"
+     on AREA when HEFF > 0.
+   - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
+     requiring that DISABLE_AREA_FLOOR *not* be defined
+  Affected verifications:
+   - 1D_ocean_ice_column (output.txt output_adm.txt)
+   - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
+ o pkg/diagnostics:
+   - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
+   - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
+     (was _RL, now integer) with option = 0 to retrieve all levels.
+   - add pieces of code to compute velocity potential at each level (new diagnostics
+     PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
+     for now, using same params as CG2D (target-resisual, max Nb of iter ...).
+   - fix few issues with counter diagnostics in diagnostics_setdiag.F &
+     diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
+     and in diagnostics_fract_fill.F (do not need a valid pointer for the
+     diagnostics counter-mate); check that definition of counter-diagnostic
+     includes a valid counter-mate (in diagnostics_set_levels.F).
+ o model/src (rStar):
+   - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
+     affect solution only if z* with full pressure in EOS;
+     update output of test-exp global_ocean.90x40x15.
+ o pkg/seaice:
+   - introduce siEps=1e-5 parameter
+   - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
+   - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
+   - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
+     For now it covers, and was tested for, ice salinity and age (attached to HEFF),
+     as well as ice cover age and ridging index (attached to AREA).
+     For now the run time parameters (in data.seaice/SEAICE_PARM03) are
+     SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
+     Up to SItrMaxNum=3 tracers can be used simultaneously.
+ o pkg/salt_plume:
+   -introduce SPsalFRAC run time parameter that sets the fraction of the
+    salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
+    that gets vertically redistributed (fluxed down) by pkg/salt_plume.
+ o model debug options:
+   - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
+     in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
+   - Refine debug-msg printing selection (3 new levels):
+     debugMode  : controls printing of debug messages (sequence of S/R calls).
+     debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
+      debLevZero =  0 ; /* level of disabled aux. msg printing */
+      debLevA =  1 ; /* level of minimum  aux. msg printing */
+      debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
+      debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
+      debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
+      debLevE =  5 ; /* level of extensive debug printing */
+     New debugLevel default: with default debugMode value (=F),
+       = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
+       and if debugMode=T, default debugLevel = 4 (debLevD).
+     Relation with previous settings:
+      debLevB (=2) corresponds to former debLevA (=1)
+      debLevD (=4) corresponds to former debLevB (=2)
+     Note:
+      a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
+      b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
+         to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
+   - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
+     detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
+ o pkg/obcs:
+   - change OBCSfixTopo default from True to False (should not change the results);
+     keep OBCSfixTopo=T in verification-exp. seaice_obcs.
+ o pkg/thsice:
+   - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
+nd layer seaice sublimation (unlikely to happen)
+   - use Interior mask for OBCS in thsice_advection.F (similar to what is
+     done in gad_advection & seaice_advection).
+ o adjoint:
+   bug fix spotted by Gael Forget:
+   seaice_advection and thsice_advection still had
+   legacy CPP options to avoid CS corner updates for adjoint
+ o pkg/seaice:
+   => Change some of the defaults (2011/05/29):
+      - change SEAICEuseFluxForm default (from False to True)
+      - change DIFF1 default (from 0.004 m/s to 0. m/s)
+      And print warnings if DIFF1 is not set in data.seaice and centered
+       avection scheme is used without any diffusion.
+   also:
+   - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
+   - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
+   - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
+     other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
+     #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
+   update results of test exp.:
+      lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
+          output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
+          output_adm.noseaicedyn (SEAICEuseFluxForm=T)
+      offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
+      seaice_obcs: output (SEAICEuseFluxForm=T)
+   and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
+       for standard fwd & AD lab_sea tests (to keep the same output).
+ o pkg/seaice/seaice_growth.F:
+   - use Ian Fenty's capping formulas for actual ice
+   thickness thoughout EVOLUTION branch.
+   - put treatment pathological case #2) in CPP brackets
+   (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
+   - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
+ o pkg/seaice:
+   - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
+   pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
+   also pass fac as a param, which can be 1. (to update the tendency
+   field) or the time step (to update the field itself).
+   - seaice_advdiff.F: for multidim, call seaice_diffusion with
+   e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
+   seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
+   - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
+   hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
+ o pkg/seaice:
+   diffusion with centered advection scheme (diffus.F & advect.F):
+   - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
+     to just compute the laplacian of input-field.
+   - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
+   - fix flux-form version in diffus.F to conserve tracer.
+   update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
+    machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
+ checkpoint62y (2011/05/26)
+ o pkg/seaice:
+  - seaice_growth.F : in EVOLUTION branch, always include
+    a_QSWbyATM_cover in qnet (as it should be).
+  - verification/global_ocean.cs32x15 : update results accordingly
+    (output.seaice.txt output_adm.seaice.txt).
+ o pkg/seaice + obcs:
+  - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
+    equivalent of assuming no tracer gradient outside the OB region.
+    update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
+  - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
+    after changes above);
+  - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
+    only at OB location (instead of over a band of OLx width).
+ o pkg/seaice:
+  - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
+    (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
+ o pkg/obcs:
+   - split header file "OBCS.h" into 4 separated files:
+     OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
+    Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
+      (contain no conditional statement which depends on OBCS options).
+   - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
+     to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
+ o ctrl, cost, grdchk & autodiff pkgs:
+   - make options file more standard (like other {PKG}_OPTIONS.h file but
+     with AD_CONFIG.h); clean-up some of the included header files.
+ o pkg/obcs:
+   - do not mask tracer when applying OB (tracer == 0 could generate problems)
+   - apply tracer OB values to tracer field only at OB location (instead of
+     over a band of OLx width)
+   - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
+   - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
+     obcs_apply_tloc.F & obcs_apply_sloc.F
+ o obcs in model/src:
+   - call OBCS_APPLY_W only if NonHydrostatic.
+   - call OBCS_APPLY_ETA only if NonLinFreeSurf.
+   - reset dEtaHdt and wVel to zero outside OB interior region ;
+   - leave tracer unchanged outside OB interior region: This has no effect
+     on the solution but just to prevent unrealistic tracer value outside OB.
+   - zero out velocity outside OB interior region: This has no effect on
+     the solution but just to prevent unrealistic velocity outside OB.
+ o obcs and non-lin free-surf:
+    move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
+    and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
+    + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
+    this fixes missing EXCH + get consistent eta OB value (+ fix restart).
+    update results of test-exp. exp4(nlfs).
+ o exp4 (nlfs) test-exp:
+    use OBC for Eta at Western & Eastern OB (to test prescribing Eta
+    with NonLin-FreeSurf); update output.nlfs.txt
+ o obcs and 2d/3d solver norm:
+    use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
+    and outside OB interior region (will allow to place OB further inside the
+    domain). Depending on the domain, can affects cg2d-Norm (previous
+    cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
+    and cg3d-Norm (previous Norm was computed before canceling OB terms),
+    e.g. in tutorial_plume_on_slope.
+   - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
+ o pkg rbcs:
+   - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
+   - add capability to apply relaxation to horizontal velocity uVel & vVel.
+ o pkg/grdchk: add gradient check for control variable xx_shifwflx
+ o pkg/shelfice/shelfice_init_fixed.F
+   fix CPP-flag combinations
+ o pkg/seaice: Merge iceage code of Pierre Rampal
+   * update/change/correct ice age calculations
+   * add age updates for pathological cases
+   Probably needs more testing...
+ checkpoint62x (2011/05/13)
+ o pkg/mom_vecinv:
+    high-order vorticity scheme: use interior masks (maskInW & S)
+    to zero-out (outside OB) gradient of vorticity.
+ o verification exp.:
+    turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
+    hs94.128x64x5 and seaice_obcs ; update results.
+ o pkg/obcs:
+   fix bug in OBeta for YZ sections in obcs_exf_load.F
+ o pkg/ctrl, pkg/shelfice, and optim:
+   - add new control variable xx_shifwflx (fresh water flux underneath ice
+     shelves). This is almost as tedious as obcs-ctrl, because the
+     variables needs its own mask.
+   - add a cost function term that penalizes the deviation of xx_shifwflx
+     from the first guess (zero) in analogy to other control variables
+ o pkg/shelfice:
+   - start basic adjoint
+ o pkg/ctrl:
+   - remove extra 2D field "for good measure" when initializing in
+     ctrl_set_globfld_[xy/xz/yz].F
+   - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
+   - improve error messages in ctrl_set_unpack_*
+ o OBC implementation in momentum:
+    use interior masks (maskInC,W & S) in momentum S/R:
+    - multiply divergence, tension and some del^i.u or del^j.v by maskInC
+    - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
+    - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
+    - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
+    Motivation: fix/clean implementation of OBC with biharmonic-viscosity
+     (and also with Leith/Smagorinsky harmonic-viscosity).
+    Update output of experiment dome and exp4 (+nlfs).
+ o exp4 test-exp:
+   - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
+     and prescribe time-varying OB (without pkg/exf) for zonal-velocity
+     at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
+     time-varying OB at Western-side for wVel (NonHyd); update output.
+   - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
+     and biharmonic-viscosity ; also use prescribed time varying OB.
+ o pkg/obcs:
+   fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
+ o model/src:
+   - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
+   - initialise startTime & nIter0 with unlikely values: allows to set one
+     from the other without ambiguity.
+ o seaice_obcs test-exp.:
+   add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
+ o pkg/obcs:
+   - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
+     no longer needed with maskInC,W,S in pkg/generic_advdiff.
+ o pkg/seaice:
+   - retired SEAICE_SALINITY and SEAICE_salinity in favor of
+     SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
+   - fixed bug in the initialization of sea ice salinity variable HSALT
+     in seaice_init_varia.F  (removed dependence on ICE2WATR)
+ o fizhi-cs test exp.:
+    switch reference output convention for these 2 non-standard test-exp,
+     from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
+       to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
+    reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
+ o model/inc:
+   - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
+     of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
+ o pkg/seaice:
+   - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
+ o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
+   - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
+     and initial HSALT
+ checkpoint62w (2011/04/26)
+ o pkg/mom_fluxform:
+   - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
+   - use parameter "sideDragFactor" in no-slip BC side-drag part.
+   - update output of exp. global_ocean.90x40x15
+ o pkg/mom_vecinv:
+   mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
+ o update seaice exp.:
+   use more consistent parameter values (remove "backward compatability only":
+    ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
+   related to thermodynamics seaice. Update output (fwd+AD) of exp.:
+D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
+ o update test-exp global_ocean.90x40x15:
+   o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
+   o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
+   o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
+   o turn on zStar & viscA4 in standard set-up (dir input/)
+     and update output files: output.txt & output.dwnslp.txt
+ o new AD-test experiment: obcs_ctrl
+   (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
+ o pkg/dic:
+   fix two bugs in handling water vapour pressure in carbonate chemistry
+   and air-sea fluxes. Found by Val Bennington and Galen McKinley
+   (add DIC Option = WATERVAP_BUG to recover old results)
+   update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
+ o adding allowInteriorFreezing option to check for water below freezing point
+   at depth and bring the negative heat anomaly to the surface level
+ o pkgs _fields_load:
+   - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
+   - use new S/R GET_PERIODIC_INTERVAL in pkgs:
+     bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
+     rbcs to get interpolation weights and time reccord number.
+   - fix multi-threading in aim_fields_load.F
+   - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
+ o external_fields_load:
+   new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
+    interpolation weights) to use in a periodic time-series ; do not divide by
+    time-step to convert to integer:
+    - this fixes case where externForcingPeriod is not multiple of time-step
+       (Thanks to Christopher L. Wolfe)
+    - this fixes case where externForcingPeriod is an odd multiple of time-step
+      (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
+   store index of time-record which is currently loaded:
+    - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
+    - needed for the adjoint but not yet used because of extensive recomputations;
+      (to be fixed soon)
+ checkpoint62v (2011/04/02)
+ o verification/1D_ocean_ice_column added to test Ian Fenty's
+   pkg/seaice_growth.F modifications for improving sea ice code differentiability
+ o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
+   (new velocity statistics after changing maskInW & maskInS definition)
+ o pkg/generic_advdiff with OBCS:
+   use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
+   equivalent to assumption of no tracer gradient outside the OB region.
+   This will affect the results if using obcs+biharmonic diffusion.
+   update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
+ o pkg/obcs:
+   change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
+   (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
+   in Interior region. No impact on solution but affects Velocity monitor stats.
+ o pkg/ptracers (adjoint)
+   New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
+   tape file for each tracer
+ o model/inc/src and pkg/autodiff: add parameters that allow to turn
+   of parts of the adjoint code at run time. For now, there are only
+   useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
+   parameters are set in data.pkg.
+   This is the lazy coward's version of doing this, but still useful for
+   debugging. In order to do it right, everything needs to be moved to
+   pkg/autodiff.
+ o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
+   the end; this fixes the adjoint balancing code for open boundaries.
+ o pkg/ctrl:
+   - change behavior of xx_${varname}period to be analogous to exf-conventions:
+     xx_${varname}period =   0.,  means time-independent control part
+     xx_${varname}period = -12., means one-year-periodic monthly control part
+   - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
+     clean up ctrl_init a little, remove unused variables
+   - ctrl_init: fixed the handling of the start/endrec for obcs-variables
+   - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
+ checkpoint62u (2011/03/15)
+ o model/src:
+   - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
+     h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
+   - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
+     INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
+ o pkg/ctrl/obcs/ecco:
+   - remove obsolete, unused, and partially broken code:
+     ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
+     ALLOW_CTRL_OBCS_BALANCE
+   - put a stop statement into ecco/cost_obcsvol.F, but also add
+     cost_obcsvol to ecco_ad_diff.list
+ o pkg/ecco: fix counting cost function contributions for obcs (code
+   by Matt M.) and diffkr for diagnostics
+ o pkg/ecco, pkg/ctrl, pkg/grdchk:
+   add cost penalty terms for initial uvel, vvel, eta controls
+   and I/O for prior error files
+ o pkg/mdsio:
+    move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
+    (new argument) to check for tiled file in mdsioLocalDir : this fix the
+    restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
+ o pkg/ctrl:
+  - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
+    ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
+    unused and superfluous variables
+  - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
+ o pkg/ecco
+  - enable adjoint of Stevens OB
+ o pkg/ctrl/ecco/grdchk:
+   - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
+     Fortunately, we do not have any tests for the numerous cpp-flagged
+     option of "obcs as control parameters" so we will never know
+     if this is an improvement (but at least now things compile).
+   - remove an obsolete initialization from ecco_cost_init_barfiles.F
+   - fix some problems within never used ifdefs to make the code compile
+ o pkg/obcs:
+  - Refine Interior mask definition to work with more complex OB (e.g.
+    if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
+    read in Interior mask from file. Check if Interior mask is consistent
+    with OB list of indices.
+ o pkg/seaice
+  - beginning code for a seaice tracer package,
+    but currently only used for seaice age: SEAICE_AGE
+    SEAICE_num = 4
+    iTracer = 1: area-weighted ice age
+            = 2: volume-weighted ice age
+            = 3, 4: template for one-year vs. multi-year ice
+    data.seaice has new namelist SEAICE_PARM03 for arrays related to
+    SEAICE_num
+ checkpoint62t (2011/03/05)
+ o pkg/obcs:
+  - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
+    then normal component. This ensures that the normal component is set
+    correctly even when it conficts with tangential setting from an other OB.
+    Affects results of test-experiment seaice_obcs: update the output.txt
+ o pkg/obcs:
+  - add code to monitor statistics of dynamical fields at OB.
+  - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
+    - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
+    - change default: balance the Net inflow through all OB (instead of balancing
+      each OB separately); keep the old method if setting OBC_balanceFacX < 0.
+  - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
+    to match Nortern OB inflow (OBCS_balanceFacN=0).
+ o pkg/seaice:
+  - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
+ o pkg/seaice (seaice_growth v 1.113):
+  - reverting seaice_growth to v 1.111 in order to have code with exact bit
+    compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
+    CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
+    runtime flag SEAICEareaFormula is kept but is inactive
+ o model/src:
+  - add new param to scale curvilinear grid distance and area when using
+    a different sphere radius from the grid-files.
+  - test/check multi-threads EXCH applied to local variable (cg2d_x)
+ o adjoint:
+  - enable adjoint of Stevens OB
+  - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
+    (a bit delicate because of potentially modified adj. common block structure;
+    current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
+ checkpoint62s (2011/02/15)
+ o pkg/seaice (seaice_growth v 1.112):
+  - introduce SEAICEareaFormula run time parameter, which selects the recipe for
+    computing the ice cover tendency from effective thickness tendencies. Include
+    Ian Fenty's formula.
+  - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
+    SEAICEareaFormula.
+  - simplify notations for the various d_HEFF/d_AREA terms.
+ o pkg/gmredi:
+  - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
+    from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
+    add a verification test-run (front_relax.bvp) to test GM_useBVP.
+ o pkg/seaice (seaice_growth v 1.111):
+  - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
+  - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
+    also melt ice.
+ o pkg/seaice:
+  - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
+  - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
+ o pkg/cheapaml:
+  - from Nico Wienders: New version of this package.
+ o pkg/flt:
+  - add CPP options to prevent floats to re-enter the opposite side of
+    a periodic domain (default: keep periodicity)
+ o pkg/gmredi:
+  - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
+    (needed for multi-dim advection).
+  - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
+ o model/src:
+  - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
+ o tutorial_tracer_adjsens
+  - extend to NLFS and replace maskC by hFacC
+    (change reference output accordingly)
+ checkpoint62r (2011/01/24)
+ o testreport:
+  - add option -deloutp (-do) to remove output file after successful run
+  - add option -mfile (-mf) for MPI machile-file and for each test-exp,
+    extract exact list of procs from this file ; adjust COMMAND by
+    replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
+ o pkg/ecco: replace old ineffective way of penalizing deviations from
+   first guess (of obcs) with code by Matt Mazloff
+ o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
+   exf/cal
+   - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
+     and handle case of obcs?period == 0
+     Not affected by these changes: There is still an inconsistency in
+     the computation of start/endrec for the obcs variables for ALLOW_CAL
+     defined (see comment by Menemenlis, 7-Mar-2003)
+   - make S/R ctrl_get_gen_rec return something meaningful even if
+     ALLOW_CAL is not defined
+   - ctrl_getobcs?: simplify code so that it does not need to use
+                    S/R exf_swapfields
+ o testreport:
+    allow to test MPI with different number of processors for each experiment:
+    create file "SIZE.h.mpi" in each build dir.
+    Note: update of "-command" argument not yet implemented.
+ o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
+   alleviate the need for additional 3D tapes when using
+   the non-inear free surface in the adjoint. This is done
+   by adding an 'update' of hfacc etc. to their current
+   value at the beginning of forward_step.F.
+ o pkg/seaice
+   seaice_lsr: move stress-divergence computations out of outer pseudo-
+   timestepping loop
+ o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
+   up, so that the calls of the ctrl_* subroutines are really at the end
+   of the routine.
+ o pkg/gmredi:
+   allow to specify a 2-D horizontal map and a 1-D vertical profil
+   as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
+ o pkg/seaice:
+   move lsr iterations from seaice_dynsolver to seaice_lsr.
+ o pkg/seaice:
+   reduce memory footprint of seaice mutldim advection tapes,
+   by using a 2D tape independent of the generic_advdiff ones,
+   and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
+ checkpoint62q (2010/12/29)
+ o model/src:
+   - check horizontal grid-spacing for unset or zero/negative values.
+   - change AD test hs94.1x64x5 to be truly a 2-D set-up.
+ o pkg/flt:
+   - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
+   - precision of input and output files set according to readBinaryPrec
+     and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
+   - initial float position from tiled file was not converted to index space
+     (looks like a bug): fixed to make it similar to initial pos. global file.
+ o global_ocean.cs32x15:
+    change SIZE.h of AD set-up to get same tiling as with MPI.
+    Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
+ o model/src:
+    add flag to control printing of domain fields (bathymetry, hFac ...) in
+    ini_mask_etc (call to plot_fieds_xy*).
+ o pkg/thsice:
+    if useEXF, some forcing fields are not valid in overlap: fixed by computing
+    over the interior only + apply EXCH at the end (like with SEAICE advection).
+ o pkg/mdsio:
+   - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
+     to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
+   - change barrier call for safe multi-threads access to 3-D shared buffer.
+   - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
+   - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
+     remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
+ o pkg/flt:
+   - add fourth-order Runge-Kutta integration
+   - add basic exch2 support (only 1 facet supported so far!)
+ o pkg/mdsio+rw:
+   new S/R to read local (or tile independent) vector (read counterpart of
+    mds_writevec_loc, and front-end write_glvec_rl/rs).
+ o global_ocean.cs32x15: additional input_ad.seaice experiment
+     that uses pkg/seaice rather than pkg/thsice.
+     (using multidim advection for seaice)
+ o towards more F95 syntax for array specification in namelist:
+   - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
+     of all verification experiments.
+        e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
+       was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
+   - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
+ o global_ocean.cs32x15: additional input.seaice experiment
+     that uses pkg/seaice rather than pkg/thsice.
+ checkpoint62p (2010/12/17)
+ o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
+     to THSICE_SIZE.h to avoid conflict with pkg/seaice.
+ o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
+     allow for use of multim. advection in seaice adjoint.
+ o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
+   - first attempt to close budgets by taking into account the freshwater
+     flux implied by the sublimation of snow and ice. So far only the
+     volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
+     SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
+ o eesupp/src:
+   new S/R with new option (NML_EXTENDED_F77) to change array specification
+   from F95 standard to commonly accepted extended F77 form.
+   This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
+   and to revert back to the original syntax (with -DNML_EXTENDED_F77)
+   for less tolerant f77 compiler (e.g., pgf77, g77).
+ o globalFiles:
+   commented out in parameter file "data" since it's not safe with MPI
+   (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
+   in this case); no longer commented out in restart test (tst_2+2).
+ o add adTapeDir to specify a special directory where adjoint tapes are
+   written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
+   and cannot be used together with mdsioLocalDir.
+ o nesting pkgs:
+   - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
+   - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
+   - add parameter files + utils dir + output from short run on beagle.
+ o pkg/seaice:
+     fix seaice_growth.F store directives; update results of exp. lab_sea.ad
+ o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
+   unnecessary copying in adjoint code, requires new parameter NMAX_ITER
+ checkpoint62o (2010/11/25)
+ o pkg/exf:
+   - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
+ o pkg/seaice:
+   - seaice_ocean_stress: split a loop for better vectorization of the
+     adjoint code
+   - seaice_growth.F: fix bug in conservation of freshwater connected to
+     capping of heff, put contribution into d_HEFFbyNEG
+   - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
+     by something more sensible (parameters that are what their name implies)
+   - change some defaults, so that by default exf-parameters are used for
+     things like rhoAir, cpAir,latent/sensible heat parameters, in order
+     to reproduce the old results, many data.seaice now contain funny values
+     for cpAir and latent heat of sublimation
+ o packages_readparms.F: move exf_readparms up in line so that
+     exf-parameters are visible for other packages (e.g. seaice)
+ o debugMode & debugLevel=2:
+   - differentiate between debugMode & debugLevel=2:
+     debugMode: controls printing of debug messages (sequence of S/R calls).
+     debugLevel: controls printing of algorithm intermediate results and stats.
+   - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
+     => allows to print debug-stats without all sequence of call messages.
+   - switch control of debug print from debugLevel to debugMode in many S/R.
+ o pkg/obcs (obcs-sponge):
+     fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
+     call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
+ o pkg/generic_advdiff:
+   - record overlap minimum size for each advection scheme;
+   - refine criteria on overlap minimum size;
+   - check and stop (in gad_check) if overlap size is too small.
+ o pkg/obcs:
+   - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
+     once, in ptracers_implicit.F)
+   - with seaice: remove test on empty file name in obcs_apply_seaice (always
+     apply OB values when tile has OB)
+ o model/src, coriolis setting:
+   - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
+     useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
+     files (selectCoriMap=3) with any grid.
+   - add parameter "fPrime" for constant second Coriolis coeff (default=0).
+ o pkg/seaice/seaice_growth.F:
+     a few cosmetic changes that reduce the number of lines of code
+ o pkg/obcs: add boundary conditions following Stevens (1990)
+   - the code follows old MOM/NAOSIM code
+   - so far it is only implemented for the eastern and western boundaries
+     and NOT for pTracers
+ o pkg/rbcs:
+   - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
+     beginning of the first rbcs forcing period.
+   - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
+     offline package, i.e., one file per time, labeled by iteration number;
+     deltaTrbcs sets the timestep with which the data was generated;
+     rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
+   - rbcsForcingCycle=0 makes forcing non-cyclic.
+   - make arithmetic safe for negative times and odd forcing periods.
+ checkpoint62n (2010/11/09)
+ o pkg/seaice:
+     fix masking in free-drift S/R ; update results of exp. lab_sea.fd
+ o pkg/obcs:
+    New S/R to copy tracer value from the OB location to narrow band region
+     (width = same as overlap) beyond the OB: preserve OB value (needed for
+     high-order scheme) which were overwritten by EXCH call if in overlap
+     region. Applied to theta, salt, ptracer and advected seaice variables.
+    With seaice: use maskInC in similar way as in gad_advection.F,
+     in seaice_advection.F and advect.F.
+    Update output of experiment seaice_obcs and change exp4 to test OBCS with
+th order Adv.Scheme. for pasive salt and ptracer.
+ o tools/genmake2:
+   - when looking for an optfile (not specified), only search for Fortran compiler
+     (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
+   - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
+     (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
+   - set default for CPP to "cpp -traditional -P" (was the case without specifying
+     an optfile, but otherwise default was just "cpp".
+   - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
+   - when "CC" is not set in the optfile, look for possible C compiler
+     (instead of just setting CC=cc)
+   - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
+     => add a ".F" to ".o" rule for source files with no "#include" (such as
+        port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
+   - move gfortran before g77 in list of possible Fortran compiler (consistent
+     with reference compiler switch from g77 to gfortran)
+ o pkg/seaice:
+   o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
+     seaice_check that stops the model, when the CPP flag is used.
+   o seaice_growth.F: make capping of ice volume conserving by returning the
+     capped ice as freshwater to EmPmR. This does not change the verification
+     experiments but will change runs where the capping is acutally active
+ o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
+   (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
+      global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
+      lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
+ o tools/genmake2:
+   - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
+   - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
+   - clean previous genmake log files before anything else.
+   - change Makefile to remove testreport log files (*.tr_log) and genmake log
+     files only with "CLEAN" target (instead of "Clean");
+ o pkg/generic_advdiff:
+   Change OBCS in multiDim advection (gad_advection.F):
+    Use maskInC to prevent intermediate update of tracer-field in OB regions,
+    thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
+    which were applying future time-step OB values.
+   This way, all explicit calculations use current-time-step OB values
+    (simpler and more consistent).
+   Affects results when set-up uses time-varying OBC and multi-dim advection;
+    update output of experiment seaice_obcs.
+ o pkg/seaice:
+   move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
+    this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
+      SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
+   Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
+    but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
+    unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
+ o pkg aim (2010/10/26):
+   - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
+     formulation with obliquity, eccentricity, ... as run-time parameters,
+   - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
+     upward shortwave radition at the surface (all-sky and clear-sky).
+ o pkg/obcs:
+   - writing sections with globalFiles=T does not work: switch to tiled-files
+     when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
+   - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
+   - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
+ checkpoint62m (2010/10/21)
+ o pkg/seaice: vectorize seaice_solve4temp.F
+   - move iterations loops outside of i/j-loops
+   - requires 2D arrays for TB and effConduct
+   - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
+     modified in this routine
+   - a little bit of clean up, adjusting indentation, etc.
+   - replaced a few TEN**a by exp(a*log(10.)) in new code for better
+     performance and '**TWO' by '**2' (because TWO is a float),
+     replaced ONE, ZERO
+ o eesupp/src:
+    fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
+ o pkg/seaice/seaice_growth.F
+   Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
+   merging process. The merged routine has two branches, and one activates the 'evolution'
+   branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
+   In summary, here is what the '10/10 revision' did consist of
+     part 1: seaice_growth.F revisions 1.71 to 1.75
+       - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
+         The emphasis here was on improving readability (e.g. by trying to use meaningful
+         variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
+     part 1.5:
+       - revising the lab_sea experiment to make it a more useful (i.e. stable
+         and representative of an actual model run). This was done by generating a
+         (winter) pickup to start from, switching back the main experiment dynamic
+         solver from evp to lsr, having one of the experiments use the free drift solution.
+     part 2: seaice_growth.F revisions 1.76 to 1.85
+       - Sorting out hard-coded constants that prevented heat and fresh water conservation.
+       - Sorting out the various fields units and sign (set early on and reset at the end)
+         to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
+         fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
+       - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
+         and simplifying logical expressions to further improve readibility.
+     part 3: seaice_growth.F revisions 1.86 to 1.89
+       - Re-organize the blocks of code more logically.
+       - Merging the '_if.F' pieces that add something new.
+ o pkg/thsice:
+   - vectorize thsice_solve4temp and thsice_get_exf.
+     Problem: thsice_solve4temp has an unvectorizable statement that
+     might also be problematic for TAF
+   - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
+     does not change the verifcation experiment, but will change all
+     experiments that have this flag undefined (not tested in verification);
+     a little reorganization to save a few 2D fields and recomputations
+   - 1st step of revisiting thsice adjoint (major recomp. sorted out)
+   - 2nd step:  fix some store dirs
+     o seems to work somewhat, i.e. using ifort but not g77
+     o likely cause are incomplete init. or recomputation
+     o start verification/global_ocean.cs32x15/input_ad.thsice
+ o pkg/obcs: add support for exch2
+   - the position of the boundary and prescribed values are specified using
+     a global domain with exch2 facets stacked
+     - in x for N,S boundaries (like W2_mapIO=-1)
+     - in y for E,W boundaries (so E,W boundaries do not overlap)
+ o pkg/mdsio: add support for writing global sections with exch2
+     file layout is as for obcs described above:
+     - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
+     - for y-z sections, facets are stacked in y
+ o pkg/thsice:
+    - change a few routines for better vectorization: thsice_albedo.F,
+      thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
+      not affected, but in particular the latter routine has changed
+      dramatically (not necessarily easier to read now).
+    - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
+    iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
+ o verification/lab_sea:
+   - overhaul of the forward model experiments. The main motivation
+     for this revision is that lab_sea has proven quite fragile (when
+     changing the sea-ice code, and switching platforms) to a point
+     when failures were very hard to attribute to specific code problems.
+   - the suspected reason for this fragility is noise amplification by evp so,
+     to start with, we decided to replace evp with lsr in the main experiment.
+   - the input.lsr experiment thus became obsolete and was removed.
+   - it was replaced with the input.fd experiment that uses an
+     analytical "free drift" solution as the ice velocity field.
+   - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
+     will hopefully allow us to discriminate problems due to dynamic solvers
+     from problems due to the thermodynamic code. input.salt_plume (lsr) allows
+     us to test additional options, along with the salt plume package.
+   - Finally a pickup was generated (at the end of a one year run) to
+     make the tests more representative of an actual model run. Previously
+     the tests starting point was a 1m thickness of ice everywhere.
+ o pkg/seaice:
+   - introducing S\R seaice_freedrift.F that compute the
+     analytical solution to an approximate ice momentum
+     equation (i.e. the simple stress/coriolis balance).
+   - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
+     of the free drift velocity field, and enable its use.
+     To actually use the free drift solution as the model ice
+     velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
+ o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
+ checkpoint62l (2010/10/04)
+ o pkg/seaice:
+   -fix the USE_ORIGINAL_SBI version (for variable freezing point);
+   -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
+    version (with USE_ORIGINAL_SBI undef);
+ o add hooks for new packages OASIS, the package will follow
+   (hooks exclude the seaice pkg for now)
  o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
    Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
    rather than mdsio_readvector.F/mdsio_writevector.F, within
    adread_adwrite.F to read/write adjoint-related tapes to disk.
- o eesup and pkg/mdsio: ALLOW_WHIO
+ o eesupp and pkg/mdsio: ALLOW_WHIO
+   Option to write/read 2D fields to files including tiles halos.
-   Option to write/read 2D fields to files including tiles halos.
+   The main purpose is for adjoint related "tape I/O".
-   The main purpose is for adjoint related "tape I/O".
    The secondary purpose is for debugging phases.
    A word on those rather specifically intended purposes.
    The code was meant to be stripped down to the bare minimum.
    Typically, there is a unique and basic mapping to the global
    buffer (tile by tile, then proc by proc, then level by level), and
    byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
    meant to generate user friendly outputs of various shapes and forms.
    Rather it is intended, for the knowledgeabale developers,
    to be largely independent of the many mdsio options, to allow
    outputs of tiles+halos in debugging phases and in adjoint runs,
    and to allow some flexibility in tuning (adoint) I/O depending on each
    file system behavior. With regard to tuning, most of the potential knobs
    (to leave files open, to allocate the I/O indep. of usesinglecpuio,
    to specify directories, to specify the typical size of I/O calls, etc.)
    are not yet included, and will be added if they prove useful.
-Line 317 
 o tools/build_options:
+Line 4540 
 o tools/build_options:
      but keep the former optfile for few weeks for smooth transition
  o pkg/ecco
    - allow user defined cost function contributions
-         CPP: ALLOW_USERCOST_CONTRIBUTION
+      CPP: ALLOW_USERCOST_CONTRIBUTION
-         USAGE: compute contributions in cost_usercost_all.F
+      USAGE: compute contributions in cost_usercost_all.F
    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
        the two options are complementary.
  o pkg/smooth

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