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-revision 1.1897 by jmc,
Sat Jul 20 00:04:02 2013 UTC
+revision 1.2074 by jmc,
Sun Sep 28 13:47:43 2014 UTC
 Line 4 
 $Name$
      Notes on tags used in MITgcmUV
      ==============================
+ 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

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