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-revision 1.1821 by mlosch,
Fri Feb  8 07:56:45 2013 UTC
+revision 1.2322 by jmc,
Thu Apr  6 16:29:09 2017 UTC
 Line 4 
 $Name$
      Notes on tags used in MITgcmUV
      ==============================
+ checkpoint66f (2017/04/06)
+ o model/src:
+   - add specific run-time param to select level of printed plot-field-maps,
+     set by default to debugLevel. Remove internal param "printDomain".
+ o pkg/seaice:
+   - add flag to add snow mass to seaiceMassC/U/V, the default is
+     SEAICEaddSnowMass=.FALSE., not to change previous results
+ o pkg/bling
+   - Bug fix in bling_production regarding unit conversion for diagnostics
+     being put in the wrong place
+ o model/src:
+   - add back recomputation of 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; was initially added on 2012/06/01 (ini_masks_etc.F
+     revision 1.51) but was removed accidentally on 2014/02/08 (v1.53).
+ o pkg/autodiff:
+   - clean-up "checkpoint.flow"
+ o pkg/rw (Contribution from Jody Klymak):
+     option to set mds file suffix as function of time in simulation:
+     *) new input parameter "rwSuffixType" (read from PARM03 namelist)
+        to select file suffix format; by default (=0), use iteration number;
+     *) add simple routine to return file suffix according to rwSuffixType;
+     *) in model/src and in most pkgs (except: atm2d, fizhi, regrid & streamice),
+        use new S/R to get file suffix, except for debug output file (diagFreq)
+        and pkgs offline & rbcs input files.
+ o pkg/rw:
+   - uniform processing of "I10" suffix across writing fld routines; used to
+     simplify debug writing of cg2/3d_b/x in solve_for_pressure.F & post_cg3d.F
+     (similar to cg3d.F, cg3d_ex0.F)
+ o pkg/mom_vecinv:
+   - highOrderVorticity in selectVortScheme=2 case: fix c4 coeff in splitted
+     vorticity flux (keep same sum in case vBarXm=vBaXp, uBarYm=uBarYp).
+ o pkg/bling:
+   - Many small changes intended to clean the code.
+     Unnecessary ADJOINT_SAFEs removed ;
+     removed BLING_COST.h BLING_CTRL.h bling_cost.F ;
+     diagnostics added.
+ checkpoint66e (2017/03/14)
+ o pkg/exf:
+   - interpolation with #undef EXF_INTERP_USE_DYNALLOC: move buffer size
+     definition outside EXF_PARAM.h in new header file: EXF_INTERP_SIZE.h;
+     use fixed size buffer (passed to S/R EXF_INTERP & EXF_INTERP_UV) to
+     avoid any dynamic allocation ;
+   - S/R EXF_CHECK: add new check & stop when file-name is defined but not
+     read-in ; add warning when file is read-in but not used within pkg/exf ;
+     + check for buffer-size (if #undef EXF_INTERP_USE_DYNALLOC).
+   - update exf_summary.F (print {FLD}RepCycle).
+ o verification/global_with_exf:
+   - switch on exf interpolation in AD test (just like the forward test)
+ o pkg/mom_vecinv:
+   - add storage directives to avoid recomputations within mom_vecinv.F
+     which were generating seg. fault with gfortran -devel
+ o pkg/ctrl, pkg/smooth:
+   - initialize array halos which were generating seg. fault with
+     gfortran -devel in adjoint mode
+ o pkg/exf:
+   - for each input field, enable to specify a field specific repeat-cycle
+     ({FLD}RepCycle) which defaults to pkg/exf main "repeatPeriod".
+ o verification/lab_sea:
+   - update AD results of primary test and noseaicedyn test after switching
+     to new version of TAF (5.3.13 vs 5.3.2 before); agreement with gradient
+     check stays about the same.
+ o pkg/exf:
+   - fix bug in exf_zenithangle.F for cases select_ZenAlbedo > 0 with useCAL=T.
+   - exf_check: MAX_LAT_INC need only be "loc_nlat-1", not equal to loc_nlat
+ o pkg/bling, USE_EXFCO2 code:
+   - add parameter "apco2RepCycle" (set to pkg/exf "repeatPeriod" by default);
+   - update calls to EXF S/R (use new version: EXF_INIT_FLD & EXF_SET_FLD).
+ o pkg/exf:
+   - rename S/R EXF_INIT to EXF_INIT_VARIA ;
+   - add arguments: fldName (for debug msg) and fldRepeatCycle (set to
+     repeatPeriod) to S/R EXF_SET_UV and to S/R EXF_SET_GEN (renamed EXF_SET_FLD)
+     and update calls in pkg/exf calling S/R (exf_getffields.F & exf_getclim.F) ;
+   - add argument: fldName (for debug msg) to S/R EXF_INIT_GEN (renamed
+     EXF_INIT_FLD) and update calls in exf_init_varia.F
+   - For now, for backward compatibility, keep a simplified version of S/Rs
+     EXF_SET_GEN & EXF_INIT_GEN in file exf_set_gen.F
+   - add and pass new arguments: fldName (for debug msg) and fldRepeatCycle
+     to S/R EXF_GetFFieldRec ; update calls in pkg/obcs/obcs_exf_load.F
+ o tools/genmake2:
+   - replace "bc -l" (only used once) by "expr" (already used).
+ o verification/global_ocean.cs32x15:
+   - turn off pkg/cal (useCAL=F) in secondary FWD exp. "icedyn".
+     Note: exf setting (data.exf) can be compared to other exf secondary exp
+     "seaice" (kept with useCAL=T) which has same time dependent forcing.
+ checkpoint66d (2017/02/13)
+ o pkg/exf:
+   - remove setting of useCAL=T when using pkg/exf (useEXF=T); add warning
+     early on (in packages_boot.F) to stress this change in pkg setting.
+   - In (most) verification exp. that use pkg/exf, add useCAL=.TRUE. to data.pkg
+ o model/src:
+   - move call to ecco_phys to end of time step; this may induce minor
+     cost function changes by shifting time averages by one time step
+     for some variables; this revision resulted in changed adjoint results
+     in MITgcm_contrib/verification_other/global_oce_cs32
+ o pkg/exf:
+   - Change EXF_READ_EVAP to only activate code within #ifdef ALLOW_ATM_TEMP ;
+     this prevents to read evap when ALLOW_ATM_TEMP is undef and other fields,
+     e.g. precip, are not available.
+ o pkg/flt:
+   - flt_init_varia.F: use pickupSuff if specified
+   - add code (within #ifdef DEVEL_FLT_EXCH2) and test case as a first,
+     intermediate, step towards completing pkg/exch2 support within pkg/flt;
+     ifdef DEVEL_FLT_EXCH2 then:
+     - flt_init_fixed.F: comment out stop
+     - flt_exch2.F: conserve ipart, jpart (grid coordinates)
+     - exch2_recv_get_vec.F: transform ipart, jpart (grid coordinates)
+     - flt_mapping.F: attempt to fix longitude diagnostic near date-line
+     - flt_init_varia.F: hack initialization (for testing purposes w. LLC90)
+ o tools/genmake2 & pkg/pkg_depend:
+   - define new type of pkg dependency rule ("=pkg_x"), less strict than
+     the "+" rule, that add the dependent pkg (pkg_x) unless it's disabled
+     (-pkg_x in packages.conf).
+   - change pkg/exf dependency rule from "exf +cal" to "exf =cal";
+   - add "+cal" to dependency list of pkg/ecco (needed to compile).
+   - simplify FWD experiment "offline_exf_seaice" by removing pkg/cal.
+ o utils/matlab:
+   - adding ocean_basin routines for defining basin masks.
+ o pkg/exf:
+   - new S/R EXF_GETFFIELD_START replacing EXF_GETFIELD_START, but with more
+     arguments, allowing to check (and stop) if parameter setting of
+      {FLD}startdate1 & date2 and of {FLD}StartTime are consistent with
+     useCAL= T or F. For now, kept a simplified version of EXF_GETFIELD_START
+     for backward compatibility.
+   - change accordingly calls in exf_init_fixed.F + default {FLD}StartTime in
+     exf_readparms.F ; apply same changes to pkg/icefront (for SGRunOff field).
+ o pkg/bling (USE_EXFCO2 code):
+   - fix missing setting of apco2StartTime according to apco2startdate1 & date2
+     by adding a call to S/R EXF_GETFFIELD_START.
+ o pkg/exf:
+   - allows to compile without pkg/cal (but disabled by current dependency
+     rules, i.e., default "pkg/pkg_depend"). Minimal changes to enable to
+     run with useCAL=F ; this involves setting directly {FLD}StartTime instead
+     of {FLD}startdate1 & date2 ; consistency check not yet coded.
+ o verification/global_ocean.cs32x15:
+   - fix all data.exf for a shift of 1 day in all field startdate1 so that it now
+     corresponds to middle of 1rst month; update outputs (2 fwd + 3 adm + 3 tlm).
+ o pkg/exf:
+   - allow to use EXF_ZENITHANGLE without pkg/cal + simplify (saving some
+     calculations); change FWD experiment global_ocean.cs32x15
+     (#define ALLOW_ZENITHANGLE) to test/check that this code compiles.
+ o pkg/exf:
+   - In preparation for addition to NAMELIST, rename internal (_RL) parameter
+      {FIELD}startdate to {FIELD}StartTime
+     Note: new name also fit better the content, i.e, a start time in second.
+ o eesupp/src:
+   - add 1 argument to S/R EEBOOT & EEBOOT_MINIMAL for interface with ESMF
+ o pkg/exf:
+   - add option ALLOW_READ_TURBFLUXES (and corresponding set of parameters)
+     to allow to read-in Sensible & Latent Heat flux ;
+   - simplify pkg/exf main options:
+) move small piece of code (case ALLOW_ATM_TEMP undef) out of
+        exf_bulkformulae.F into exf_wind.F so that exf_bulkformulae.F is
+        compiled only when both ALLOW_ATM_TEMP & ALLOW_BULKFORMULAE are defined;
+) make call to EXF_RADIATION and to EXF_WIND independent of CPP option
+        ALLOW_BULKFORMULAE which now only applies to S/R EXF_BULKFORMULAE ;
+) improve options documentation in EXF_OPTIONS.h.
+ o pkg/ecco:
+   - cost_gencost_customize.F,ecco.h,ecco_phys.F,ecco_readparms.F, and
+     ecco_summary.F: add passive tracer cost functions to gencost;
+     m_ptracer and m_boxmean_ptracer
+ o pkg/ctrl:
+   - ctrl_map_forcing.F: pass myIter and myTime to ctrl_map_forcing as input
+     parameters; move myIter .EQ. nIter0 inside ctrl_map_forcing; add to list
+     of implemented gentim2d contol parameters: xx_qnet, xx_empmr, xx_qsw,
+     xx_sst, xx_sss, xx_pload, xx_saltflux, xx_fu, xx_fv, xx_fe, xx_fn
+ o model/src:
+   - forward_step.F: pass myIter and myTime to ctrl_map_forcing as input
+     parameters; move myIter .EQ. nIter0 inside ctrl_map_forcing
+ o pkg/exf:
+   - exf_getffields.F: add to list of implemented gentim2d contol parameters:
+     xx_lwflux, xx_swflux, xx_evap, xx_apressure, xx_areamask
+ checkpoint66c (2017/01/19)
+ o verification:
+   - add new option "-src" to testreport to only produce source code (*.f),
+     including taf output src code (if using '-adm'/'-tlm' option).
+ o pkg/exf:
+   - add saltflx :: Net upward salt flux in psu.kg/m^2/s
+ o pkg/diagnostics:
+   - add run-time variable diagMdsDir to specify a subdirectory for
+     diagnostic output when mds is being used and mdsioLocalDir is not.
+ o pkg/mnc:
+   - mnc_utils.F: edit stop message
+ o pkg/autodiff:
+   - autodiff_ini_model_io.F: PRINT_MESSAGE, clean-up comments, add _*_MASTER,
+     add HAVE_SYSTEM bracket around system call to mkdir
+ o pkg/profiles:
+   - profiles_findunit.F, profiles_init_fixed.F, profiles_interp.F,
+     profiles_readparms.F: call ALL_PROC_DIE before 'stop'
+   - profiles_ini_io.F: use PRINT_MESSAGE, clean-up comments, add _*_MASTER,
+     add HAVE_SYSTEM bracket around system call to mkdir
+ o pkg/smooth:
+   - smooth_filtervar2d.F, smooth_filtervar3d.F: call ALL_PROC_DIE before 'stop'
+   - smooth_init2d.F, smooth_init3d.F: move print statements to readparms
+   - smooth_readparms.F: add cleaner print statements from smooth_init?d.F
+ o pkg/exf:
+   - check: count errors and stop cleanly at the end (call to ALL_PROC_DIE);
+     issue error message when climsst_interpMethod.GT.0 and climsst_lon_inc > 500
+     generalize tests on interpMethod, nlat, and lon_inc to all exf variables.
+   - summary: skip detailed field report if not used (empty file-name).
+ o tools/xmakedepend:
+   - In case line editor "ed" is missing, switch to "sed" command to clean-up
+     Makefile from previous dependencies (anything after "# DO NOT DELETE" line).
+ o pkg/exf:
+   - change definition of "hflux" input file to always include Short-Wave;
+     this is now consistent with hflux computation (if using bulk-formulae)
+     and hflux diagnostic & documentation (in EXF_FIELDS.h).
+ checkpoint66b (2016/12/01)
+ o model & momentum pkgs:
+   - implement fully implicit bottom friction combined with implicit surf.
+     pressure, for now, only in hydrostic formulation:
+     + to use: compile with #define ALLOW_SOLVE4_PS_AND_DRAG in CPP_OPTIONS.h
+       and run with selectImplicitDrag=2 ;
+     + currently missing diagnostics of bottom drag and vert. viscosity tendency;
+   - partial implicit time-stepping (bot. friction + vert. visc first, then
+     surf. press) corresponding to selectImplicitDrag=1 should be applicable
+     to NH formulation but not available until we solve for surf. pressure
+     increment (instead of full etaN).
+   - change exp. global_ocean.cs32x15.thsice to test implicit bottom drag
+     with implicit vertical viscosity.
+ o pkg/seaice: add linear remapping scheme (Lipscomb 2001) to ITD model
+   - this is a first version that includes many regularisations that may
+     not all be necessary, to be sorted out,
+   - turned on by runtime parameter SEAICEuseLinRemapITD (true by default)
+   - change one verification experiment in seaice_itd to use and test new code
+   - seaice_growth: catch a case where the argument of log can be zero
+     or smaller (important for code stability)
+ o model/src:
+   - modify SOLVE_DIAGONAL_LOWMEMORY version of solve_tridiagonal.F
+     & solve_pentadiagonal.F to enable to re-used inverse matrix for solving
+     similar A.X'=Y' system (with same matrix A) in subsequent calls;
+     switch based on errCode (In/Out) argument value; in calling routines,
+     initialise errCode before first call.
+ checkpoint66a (2016/10/18)
+ o pkg/bling:
+   - BLING package now loads in atmospheric pCO2 file using exf package routines
+     Enable with #define USE_EXFCO2 in BLING_OPTIONS.h
+ o model/src & pkg/ptracers:
+   - with INCLUDE_IMPLVERTADV_CODE defined, also call MOM_U,V_IMPLICIT_R &
+     GAD_IMPLICIT_R (instead of IMPLDIFF) when just implicitViscosity and
+     implicitDiffusion (respectively) are used (even without momImplVertAdv
+     or temp,salt,PTRACERS_ImplVertAdv).
+ o model/src & generic_advdiff:
+   - add parenthesis in main diagonal calculation of implicit vertical
+     diffusion matrix (impldiff.F & gad_implicit_r.F).
+     This affects results at machine truncation level; update output of many
+     verification experiments (31 fwd ; 10 adm ; 8 tlm ; 3 oad).
+ o pkg/mom_commom & generic_advdiff:
+   - add deep atmosphere and anelastic scaling factor in implicit vertical
+     advection routines (mom_u,v_implicit_r.F & gad*_impl*_r.F).
+ o model/src:
+   - remove few unnecessary temp array copies in solve_tridiagonal.F
+     & solve_pentadiagonal.F
+ checkpoint65z (2016/09/28)
+ o pkg/seaice: fix multithreading for seaice_fgmres.F
+   - remove unecessary variables from common blocks
+   - use extra dimension MAX_NO_THREADS for all variables of the Krylov space
+     basis, that are stored in commom blocks (including integer variable i1)
+   - clean up code a little by removing commented lines that refer to
+     original code
+   - turn on multi-threaded test for experiment offline_exf_seaice.dyn_jfnk.
+ o MITgcm manual:
+   - add uptodate pkg/ecco documentation to the manual (section 8.1; ecco.tex),
+     preliminary documentation for generic controls (8.3; ctrl.tex),
+     a placeholder for smooth (8.4; smooth.tex), and comment out the deprecated
+     ecco_costfunction.tex
+ o pkg/ecco:
+   - update and cleanup list of CCP options
+   - re-assign gencost_mask to specify masks rather than gencost_errfile; 'c'
+     is now always passed to cost_generic; gencost_mask is now MAX_LEN_FNAM
+   - add checks that retired run-time options are not used, and in relation
+     to gencost_mask and gencost_errfile
+   - finish deprecating gencost_scalefile, gencost_smooth2Ddiffnbt, and
+     gencost_nrecperiod
+   - fix m_eta computation for virtual salt flux case
+   - add m_horflux_vol case (selected via gencost_barfile) that computes
+     transports via cost_gencost_boxmean (gencost_flag=-3)
+   - use gencost_flag more systematically (i.e., avoid using gencost_name)
+     for code switches (aside from physical variable selection)
+ o pkg/seaice: make seaice_fgmres.F fit for multithreading; this first
+   attempt appears to be a bit of a hack and my need some repair down the road
+ o pkg/exf:
+   - interpolation near South Pole: fix criteria on input field latitude.
+ o pkg/icefront & pkg/exf:
+   - move setting of icefront Sub-Glacial RunOff forcing (currently unused)
+     from pkg/exf (read from data.exf) to pkg/icefront (read from data.icefront)
+ o pkg/exf:
+   - replace CPP option ALLOW_EXF_OUTPUT_INTERP with run-time parameter
+     "exf_output_interp" (in namelist: EXF_NML_04); change output file name
+     (add suffix "_out" instead of a prefix); keep same record number as in
+     input file but always write record 1 first (to avoid a STOP in I/O S/R).
+     Change output file content by writing interpolated field before applying
+     land-sea mask (helpful for debug).
+   - 2 compon. vector interpolation with rotation: apply scaling factor on
+     each compon. (Eastward and Northward) just before rotation.
+ o pkg/bling:
+   - Cleaned package. Removed not needed code and comments.
+   - adjoint example now works
+     (MITgcm_contrib/verification_other/global_oce_biogeo_bling/code_ad)
+ o pkg/ptracers:
+   - add Bruno Deremble's code to complete the linear surface correction
+     for tracer conservation;
+   - enabled for individual ptracers by PTRACERS_linFSConserve(iTr)=.TRUE.
+ checkpoint65y (2016/07/29)
+ o pkg/debug (stats):
+   - change GLOBAL_SUM to GLOBAL_SUM_TILE (result independent of tile to
+     proc/thread mapping);
+   - fix Min & Max for case where 1 thread has only empty tiles;
+   - use RL variable to count number of wet grid points (with big domain,
+     can be too large to fit into integer*4).
+ o pkg/monitor:
+   - use RL variable to count number of wet grid points (but used only for del2)
+   - add new routine to compute Advective CFL within tracer time-stepping with
+     writing delayed until next monitor output.
+ o pkg/obcs:
+   - fix bug in OBCS_BALANCE_FLOW (OBCS_balanceFacN misspelled OBCS_balanceFacW)
+ o pkg/cal:
+   - calandar-dump: treat case myTime < timePhase in the same way as in
+     eesupp/src/diff_phase_multiple.F (when not using calandar-dump).
+ o pkg/dic & seaice:
+   - fix compilation of ocean component for coupled atm+ocn model with
+     seaice dynamics & dic.
+ checkpoint65x (2016/06/11)
+ o add a license text file in main MITgcm tree.
+ o added pkg/bling:
+   - intermediate complexity biogeochemical model
+   - see bling_description.txt for details
+   - verification experiment is global_oce_biogeo_bling (for now, in
+     Contrib/verification_other/); tested daily on baudelaire with gfortran.
+   - add entry point in pkg/gchem for new pkg "bling".
+ o pkg/seaice: fix tensile stength computation
+   - replace global field tensileStrength by tensileStrFac
+   - tensileStrFac can be computed once in S/R seaice_init_varia
+   - fortunately that does not affect any verification results
+ checkpoint65w (2016/05/12)
+ o pkg/ctrl/ctrl.h: fix a comma in common block list, so that code compiles
+      with ECCO_CTRL_DEPRECATED defined
+ o verification/global_ocean.cs32x15:
+   - change secondary test "viscA4" to also test "selectP_inEOS_Zc=3"
+     with "selectNHfreeSurf=1".
+ o model/src (non-hydrostatic free-surface):
+   - More "natural" expression of NH free-surface term (case selectNHfreeSurf=1):
+     was: tmpSurf/(1+tmpSurf); changed to: 1/(1+Gamma) with Gamma=1/tmpSurf.
+   - Calculate surface vertical velocity after 2-D solver adjustment (accounts
+     for EmPmR if RealFreshWaterFlux); used in RHS (cg3d_b) if exactConserv
+     and used to compute dPhiNH (in post_cg3d.F) if selectNHfreeSurf=1.
+     This fixes EmPmR contribution when selectNHfreeSurf=1 & RealFreshWaterFlux.
+   - Update output (changes at machine truncation level) of verification exp:
+     exp4 (11 digits for cg2d), global_ocean.cs32x15.viscA4 (11.d),
+     short_surf_wave (13.d) and tutorial_deep_convection.smag3d (12.d).
+ o pkg/seaice: ITD code
+   - fix picking up from a single category model by initialising
+     heff/area/hsnowITD = 0. in seaice_itd_pickup.F
+   - split a long warning message in seaice_check_pickup.F into two lines,
+     because NEC SX-ACE cannot deal with the long line.
+ o model/src:
+   - fix missing dPhiNH in pressure_for_eos.F (case: selectP_inEOS_Zc=3)
+ o pkg/seaice:
+   - add missing checks for SEAICE_ALLOW_KRYLOV and SEAICE_ALLOW_BOTTOMDRAG
+ o pkg/seaice:
+   - add basal stress as parameterisation for grounding ice
+     following Lemieux et al. (2015)
+   - turn on by setting new parameter SEAICEbasalDragK2 to a value
+     larger than 0. Lemieux et al. (2015) recommend 15.
+   - The adjoint complains with extra recomputations so there is also a
+     new cpp-flag SEAICE_ALLOW_BOTTOMDRAG that is undefined by default in
+     order to postpone the problem
+   - compile the new code in lab_sea
+ o verification/halfpipe_streamice:
+   - update both TAF and OpenAD adm output (machine truncation differences)
+ checkpoint65v (2016/04/08)
+ o verification/advect_xz:
+   - increase overlap size from 3 to 4 and add new secondary test for PQM
+     advection scheme (with mono & wino limiter).
+   - change main exp. to test PPM (with weno limiter) adv.scheme on Temp.
+ o model/src:
+   - new parameters "top_Pres" & "seaLev_Z" (replacing Ro_SeaLevel and recently
+     added phi0Ref) to set vertical axis origin and phiRef origin;
+     keep Ro_SeaLevel for backward compatibility (with a warning).
+    According to coordinate and fluid type:
+     OCN in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(1), @ the top)
+     ATM in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(Nr+1) @ bottom)
+     OCN in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(Nr+1)/g, @ the top)
+     ATM in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(1)/g, @ the bottom)
+   - remove Ro_SeaLevel from ATM experiment parameter files;
+   - in tutorial_global_oce_in_p, remove Ro_SeaLevel and set top_Pres to the
+     complement; update output.txt (changes at machine truncation level).
+ o pkg/seaice/seaice_evp.F
+   - simplify computation of deltaZ and zetaZ to simple averaging following
+     Bouillon et al. (2013). This removes a lot of code, but also changes
+     verification experiment lab_sea.hb87 -> updated
+ checkpoint65u (2016/03/14)
+ o pkg/generic_advdiff:
+   - from Darren: add PPM and PQM advection schemes (number 40-42 and 50-52)
+     with 2 types of limiter (see: Engwirda & Kelley, submit. to JCP);
+     Note (from Darren): unlimited PPM/PQM scheme (40 & 50) are just for
+     testing and not for actual use.
+ o model/src:
+   - add parameter "phi0Ref" to specify reference [pressure/geo] potential at
+     origin r = rF(1);
+   - add options (parameter selectP_inEOS_Zc) to select which pressure to use
+     in EOS for height coordinate: enable to include NH Pressure or to use
+     more accurate pressure vertical profile; options not linked to EOS type
+     (as previously, e.g., JMD95P/JMD95Z) but set default according to EOS type;
+   - start to implement variable gravity (along vertical): for now, only with
+     z-coords (not even z*).
+   - add Ideal Gas equation of state for height coordinate.
+   - update OpenAD output (affected at machine truncation level) of exp:
+     global_ocean.90x40x15, OpenAD (std) and tutorial_global_oce_biogeo.
+ o pkg/exf:
+   - add ALLOW_EXF_OUTPUT_INTERP cpp switch to output the result
+     of exf interpolation (before any rescaling, rotation or interpolation
+     to velocity point) for each field that gets loaded from file. This option
+     identically mimics the input file organization (e.g. record numbers in year
+     by year input files) besides the change in horizontal grid.
+   - add rotateStressOnAgrid run-time switch so that wind stress fields
+     can be provided on the A-grid in zonal/meridional direction and
+     rotated on the fly. This only applies to the case when the exf
+     interpolation is off and rotateStressOnAgrid is false by default.
+ o model/src:
+   - rename internal parameter "useDynP_inEos_Zc" to "storePhiHyd4Phys" (since
+     it's also used with pkg/atm_phys) and add few more parameters (but still
+     inactive, src code yet to come)
+ checkpoint65t (2016/02/10)
+ o pkg/atm_phys:
+   - from Ruth Geen: add optical depth dependence on CO2 concentration.
+ o model/src:
+   - fix vertical inter/extra-polation of density factor rhoFacF (for anelastic)
+     for the case setCenterDr=T (delRc set from "data"); add output of rhoFacC&F.
+     Update output of exp. deep_anelastic (changes at truncation level).
+ o tools:
+   - add a hack in "remove_comments_sed" (used only with TAF) for recent
+     version of OpenMPI (shipped with FC.23): comment out the new header
+     file "mpif-sizeof.h" which causes problems to TAF.
+ o pkg/seaice:
+   - change the termination criterion so that maxits (SEAICElinearIterMax)
+     has an effect
+   - unify iteration parameters for implicit solvers (JFNK and Picard)
+     SEAICEnonLinIterMax replaces SEAICEnewtonIterMax/NPSEUDOTIMESTEPS
+     SEAICElinearIterMax replaces SEAICEkrylovIterMax/SOLV_MAX_ITER
+     SEAICEpreLinIterMax replaces SOLV_MAX_ITER in preconditioner
+     SEAICEpreNL_IterMax replaces NPSEUDOTIMESTEPS in preconditioner
+     SEAICEnonLinTol     replaces JFNKgamma_nonlin
+   - remove S/R SEAICE_FGMRES_DRIVER and put content into S/R SEAICE_JFKN
+   - add new Picard-Krylov solver, compile with SEAICE_ALLOW_KRYLOV and
+     use with SEAICEuseKrylov
+ o pkg/seaice/seaice_lsr.F
+     fix small bug: replace zetaZ by zetaZloc in S/R seaice_lsr_rhsu/v; only
+     relevant if SEAICEuseStrImpCpl=T, and even then it does not seem to have
+     an effect.
+ o pkg/seaice: add two new parameters
+   - SEAICEuseLSR to simplify the logic in seaice_dynsolver (this
+     parameter is not in any namelist)
+   - SEAICEusrPicardAsPrecon to allow s/r seaice_lsr to be used as
+     a preconditioner for the non-linear Newton iteration of the JFNK
+     solver
+ o pkg/seaice/seaice_lsr.F: replace 1./SEAICE_deltaTdyn with recip_deltaT,
+   affects some experiments at truncation level:
+   - global_ocean.cs32x15.icedyn (11 digits),
+   - global_ocean.cs32x15.seaice (11 digits),
+   - seaice_itd (12 digits), seaice_itd.lipscomb07 (12 digits) -> update
+   - also update global_ocean.cs32x15 adjoint and tangent-linear results
+ o pkg/salt_plume & pkg/thsice:
+   - for coupled  set-up with pkg/thsice in ATM and pkg/salt_plume in OCN,
+     connect salt_plume flux to ATM-OCN coupling pkgs interface:
+    a) in ATM: also cumulate salt-plume flux in S/R THSICE_SALT_PLUME (for
+      export to coupler interface) even without compiling pkg/salt_plume ;
+    b) in OCN: apply coupler salt-plume flux to pkg/salt_plume field
+      (saltPlumeFlux) just before exch call, in S/R SALT_PLUME_DO_EXCH.
+ o pkg/dic:
+   - use the updated seaice fraction (from seaice pkgs) for DIC forcing
+     instead of the previous time-step value ; done in new S/R DIC_FIELDS_UPDATE
+     called from the top of dic_biotic_forcing.F (instead of in DIC_FIELDS_LOAD);
+   - move also update with values from ATM-OCN Coupler in the same new S/R
+     (previously done in ocn_apply_import.F).
+ o tools/adjoint_options:
+   - specify explicitly "-f77" or "-f90" in default ad-optfile since TAF (default)
+     has been changed on Jan 14, 2016.
+ o pkg/ggl90:
+   - add alternative discretisation of vertical shear (off by default), to
+     compute the mean (@ grid-cell center) of vertical shear compon instead of
+     vertical shear of mean flow (@ grid-cell center).
+   - add correct parenthesis in ALLOW_GGL90_SMOOTH code to get the same truncated
+     results on adjacent faces of cubed-sphere grids; this fix the restart.
+ o pkg/atm_compon_interf:
+   - skip time-ave over cpl_atmSendFrq of Sea-Level Pressure (atmSLPr) and just
+     pass last value, stored directly before export to CPL ;
+     Note: this affects results of Coupled set-up where OCN uses useImportSLP=T
+   - remove atmSLPr from pickup files (no longer needed for restart)
+ checkpoint65s (2016/01/13)
+ o eesupp & genmake2:
+    - first check for Function ETIME and, if it fails, then check for subroutine
+      ETIME and consistent output; use the appropriate version in timers.F
+ o model/src:
+   - to check restart test, add option to apply EXCH to U,V earlier, just before
+     integr_continuity; turned off by default.
+ o pkg/dic:
+   - remove CPP option USE_ATMOSCO2 (not needed)
+ o tools/tst_2+2:
+   - try to ignore difference between +0 and -0 in binary file, causing test
+     to fail for no good reason.
+ o eesupp & genmake2:
+   - put back modif from Jinxuan Zhu - change etime fct call to S/R call -
+     but also check (in genmake2) that test runs and returns meaningful results.
+ o coupler pkgs:
+   Finish implementation of optionally-exchanged variable switches (started on
+    Nov 12) with addition of few more exchanged fields, including 2-way exchange
+    of pkg/thsice vars to allow to use seaice dynamics (from pkg/seaice) & seaice
+    advection in OCN component; this requires sequential coupling.
+   coupler (pkg/atm_ocn_coupler):
+   - add argument msgUnit and iter number to CPL_SEND/RECV_ATM/OCN_FIELDS
+     routines (useful for debug).
+   - only export/import optionally exchanged fields (RunOff, seaice, Salt-Plume
+      flux, DIC fields) if corresponding switch is ON.
+   - add option to export RunOff to OCN (to use for DIC river input)
+   - add 2-way thSIce vars exchange; check for consistent cpl_sequential setting.
+   components (pkg/atm_ & ocn_compon_interf):
+   - to save memory space in ATM & OCN comp: add some #ifdef ALLOW_${PKG} around
+     optionally exchanged fields; add a check & stop in cpl_readparms.F.
+     ATMCPL.h: ALLOW_LAND for RunOff, ALLOW_THSICE for seaice, ALLOW_AIM for CO2;
+     OCNCPL.h: ALLOW_SALT_PLUME, ALLOW_DIC for DIC, ALLOW_THSICE for 2-W thsice.
+   - rename:   fracIce     -> sIceFrac_cpl (<- match coupler var name)
+     + in ATM: fracIceTime -> sIceFracTime ; seaIceTime -> sIceMassTime.
+   - add 2-way thSIce vars exchange ; add Salt-Plume flux ; add RunOff in OCN.
+   - hold in common block coupler optionally-exchanged variable switch
+     and set default "useImportXXX" accordingly; + check & stop if inconsistent.
+   - add diagnostics for all imported fields from coupler (in both OCN & ATM);
+     this is intended to replace the OCN cplFldtave.* output files (not updated
+     to contain new additional exchanged fields).
+ o pkg/dic:
+   - fix an other bug (also from 2014/08/30) in dic_atmos.F, in dic_int1=3 code.
+ o pkg/thsice:
+   - when coupled to ATM (useCoupler) with thSIce_skipThermo=T, skip reading
+     and writing of thsice pickup files.
+ o pkg/atm_compon_interf:
+   - move all field individual export-call out of cpl_export_import_data.F
+     into new S/R ATM_EXPORT_FIELDS
+ o pkg/atm_compon_interf:
+   - store state variables (for now, only thSIce fields) just before beeing
+     exported (in cpl_export_import_data.F, like on ocean side) instead of from
+     atm_store_my_data.F like all exported fluxes.
+   - new version of pickup_cpl: write field names into meta file and read meta
+     file to find field postion in pickup. Also only write/read fields meeded for
+     restart (same logic as main pickup file ; also using pickupStrictlyMatch)
+ o pkg/dic:
+   - fix bug (added on 2014/08/30) in dic_atmos.F for the case dic_int1= 2 or 3.
+ o pkg/seaice: add new parameter SEAICEpressReplFac to choose between
+     pressure replacement method (=1., default) or original Hibler (1979) (=0.)
+     value can be from domain [0,1] to average between the two methods
+ o pkg/atm_phys:
+   - allow to provide 2-d map of albedo and mixed-layer depth from files (but
+     hold fixed in time).
+ checkpoint65r (2015/12/21)
+ o pkg/seaice:
+     fix bug in tridiagonal solvers for SEAICE_OLx/y>0, this affects the JFNK
+     solver (offline.dyn_jfnk) and global_ocean.cs32x15.seaice -> updated
+ o pkg/seaice:
+   - fix a bug in computing areaS in (J-J -> J-1) that affects runs
+     when SEAICEscaleSurfStress=.TRUE.,
+   - apply areaW and areaS in S/R seaice_calc_lhs
+ o pkg/atm_phys:
+   - add diagnostics for 3-D, Nr+1 levels diagnostics of radiative fluxes
+     (shortwave & longwave, net & downward) and diagnostics of temp. tendency
+     for individual contribution (convection, LSC cond, radiation)
+   - add Ruth Geen etal, GRL 2016, radiation options (see paper supp.
+     information); activated with: solar_exponent=0. and wv_exponent=-1.
+ o pkg/ggl90:
+   - within IDEMIX add upper limit for horizontal group velocity to
+     avoid instability problems in the explicit horizontal diffusion term for
+     long time steps or high resolution
+ o pkg/diagnostics:
+   - simplify setting of local-array size in diagstats_output.F: uses "numLevels"
+     (from DIAGNOSTICS_SIZE.h) to allow to write out more than Nr levels.
+ o testreport:
+   - remove "-v" (verbose option) in default mpirun command.
+ o pkg/seaice/seaice_growth:
+   - catch potential division by zero in ITD code, does not change
+     verification results
+ o pkg/ecco:
+   - retire old codes to the Attic. The calls to retired functions are
+     left in a commented form in case they ever need to be re-activated.
+   - ecco_check.F: issue warning if any old CPP option is
+     defined that corresponds to retired codes -- then stop.
+ o pkg/atm_compon_interf:
+   - change seaice fraction (use for OCN dic surf.flux) stored and sent to
+     coupler: use last time-step value instead of average over cplSendFrq_iter
+     time-step, similar to what is done for seaIceMass.
+     This will affect results (pkg/dic) of coupled ATM-OCN+dic set-up.
+ o eesupp & genmake2:
+   - from Jinxuan Zhu: change etime fct call to S/R call (fix gfortran ETIME);
+     <= remove until a fix is found for some ifort version on ia32 machine.
+ o pkg/seaice/seaice_evp:
+   - refine residual computation
+ checkpoint65q (2015/11/18)
+ o pkg/seaice/seaice_evp:
+   - fix residual computations so that they no longer affect the actual
+     simulation code
+   - fix seaice_readparams to be able to actually set new parameters
+     SEAICEaEVPcStar and SEAICEaEVPalphaMin, also fix logic a little
+ o model/src:
+   - fix wrong truncation (single prec) from "FLOAT" function in expressions
+     like: deltaT*FLOAT(myIter) when myIter is large:
+      a) replaced by DFLOAT (if not seen by TAF);
+      b) remove "FLOAT" and use implicit type conversion (if seen by TAF).
+ o pkg/aim_v23:
+   - write/read the expected CO2 pickups (from S/R AIM_DO_CO2): fix reading
+     when pickupSuff is set ; do write rolling pickups + at the end of the run.
+ o pkg/atm_ocn_coupler + ocn_compon_interf:
+   - in prep for using pkg/seaice Dyn in coupled set-up, implement sequential
+     coupling option-1: ATM -(cpl)-> OCN and then OCN -(cpl)-> ATM ;
+     add corresponding call in DO_OCEANIC_PHYS.
+ o coupler pkgs:
+   Start a new way to set-up optionally-exchanged variables (previously, only
+    there for exchange_DIC): switch on/off from 1 place, at run-time, in coupler
+    data.cpl (new) instead of at compile time in ATMIDS.h & OCNIDS.h ;
+    send switch to ATM & OCN compon before reading their own "data.cpl" (so that
+    compononent param default can be set accordingly).
+   Note: this new switch (cpl_exchange_[xxx]) is not a per variable switch
+    but rather applies to a group a fields (going both ways like for DIC)
+    and corresponds to an option of coupling config.
+   coupler (pkg/atm_ocn_coupler):
+   - change parameter file from "data" to "data.cpl" (in cpl_read_params.F),
+     and read namelist directly (without eessup S/R calls) instead of
+     in the very un-flexible old way, 1 param per line, in fixed order;
+   - add error-counter to track errors (e.g., missing "data.cpl") and to stop
+     cleanly in CPL_CHECK_CPLCONFIG
+   - add new coupling-exchange selectors (some not yet active) including
+     cpl_exchange_DIC (to set to 3 to replace atmCpl_exchange_DIC=T in ATMIDS.h
+                                          and ocnCpl_exchange_DIC=T in OCNIDS.h);
+   - add 2 new S/R (CPL_SEND_ATM/OCN_CPLPARMS) to send coupler-params to each
+     component ; called directly from coupler.F, after comp. registrations;
+   - rename few variable-ID names (in ATMIDS.h & OCNIDS.h):
+      atm/ocnSeaIceName --> atm/ocnSIceMassName ; atm/ocnFCO2Name ->
+       -> atm/ocnCO2FluxName ; atm/ocnWSpdName --> atm/ocnWindSpdName
+   components (pkg/atm_ & ocn_compon_interf):
+   - add ATM/OCN_CPL_OPTIONS.h in component pkgs and include the corresponding
+     CPP header file in all pkg source files.
+   - move checking of comp. configs out of cpl_exch_configs.F into new S/R
+     ATM/OCN_CHECK_CPLCONFIG;
+   - add error-counter to track errors (e.g., in "data.cpl") and to stop
+     cleanly in ATM/OCN_CHECK_CPLCONFIG;
+   - add new S/R CPL_IMPORT_CPLPARMS to import coupling-exchange selectors
+     from coupler ; called from initialise_fixed.F, after PACKAGES_BOOT and
+     before PACKAGES_READPARMS;
+   verification/cpl_aim+ocn/:
+   - update ATMIDS.h & OCNIDS.h (in shared_code) and use new parameter file
+     "data.cpl" for coupler (in input_cpl).
+ o eesupp/inc:
+   - change the MPI-global-sum default (in CPP_EEOPTIONS.h) to:
+     #define GLOBAL_SUM_ORDER_TILES (only affects MPI built of global_sum_tile.F)
+     to always cumulate tile local-sum in the same order (still uses
+     MPI_Allreduce like standard code).
+   - in verification experiment code, remove local CPP_EEOPTIONS.h_mpi files
+     that are now identical to standard version (in eesupp/inc).
+ o pkg/shelfice:
+   - add SHELFICETransCoeffTFile for initializing spatially varying
+     heat and salt transfer coefficients
+ o pkg/atm_compon_interf & ocn_compon_interf:
+   - combine into 1 (new) S/R CPL_EXPORT_IMPORT_DATA the two previous
+     S/R CPL_EXPORT_MY_DATA & CPL_IMPORT_EXTERNAL_DATA
+   - move bi,bj loops inside S/R OCN_STORE_MY_DATA
+ o pkg/atm_ocn_coupler:
+   - initialise to zero ATMVARS.h & OCNVARS.h arrays.
+ o pkg/rbcs:
+   - select RBCS-mask for Temp & Salt the same way as for pTracer ; this allows
+     to compile with maskLEN=1 when all tracers use the same RBCS-mask.
+   - add a short report (to STDOUT) about RBCS-mask settings.
+ checkpoint65p (2015/10/23)
+ o pkg/seaice/seaice_evp.F: fix store directives and key computations, since
+     there is no adjoint test for EVP, we don't know what it does to the adjoint
+     solution, but at least there are no more recomputation warnings left
+ o pkg/seaice/seaice_evp.F: slight modification of averaging so that EVP stands
+     a chance of giving the same results as a fully converged VP (JFNK) solver
+ o tools/adjoint_options/adjoint_diva:
+   - fix bug (typo) in Tang-Linear FLAGS setting for MPI + DIVA
+ o pkg/streamice:
+   - spotted bug in streamice_driving_stress using dyG where should have been dxG
+ o pkg/exf:
+   - remove STOP statement that prevented to use wind or (wind-)stress
+     interpolation for constant-in-time forcing fields (wind/stress period = 0).
+ o pkg/seaice:
+   - replace SEAICE_EVP_USE_ADAPTATION by run time parameters, requires
+additionals 2D fields and 6 new store directives
+   - change logic in seaice_readparms.F: EVP code can now be turned on in
+     various ways, setting SEAICE_deltaTev is no longer required,
+     alternatively set SEAICE_evpAlpha/Beta, SEAICEuseEVPstar, SEAICEuseEVPrev,
+     or SEAICEaEVPcoeff
+ o pkg/shelfice/shelfice_thermodynamics.F
+   - redefining uLoc/vLoc to u/v, instead of 2u/v
+ o pkg/seaice/seaice_evp.F: introduce "adaptive EVP" by Madlen Kimmritz
+   - this is an intermediate state of a truely converging EVP that has
+     the potential of outperforming implicit VP methods, I do not recommend
+     using it yet.
+   - for now, "adaptive EVP" is turned on by setting SEAICE_EVP_USE_ADAPTATION
+     and all parameters are hardwired
+   - for convergence it still requires very smooth regularisations, that means,
+     if SEAICE_DELTA_SMOOTHREG is defined, deltaCreg=deltaC+deltaMin, which is
+     different from the VP case with deltaCreg=sqrt(deltaC**2+deltaMin**2); also
+     specific averaging appears to be required, still subject to tuning
+   - still needs cleaning and I need to turn parameter into runtime parameters
+   - add code to compute and print residuals of iteration, compile with
+     defining ALLOW_SEAICE_EVP_RESIDUAL to enable it
+ o pkg/seaice/seaice_evp.F: fix a bug (factor of four in front of e12Csq)
+   that entered with r1.54 on Sep04, 2015, -> update results
+ checkpoint65o (2015/09/14)
+ o pkg/mom_vecinv & mom_common:
+   - add deep-atmosphere geometry factor in mom_calc_visc.F + in routines
+     called from there.
+   - add anelastic and deep-atmosphere geometry factor in pkg/mom_vecinv ; this
+     allows to use Vector-Invariant form in deep atmos and anelastic formulation
+ o pkg/seaice: introduce fast ice parameterisation following Itkin et al. (2015)
+   and Koenig-Beatty+Holland (2012)
+   - two new parameters SEAICE_tensilFac and SEAICE_tensilDepth
+   - global 2D field tensileStrength, computed in seaice_calc_ice_strength
+   - requires an extra input argument for S/R seaice_calc_viscosities
+   - tensileStrength's depth dependence is different from Itkin et al. (2015)
+     (to be changed and played with, for now exponential)
+ o pkg/seaice: introduce new parameter SEAICEscaleSurfStress (default = .FALSE.)
+   - if TRUE scale ice-ocean and ice-atmosphere stress acting on sea ice
+     by AREA according to Connelly et al. (2004), JPO.
+   - For EVP and the LSR solver, the implicit part of the drag term is
+     the only non-zero term in the denominator when there is no ice (which
+     prevented running the model with zero ice-ocean drag). If
+     SEAICEscaleSurfStress = .TRUE., this results in a division by zero
+     (or zero main diagonals BU/BV) which need to be caught. A practical
+     consequence is that for open water, the momentum equation reduce
+     to trivially 0 = 0 + 0 (for EVP). For LSR, BU/BV are reset to 1, if
+     they happen to be zero, often leading to a non-zero solution over
+     open water.
+ o pkg/seaice: revise EVP code (seaice_evp.F) in preparation for a more
+     efficient EVP method.
+   - introduce area-weighted averages for e12 (analogously to
+     seaice_calc_viscosities.F); this totally changes lab_sea.hb87 (2 digits
+     remain, but also changing the order of terms in the previous average
+     changed the results as much) -> update experiment
+   - add SEAICE_DELTA_SMOOTHREG code
+   - disentangle computation of zetaC/deltaC and zetaZ/deltaZ, also for
+     TEM-code
+   - adjust loop bounds so that only required fields are computed
+   - add new averaging code for zetaZ/deltaZ (again similar to
+     seaice_calc_viscosities.F), inactive by default for now (will change
+     results again), but will replace old code eventually
+ o eesupp/src:
+   - add an other alternative for multi-proc GLOBAL_SUM (in global_sum_tile.F)
+     to always cumulate tile local-sum in the same order
+     (option #define GLOBAL_SUM_ORDER_TILES in CPP_EEOPTIONS.h).
+     Still uses MPI_Allreduce (like standard code) but on array of tiles
+     and should be faster than GLOBAL_SUM_SEND_RECV code.
+   - switch almost all verification experiments that use GLOBAL_SUM_SEND_RECV
+     (defined in CPP_EEOPTIONS.h_mpi) to GLOBAL_SUM_ORDER_TILES instead.
+   - add CPP_EEOPTIONS.h_mpi with GLOBAL_SUM_ORDER_TILES defined in 14 more exp.:
+      aim.5l_cs, cheapAML_box, deep_anelastic, dome, fizhi-cs-32x32x40,
+      fizhi-cs-aqualev20, fizhi-gridalt-hs, global_ocean_ebm, matrix_example,
+      natl_box, solid-body.cs-32x32x1, tutorial_advection_in_gyre,
+      tutorial_baroclinic_gyre and tutorial_held_suarez_cs.
+ checkpoint65n (2015/07/29)
+ o pkg/thsice:
+   - add a warning when used with pkg/aim but without updating SST
+     (stepFwd_oceMxL=F & useCoupler=F & tauRelax_MxL<>-1 ).
+ o pkg/offline:
+   - change where Offline-Fields are loaded, from load_fields_driver.F to
+     directly within FORWARD_STEP, just after updating iter number and time;
+   - move setting of GM and KPP diffusivity out of OFFLINE_FIELDS_LOAD into new
+     S/R OFFLINE_GET_DIFFUS that is called towards the end of DO_OCEANIC_PHYS;
+    These changes allow:
+     a) to recover exactly on-line results using deltaToffline=deltaTClock,
+     tested (using offlineIter0= nIter0 -1 and offlineTimeOffset= -deltaT/2)
+     both with Lin & Non-Lin Free-Surf, both with staggerTimeStep & synchronous
+     time-step, both with GM & KPP files and with recomputing these fields;
+     b) no needs to switch on staggerTimeStep anymore;
+     c) simplify rescaling of offline horiz. velocity with Non-Lin Free-Surf.
+   - update output of experiment tutorial_dic_adjoffline (only 3 digits left).
+ o pkg/offline:
+   - change (rarely used) offset-iteration parameter to an offset time (in s):
+     can easily recover previous offset-iter effect by setting offset-time
+     (offlineTimeOffset) to offset-iter x deltaToffline;
+   - do not turn-off Temp & Salinity surface relaxation when using KPP (used
+     in KPP as part of surface buoyancy forcing) in offline run.
+   - fix ptracers KPP non-local term in the case where KPP is re-computed.
+ o OpenAD
+   - Adding preliminary ggl90 test to OpenAD verification.
+     Config. with ggl90 currently diverges after 64 time steps
+     so will need more work to become more stable
+   - Adding preliminary kpp test to OpenAD verification.
+     required small tweakes in kpp_routines.F
+   - Merge and update from Krishna Narayanan's contrib area:
+     * Add one variable for preliminary OpenAD DIVA
+     * Add replacement time-stepping for OpenAD DIVA
+     * genmake2 flag -diva (but only for OpenAD; preliminary)
+     * required modifs for OAD_support
+     successful preliminary test for tutorial_global_oce_biogeo/
+ o pkg/seaice:
+   - initialise deltaC in seaice_lsr, cosmetic changes in seaice_lsr
+   - add cpp-flag SEAICE_DELTA_SMOOTHREG for option of regularising
+     delta with a smooth function in s/r seaice_calc_viscosity
+     (no effect on EVP)
+   - rename local suffix "sqr" into "sq" for more consistent variable names
+ o pkg/seaice:
+     add new parameter SEAICE_deltaMin that is used ***only***
+     for regularizing Delta (and nothing else, like the parameter
+     which is also used for all sorts of things SEAICE_EPS).
+     Defaults to SEAICE_EPS for backward compatibility only.
+ o pkg/seaice: replace erroneously storing e12Csqr on the wrong tape with
+     the wrong key by inialising it before use -> fixes a recomputation
+     problem but does not fix the gradient
+ o pkg/layers:
+   - move resetting of flux arrays to outside the iLa loop
+     (this caused layers_diapycnal to not work with more than one layer coord.)
+   - fix bug in calculation of layers_recip_delta in layers_init_fixed.F
+ o pkg/layers:
+   - remove from common block 3D layers fields (used to diagnose transport
+     in tracer coords) and declare them as local arrays in layers_calc.F
+ o pkg/seaice:
+   - Rename SEAICE_VECTORIZE_LSR_ZEBRA to SEAICE_LSR_ZEBRA and define it
+     in lab_sea forward experiment (changes results -> updated)
+   - update adjoint experiment lab_sea after cleaning up seaice_lsr_tridiagu/v
+ o pkg/seaice: modify seaice_lsr.F in order to improve the gradient
+    computations; for SEAICE_VECTORIZE_LSR
+   - move the loops over which the tridiagonal solvers (seaice_lsr_tridiagu/v)
+     sweep to the outside,
+   - remove store directives and add "CADJ loop sequential" directives
+     in analogy to model/src/solve_tridiagonal.F
+   - replace many "#ifdef SEAICE_VECTORIZE_LSR_ZEBRA" by variable loop
+     boundaries to yield more readable code. This has also the charming side
+     effect that your can use SEAICE_VECTORIZE_LSR_ZEBRA without
+     SEAICE_VECTORIZE_LSR (i.e. adjoint without recomputations in
+     seaice_lsr_tridiagu/v now requires either of these flags, vectorization
+     still requires SEAICE_VECTORIZE_LSR with SEAICE_VECTORIZE_LSR_ZEBRA as
+     an additional option)
+    The tridiagonal solvers are now completely analoguous to solve_tridiagonal.F
+    but the adjoint gradients (which are affected by this change) still explode.
+ o coupler (atm & ocn _compon_interf):
+   - avoid using Exch2 IO mapping if not suitable.
+ checkpoint65m (2015/06/15)
+ o pkg/layers:
+   - clean-up old parameters setting (from Sep 2012):
+     + remove old parameters setting from common block (declared locally);
+     + stop if any old parameter is mixed with new parameters;
+     + check for valid or consistent parameter setting (e.g., layers_name)
+   - check that layers_bounds for Pot.Density are in the right range;
+     this is supposed to catch un-updated setting after recently shifting
+     potential density field "prho" by -1000 (now in "sigma" scale).
+ o pkg/layers:
+   - Added missing call to layers_fill for keeping track of tottend in
+     pkg/diagnostics/diagnostics_fill_state.F
+ o pkg/layers:
+   - added CPP flux LAYERS_FINEGRID_DIAPYCNAL to disable fine-grid binning
+     of diapycnal fluxes
+ o pkg/layers:
+   - reverted changes to interpolation to previous treatment; there
+     was never actually a problem
+ o pkg/layers:
+   - fix interpolation of layers tracers in the presence of partial cells
+   - add lots of new functionality to compute water mass transformation
+     (enabled by CPP flag LAYERS_THERMODYNAMICS)
+   - add new calls from main code (diags_oceanic_surf_flux.F,
+     thermodynamics.F, impldiff.F) and gad to save the necessary fields
+     for layers_thermodynamics calculations
+ o pkg/ptracers:
+   - add capability of stepping a passive tracer forward without advection
+     by setting PTRACERS_advScheme to 0.
+ o pkg/diagnostics:
+   - add few (threads) _BARRIER around any update of "diag_pkgStatus".
+ o pkg/layers:
+   - shift potential density field "prho" by -1000 for density layer averaging so
+     that it corresponds to usual "sigma" definition (i.e., rho(p=const)-1000);
+     Note that density bin boundaries (layers_bounds in data.layers) have
+     to be set accordingly (i.e., shifted, in sigma scale).
+ o pkg/layers:
+   - fix snap-shot output of layer thickness @ V.pt and output of pot.density
+   - fix calculation of layer non-weighted velocity and layer probability
+   - add diagnostics for pot.density used for layer averaging
+ o pkg/seaice:
+   - seaice_calc_viscosity.F: change computation of deltaC**2 to ensure
+     positiveness, modify a few comments and improve variable names,
+   - the changed computation of deltaC affects most seaice-related
+     experiments at the truncation level.
+     seaice_itd.thermo is affected by far the most, with
+     only 7 digits of agreement remaining; update experiments.
+ checkpoint65l (2015/05/04)
+ o pkg/shelfice:
+   - in shelfice_thermodynamics.F, if SHELFICEBoundaryLayer=.true., then set
+     factor drKp1 to zero where it is negative (ie. do not use
+     SHELFICEBoundaryLayer if hFacC>1)
+   - the same for factor drLoc in shelfice_forcing.F
+ o tools/genmake2: move FEXTRAFLAGS from FFLAGS to FOPTIM to avoid a problem
+     with modules in ptracers, when using testreport option "-small_f"
+ o pkg/seaice/seaice_growth.F (in case of SEAICE_ITD)
+   - replace tmpscal1**1.36 by faster exp(1.36*log(tmpscal1))
+ o verification/testreport
+   - add new option -small_f
+     with this option testreport first makes the target small_f (*.f files)
+     before running make (all). This is useful for explicit inlining when
+     all sources need to be full available.
+ o pkg/exf/exf_interp.F:
+     remove previous changes related to reverse (decreasing) input grids latitude
+ checkpoint65k (2015/04/01)
+ o pkg/ecco:
+     fix missing cosphi initialization; use eccoiter in place of optimcycle;
+     if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
+     instead of active read/write
+ o pkg/ctrl:
+     if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
+     instead of active read/write.
+ o pkg/autodiff: make autodiff_readparms.F and autodiff_whtapeio_sync.F
+     return if .NOT.useAUTODIFF
+ o pkg/seaice: add CPP brackets (cost function related).
+ o model/src:
+     add useAUTODIFF run time switch.
+ o pkg/exf/exf_interp.F:
+     add code to allow input grids with latitude starting in the north (i.e. when
+     j=1 corresponds to northern edge of field); modify global_with_exf to test
+     this feature.
+ o verification/testreport:
+   - replace "grep -A3" with POSIX conformal sed command, because there are
+     implementations of grep that cannot do contextual searches
+   - replace "cat -n" by "nl" (two occurrences), because not all implementations
+     of "cat" have the option "-n"
+ o model/src:
+     add new file gsw_teos10.F that contains 3 functions, more or less a copy
+     of the gsw_toolbox.f90 of the TEOS-10 fortran interface, that are used to
+     convert from conservative to potential temperature. For now they are not
+     called anywhere.
+ o pkg/ggl90: make "useIDEMIX" useful
+   - re-organize code in s/r ggl90_calc a little to move computations that
+     are different for idemix into separate loops (changes verification
+     experiment idemix at truncation level, 12 digits remain -> updated)
+   - requires 2 new 2D fields KappaM, verticalShear
+   - make hFacI and recip_hFacI local 3D variables that are passed to
+     s/r ggl90_idemix
+   - fix and improve some comments
+ checkpoint65j (2015/02/25)
+ o pkg/openad
+   - synchronize seawater.F with version in model/src: replace routine
+     body of sw_temp by calling sw_ptmp and fix/add a few comments.
+ o pkg/mnc:
+   - change default value of pickup_read/write_mnc params to FALSE
+     (since few features are missing in reading MNC pickup files).
+ o model/src:
+   - change default (background) vertical diffusivity for salt to be the
+     temperature (background) vertical diffusivity.
+   - change background vertical diffusivity in vertical mixing pkgs ggl90,
+     kl10, my82 and pp81 from temperature diffusivity to salinity diffusivity.
+     This makes ptracers default diffusivity (that uses salt diffKr) more
+     consistent with vertical mixing schemes.
+ o verification/testreport:
+   - fix typo in "-pcls" option ;
+   - put temp files in /tmp (instead of in local dir)
+   - add option "-ncad" to use genmake2 new option "-nocat4ad"
+   - allow to use "-j" option (for multi-procs make) for AD, OAD and TLM.
+ o pkg/ggl90 (idemix code):
+   - apply few fixes ; add some missing "_d 0" ; update output of exp.
+     global_ocean.90x40x15.idemix
+ o OpenAD
+   - enable active file I/O and begin removal of work-around code
+     for OpenAD for handling control variables (memory vs. active files)
+   - new CPP options file OPENAD_OPTIONS.h
+   - revert to genarr2d gradient check for hs94.1x64x5
+   - (genarr3d tested by tutorial_global_oce_biogeo, tutorial_tracer_adjsens)
+   - gentim2d works for halfpipe_streamice but not yet hs94.1x64x5
+ o tools/genmake2:
+   - add option for an alternative Makefile (from Martin) where multiple
+     source files are sent to TAF (instead of all in one file).
+ o pkg/ggl90: add IDEMIX (Olbers and Eden, 2013)
+   - code provided by Carsten Eden as an extension of ggl90
+   - so far the code is turned on within ggl90 by setting a CPP-flag at
+     compile time; a runtime flag implementation is not yet complete
+   - tested in new verification experiment global_ocean.90x40x15.idemix
+ o verification:
+   - reduce length of the AD test run by half for experiments
+     global_ocean.cs32x15 (std + thsice) and isomip
+   - enable active file I/O for OpenAD, adjust verifications accordingly
+   - halfpipe_streamice: change gradient check from genarr2d to gentim2d
+ o verification/testreport:
+   - fix two non-POSIX sed statements so that there are no error messages
+     on Mac OS X
+   - replace hostname -s with hostname | sed 's/\..*$//'
+ o model/src/seawater.F:
+   - simplify SW_TEMP to just calling SW_PTMP with P and PR exchanged
+     (following the matlab code), which would have avoided the bug caught
+     by Matt (see below) in the first place
+ o pkg/shelfice:
+   - implement alternative discretisation of quadratic drag (selectBotDragQuadr)
+     and true distance in no-slip BC (bottomVisc_pCell) similar to bottom-drag.
+   - fix sign of friction tendency (no-slip BC) and fix u,v drag for thin
+     ice-shelf case (i.e., within surface level).
+   - add config summary in shelfice_check.F
+   - remove global variable recip_SHELFICElatentHeat and replace by a local
+     variable recip_latentHeat
+   - introduce diagnostics for friction velocity uStar (in case of
+     SHELFICEuseGammaFrict)
+   - change verification experiment isomip.htd:
+     + start from pickup (as input_ad at nIter0=8640)
+     + start from SHELFICEmassFile instead of SHELFICEloadAnomaly file
+     + test SHELFICEuseGammaFrict = .TRUE.
+     + test SHELFICEadvDiffHeatFlux = .TRUE.
+ o model/src:
+   - fix bug (Thanks to Matt) in function SW_TEMP (to convert Pot.Temp to
+     in-situ Temp) and in routine SW_TEMP (in pkg/openad);
+     update output of experiments global_with_exf.yearly and isomip (all 6).
+ o pkg/shelfice:
+   - change setting of kTopC to also be zero where there is no ice-shelf.
+   - zero out surface forcing arrays (for now, for T & S + EmPmR) where
+     ice-shelf is.
+   - first attempt to get RealFreshWaterFlux effects: for now, only without
+     SHELFICEboundaryLayer ; not consistent if using synchronous time-stepping.
+ o pkg/seaice: add the option to prescribe a fixed thickness PDF
+   for thermodynamic calculations
+   - because of divisions of the type 7/7 not exactly equal to 1, this change
+     affects results of some verification experiments by up to 4 digits:
+     global_ocean.cs32x15.seaice, lab_sea, lab_sea.fd, lab_sea.salt_plume,
+     seaice_obcs, seaice_obcs.seaiceSponge, seaice_obcs.tides
+     adjoint: lab_sea, lab_sea.noseaicedyn
+     -> updated
+ checkpoint65i (2015/01/23)
+ o model/src:
+   - change units of frictionHeating field from W to W/m^2
+   - fix bug in frictional heating from stratospheric drag in
+     S/R ATM_PHYS_TENDENCY_APPLY_V
+   - with synchronous time-stepping: move resetting to zero of frictionHeating
+     field from load_fields_driver.F to thermodynamics.F ;
+   - add diagnostics for frictional heating.
+ o model/src & gmredi K3D:
+   - add frictionHeating field to pickup-files (for synchronous time-stepping)
+   - move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h
+   - rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name
+     and name in pickup file).
+   - fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F
+ o model/src:
+   - move (from ini_forcing.F) initialisation of all arrays in header file
+     FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart
+     (since Nov 2012) with option selectAddFluid=1.
+ o pkg/shelfice:
+   - change units (+ document) of newly added field "shelfIceMassDynTendency"
+   - upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays.
+ o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers
+ o pkg/seaice: two new runtime parameters:
+   - SEAICE_cStar replaces the hard wired "20" in the strength formulation,
+     long overdue
+   - SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012)
+     parameterization of tensil stress for fast ice (does not do anything yet)
+ o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method
+     for LSR: move checking overlaps out of JFNK-if-block
+ o pkg/atm_phys:
+   - move copy of grid and dynamical fields out of atm_phys_driver.F into
+     new S/R ATM_PHYS_DYN2PHYS.
+   - fix level height for Linear Free-Surf case (to be consistent with
+     fixed-in-time pressure levels).
+ o pkg/mom_common (bottomdrag):
+   - average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center
+     to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG;
+     update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag.
+ o pkg/shelfice (u/v_drag):
+   - add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG;
+   - use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F
+     (now similar to shelfice_u_drag.F)
+   - remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG
+     from mom_vecinv.F (similar to mom_fluxform calls).
+ o pkg/mom_common (bottomdrag):
+   - add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG;
+   - add options for alternative discretisation of velocity norm in quadratic
+     bottom drag: averaging of grid-cell-center KE to U.point and V.point
+     (selectBotDragQuadr=0, original code) can produce noisy patterns; this
+     improves when averaging only the other component (e.g. vVel for U bottom
+     drag) using wet-point method (selectBotDragQuadr=2) or not (=1).
+   - add options (bottomVisc_pCell) to account for partial-cell in bottom
+     friction (no-slip BC) thus getting the true distance from the bottom;
+     off by default since this also reduces model stability (explicit bottom
+     friction). Changes produce different machine truncation with linear-drag
+     + no-slip BC: update output of experiments exp4.stevens (10 digits) and
+     front_relax (bvp & mxl, 10 & 11 digits).
+ o model/src & mom pkgs:
+   - add one more level to vertical viscosity local arrays (Nr+1, previously Nr)
+     since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k
+   - for now and until vertical mixing scheme are updated to fill up level Nr+1,
+     just copy level Nr value to level Nr+1.
+ o doc:
+   - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
+ o pkg/shelfice:
+   - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
+     SHELFICE.h: move array shelficemass to init_varia, initialise
+     from array shelficemassinit, which is set in init_fixed and
+     has option to be set from file; introduce array
+     shelficeMassDynTend array, set thru file in init_fixed
+   - NEW FILE: shelfice_step_icemass.F: update shelficemass from either
+     shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in
+     pkg/streamice
+   - shelfice_thermodynamics.F: call shelfice_step_icemass if
+     SHELFICEMassStepping = .true.
+   - shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f
+ checkpoint65h (2014/12/17)
+ o verification/global_ocean.90x40x15, global_ocean_ebm:
+   - update to generic controls.
+ o pkg/ctrl:
+   - ctrl_map_ini_genarr.F: test for igen>0
+   - ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D.
+   - move gentim2d part of ctrl_map_ini_genarr.F to
+     new separate routine : ctrl_map_ini_gentim2d.F
+   - ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F:
+     add time variable weights and cyclic controls (time mean,
+     seasonal cycle, etc) capabilities to gentim2d
+ o pkg/ecco:
+   - move reading of error, conversion to weights from
+     ecco_cost_init_fixed.F to ecco_toolbox.F (ecco_readwei)
+ o global_oce_llc90, cs32:
+   - activte sbo.
+   - CTRL_SIZE.h : add maxCtrlProc.
+   - activate the new genctrl capabilities.
+   - update following reorganization of global_oce_input_fields.tar.gz
+ o pkg/ctrl/ctrl_ad_diff.list:
+   - add missing ctrl_init_rec.f
+ o tools/OAD_support/keepOriginal:
+   - add ctrl_init_rec.F
+ o model/src/the_main_loop.F, pkg/ctrl/ctrl_map_ini_genarr.F:
+   - avoid recomputations of xx_gentim2d_dummy.
+ o momentum diagnostics:
+   - move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and
+     mom_vecinv.F to timestep.F (to include Smag-3D contribution).
+ o pkg/seaice/seaice_lsr.F:
+   - fix computation of BU/BV, make sure they are non-zero, only necessary
+     for cubed sphere exchanges and SEAICE_OLx/y>0.
+     This makes calling s/r fill_cs_corner_rl obsolete (removed).
+ o verification/global_ocean.cs32x15/input.seaice
+   - add test for strong implicit coupling and restricted addtive Schwarz
+     methods for LSR
+   - update results/output.seaice.txt
+ o verification/tutorial_global_oce_biogeo:
+   - AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up)
+     and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK);
+     update output_adm,_oadm,_tlm.txt
+ o pkg/dic:
+   - change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h
+   - add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn
+     for tracer 1 & 2 is set (to avoid double counting of dilution effect).
+ o verification/tutorial_global_oce_biogeo:
+   - AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since
+     dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ;
+     update output_adm,_oadm,_tlm.txt
+ o eesupp/src:
+   - add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F)
+     and call it in seaice_lsr when using nonzero SEAICE_OLx/y
+ o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing
+   LSR (following Hutchings et al. 2004)
+   - introduce zetaZ as a global variable (requires adjustments in
+     seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ
+     in seaice_calc_viscosities.F
+   - new flag SEAICEuseStrImpCpl (default off)
+   - add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the
+     momentum equations
+   - JFNK-solver (preconditioner) adjusted to allow using this method
+     (where it does not have any positive effect)
+ o pkg/seaice
+   - add overlap for restrictive additive Schwartz method also to LSR, but
+     turn it off by default (because it only seems to work for non-cubed
+     sphere/llc topologies)
+ o pkg/autodiff
+   - add extra exchanges in addummy_in_steppging also for mnc output
+ o pkg/seaice:
+   - add extra exchanges before dumping adjoint fields in seaice_ad_dump.F
+     to avoid stripes in the adjoint output (similar to addummy_in_stepping.F)
+ o pkg/obcs:
+   - add option to specify domain-connected piece Id along OB though files
+     (for now, only used to diagnose PhiVel; default =1 -> global correction)
+   - modify obcs_diag_balance.F to process each connected-part separately;
+     exclude OB where Id = 0 but keep the full divergence there (-> constant
+     Psi along this portion of OB and all inflow derived from grad(Phi))
+   - add example of OB-conect files in verification/so_box_biogeo/input.
+ o pkg/diagnostics:
+   - improve treatment of Open-Boundaries in Velocity-Potential calculation:
+   a) use non zero matrix element across OB and solve for Phi 1 grid point
+      outside OB (i.e, where tracer OBCS are applied).
+   b) global imbalance of inFlow/outFlow across OB: instead of modifying
+      velocity across OB, spread it uniformly along the OB in the RHS.
+ checkpoint65g (2014/11/19)
+ o pkg/diagnostcis:
+   - add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param
+ o pkg/my82,pp81,kl10:
+   - fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D
+     field diffKr as background diffusivity to set minimum diffusivity value.
+ o pkg/seaice:
+   - add new parameter SEAICEuseEVPrev (for revisited EVP by
+     Bouillon et al 2013)
+   - add SEAICE_evpAlpha/Beta to namelist
+   - modify seaice_evp code to able to use SEAICEuseEVPrev. These changes
+     involve trivial re-ordering of divisions/multiplications that should not
+     have any effects, but ... they do change the results of lab_sea.hb87 so
+     that only 2 digits of agreement remain, in line with the general
+     instability/fragility of the evp-code. For now, I do not care and just
+     update the verification experiment
+ o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc)
+   - remove xx_genarr2d_numsmooth etc
+   - use xx_genarr2d_preproc etc instead
+   - carry out smooth_correl2D at initialization stage rather than during
+     time stepping.
+   - get smoothOpNb from xx_gentim2d_preproc
+ o global_oce_cs32 :
+   - add test of generic ecco capabilities.
+ o pkg/exf/exf_getsurfacefluxes.F :
+   - add to tmpUE/tmpVN rather than re-initializing them (conventional behavior).
+ o pkg/ctrl,ecco :
+   - omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED
+     is defined.
+ o pkg/seaice: add diagnostics for Delta (deformation parameter)
+ o model/src:
+   - when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical
+     diffusivity (background) is specified but ignored.
+ o verification:
+   - in testreport, convert hostname to lower case for default output dir name
+ o model, pkg : add useCTRL, useECCO parameters (on/off run time switch).
+ o pkg/dic: add modifications from Hajoon:
+   - add iron sedimentation flux function of the flux of PO4 out of bottom layer
+   - light attenuation: add self-shading effect by climatological Chlorophyll
+     (read from file).
+ o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also
+     compiles when SEAICE_ALLOW_DYNAMICS is undefined
+ o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate
+     AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than
+     ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted,
+     approach where CPP_OPTIONS.h includes an omnipotent
+     ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h').
+ o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where
+     ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong.
+ o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF
+     to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included
+     (it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...)
+ o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl :
+   add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed
+   - ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h
+   - AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h
+   - CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc
+ o pkg/ctrl,ecco,exf :
+   - remove variables associated with NON-generic costs,
+     unless ECCO_CTRL_DEPRECATED is defined.
+   - remove NON-generic NON-obcs controls,
+     unless ECCO_CTRL_DEPRECATED is defined.
+ o pkg/ctrl : added ctrl_local_params.h
+ o pkg/ecco : added ecco_local_params.h
+ o verification : added ECCO_CTRL_DEPRECATED to most as and oad
+     experiments, which will progressively be removed once the
+     experiments are revised to use only generic controls/costs.
+ checkpoint65f (2014/10/13)
+ o pkg/ctrl, ecco, seaice : minor changes in headers
+ o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic
+     cost function and control capabilities added since checkpoint65c.
+ o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h.
+ o pkg/ecco: increase modularity and improve logic
+   - ecco_toolbox.F (new) : basic operations that are often used,
+     including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk,
+     ecco_addcost, ecco_add, ecco_div, ecco_readbar.
+   - cost_gencal.F (new) : determine filnames and records.
+   - cost_genread.F, cost_generic.F : condense code using ecco_toolbox.
+   - cost_generic.F : use spzeroloc rather than hard-coded -9999,
+     and exploit the above functions leading to more compact code.
+   - cost_genread.F : rm un-necessary arguments, re-arrange args order.
+   - ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj,
+     using_ers, using_gfo, using_mdt is now only defined within gencost)
+ o pkg/ecco: extend generic cost capabilities
+   - pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost
+     capabilities via gencost_preproc (+ _c,_i,_r related params),
+     gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod,
+     gencost_outputlevel arguments to cost_generic
+   - pkg/ecco/cost_genread.F (new) : interface between cost_generic
+     and active_read, making room for gencost_preproc to take effect.
+     Added preproc code ('climmon') to replace GENERIC_BAR_MONTH.
+   - pkg/ecco/cost_generic.F :
+     compute and store misfit maks*(model-data) in localdif that is
+     then used in cost and for output, output misfit if outlev.GT.0
+   - pkg/ecco/cost_averagesfields.F : depend on gencost_barskip
+     rather gencost_barfile for deciding whether to write barfile
+   - pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd
+   - pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from
+     ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip
+   - pkg/ecco/ecco_summary.F : report gencost variables
+   - pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs
+ o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA
+ o pkg/ecco: internal re-organization
+   - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl
+     (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,
+     mv relevant variables definition from ecco_cost.h to ecco.h,
+     make sure gencost routines only include ecco.h)
+   - throughout : add missing CCP switches, rm unused variables,
+     and rm un-necessary CPP switches
+   - throughout gencost routines : replace modelstartdate with
+     gencost_startdate when needed
+   - cost_bp_read.F : use arguments, instead of common blocs
+     so that it can be used also by (new) cost_gencost_bpv4.F
+   - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0
+   - ecco_phys.F : compute etanFull
+   - ecco_readparms.F : rename using_topex as using_tpj, add
+     bpv4-grace to gencost list, initialize added parameters
+   - ecco_summary.F : include SIZE.h needed for augmented ecco.h
+ checkpoint65e (2014/09/28)
+ o pkg/obcs:
+   - replaced the just-added CPP options with run-time variables
+     (see pkg/obcs/OBCS_PARAMS.h for details)
+ o pkg/obcs:
+   - add additional CPP options for sponge boundary layers
+     (see pkg/obcs/OBCS_OPTIONS.h for details)
+ o pkg/atm_phys:
+   - implement simple (obliquity only, assuming circular planet orbit)
+     seasonal cycle for incoming insolation ; used when run-time parameter
+     "select_incSW" is set to 1 ; by default (=0), uses old unchanged formula.
+ o pkg/exf, pkg/ecco, pkg/ctrl:
+   - add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets
+   - activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip
+   - implement gentim2d for xx_tauu, xx_tauv
+ o pkg/ctrl, pkg/ecco :
+   - fix and complement the generic controls implementation
+ o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F,
+     pkg/shelfice/shelfice_thermodynamics.F,
+     verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F,
+     verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F :
+   - add weight in CTRL_GET_GEN calls
+ o pkg/ctrl :
+   - ctrl_get_gen.F : add weight as input parameter, and apply
+     it directly rather than using smooth_correl2Dw (to be retired).
+   - ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call
+ o pkg/ctrl :
+   - introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F,
+     ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F)
+   - re-activate ctrl_summary (call in ctrl_init.F)
+ o pkg/ctrl/ctrl_cost_gen.F :
+   - fix CCP brackets, remove un-necessary myiter, mytime
+ o pkg/ecco, pkg/ctrl :
+   - remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F)
+   - remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F)
+   - add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F)
+   - add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F)
+ checkpoint65d (2014/09/15)
+ o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F :
+   - add xx_genarr2d_bounds,xx_genarr3d_bounds,
+     xx_genarr2d_numsmooth, xx_genarr3d_numsmooth
+ o pkg/ctrl/ctrl_map_ini_genarr.F :
+   - remove compilation failure
+   - replace hard coded example
+   - use ctrl_map_ini_gen2D, 3D
+ o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F :
+   - on/off switch based upon xx_genarr2d_weight,3d
+ o src/packages_init_variables.F :
+   - regroup pkg/estimation calls
+   - remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO
+     (moved to ctrl_init_variables)
+ o cost/cost_init_varia.F :
+   - remove ecco_cost_init_varia
+     (moved to ecco_init_varia)
+ o ctrl/ctrl_init_variables.F :
+   - add CTRL_MAP_INI, CTRL_MAP_INI_ECCO
+   - add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI
+ o ctrl/ctrl_map_ini.F :
+   - remove ctrl_map_ini_genarr, seaice_ctrl_map_ini
+     (moved to ctrl_init_variables)
+ o ctrl/ctrl_map_ini_ecco.F :
+   - remove ECCO_PHYS (mv to ecco_init_varia)
+   - remove seaice_ctrl_map_ini (mv to ctrl_init_variables)
+ o ecco/ecco_ad_diff.list :
+   - add ecco_init_varia.f
+ o ecco/ecco_init_varia.F
+   - new routine
+ o pkg/streamice:
+   - move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F
+     to streamice_init_fixed.F ; fix setting of STREAMICEisOn.
+   - from model/src, only call pkg/streamice routines if useStreamIce is TRUE.
+ o pkg/generic_advdiff:
+   - fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014.
+ o pkg/exf:
+   - exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown,
+      xxg_precip capability
+   - exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch
+ o pkg/ctrl:
+   - ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d
+ o model/src/load_fields_driver.F :
+   - move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING
+     so xx_gentim2d can be applied to e.g. exf fields in a timely manner.
+ o OpenAD verification experiments:
+   - Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h
+     in src files (to enable to skip the ECCO_CPPOPTIONS.h);
+     for now, only in pkgs used in OpenAD verification experiments.
+   - Change all except one (halfpipe_streamice) OpenAD experiments to use pkg
+     specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h)
+     instead of using ECCO_CPPOPTIONS.h (with all relevant options in it).
+     This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests.
+ o OpenAD verification tests:
+   - finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD);
+   - finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for
+     tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp.
+   - leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/)
+     and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC).
+ o model/src & generic_advdiff:
+   - change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S
+     forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model
+     dynamics requires valid tracer forcing only over tile interior but, for
+     some diagnostics, may need to extend it over 1 point in tile halo region.
+   - in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid
+     tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max
+     setting in temp/salt/ptracer_integrate.F
+ o pkg/dic:
+   - multiply tracer tendencies by maskInC (if ussing OBCS) before updating
+     gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER
+     in gchem_forcing_sep.F
+ o pkg/autodiff & obcs:
+   - add storage of current OB values for U & V (was already done for T & S).
+ checkpoint65c (2014/08/30)
+ o pkg/dic:
+   - take out of dic_atmos.F the initialisation part (corresponding to istate=0)
+     and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for
+     AD compilers (but still a Pb with multi-threading and Ajoint dependencies).
+ o verification:
+   - new experiment testing OBCS and DIC pkgs, using params & output from
+     tutorial_global_oce_biogeo but limited to a sub-domain around Drake
+     passage: take OBCS from the last year of a 2 yrs simulation and initial
+     conditions from t=1.yr while keeping the same forcing.
+ o model/src:
+   - when allowFreezing=T, only reset below freezing initial Temp to Tfreezing
+     (at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T).
+ o pkg/diagnostics (Stats-Diags):
+   - re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to:
+     a) refine region where stats are computed, excluding where arrhFac=0 ;
+     b) fix missing interior mask (use with OBCS) in 3-D fields statistics;
+     c) extend regional stats over the region edges (for U or V pt location).
+ o pkg/gchem:
+   - add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since
+     pkg/dic is currently changing/updating ptracers values beyond the OB).
+ o verification (hs94):
+   - convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords
+     bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments
+     hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of
+     apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged.
+ o pkg/ptracers:
+   - implement Adams-Bashforth on pTracers (instead of on tracer tendency),
+     switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs)
+   - change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer
+     with AB-2 code (so that it get tested).
+ o model/src:
+   - allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS)
+     with AB-2 code (previously only available with AB-3 code).
+     Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F
+     to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done
+     there, by calling CYCLE_AB_TRACER).
+ o pkg/generic_advdiff:
+   - change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS,
+     GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R
+     + also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in
+     S/R temp/salt/ptracers_integrate.F
+ o model/src & pkg/ptracers:
+   - remove common block variables gT,gS (in DYNVARS.h), except when
+      USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly.
+   - remove common block variable gPtr.
+ o model/src & pkgs:
+   - change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R
+      ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G,
+      IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT,
+      GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T
+   + change accordingly all calling S/R.
+   - use local temperature/salinity/ptracer tendency array (without bi,bj)
+     in S/R temp/salt/ptracers_integrate.F
+ o pkg/seaice:
+   - move computation of stress contributions to rhsU/V in s/r seaice_lsr
+     to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code
+   - make u/vIceC local variables if SEAICE_CGRID is defined only to be used
+     in seaice_lsr
+   - seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D
+     in s/r seaice_lsr_calc_coeffs
+ o pkg/mdsio:
+   - in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long
+     (e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is
+     too long (e.g., > MAX_LEN_FNAM/2 )
+ checkpoint65b (2014/08/12)
+ o pkg/matrix:
+   - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP
+ o model/src:
+   - fix initialisation of geothermalFile; compile geothermal-flux code in
+     natl_box verification experiment.
+ o model/src & pkg/down_slope:
+   - push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop).
+   - in dwnslp_apply.F, update tracer tendency instead of the future tracer
+     field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects
+     results at machine truncation level: update output of experiments
+     global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD).
+ o pkg/diagnostics (Stats-Diags):
+   - do not cumulate the full volume when DIAGNOSTICS_FILL is
+     called with bibjFlg < 0 (no increment of the counter for 2D/3D diag);
+     This fix the mean statistics when DIAGNOSTICS_FILL is called multiple
+     times (but Min,Max and StD are still wrong).
+ o model/src:
+   - add geothermal flux forcing: read in ini_forcing.F as time-constant
+     field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F)
+ o model/src:
+   - move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer
+     _integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac
+     arrays are already updated while adjustments (filters, conv.adjustment) are
+     still applied later, in S/R TRACERS_CORRECTION_STEP.
+ o model/src:
+   - store in common bloc array "rhoInSitu" the virtual potential temperature
+     anomaly that is used to compute geopotential: this make the atmos code
+     more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F
+ o pkg/seaice/seaice_lsr.F
+   - rename integer variable ilcall to ipass (that's what it is called
+     in the residual diagnostics
+   - change time stepping for NPSEUDOTIMESTEP > 2 (does not change the
+     default) for improved non-linear convergence of the first few steps
+   - adjust a few comments and add new ones to explain some of the store
+     directives
+ o pkg/generic_advdiff (& ptracers):
+   - re-work the code to check for valid advection scheme and for minimum
+     size of overlap (now stored in local common bloc in gad_advscheme.F)
+ o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics
+   - re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1
+   - add an auxilliary variable "bet" and fix store directives and keys in
+     seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or
+     less exact gradients in my tests); but there are still
+     recomputation warning (although gradients are sort of OK), when
+     SEAICE_LSR_VECTORIZE is not defined, so this flag and
+     SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency.
+   - update verification experiments lab_sea.
+   - change some comments in S/R seaice_calc_viscosities
+ o model/src:
+   - if staggerTimeStep=T, always apply exchange to velocity field in
+     do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F
+     (independent of using multi-dim advection or not); no effect on FWD run
+     but affects AD results (at machine truncation level): update output of
+     experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d)
+     and isomip (oad: 12.d).
+ o pkg/generic_advdiff:
+   - stop if doAB_onGtGs is set to FALSE but ignored
+   - refine warning related to stability of tracer time-stepping
+     regarding internal wave dynamics.
+   - setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition
+     on staggerTimeStep & implicitIntGravWave (will now get a warning
+     if potentially unstable).
+ o pkg/kl10:
+   - add new pkg "kl10" for mixing due to internal wave breaking, from
+     http://www.sciencedirect.com/science/article/pii/S1463500310000144
+     (contribution from Jody Klymak), tested in verification experiment
+     verification/internal_wave/input.kl10/
+ o isomip experiment:
+   - test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up
+     (input.htd) and update the output.
+ o cd_code experiments:
+   - use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM &
+     #undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd)
+     global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and
+     update the corresponding output.
+ o pkg/seaice:
+   - reduce the number of include files and store directives in
+     S/R seaice_lsr_tridiagu/v
+   - change the order of loops in one case in S/R seaice_lsr_tridiagv
+     (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to
+     get rid off one store directive (a TAF bug?)
+   - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in
+     S/R seaice_lsr_tridiagv to change the loop range for consistency
+   - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v
+   - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in
+     S/R seaice_lsr_tridiagu/v (requires update of
+     offline_exf_seaice/input.dyn_jfnk)
+ checkpoint65a (2014/07/27)
+ o model/src:
+   - Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than
+     surrounding hFacC=1 @ edge of a step with different kSurfC on either side
+     (topo in p-coords, ice-shelf in z-coords); update output of experiments
+     tutorial_global_oce_in_p and isomip (both AD and OpenAD output).
+ o model/src:
+   - collect momentum forcing tendency into local 2-D array (passed as argument
+     to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE
+     parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default);
+     affects results at machine truncation level (e.g., if using OBCS_SPONGE).
+   - collect T & S forcing tendency into local 2-D array (passed as argument to
+     apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.
+     affects results at machine truncation level (e.g., ocean: if using
+     SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist
+     correction due to vertical advection).
+   - update output of experiments: fizhi-cs-32x32x40 (13 digits),
+     global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
+     seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),
+     obcs_ctrl (ad & fwd grd @ 12 & 7).
+ o pkg/ptracers & diagnostics:
+   - use ptracers (short) name (instead of long one) to make ptracers diagnostics
+     title (to avoid some unexpected truncation); sort out ptracers diags units.
+   - collect ptracer forcing tendency into local 2-D array (passed as argument
+     to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency.
+ checkpoint65 (2014/07/18)
+ o pkg/fizhi:
+   - add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this
+     affects results at machine truncation level. Update output of experiments
+     fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits).
+ o pkg/seaice: more clean up
+   - rename TAF common block tapes to be more consistent and remove
+     unnecessary duplicates
+   - add store directives to remove more recomputations, but use smaller
+     tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined.
+     The idea behind this flag is to reduce the memory footprint when the
+     adjoint of the LSR is not required. As of now, defining the flag
+     SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by
+     a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h).
+     For experiment offline_exf_seaice, this means on a linux box with gfortran
+     nearly a factor of 10 (but keep in mind there is mostly seaice code in
+     this experiment):
+     > size mitgcmuv_ad
+     text    data        bss     dec        hex
+     5100659 1216  220458952  225560827  d71c8fb
+     5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
+     but only a moderate increase of 36% for global_ocean.cs32x15:
+     text    data        bss     dec        hex
+     6695027 1648 1014578664 1021275339 3cdf6ccb
+     6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER)
+   - note: there are still recomputations in global_ocean.cs32x15 and
+     offline_exf_seaice and the gradient agreement changes (gets a
+     little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt)
+   - in general, the AD gradients still are wrong
+ o OpenAD
+   - clean up code_oad/ directories somewhat by moving files
+     dontCompile, dontTransform, keepOriginal to OAD_support/
+ o model/src:
+   - using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F
+     (not currently tested): add dissipation terms before NLFS rescaling of
+     tendencies (previously done after).
+ o pkg/diagnostics:
+   - write stats-diags in ascii file with more digits (same as in monitor).
+ o pkg/down_slope:
+   - drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with
+     NLFS (not tested), use new recip_hFac value in order to conserve tracer.
+ o model/src:
+   - new file "apply_forcing.F" containing all the code previously in
+     external_forcing.F, but with new argument list: pass, as new argument,
+     the current level tendency array to update (instead of a direct update
+     of the common bloc array). Change the corresponding calls.
+   - add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use
+     EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility).
+ o pkg/seaice/seaice_lsr, a little bit of clean up
+   - rearrange some code blocks, so that now all calculations for
+     setting up the right-hand-sides done within one single block
+     (I find that easier to read and understand)
+   - rearrange freedrift-code to reduce the number of ifdefs
+   - adjust some indentations and comments
+ checkpoint64z (2014/07/10)
+ o model/src and several pkgs:
+   - change argument list of all S/R called from external_forcing.F and
+     called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F)
+     to pass, as argument, the current level tendency array to update
+     (instead of a direct update of the common bloc array).
+   - change also (in the same way) argument list of PTRACERS_APPLY_FORCING;
+   - rename taueddy_external_forcing.f to taueddy_tendency_apply.F
+ o pkg/seaice/seaice_lsr.F
+   - always initialize local arrays in seaice_lsr_tridiagu/v
+   - add more local tapes to seaice_lsr_tridiagu/v
+   - move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but
+     keep it in bi/bj loop; this seems to be essential
+   - gradients are still wrong but only by 4-7 orders of magnitude
+     instead of 15 orders of magnitude, lab_sea improves a little
+ o pkg/seaice
+   - (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that
+     generates unnecessary code in seaice_lsr_ad
+   - add more store directives in seaice_lsr to avoid unnecessary code
+     in seaice_lsr_ad
+   - exclude some residual computations in seaice_lsr when
+     ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code
+     in seaice_lsr_ad
+   - add more storing, a new tape (model/src/the_main_loop.F) and
+     another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey
+     and klockey should be checked by a specialist)
+   - modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER )
+     and update lab_sea after previous changes in pkg/seaice below
+ o pkg/autodiff:
+   - introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and
+     viscFacInAd : run time parameters allowing for adjoint switches
+     note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F
+ o pkg/ecco:
+   - introduce cost_gencost_boxmean.F that computes a box mean
+     temperature (for use in adjoint sensitivity studies).
+ o model/src/set_defaults.F : initialize viscFacAdj to 1.
+ o pkg/mom_common/mom_calc_visc.F:
+   - ifdef ALLOW_AUTODIFF then include viscFacAdj factor.
+ o pkg/seaice/seaice_summary.F:
+   - statement for SEAICEadjMODE now in autodiff_readparms.F
+ o pkg/seaice:
+   - remove some store directives and add new ones in an effort to get
+     finally rid off the recomputation warnings. This is successful
+     when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are
+     defined (i.e. no extensive recomputation warnings left), but there
+     are still too many recomputations on the solver iteration level
+   - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h
+   - move definition of MPSEUDOTIMESTEPS into TAMC-block in
+     SEAICE_SIZE.h
+   - add a store directive in S/R seaice_calc_viscosities
+ o pkg/seaice (ITD code):
+   - fix definition of Hlimit for multi-threaded case
+   - use double precision arithmetic to compute Hlimit: this affects results;
+     update output of experiment seaice_itd.
+ o replace content of verification/seaice_itd
+   - instead of a 1D column use the configuration of offline_exf_seaice
+     to test the ice thickness distribution code with ridging
+   - this is a first shot at this experiment
+   - change of some defaults of ridging parameters SEAICEhStar (from
+to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F
+     and lot of new comments.
+ checkpoint64y (2014/06/20)
+ o pkg/seaice/seaice_reg_ridge.F:
+   - modify the regularization of very small volumes of ice; only check
+     total volume HEFF, and do not apply correction to individual ice
+     classes because that leads to funny patterns in the heat and fw-fluxes
+     into the ocean. Adjust seaice_itd/results/output.txt
+   - replace nITD by SEAICE_multDim in loop-ranges
+ o pkg/exf:
+   - add code to process the case field period = -12. with UV interpolation.
+   - move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec
+     into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F)
+ o verification/global_with_exf:
+   - switch all fields period to -12. (was previously untested) in input/data.exf
+     (but keep secondary test ".yearly" unchanged); update the reference output.
+ o pkg/cal:
+   - new calendar type "noLeapYear" for 365 days calendar without any leap year.
+ o pkg/exf:
+   - new integer parameter "exf_debugLev" (default set to main model debugLevel)
+     to replace logical switch "exf_verbose"
+   - report in STDOUT when loading a new record (if exf_debugLev >= 3)
+ o pkg/sbo:
+   - update from Katherine Quinn: evaluate mass directly from density and SSH
+     (budget using Finite Volume method) instead of from bottom pressure.
+   - allow testreport to collect few selected SBO output ; tested in exp.
+     global_ocean.90x40x15 (after updating the results, to include SBO output).
+   - fix some multi-threading issues (in output part).
+ o model/src & most packages:
+   - always call {PKG}_READPARMS even if corresponding use{PKG}=F;
+   - in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R
+     PACKAGES_UNUSED_MSG to print a weak warning when parameter file
+     "data.{pkg}" exist ; and leave the S/R (return) just after.
+   - more standard LAND pkg interface (land_init_fixed.F, land_check.F).
+     + call LAND_READPARMS from packages_readparms.F
+ o pkg/seaice:
+   - remove code that resets useThSice in S/R seaice_readparms and
+     replace it by a warning in S/R seaice_check
+   - remove parameter MULTDIM, replace with nITD and runtime
+     parameter SEAICE_multDim (still hard-wired to nITD if
+     SEAICE_ITD is defined)
+ checkpoint64x (2014/05/24)
+ o verification/lab_sea:
+   - update adjoint and TLM output following changes to pkg/salt_plume
+   - un-do the update after putting back local recip_Cp in few places.
+ o pkg/salt_plume: modifications by An Nguyen:
+   - add capability to do brine rejection (salt-plume) as function of
+     volume+tracers (instead of only salinity tracer).
+   - conserve volume by exchanging volume from each kLev to above to
+     accommodate in-coming brine volume
+   - store surface and klev exchanged fraction + volume in 4 new 3-d arrays
+   - switch KPP surf buoyancy due to brine forcing to 3-d
+     (3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume)
+   - add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t
+   - unrelatedly, also add ad-hoc capability to vary salt_plume scheme
+     in East/West Arctic.
+ o pkg/sbo:
+   - incorporate modifications from Katherine Quinn to enable the use of sbo
+     pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like
+     output for future testreport verification (unfinished).
+ o pkg/atm_phys:
+   - change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R:
+     skip the reseting of t_ref & q_ref to initial t & q ; this preserve the
+     output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics.
+ o pkg/seaice
+   seaice_calc_ice_strength.F: modify expression to avoid divisions
+     (affects truncation)
+   seaice_do_ridging.F: clean up the insectarium
+   - fix a bug that was compensated by areaScaling (-> remove areaScaling code)
+   - added SEAICEsnowFracRidge to redistributed snow (2nd bug)
+   - set closing/openingRate to zero where no extra iteration is need (3rd bug)
+   - add some debugging information and error messages (warnings)
+ o model/src: modifications relatd to atmosphere p*:
+   - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)
+   - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead
+     of vertical profile tRef in geopotential background and anomaly.
+   - Acount for true p* correction in theta <-> T conversion in pkg/aim_v23
+     and pkg/atm_phys.
+   - Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40,
+     fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn.
+ o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt
+ o pkg/ptracers: compute ptracer source/sink due to linear free surface.
+     not used right now, but can be used in BGC packages to fix conservation.
+ o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by
+     other packages too.
+ o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by
+     SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix)
+ o model/src:
+   - since we have several heat capacity (even in model/src), define "recip_Cp"
+     as local variable (no longer in common block) to avoid any confusion.
+   - add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords).
+ o pkg/exf:
+   - from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local
+     air density as function of air Temp, Humidity and atm pressure.
+ checkpoint64w (2014/05/02)
+ o verification:
+   - update output_adm.txt files for experiment global_ocean.cs32x15 (seaice &
+     seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing
+     code from seaice_growth.F & seaice_advdiff.F to new ridging routines
+     seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient
+     (down to 8-7 matching digits for global_ocean and 5-6 for lab_sea).
+ o model/src: for atmosphere in p* coords:
+   - store factor rStarFacC**atm_kappa (= pStarFacK) in common block
+   - implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F),
+     but not yet activated.
+ o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation:
+   - move computation of opnWtrFrac = 1-AREA to before computing ice strength
+   - this changes the results (but not for any verification experiment, because
+     none tests this), but avoids having an extra field in the restart files
+ o pkg/seaice: remove global variable TICE (not needed)
+   - replace by TICES or local variable where necessary (cost_seaice_test,
+     seaice_diagnostics_state)
+   - move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup
+   - use specific read/write routines for reading and writing individual leves
+     of a multilevel field
+ o pkg/ctrl & model/inc:
+   - move additional anomaly fields of control vars (related to options:
+      ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL)
+     from DYNVARS.h into new header file: CTRL_FIELDS.h
+ o pkg/seaice: some small modifications to the ridging code
+   - make fw2ObyRidge a global variable and add the freshwater flux to
+     seaice_growth
+   - pass actual thickness from seaice_prepare_ridging, so that it is
+     computed only in one place and compute it in the same way as in
+     seaice_growth
+   - initialise more fields in seaice_do_ridging that where cause floating
+     point exceptions over land
+ o pkg/seaice: preparations for ridging code and first real ridging code
+   - move most of "PART 1" of S/R seaice_growth into a new and separate
+     S/R seaice_reg_ridge that will both regularize the state variable after
+     advection call the actual ridging routine;
+   - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,
+     d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;
+   - remove ridging code from seaice_advdiff
+   - clean up remaining part 1 of seaice_growth in an attempt to make it
+     more readable (this is probably subjective)
+   - call seaice_itd_redist once in the initialisation phase to have the initial
+     conditions in the correct category
+   - 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

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