Contents of /MITgcm/doc/tag-index

$Header: /u/gcmpack/MITgcm/doc/tag-index,v 1.2321 2017/04/05 03:49:11 jmc Exp $
$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:
    1) 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;
    2) make call to EXF_RADIATION and to EXF_WIND independent of CPP option
       ALLOW_BULKFORMULAE which now only applies to S/R EXF_BULKFORMULAE ;
    3) 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
    5 additionals 2D fields and 6 new store directives
  - change logic in seaice_readparms.F: EVP code can now be turned on in
    various ways, setting SEAICE_deltaTev is no longer required,
    alternatively set SEAICE_evpAlpha/Beta, SEAICEuseEVPstar, SEAICEuseEVPrev,
    or SEAICEaEVPcoeff
o pkg/shelfice/shelfice_thermodynamics.F
  - redefining uLoc/vLoc to u/v, instead of 2u/v
o pkg/seaice/seaice_evp.F: introduce "adaptive EVP" by Madlen Kimmritz
  - this is an intermediate state of a truely converging EVP that has
    the potential of outperforming implicit VP methods, I do not recommend
    using it yet.
  - for now, "adaptive EVP" is turned on by setting SEAICE_EVP_USE_ADAPTATION
    and all parameters are hardwired
  - for convergence it still requires very smooth regularisations, that means,
    if SEAICE_DELTA_SMOOTHREG is defined, deltaCreg=deltaC+deltaMin, which is
    different from the VP case with deltaCreg=sqrt(deltaC**2+deltaMin**2); also
    specific averaging appears to be required, still subject to tuning
  - still needs cleaning and I need to turn parameter into runtime parameters
  - add code to compute and print residuals of iteration, compile with
    defining ALLOW_SEAICE_EVP_RESIDUAL to enable it
o pkg/seaice/seaice_evp.F: fix a bug (factor of four in front of e12Csq)
  that entered with r1.54 on Sep04, 2015, -> update results

checkpoint65o (2015/09/14)
o pkg/mom_vecinv & mom_common:
  - add deep-atmosphere geometry factor in mom_calc_visc.F + in routines
    called from there.
  - add anelastic and deep-atmosphere geometry factor in pkg/mom_vecinv ; this
    allows to use Vector-Invariant form in deep atmos and anelastic formulation
o pkg/seaice: introduce fast ice parameterisation following Itkin et al. (2015)
  and Koenig-Beatty+Holland (2012)
  - two new parameters SEAICE_tensilFac and SEAICE_tensilDepth
  - global 2D field tensileStrength, computed in seaice_calc_ice_strength
  - requires an extra input argument for S/R seaice_calc_viscosities
  - tensileStrength's depth dependence is different from Itkin et al. (2015)
    (to be changed and played with, for now exponential)
o pkg/seaice: introduce new parameter SEAICEscaleSurfStress (default = .FALSE.)
  - if TRUE scale ice-ocean and ice-atmosphere stress acting on sea ice
    by AREA according to Connelly et al. (2004), JPO.
  - For EVP and the LSR solver, the implicit part of the drag term is
    the only non-zero term in the denominator when there is no ice (which
    prevented running the model with zero ice-ocean drag). If
    SEAICEscaleSurfStress = .TRUE., this results in a division by zero
    (or zero main diagonals BU/BV) which need to be caught. A practical
    consequence is that for open water, the momentum equation reduce
    to trivially 0 = 0 + 0 (for EVP). For LSR, BU/BV are reset to 1, if
    they happen to be zero, often leading to a non-zero solution over
    open water.
o pkg/seaice: revise EVP code (seaice_evp.F) in preparation for a more
    efficient EVP method.
  - introduce area-weighted averages for e12 (analogously to
    seaice_calc_viscosities.F); this totally changes lab_sea.hb87 (2 digits
    remain, but also changing the order of terms in the previous average
    changed the results as much) -> update experiment
  - add SEAICE_DELTA_SMOOTHREG code
  - disentangle computation of zetaC/deltaC and zetaZ/deltaZ, also for
    TEM-code
  - adjust loop bounds so that only required fields are computed
  - add new averaging code for zetaZ/deltaZ (again similar to
    seaice_calc_viscosities.F), inactive by default for now (will change
    results again), but will replace old code eventually
o eesupp/src:
  - add an other alternative for multi-proc GLOBAL_SUM (in global_sum_tile.F)
    to always cumulate tile local-sum in the same order
    (option #define GLOBAL_SUM_ORDER_TILES in CPP_EEOPTIONS.h).
    Still uses MPI_Allreduce (like standard code) but on array of tiles
    and should be faster than GLOBAL_SUM_SEND_RECV code.
  - switch almost all verification experiments that use GLOBAL_SUM_SEND_RECV
    (defined in CPP_EEOPTIONS.h_mpi) to GLOBAL_SUM_ORDER_TILES instead.
  - add CPP_EEOPTIONS.h_mpi with GLOBAL_SUM_ORDER_TILES defined in 14 more exp.:
     aim.5l_cs, cheapAML_box, deep_anelastic, dome, fizhi-cs-32x32x40,
     fizhi-cs-aqualev20, fizhi-gridalt-hs, global_ocean_ebm, matrix_example,
     natl_box, solid-body.cs-32x32x1, tutorial_advection_in_gyre,
     tutorial_baroclinic_gyre and tutorial_held_suarez_cs.

checkpoint65n (2015/07/29)
o pkg/thsice:
  - add a warning when used with pkg/aim but without updating SST
    (stepFwd_oceMxL=F & useCoupler=F & tauRelax_MxL<>-1 ).
o pkg/offline:
  - change where Offline-Fields are loaded, from load_fields_driver.F to
    directly within FORWARD_STEP, just after updating iter number and time;
  - move setting of GM and KPP diffusivity out of OFFLINE_FIELDS_LOAD into new
    S/R OFFLINE_GET_DIFFUS that is called towards the end of DO_OCEANIC_PHYS;
   These changes allow:
    a) to recover exactly on-line results using deltaToffline=deltaTClock,
    tested (using offlineIter0= nIter0 -1 and offlineTimeOffset= -deltaT/2)
    both with Lin & Non-Lin Free-Surf, both with staggerTimeStep & synchronous
    time-step, both with GM & KPP files and with recomputing these fields;
    b) no needs to switch on staggerTimeStep anymore;
    c) simplify rescaling of offline horiz. velocity with Non-Lin Free-Surf.
  - update output of experiment tutorial_dic_adjoffline (only 3 digits left).
o pkg/offline:
  - change (rarely used) offset-iteration parameter to an offset time (in s):
    can easily recover previous offset-iter effect by setting offset-time
    (offlineTimeOffset) to offset-iter x deltaToffline;
  - do not turn-off Temp & Salinity surface relaxation when using KPP (used
    in KPP as part of surface buoyancy forcing) in offline run.
  - fix ptracers KPP non-local term in the case where KPP is re-computed.
o OpenAD
  - Adding preliminary ggl90 test to OpenAD verification.
    Config. with ggl90 currently diverges after 64 time steps
    so will need more work to become more stable
  - Adding preliminary kpp test to OpenAD verification.
    required small tweakes in kpp_routines.F
  - Merge and update from Krishna Narayanan's contrib area:
    * Add one variable for preliminary OpenAD DIVA
    * Add replacement time-stepping for OpenAD DIVA
    * genmake2 flag -diva (but only for OpenAD; preliminary)
    * required modifs for OAD_support
    successful preliminary test for tutorial_global_oce_biogeo/
o pkg/seaice:
  - initialise deltaC in seaice_lsr, cosmetic changes in seaice_lsr
  - add cpp-flag SEAICE_DELTA_SMOOTHREG for option of regularising
    delta with a smooth function in s/r seaice_calc_viscosity
    (no effect on EVP)
  - rename local suffix "sqr" into "sq" for more consistent variable names
o pkg/seaice:
    add new parameter SEAICE_deltaMin that is used ***only***
    for regularizing Delta (and nothing else, like the parameter
    which is also used for all sorts of things SEAICE_EPS).
    Defaults to SEAICE_EPS for backward compatibility only.
o pkg/seaice: replace erroneously storing e12Csqr on the wrong tape with
    the wrong key by inialising it before use -> fixes a recomputation
    problem but does not fix the gradient
o pkg/layers:
  - move resetting of flux arrays to outside the iLa loop
    (this caused layers_diapycnal to not work with more than one layer coord.)
  - fix bug in calculation of layers_recip_delta in layers_init_fixed.F
o pkg/layers:
  - remove from common block 3D layers fields (used to diagnose transport
    in tracer coords) and declare them as local arrays in layers_calc.F
o pkg/seaice:
  - Rename SEAICE_VECTORIZE_LSR_ZEBRA to SEAICE_LSR_ZEBRA and define it
    in lab_sea forward experiment (changes results -> updated)
  - update adjoint experiment lab_sea after cleaning up seaice_lsr_tridiagu/v
o pkg/seaice: modify seaice_lsr.F in order to improve the gradient
   computations; for SEAICE_VECTORIZE_LSR
  - move the loops over which the tridiagonal solvers (seaice_lsr_tridiagu/v)
    sweep to the outside,
  - remove store directives and add "CADJ loop sequential" directives
    in analogy to model/src/solve_tridiagonal.F
  - replace many "#ifdef SEAICE_VECTORIZE_LSR_ZEBRA" by variable loop
    boundaries to yield more readable code. This has also the charming side
    effect that your can use SEAICE_VECTORIZE_LSR_ZEBRA without
    SEAICE_VECTORIZE_LSR (i.e. adjoint without recomputations in
    seaice_lsr_tridiagu/v now requires either of these flags, vectorization
    still requires SEAICE_VECTORIZE_LSR with SEAICE_VECTORIZE_LSR_ZEBRA as
    an additional option)
   The tridiagonal solvers are now completely analoguous to solve_tridiagonal.F
   but the adjoint gradients (which are affected by this change) still explode.
o coupler (atm & ocn _compon_interf):
  - avoid using Exch2 IO mapping if not suitable.

checkpoint65m (2015/06/15)
o pkg/layers:
  - clean-up old parameters setting (from Sep 2012):
    + remove old parameters setting from common block (declared locally);
    + stop if any old parameter is mixed with new parameters;
    + check for valid or consistent parameter setting (e.g., layers_name)
  - check that layers_bounds for Pot.Density are in the right range;
    this is supposed to catch un-updated setting after recently shifting
    potential density field "prho" by -1000 (now in "sigma" scale).
o pkg/layers:
  - Added missing call to layers_fill for keeping track of tottend in
    pkg/diagnostics/diagnostics_fill_state.F
o pkg/layers:
  - added CPP flux LAYERS_FINEGRID_DIAPYCNAL to disable fine-grid binning
    of diapycnal fluxes
o pkg/layers:
  - reverted changes to interpolation to previous treatment; there
    was never actually a problem
o pkg/layers:
  - fix interpolation of layers tracers in the presence of partial cells
  - add lots of new functionality to compute water mass transformation
    (enabled by CPP flag LAYERS_THERMODYNAMICS)
  - add new calls from main code (diags_oceanic_surf_flux.F,
    thermodynamics.F, impldiff.F) and gad to save the necessary fields
    for layers_thermodynamics calculations
o pkg/ptracers:
  - add capability of stepping a passive tracer forward without advection
    by setting PTRACERS_advScheme to 0.
o pkg/diagnostics:
  - add few (threads) _BARRIER around any update of "diag_pkgStatus".
o pkg/layers:
  - shift potential density field "prho" by -1000 for density layer averaging so
    that it corresponds to usual "sigma" definition (i.e., rho(p=const)-1000);
    Note that density bin boundaries (layers_bounds in data.layers) have
    to be set accordingly (i.e., shifted, in sigma scale).
o pkg/layers:
  - fix snap-shot output of layer thickness @ V.pt and output of pot.density
  - fix calculation of layer non-weighted velocity and layer probability
  - add diagnostics for pot.density used for layer averaging
o pkg/seaice:
  - seaice_calc_viscosity.F: change computation of deltaC**2 to ensure
    positiveness, modify a few comments and improve variable names,
  - the changed computation of deltaC affects most seaice-related
    experiments at the truncation level.
    seaice_itd.thermo is affected by far the most, with
    only 7 digits of agreement remaining; update experiments.

checkpoint65l (2015/05/04)
o pkg/shelfice:
  - in shelfice_thermodynamics.F, if SHELFICEBoundaryLayer=.true., then set
    factor drKp1 to zero where it is negative (ie. do not use
    SHELFICEBoundaryLayer if hFacC>1)
  - the same for factor drLoc in shelfice_forcing.F
o tools/genmake2: move FEXTRAFLAGS from FFLAGS to FOPTIM to avoid a problem
    with modules in ptracers, when using testreport option "-small_f"
o pkg/seaice/seaice_growth.F (in case of SEAICE_ITD)
  - replace tmpscal1**1.36 by faster exp(1.36*log(tmpscal1))
o verification/testreport
  - add new option -small_f
    with this option testreport first makes the target small_f (*.f files)
    before running make (all). This is useful for explicit inlining when
    all sources need to be full available.
o pkg/exf/exf_interp.F:
    remove previous changes related to reverse (decreasing) input grids latitude

checkpoint65k (2015/04/01)
o pkg/ecco:
    fix missing cosphi initialization; use eccoiter in place of optimcycle;
    if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
    instead of active read/write
o pkg/ctrl:
    if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
    instead of active read/write.
o pkg/autodiff: make autodiff_readparms.F and autodiff_whtapeio_sync.F
    return if .NOT.useAUTODIFF
o pkg/seaice: add CPP brackets (cost function related).
o model/src:
    add useAUTODIFF run time switch.
o pkg/exf/exf_interp.F:
    add code to allow input grids with latitude starting in the north (i.e. when
    j=1 corresponds to northern edge of field); modify global_with_exf to test
    this feature.
o verification/testreport:
  - replace "grep -A3" with POSIX conformal sed command, because there are
    implementations of grep that cannot do contextual searches
  - replace "cat -n" by "nl" (two occurrences), because not all implementations
    of "cat" have the option "-n"
o model/src:
    add new file gsw_teos10.F that contains 3 functions, more or less a copy
    of the gsw_toolbox.f90 of the TEOS-10 fortran interface, that are used to
    convert from conservative to potential temperature. For now they are not
    called anywhere.
o pkg/ggl90: make "useIDEMIX" useful
  - re-organize code in s/r ggl90_calc a little to move computations that
    are different for idemix into separate loops (changes verification
    experiment idemix at truncation level, 12 digits remain -> updated)
  - requires 2 new 2D fields KappaM, verticalShear
  - make hFacI and recip_hFacI local 3D variables that are passed to
    s/r ggl90_idemix
  - fix and improve some comments

checkpoint65j (2015/02/25)
o pkg/openad
  - synchronize seawater.F with version in model/src: replace routine
    body of sw_temp by calling sw_ptmp and fix/add a few comments.
o pkg/mnc:
  - change default value of pickup_read/write_mnc params to FALSE
    (since few features are missing in reading MNC pickup files).
o model/src:
  - change default (background) vertical diffusivity for salt to be the
    temperature (background) vertical diffusivity.
  - change background vertical diffusivity in vertical mixing pkgs ggl90,
    kl10, my82 and pp81 from temperature diffusivity to salinity diffusivity.
    This makes ptracers default diffusivity (that uses salt diffKr) more
    consistent with vertical mixing schemes.
o verification/testreport:
  - fix typo in "-pcls" option ;
  - put temp files in /tmp (instead of in local dir)
  - add option "-ncad" to use genmake2 new option "-nocat4ad"
  - allow to use "-j" option (for multi-procs make) for AD, OAD and TLM.
o pkg/ggl90 (idemix code):
  - apply few fixes ; add some missing "_d 0" ; update output of exp.
    global_ocean.90x40x15.idemix
o OpenAD
  - enable active file I/O and begin removal of work-around code
    for OpenAD for handling control variables (memory vs. active files)
  - new CPP options file OPENAD_OPTIONS.h
  - revert to genarr2d gradient check for hs94.1x64x5
  - (genarr3d tested by tutorial_global_oce_biogeo, tutorial_tracer_adjsens)
  - gentim2d works for halfpipe_streamice but not yet hs94.1x64x5
o tools/genmake2:
  - add option for an alternative Makefile (from Martin) where multiple
    source files are sent to TAF (instead of all in one file).
o pkg/ggl90: add IDEMIX (Olbers and Eden, 2013)
  - code provided by Carsten Eden as an extension of ggl90
  - so far the code is turned on within ggl90 by setting a CPP-flag at
    compile time; a runtime flag implementation is not yet complete
  - tested in new verification experiment global_ocean.90x40x15.idemix
o verification:
  - reduce length of the AD test run by half for experiments
    global_ocean.cs32x15 (std + thsice) and isomip
  - enable active file I/O for OpenAD, adjust verifications accordingly
  - halfpipe_streamice: change gradient check from genarr2d to gentim2d
o verification/testreport:
  - fix two non-POSIX sed statements so that there are no error messages
    on Mac OS X
  - replace hostname -s with hostname | sed 's/\..*$//'
o model/src/seawater.F:
  - simplify SW_TEMP to just calling SW_PTMP with P and PR exchanged
    (following the matlab code), which would have avoided the bug caught
    by Matt (see below) in the first place
o pkg/shelfice:
  - implement alternative discretisation of quadratic drag (selectBotDragQuadr)
    and true distance in no-slip BC (bottomVisc_pCell) similar to bottom-drag.
  - fix sign of friction tendency (no-slip BC) and fix u,v drag for thin
    ice-shelf case (i.e., within surface level).
  - add config summary in shelfice_check.F
  - remove global variable recip_SHELFICElatentHeat and replace by a local
    variable recip_latentHeat
  - introduce diagnostics for friction velocity uStar (in case of
    SHELFICEuseGammaFrict)
  - change verification experiment isomip.htd:
    + start from pickup (as input_ad at nIter0=8640)
    + start from SHELFICEmassFile instead of SHELFICEloadAnomaly file
    + test SHELFICEuseGammaFrict = .TRUE.
    + test SHELFICEadvDiffHeatFlux = .TRUE.
o model/src:
  - fix bug (Thanks to Matt) in function SW_TEMP (to convert Pot.Temp to
    in-situ Temp) and in routine SW_TEMP (in pkg/openad);
    update output of experiments global_with_exf.yearly and isomip (all 6).
o pkg/shelfice:
  - change setting of kTopC to also be zero where there is no ice-shelf.
  - zero out surface forcing arrays (for now, for T & S + EmPmR) where
    ice-shelf is.
  - first attempt to get RealFreshWaterFlux effects: for now, only without
    SHELFICEboundaryLayer ; not consistent if using synchronous time-stepping.
o pkg/seaice: add the option to prescribe a fixed thickness PDF
  for thermodynamic calculations
  - because of divisions of the type 7/7 not exactly equal to 1, this change
    affects results of some verification experiments by up to 4 digits:
    global_ocean.cs32x15.seaice, lab_sea, lab_sea.fd, lab_sea.salt_plume,
    seaice_obcs, seaice_obcs.seaiceSponge, seaice_obcs.tides
    adjoint: lab_sea, lab_sea.noseaicedyn
    -> updated

checkpoint65i (2015/01/23)
o model/src:
  - change units of frictionHeating field from W to W/m^2
  - fix bug in frictional heating from stratospheric drag in
    S/R ATM_PHYS_TENDENCY_APPLY_V
  - with synchronous time-stepping: move resetting to zero of frictionHeating
    field from load_fields_driver.F to thermodynamics.F ;
  - add diagnostics for frictional heating.
o model/src & gmredi K3D:
  - add frictionHeating field to pickup-files (for synchronous time-stepping)
  - move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h
  - rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name
    and name in pickup file).
  - fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F
o model/src:
  - move (from ini_forcing.F) initialisation of all arrays in header file
    FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart
    (since Nov 2012) with option selectAddFluid=1.
o pkg/shelfice:
  - change units (+ document) of newly added field "shelfIceMassDynTendency"
  - upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays.
o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers
o pkg/seaice: two new runtime parameters:
  - SEAICE_cStar replaces the hard wired "20" in the strength formulation,
    long overdue
  - SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012)
    parameterization of tensil stress for fast ice (does not do anything yet)
o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method
    for LSR: move checking overlaps out of JFNK-if-block
o pkg/atm_phys:
  - move copy of grid and dynamical fields out of atm_phys_driver.F into
    new S/R ATM_PHYS_DYN2PHYS.
  - fix level height for Linear Free-Surf case (to be consistent with
    fixed-in-time pressure levels).
o pkg/mom_common (bottomdrag):
  - average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center
    to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG;
    update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag.
o pkg/shelfice (u/v_drag):
  - add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG;
  - use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F
    (now similar to shelfice_u_drag.F)
  - remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG
    from mom_vecinv.F (similar to mom_fluxform calls).
o pkg/mom_common (bottomdrag):
  - add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG;
  - add options for alternative discretisation of velocity norm in quadratic
    bottom drag: averaging of grid-cell-center KE to U.point and V.point
    (selectBotDragQuadr=0, original code) can produce noisy patterns; this
    improves when averaging only the other component (e.g. vVel for U bottom
    drag) using wet-point method (selectBotDragQuadr=2) or not (=1).
  - add options (bottomVisc_pCell) to account for partial-cell in bottom
    friction (no-slip BC) thus getting the true distance from the bottom;
    off by default since this also reduces model stability (explicit bottom
    friction). Changes produce different machine truncation with linear-drag
    + no-slip BC: update output of experiments exp4.stevens (10 digits) and
    front_relax (bvp & mxl, 10 & 11 digits).
o model/src & mom pkgs:
  - add one more level to vertical viscosity local arrays (Nr+1, previously Nr)
    since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k
  - for now and until vertical mixing scheme are updated to fill up level Nr+1,
    just copy level Nr value to level Nr+1.
o doc:
  - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
o pkg/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
    100 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:
     1.leith  -> A4FlxF  + switch to flux-form & add side-drag
     0.leithD -> AhFlxF  + switch to flux-form
     0.smag   -> AhVrDv  (use Vorticity-Div. visc form) + add side-drag
     0.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
    8 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:
   1) Rain has same temp as Air.
   2) Snow has no heat capacity (consistent with seaice & thsice pkgs)
   3) Run-Off comes at the temp of surface water (with same Cp)
   4) 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.
   5) Evap over snow/seaice (pkg/thsice) assumes constant Lf+Lv (consistent
    with snow having no Cp) => water vapor is released to Atmos @ 0^oC (=ERL).
o pkg/seaice: simplify the use of CPP flags in JFNK-related files
    (compile when SEAICE_ALLOW_JFNK is defined)
o pkg/thsice:
  - fix oceanic flux diagnostics & timeave (left from new sequence of calls
    implementation): move THSICE_AVE call after the advection (called directly
    from thsice_do_advect.F).
o verification/global_ocean.90x40x15 and OpenAD:
  New experiment for OpenAD is identical to the one in input_ad except that
    multiDimAdvection=.FALSE.,
  There is still an issue with this.
o pkg/thsice:
  - account for ice velocity (ocean relative velocity) in turbulent heat flux
    at the base of the ice; update output of global_ocean.cs32x15 (icedyn)
    and offline_exf_seaice (main test).

checkpoint64f (2013/03/31)
o verification/OpenAD:
  - new (smaller, without OAD_DEBUG) output_oadm.txt generated using gfortran.
o verification/isomip, pkg/shelfice and OpenAD:
  - add OpenAD setup to this exp and make shelfice package work with OpenAD
o verification/tutorial_global_oce_biogeo:
  - update AD and TLM output after turning off ALLOW_FE (in DIC_OPTIONS.h)
o verification/offline_exf_seaice:
  - replace adjoint experiment (now similar to fwd input.thermo/ setup).
o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD:
  - add OpenAD setup to this exp and make ptracers package work with OpenAD
o pkg/seaice/seaice_evp.F:
   mask the asymmetric contribution of the ice-ocean stress (when
   the turningAngle is non-zero) over open water to avoid stripes
   in the EVP-solutions after many EVP-substeps. This does not change
   the verification experiment (because turningAngle=0 in that experiment),
   but will affect other EVP solutions with turningAngle.ne.0
o verification, AD & TLM output:
  - new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple
    additions and multiplications which affect results at machine truncation
    level. Update few AD output (1D_ocean_ice_column, bottom_ctrl_5x5,
    lab_sea.noseaicedyn & offline_exf_seaice) and TLM output
    (1D_ocean_ice_column & tutorial_tracer_adjsens.som81) which had only 12
    digits of matching.
o pkg/seaice:
   modify lsr-algorithm so that it vectorizes AND converges by using a
   "zebra" method: split vector loop into two with step size 2; this
   solves a general convergence problem for the JFNK solver on a vector
   computer. It has the potential to even improve convergence for
   non-vector machines, but it does change the results so it is turned
   off by default. To turn on define CPP-flags SEAICE_VECTORIZE_LSR and
   SEAICE_VECTORIZE_LSR_ZEBRA in SEAICE_OPTIONS.h

checkpoint64e (2013/03/05)
o pkg/ecco and several verification experiments:
   Remove special versions of the_model_main.F, the_main_loop.F, forward_step.F
   from ecco package, and revert to unified routine in model/src/
   Adjust verification experiments accordingly, especially gloal_oce_llc90
   Should conclude long-standing work by Gael to reconsile the_main_loop with
   ECCO and will enable OpenAD's revolve loop in ECCO setup.
o pkg/generic_advdiff:
  - implement compressible flow method for multi-dim advection (similar to
    gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since
    TAF generates many recomputations) to use it; no yet coded with implicit
    vertical advection.
  - change experiment advect_cs (new output) and advect_xy (same output)
    to test compressible flow multi-dim advection.
o pkg/generic_advdiff:
  - fix SOM advection for unusual cases (linear Free-Surf in r*, other
    cases where linear Free-Surf is not @ k=1, e.g., useShelfIce)
o pkg/seaice:
  - fix bug in the no-slip implementation in seaice_calc_strainrates.F, this
    bug affects two verification experiments (lab_sea and lab_sea.hb87),
    recover old (wrong) results by setting noSlipFac = 2. in
    seaice_calc_strainrates.F;
  - add another averaging method for etaZ (etaZmethod=3), a mix of 2 and 0
  - add runtime parameter SEAICE_JFNKepsilon for that finite difference
    gradient in the Jacobian times vector operation (s/r seaice_jacvec)
  - fix line search in seaice_jfnk.F (s/r seaice_jfnk_update)
o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code:
  - new subroutines seaice_lsr_tridiagu/v
  - introduce loop bounds i/jmin/max to be able to use a restricted
    additive Schwarz method, but not used for now.
  - rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS
  - use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner
o OpenAD support
   Reorganize S/R call for overall time-stepping loop to facilitate
   OpenAD revolve loop replacement
   (new S/R main_do_loop.F)
o model/src:
  - add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3;
  - pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R
    ADAMS_BASHFORTH2.
o pkg/cheapaml:
  - add new parameter (default=F, same as before) to disable full domain
    (including land) periodicity in X & Y dir.
  - new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of
    prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer
    into single S/R CHEAPAML_TIMESTEP.

checkpoint64d (2013/02/17)
o pkg/monitor (angular momentum):
  - do not add Eta contribution to the total AM if using rigid-lid;
  - correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta).
  - horizontal discretisation: compute Zonal wind contribution separately for
    each component (instead of from cell centered averaged) and use the 4
    grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part.
  - Check that AM is conserved with linear dynamics (momAdvection=F and linear
    FreeSurf) if using vectorInvariant momentum.
o model/src (horizontal grid):
  - move initialisation of all horizontal grid arrays to null value
    from specific horizontal grid S/R to main S/R INI_GRID;
  - add 2 new arrays to project model C-grid velocity on to zonal direction
    (similar to AngleCosC & -AngleSinC but at U and V point location) and
    compute them in S/R CALC_GRID_ANGLES.
o pkg/seaice: replace a hard coded parameter by a runtime parameter
    SEAICE_JFNK_tolIter
o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in
    preconditioner for JFNK (run LSR into the overlaps as far as possible,
    i.e OLx/y-2, but overwrite the solution in the overlaps)
  - extend loop range in seaice_calc_viscosity
  - add new parameters SEAICE_OLx/y (default = OLx/y-2)
  - add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs
  - slightly modify loops in tridiagonal solver lsr-preconditioner
  - by default remove the extra exchange in seaice_preconditioner with a
    replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE
  - modify offline_exf_seaice so that old results without RAS are reproduced
    for output.dyn_jfnk.txt
  in seaice_fgmres.F (unrelated to RAS)
  - add a cpp-flag option for a re-ordered mapping (potentially more
    efficient), but because this changes the results, turn it off by
    default
  - replace the save statement by local common blocks
o utils/matlab:
  - fix tile-offset in rdmnc.m when output was produced using EXCH2.
  - update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab)
    instead of local script "load_cs.m".
o pkg/seaice:
  - fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected
    to the scalarProductMetric and the unrolling. By chance this does not
    change the verification experiment, because of the particular domain
    decomposition
o pkg/diagnostics:
  - change default missing_value from UNSET_RL to -999.
o pkg/layers: improve vectorization of layers_fluxcalc.F
  - step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu
    time spent in this routine by more than a factor of 3 on an NEC-SX8
  - step 2: replace search algorithm by a bisection algorithm found in
    Press et al. Numerical Recipes in Fortran. This algorithm can be
    vectorized and finds the correct bin in approx. log2(Nlayers) steps.
    For now, use this algorithm only for TARGET_NEC_SX defined.
  - moved the search algorithm into a separate subroutine, that is kept
    within the same file for automatic inlining.
  - modified catching potential errors
o pkg/ecco:
  - add compile switches ALLOW_SHALLOW_ALTIMETRY and ALLOW_HIGHLAT_ALTIMETRY.
o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk :
  - modifications for ALLOW_GENTIM2D_CONTROL
  -- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes.
  -- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid )
  -- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc
  -- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F
o model/src:
  - account for moist thermodynamics in (dry) potential temperature equation;
    update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev)
    and cpl_aim+ocn.
  - also switch to standard compiler (gfortran, was using ifort previously)
    for fizhi-cs experiments reference output.
o pkg/ctrl:
  - 1st step toward generic time-varying control variable (2D) via CPP option
    ALLOW_GENTIM2D_CONTROL
  - note new namelist ctrl_nml_genarr in data.ctrl
o verification/global_ocean.cs32x15:
  - switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new
    thsice calling sequence and update "output.icedyn.txt" output file.
o pkg/ptracers:
  - from Ryan A.: code to allow to restart a tracer at regular time interval
    specifying a reset frequency and a reset-phase (for each tracers).
o pkg/thsice:
  - implement new sequence of calls for thsice+seaice:
      previously:   ice-Dyn,ice-Advect,ice-Thermo(thsice)
      new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect
  - allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE"
    in CPP_OPTIONS.h) to recover old sequence;
  - update diagnostics for Intermediate State thsice diagnostics: now filled
    just before advection (instead of just after advection in old sequence);
  - update output of experiment offline_exf_seaice (standard test);
  - in global_ocean.cs32x15 exp., postpone output.icedyn.txt update
    by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h
o pkg/aim_v23:
  - use tiled array for aim_CO2 and surface wind speed for export to coupler;
  - use standard pkg/mdsio routines to read & write CO2 pickup file;
  - in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F;
  - Implement new sequence of calls for seaice advection (with thsice and
    seaice diffusion): do ice advection after ice-Thermodynamic (previously
    was done before); change aim_do_physics.F (split the bi,bj loops block);
  - use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence;
o pkg/thsice:
  - add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case
    where just seaice diffusion is used without seaice-dynamics.

checkpoint64c (2013/01/18)
o pkg/seaice:
  - add a parameter JFNKres_tFac that can replace JFNKres_t
    (= JFNKres_tFac*JFNKresidual before JFNK solver)
  - add a line search option to the JFNK solver
  - move update of u/vIce and computation of initial residual into a separate
    routine (same file); makes the code a little easier to read (?)
  - the line search requires computation of the residual and for some reason
    I cannot do the update of u/vIce at the beginning of the Newton loop
    without changing the results, so we move computation of the new residual
    also to the end of the Newton loop, even without the line search
o pkg/mdsio:
  - write missing value (corresponding to undefined array value) to meta files;
    skip this if missing value is one (UNSET_RL would be a better value for the
    case of undefined missing value but it's current the default missing-value);
    Also update mdsio_read_meta.F (reading timeInterval & missing-value).
o pkg/exf & thsice:
  - for diagnostics purpose, fill-up and update Qsw array (+ fill the
    diagnostics) even when SHORTWAVE_HEATING is #undef;
o verification/cfc_example:
  - turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to
    illustrate how to use it).
o verification/offline_exf_seaice:
  in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing
    files to only one time-record.
  in input.thermo: narrow the 2 bands of low initial ice-concentration near
    N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for
    snapshot output; same mcPheePiston value as in thsice with
    surf-current=0.2m/s.
  in input.thsice: similar set-up as in input.thermo (channel with same seaice
    initial conditions).
o verification/cfc_example:
  - update file "data" with more standard choice (default rotationPeriod,
    exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F,
    set deltaTFreeSurf to deltaTtracer) and update the output.
o pkg/layers:
  - fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC;
  - ensure that "layers_bolus" is switched to False when useGMRedi=False.
o verification/offline_exf_seaice:
  - set all {field}period to zero for constant-in-time forcing (not tested
    anywhere else).
o verification/offline_exf_seaice:
  - dyn_lsr  : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice;
  - dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice.
o model/src:
  - implement Finite-Volume method for (hydrostatic) presure gradient
    from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate.
o pkg/seaice: implement EVP* by Lemieux et al. (2012).
  - In order to be compatible with the default EVP code, this requires changing
    the EVP code around a little; and because any small change immediately
    breaks the lab_sea.hb87 verification experiment, the reference output is
    updated two times (each time the remaining aggrement was only 2 digits):
    - after replacing 1/dt by 1*recip_dt with a precomputed recip_dt
    - after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt
    The adjoint test lab_sea.evp also needed to be updated.
  - Turn on EVP* by setting SEAICE_deltaTevp as before, and setting
    SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be
    a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps
    explicitly with SEAICEnEVPstarSteps (thereby overriding the default of
    INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately
    kept obscure, because I need to test it a little more.
o pkg/cheapaml:
  - fix few incorrect type (_RL/_RS) in subroutine calls.
o pkg/seaice:
  - new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays
    to _RL vector; this fixes JFNK code when compiling with "-use_r4" option.
o model/src:
  - add a warning if using select_rStar=2 with nonlinFreeSurf <> 4;
    change (in input_ad*/data) select_rStar from 2 to 1 for AD verification
    experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output)
o pkg/cheapaml:
  - replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and
    update output of experiment cheapAML_box.
  - store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity,
    and set them only in one place (cheapaml_readparms.F).
  - replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI"
  - remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms)
    and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia).
o model/src/the_main_loop.F:
  - fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION.
o pkg/seaice:
  - remove legacy branch code.
  - retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly.
o verification/*/code*/SEAICE_OPTIONS.h:
  - remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY,
    SEAICE_CAP_HEFF).
o pkg/cheapaml:
  - use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time
    to load new forcing fields.
  - add missing "_d 0" where it's needed; + some editing (improve indentation).
  - remove switch to "-r8" compiler option (no longer needed) in verification
    cheapAML_box, keep same output (small trucation error differences).
o verification/offline_exf_seaice:
  - add thermodynamics only test.
o verification/cheapAML_box:
  - split the domain in 8 (2x4) tiles; add MPI and multi-threaded test;
    keep same output (same 14 digits for cg2d).
  - switch on "-r8" compiler option (some numerical values are missing
    the "_d 0") and update output (only 6 digits for cg2d were preserved).

checkpoint64b (2012/12/24)
o pkg/cheapaml:
  - remove un-used variables (Qnet,EmPmR) from pickup files.
  - store tendency of advected variables into cheapaml pickup file
    and fix the AB-2 restart.
o verification/offline_exf_seaice and lab_sea adjoint:
  - switch to new code (#undef SEAICE_GROWTH_LEGACY).
  - switch to 4 time steps in offline, consistent with lab_sea.
  - match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice.
  - update results after change of experiment seaice.
o pkg/seaice:
  - remove option SEAICE_MULTICATEGORY; has been replaced with run-time
    parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is
    still defined since SEAICE_multDim needs to be set to MULTDIM value (from
    SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default.
o model/src:
  - add run-time parameter to select CG2D solver minimum-residual solution
    (in case of a poor convergence).
o pkg/seaice/seaice_lsr.F
  - move calculation of matrix coefficients into new
    S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same
    file; the main purpose of this change is to be able to reuse the code
    in S/R SEAICE_PRECONDITIONER
  - modify the computation of the residual so that the mass of sea-ice
    is not used twice; this simplifies the calculations, but since
    the residual is never used except when LSR_mixIniGuess.ge.4---and this is
    not tested in testreport---this does not affect the testreport results.
o verification/seaice_obcs:
  - disable SEAICE_GROWTH_LEGACY; reset input files to match those of
    verification/lab_sea/input.salt_plume; changes results/output.txt*
o model/src:
  - adapt quasi-hydrostatic formulation to work with p or p* coordinate.
o pkg/seaice:
  - improve description of parameters in seaice_fgmres.F and start
    cleaning up the code
  - change name of SCALPROD to SEAICE_SCALPROD and modify meaning of
    second argument
  - add a metric based on grid cell area to SEAICE_SCALPROD; update
    results of offline_exf_seaice.dyn_jfnk
  - compute initial residual norm in seaice_jfnk based on SEAICE_SCALPROD
o pkg/aim_v23:
  - fix an other bug in dissipation heating (grid-cell area was missing).
o model/src + pkg/seaice:
  - add global (multi-tile) linear solver for pair of tri-diagonal system
    along X and Y lines, respectively for U and V component.
    Note: 1) MPI and cube-exchange not yet coded.
        2) probably not accurate for poorly conditioned / large size problem.
  - add option for SEAICE_LSR to use global (multi-tile) tri-diagonal solver;
    default: not compiled and not used.
o pkg/seaice:
  - first attempt at a multi-threaded fgmres solver for the JFNK solver:
    introduce bi/bj loops and use global_sum_tile_rl instead of
    mpi_allreduce in seaice_fgmres.F
  - improve diagnostics output for fgmres solver (seaice_fgmres.F)
  - replace a few unnecessary goto statements by if-blocks  (seaice_fgmres.F)
  - add a verification experiment for JFNK in offline_exf_seaice
o verification:
  - change (for now, only fwd test) offline_exf_seaice experiment:
    use a re-entrant channel with idealized coastline (trapezoidal shape)
    at southern boundary to explore seaice dynamics and thermodynamics
    with simple forcing. Main set-up has dynamics+thermo and SST relaxation;
    secondary test (input.thsice) use thermodynamics only with SST relaxation.
  - add seaice-dynamics only secondary test using LSR and pkg/thsice advection.
o pkg/exf:
  - disable "sstExtrapol" when Nr=1
o verification:
  - add new experiment "cheapAML_box" (simple 1 layer set-up from Bruno Deremble)
    to test pkg/cheapaml.
o pkg/aim_v23 & pkg/shap_filt:
  - fix dissipation heating (erroneous gravity multiplication factor).
o pkg/seaice:
  - remove unused field pressPre from jfnk solver
  - rename two subroutines in seaice_preconditioner.F
o eesupp/src:
   - S/R MDSFINDUNIT avoids reserved unit numbers (scrUnit1, eeDataUnit ...)
o pkg/seaice/seaice_preconditioner.F: fix preconditioner once again
   - remove wrong parts of the rhs and the lhs (were in there
     because I did not understand the concept of this preconditioner)
   - add an exchange between u- and v-sweep. This increases communication
     by a factor of two but improves the convergence of jfnk. Ideally,
     one would like the u- and v-sweep to be independent. So far within
     undocumented ifdefs
   - reorganize the extra computations for printing the residuals
o tools/genmake2:
  - comment out the "mpif.h" include in NetCDF test programm (for MPI built)
    since it's not necessary (and was preventing to use MNC in some cases).

checkpoint64a (2012/11/16)
o pkg/autodiff:
  - improve pkg-internal logical parameter switch (inAd/inFwd mode) so that
    autodiff_readparms.F no longer depends on calling order (within
    packages_readparms.F) and no longer requires to include ${PKG}_PARMS.h):
    rename param turnFreeDriftInAdMode to SEAICEuseFREEDRIFTswitchInAd
    and change param SEAICEuseDYNAMICSinAdMode to SEAICEuseDYNAMICSswitchInAd.
o pkg/obcs:
  - adding tidal velocity forcing capability to obcs
    for usage example, see verification/seaice_obcs/input.tides
o pkg/seaice:
  - turn the LSR-relaxation parameters WFAU/V into runtime parameters
    SEAICE_LSRrelaxU/V
  - introduce runtime parameter SEAICEetaZmethod (=0 by default)
o pkg/aim_v23:
  - implement heating from friction (bottom friction and stratospheric drag).
o pkg/shap_filt:
  - fix diagnostic "SHAP_dKE" (was 2 time smaller); implement heating from
    dissipation but only for Shap_funct=2, active when addFrictionHeating=T.
o model/src:
  - move AddMass common block from DYNVARS.h to FFIELDS.h; allow to read-in
    time-constant addMass field from file (addMassFile);
  - support for heating due to friction (and Kinetic Energy dissipation):
    add option, run-time switch and 3-D field array + support code ; each pkg
    or S/R can add heating contribution (if there is a sink of KE); the sum is
    accounted for as a Temperature tendency term (EXTERNAL_FORCING_T).
o pkg/seaice:
  - complete merge of ITD code into seaice_growth.F
    from MITgcm_contrib/torge/itd/code/
    no verification so far, but Torge Martin tested
    "1-D test case and Beaufort set up;
    deliver okay results after 1 model year."
  - complete merge of SEAICE_SIZE.h into all relevant routines
  - move computation of eta at Z-points into calc_viscosities
    + introduce global field etaZ
    + add different methods for computing etaZ, for now the old
      method (simple averages of eta to Z-points) is hardwired
    + replace etaMeanZ by etaZ in seaice_lsr, seaice_calc_residual,
      seaice_preconditioner
  - simplify computations for SEAICE_ZETA_SMOOTHREG
  - seaice_preconditioner:
    + replace one remaining press by pressLoc (mistake)
    + adjust printing of residuals
  - improve I/O of diagnostics of JFNK in seaice_jfnk.F:
    + add (SEAICE.h) and rename some counters (initiliased in
      seaice_init_fixed.F)
    + add _BEGIN/END_MASTER (myThid)  around print statements
    + print total number of iterations and failures over SEAICE_monFreq
      interval to STDOUT
  - move control over output-messages by fgmres to seaice_jfnk to save
    some operations
  - move resetting initial guess for fgmres outside of seaice_fgmres_driver
    in order to make restarts with sol .ne. zero (fgmres with restarts)
    (seaice_jfnk.F, seaice_fgmres.F)
  - seaice_calc_l/rhs.F: replace maskW/S by maskInW/S; this fixes
    a serious convergence problem when open boundaries are involved
o pkg/ggl90: fix computation of control volumes for the case of
  ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes
  up half a grid cell from C-centered to W-centered (pointed out by C. Eden)
o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC
o pkg/autodiff
  - Add inAdMode switch for SEAICEuseDYNAMICS:
    SEAICEuseDYNAMICSinAdMode
    (extend logic in ADAUTODIFF_INADMODE_SET)
o pkg/seaice
  - Step 1 of merging ice-thickness distribution (ITD) code from
    MITgcm_contrib/torge/itd/ (author: Torge Martin)
    The code implements concept laid out in Thorndike et al. (1975);
    code is enabled via CPP flag SEAICE_ITD
    nITD (in SEAICE_SIZE.h) defines number of ice thickness categories;
    code is not complete yet!!
  - SEAICE_SIZE.h now included in almost all seaice routines
o verification (using seaice):
  - switch back seaice-dynamics (+ lower SOLV_MAX_ITERS) in ADM exp.
    global_ocean.cs32x15.seaice ; update results.
  - compile B-grid dynamics in FW test exp 1D_ocean_ice_column ;
  - compile C-grid dynamics with #define SEAICE_ALLOW_JFNK in FW test exp
    offline_exf_seaice (previously compiling B-grid).
o pkg/exf:
  - fix some STOP conditions in exf_check.F (from Aug 28, modifs did not allow
    to specify neither just 1 comp of wind or wind-stress, nor no surface momentum
    forcing): just replace CPP option ALLOW_ATM_WIND with run-time param useAtmWind.
o pkg/layers (adjust changes from Sept 19):
  - do snap-shot output and fill diagnostics from inside iLa loop (layers_calc.F)
    this allows to remove "layers_maxNum" dimension from all layers arrays.
o pkg/layers (adjust changes from Sept 19):
  - remove ALLOW_LAYERS_OUTPUT ; fix snap-shot and time-ave output ;
  - snap-shot extended to all type of layers (not just the 1rst type);
  - remove layers variables when corresponding CPP option is undef.
o pkg/layers:
  - rename pkg/layers variable and add new output (layer exist & un-weighted
    velocity in layer)
o pkg/seaice:
  - simplify (?) ocean-drag coefficent computations by using
    the same routine in all three solvers (saves some code lines)
  - remove global fields DRAGA and DRAGS from C-grid code and
    declare them locally in lsr.F (the only place where they are
    still used)
  - update AD output of lab_sea.evp (very sensitive anyway).
o pkg/seaice: add Jacobian-free Newton Krylov solver for ice dynamics
  (Lemieux et al. 2010, 2012). Turn on with the usual SEAICE_ALLOW_JFNK
  and SEAICEuseJFNK=.true. A few things to note:
  - involves a FGMRES, that is parallel but very inefficient,
    because of many scalar products (global sums) in the Gram-Schmidt
    orthogonalization method. Needs to be replaced. Original code
    from J.-F. Lemieux
  - preconditioner for FGMRES is a stripped down version of LSOR
  - SOLV_MAX_ITERS is now used for LSOR as a solver and as a
    preconditioner. For the preconditioner, the default is set to 10.
  - Jacobian times vector is computed with finite differences
  - marginally related to JFNK-solver: add a smooth regularization for
    zeta with tanh that will improve convergence (Lemieux and Tremblay,
    2009) for any implicit solver (not implemented for EVP because EVP
    does not need this regularization in the first place). Define
    SEAICE_ZETA_SMOOTHREG in SEAICE_OPTIONS.h to use.
o eesupp/src:
  - check in genmake2 that intrinsic S/R flush is available.
  - add S/R to flush IO unit (if intrinsic S/R flush is available)
  - flush standard & error msg unit before MPI termination
  - if debugMode, flush IO unit after printing msg
o pkg/ctrl:
  - ctrl_unpack.F, ALLOW_GENARR3D_CONTROL code: fix missing argument in call
    to ctrl_set_unpack_xyz.

checkpoint64 (2012/10/09)
o pkg/shelfice
  - in mom_fluxform.F, mom_vecinv.F:
    CALL SHELFICE_V_DRAG(bi,bj,k,vFld,KE,KappaRU,vF,myThid)
    Bug fix KappaRU -> KappaRV
    does not change verification/isomip but may change other setups
    (presumably constant KappaRU=KappaRV)
  - fix diagnostics SHIU/Vdrag (thanks to Tom Millgate)
o pkg/obcs:
  - fixed some indexing bugs in obcs_seaice_sponge.F
  - added obcs relaxation subroutines for HSALT and HSNOW
  - changes verification/seaice_obcs/results/obcs_seaice_sponge.F
o pkg/seaice:
  - add "multicategory" parameterization for snow in analogy to ice,
    default is off for now.
o pkg/obcs:
  - added obcs_seaice_sponge.F for obcs relaxation of seaice variables;
    see verification/seaice_obcs/input.seaiceSponge for example application.
  - remove local commom bloc "OBCS_GLOBAL" in obcs_readparms.F and do all the OB
    index setting by master-thread. This fix multi-threads Pb in previous modifs.
o pkg/layers :
  - add diagnostics to pkg/layers
  - move the meat of pkg/layers from layers_calc.F to layers_fluxcalc.F
    (from R.Tulloch). Layers_calc.F now calls layers_fluxcalc.F accordingly.
o pkg/generic_advdiff/gad_implicit_r.F :
  - fix ADVr diagnostics in case of both implicit vertical advection and diffusion.
o pkg/seaice/seaice_growth.F:
  - fix SItflux diagnostics in virtual salt flux + balanceEmpmr case.
o pkg/obcs:
  - change default setting of OBCS_UVICE_OLD from defined to undef;
  - use new parameter OB_indexNone for null index value (instead of hard-coded 0)
    in all pkg/obcs code and in other pkgs; remove k loop in obcs_check_depths.F;
  - pass OB_indexNone as (new) argument to S/R CTRL_MASK_SET_[X,Y]Z;
  - change OB null index value (OB_indexNone) to -99 ; this fix the problem
    with Southern & Western OB at a tile edge (at least in a simple set-up).
o pkg/obcs:
  - change settings of OB index in case OB coincides with tile edge (shared by
    2 tiles), so that common OB location is registered by both tiles (instead of
    only 1). However, for Southern and Western OB, index value = 0 is not
    recognized as valid OB index (=default null value) and needs to be fixed.
  - modify accordingly OBCS_BALANCE_FLOW and OBCS_MONITOR (avoid double counting)
  - new parameter "OB_indexNone" for null index value (for now, still zero)
    to replace hard-coded null index value of zero.
o pkg/exch2:
  - improve W2_USE_E2_SAFEMODE (faster) and W2_E2_DEBUG_ON:
    always check buffer-size (but outside the loop); move checking for valid
    index from W2_USE_E2_SAFEMODE to W2_E2_DEBUG_ON; in W2_E2_DEBUG_ON,
    print each tile and point connection only if |W2_printMsg|>= 2 and 3.
o pkg/ctrl (pack & unpack):
  - in ctrl_pack.F & ctrl_unpack.F, use the same local file-name variable
    (locally defined) for different variables (+ remove the variable-specific
    file name in CTRL_GENARR.h). For now, only implemented for GENARR2/3D_CONTROL
    (to be extended to other local file names in ctrl.h).
o pkg/flt:
  - add a FLT_Iter0 option (similar to PTRACERS_Iter0).
o pkg/mdsio:
  - fix missing STOP in mdsio_readvec_loc.F (case ioUnit=0) when file is missing
o tools/genmake2:
  - add similar dependences for target EXE_AD & EXE_FTL as we have for EXECUTABLE
    (added by Alistair in version 1.51 for building without make depend);
  - remove Header files list (H_SRC_FILES) from the dependence of targets
     ad_input_code.f & ftl_input_code.f (not clear why it was added in the first
    place in version 1.23): this save going through staf when unrelated header
    file has been modified.
   Note: for an intermediate target (e.g., ad_input_code.f or adtaf) without
    "make depend" step, still need to do "make links" before "make adtaf".
o eesupp/src (+ few pkg src files) & genmake2:
  - finish to remove ALWAYS_USE_MPI in source code that TAF does not see;
  - no longer set ALWAYS_USE_MPI in Makefile (was done by genmake2).
  - improve genmake2 checking for ALLOW_${PKG} in CPP_OPTIONS.h files (distinguish
     upper/lower case ; account for space between "#" and undef/define)
o pkg/flt (with exch2):
  - cleaning: fix so that it compiles; move remaining MPI calls out of flt_exch2.F;
  - simplify threads synchronisation; fix (many issues) multi-threaded with MPI.

checkpoint63s (2012/09/05)
o pkg/ecco:
  - remove #ifdef ALLOW_SMOOTH_CORREL3D brackets.
  - add more relevant #ifdef ALLOW_SMOOTH ones.
  - sort out useAtmWind, useSMOOTH, ctrlSmoothCorrel2D.
o pkg/ctrl:
  - CTRL_OPTIONS.h : document CPPs related to smoothing; ALLOW_SMOOTH_CORREL2D/3D,
    ALLOW_CTRL_SMOOTH, ALLOW_SMOOTH_CTRL2D, ALLOW_SMOOTH_CTRL3D.
  - ctrl.h : document run time params doInitXX, doMainPack, doMainUnpack, doPackDiag,
    doSinglePrecTapelev (audodiff param!), ctrlSmoothCorrel2D (new) and
    ctrlSmoothCorrel3D (new).
    The added ctrlSmoothCorrel2D/3D replace the old ALLOW_SMOOTH_CORREL2D/3D CPP.
  - ctrl_readparms.F : initialise ctrlSmoothCorrel2D/3D and read from namelist.
  - ctrl_init.F ctrl_pack.F ctrl_unpack.F : switch off ustress/vstress
    controls when useAtmWind, and vice versa.
  - ctrl_map_ini_ecco.F : UVEL0, VVEL0, edtaux, edtauy cannot be smoothed as tracers.
  - ctrl_get_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL2D with
      #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel2D, IF useSMOOTH.
  - ctrl_map_ini_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL3D with
      #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel3D, IF useSMOOTH.
  - ctrl_set_pack_xy[z].F, ctrl_set_unpack_xy[z].F:
    replace ALLOW_SMOOTH_CORREL2D/3D brackets with ctrlSmoothCorrel2D/3D.
o pkg/smooth:
  - remove un-necessary includes.
  - remove ALLOW_SMOOTH*D and ALLOW_SMOOTH_CORREL*D brakets.
    Those CPP options were never defined, and not necessary.
o model/src:
  - fix CPP brackets in ini_mixing.F (GM_background_K belongs to gmredi).
  - standard treatment of useSMOOTH.
o pkg/autodiff:
  - add LOGICAL useGGL90inAdMode, useGGL90inFwdMode, useSALT_PLUMEinAdMode,
    useSALT_PLUMEInFwdMode allowing to switch off ggl90 and salt_plume adjoint.
o pkg/exch2:
  - add "if usingMPI" where it was missing (in exch2_rx?_cube*.template)
    + start to remove ALWAYS_USE_MPI in source code that TAF does not see.
  - make new S/R W2_MAP_PROCS out of w2_eeboot.F to setup exch2 CommonFlag
    and tiles to process mapping.
  - re-arrange 3 header files (W2_EXCH2_PARAMS.h, _BUFFER.h & _TOPOLOGY.h)
    moving /EXCH2_FILLVAL_RX/ & /W2_EXCH2_COMMFLAG/ to W2_EXCH2_TOPOLOGY.h;
    rename "exch2_tProc" to "W2_tileProc" and move seting of e2FillValue_RX
    from w2_eeboot.F to w2_readparms.F.
o eesupp/src:
  - set exchNeedsMemsync & exchUsesBarrier according to "usingMPI" (instead of
    ALWAYS_USE_MPI) + moved from ini_communication_patterns.F to eeset_parms.F;
    also move setting of exchCollectStatistics from exch_init.F to eeset_parms.F
  - in eedie.F and all_proc_die.F, always call MPI_FINALIZE when ALLOW_USE_MPI
    is defined (remove condition on usingMPI) to match cases where MPI_INIT
    has been called.
  - fix bug I put in previous modif of exch_sm_3d_rx.template (not much used);
  - change default (non-MPI) value of myPid (from 1 to 0) to match MPI settings
    (so that on 1 proc, get same myPid independently of usingMPI)
  - add a stop if multi-procs but usingMPI=F ; stop also if usingMPI=T and
    useCubedSphereExchange with EXCH-1 (safer).
  - add "if usingMPI" where it was missing (+ start to remove ALWAYS_USE_MPI).
o pkg/ggl90:
  - fix bug in filling corner mask array "mskCor" (FILL_CS_CORNER_TR_RL call)
    used in ALLOW_GGL90_SMOOTH code.
o pkg/flt:
  - fix typo in FLT_WITHOUT_Y_PERIODICITY (the effect was to ignore stopping
    floats at the Southern end of the domain).
o eesupp/inc:
  - add a list of CPP-options which can be set by Makefile (DEF_IN_MAKEFILE.h);
    but not used (and not to be used) anywhere, just for documentation.
o pkg/autodiff, exf, ptracers & seaice (AD & TL output):
  - comment out the very nasty "writeBinaryPrec = writeStatePrec" line, since:
    a) can damage previously written records in any other multi-record files.
    b) if needed, can easily do it cleanly, by calling S/R WRITE_REC_3D_RL/S.
o tools/genmake2:
  - define variable MAKE within Makefile and use it in place of 'make';
  - update AD_CONFIG.h (if needed) before building any of the executable
    (forward, adjoint or tangent-lin); this involves a 2nd invocation of make;
    and add the usual #ifndef/#define AD_CONFIG_H in AD_CONFIG.h;
  - always print usual warning comment 'this file is automatically generated'
    from script convert_cpp_cmd2defines (+ remove this warning from genmake2).
o pkg/cheapaml:
  - updated to correspond to the code used in accepted paper (Nico Wienders).
o pkg/exf:
    added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch.
    ALLOW_ATM_WIND now just sets the useAtmWind default (see exf_readparms.F)
    and force defines ALLOW_BULKFORMULAE (EXF_OPTIONS.h).
o pkg/exf, autodiff, ctrl, ecco and seaice:
    remove ALLOW_ATM_WIND brackets, or replace them with useAtmWind ones.
o pkg/ctrl, ecco:
    allow to compile both ALLOW_U/VSTRESS_CONTROL and ALLOW_U/VWIND_CONTROL.
    Depending on useAtmWind, one is inactive, and the other is active (see
    exf_getffields.F/exf_getsurfacefluxes.F).
o tools/genmake2:
  - improve error msg when failing in 2nd test of check_for_broken_Ff
  - fix option '-makefile' short-name (-mf according to genmake2 -help)
  - source local config file "genmake_local" just after processing the genmake2
    command arguments (previously done before processing arg).
o pkg/grdchk:
  - add a call to TURNOFF_MODEL_IO for Tangent-Linear run (in this case, call
    to this routine from cost_final has been dropped in g_cost_final)
  - improve printed information (more explicit msg, no longer using "print *,"
     fix fcpertminus printed value).
o model/src:
  - move call to COST_INIT_VARIA out of packages_init_variables.F directly
    into initialise_varia.F (just after calling PACKAGES_INIT_VARIABLES):
    this prevents getting cost-funct reset in adinitialise_varia recomputations.
o pkg/dic:
  - move initialisation of "freefe" array from from dic_biotic_forcing.F to
    fe_chem.F: this prevents TAF from dropping this initialisation in TLM code.
o pkg/grdchk:
  - grdchk_main.F : added CALL GLOBAL_SUM_INT( ierr , myThid )
  - grdchk_getadxx.F etc. : omit I/O if ierr.EQ.0
o pkg/autodiff/ctrl/grdchk :
  - attempt to sort out what works and what does not,
    with regard to I/O, and to warn/stop accordingly.
o pkg/grdchk:
  - attempt to fix grdchk in the case of useSingleCpuIO.
  - "if ( myProcId .EQ. grdchkwhichproc .AND. ierr .EQ. 0 )"
   statements were moved from grdchk_main.F and into
   grdchk_getadxx.F grdchk_getxx.F grdchk_setxx.F.
  - a global sum is applied to record numbers icvrec/layer
   out of grdchk_loc so that they be passed to I/O routines.
o pkg/smooth:
  - fix recomputation that appeared with nlfs : use smooth_recip_hFacC,
    smooth_hFacW, smooth_hFacS (copied at init_fixed) in 3d case.
o verification/testreport:
  - add option '-tlm' for Tangent-Linear test (-adm,-oad,-tlm are all exclusive);
  - can also use compressed (gzip) reference output file;
  - change format (in pkg/grdchk) of TLM output (+ add forward gradient)
    to be easier to collect by testreport.
  - update existing TLM output (half out-of-date by more than 3 yrs).
  - report NETCDF & LAPACK settings (from genmake2) in output dir.
  - report run-time in each individual summary (previously only for AD test);
    for TLM test, add also TAF version.
  - add daily TLM test on (old) aces cluster + weekly test on baudelaire.

checkpoint63r (2012/08/15)
o tools/genmake2:
  - fix Makefile for target ftlall (+ update files to clean after make ftlall)
o pkg/ecco/ecco_cost_final.F :
  - fix fc print statements (to stdout and costfunction0000) so
    that the printed value is always after the global sum.
o pkg/seaice/seaice_dynsolver.F :
  - fix ice strength assymptote at SEAICE_area_max<1
    (no change for the standard case of SEAICE_area_max=1)
o some cleaning:
  - pkg source files: ensure that all *.F files from each pkg included the
    corresponding ${PKG}_OPTIONS.h file (except stand-alone src file which
    only includes CPP_EEOPTIONS.h); fix S/R CTRL_SMOOTH ; update AD experiment
    code_ad/*.F src files; add new option-file in pkg/admtlm + corresponding
    includes;
  - model/src: add PACKAGES_CONFIG.h wherever ALLOW_AUTODIFF[_TAMC] is used.
  - ALLOW_DIFFKR_CONTROL: add a stop in S/R CTRL_CHECK in case ALLOW_3D_DIFFKR
    is undef; also define /DYNVARS_DIFFKR/ common block in DYNVARS.h when
    ALLOW_DIFFKR_CONTROL is defined, to allow to compile and reach this stop.
  - update option-file CPP_OPTIONS.h of all AD experiments:
    * no longer include PACKAGES_CONFIG.h ;
    * includes ECCO_CPPOPTIONS.h if PACKAGES_CONFIG.h has been included ;
    * def/undef ALLOW_3D_DIFFKR independently of ALLOW_DIFFKR_CONTROL (before
      including ECCO_CPPOPTIONS.h).
o pkg/cost, pkg/ctrl, pkg/ecco option-file:
  - clean-up and split content of old pkg/ecco/ECCO_CPPOPTIONS.h file into
    separated pkg option-file (done according to old doc from ECCO_CPPOPTIONS.h,
    not necessary accurate).
  - add a template for option-file ECCO_CPPOPTIONS.h, mostly empty, in
    pkg/autodiff, i.e., the 1rst pkg to compile for adjoint built, with lines to
    deliberately break compilation (a remainder that it needs to be customized)
  - in pkg/ecco, includes ECCO_OPTIONS.h instead of COST_OPTIONS.h
  - rename COST_CPPOPTIONS.h to COST_OPTIONS.h
  - rename CTRL_CPPOPTIONS.h to CTRL_OPTIONS.h
o tools/genamke2:
  - check for lapack.
o pkg/cost and pkg/ecco : attempt to sort out some of the limiting intricacies.
  - pkg/cost.cost_final.F : allow for use of pkg/ecco and pkg/cost cost functions
    jointly. The exclusive ifdefs were removed, to add costs terms (when defined)
    from both packages.
  - the fc global sum in pkg/ecco/ecco_cost_final.F was removed accordingly.
  - for objf_atl we use either the pkg/ecco or the pkg/cost term depending on CPPs.
  - pkg/ecco and model/src : add CPP brackets around pkg/cost and pkg/ctrl includes
    of "CTRL_SIZE.h" "ctrl.h" "ctrl_dummy.h" "optim.h" / "cost.h" accordingly.
o pkg/cost : add comments to explain special and/or untested setups.
o pkg/exf:
  - use EXF_OPTIONS.h to set pkg/exf options except if done in ECCO_CPPOPTIONS.h
    (previously, ALLOW_AUTODIFF_TAMC was controling this switch).
o verification/*/code_ad:
  mimimal cleaning of AD experiments ECCO_CPPOPTIONS.h option-file:
  - reccord when this file is included (define ECCO_CPPOPTIONS_H)
  - remove the most obvious obsolete features (e.g., #define ALLOW_COST not
    allowed since Oct 2003 in any option-file except in PACKAGES_CONFIG.h)
o pkg/seaice :
  - added possibility to change ice strength/PRESS0 relationship to
    HEFF, according to the following run time parameters
    SEAICEpresPow0 :: HEFF exponent for ice strength below SEAICEpresH0 (integer, >0)
    SEAICEpresPow1 :: HEFF exponent for ice strength above SEAICEpresH0 (integer, >0)
    SEAICEpresH0   :: HEFF threshold for ice strength            (m)
o pkg/ggl90 :
  - added run time flag mxlSurfFlag to include the code that ensure
    mixing between first and second level (previously included as a comment)
o verification/1D_ocean_ice_column/input_ad/data.autodiff :
  - add test of newly added dumpAdByRec=T option where
    we write all records to one file per variable.
o verification/global_ocean.cs32x15/code_ad/CPP_OPTIONS.h :
  - switch to #define ALLOW_BALANCE_RELAX and ALLOW_BALANCE_FLUXES
    to check that this code is ok with taf and compiles in adjoint.
o pkg/autodiff :
  - added run time param dumpAdByRec : ad dump format switch.
    If true then write all records to one file per variable.
    Else write one file per record (remains the default).
  - revise seaice_ad_dump.F and exf_adjoint_snapshots_ad.F accordingly.
o pkg/seaice:
 - Added SEAICEuseTILT run time switch : if set to
   false then omit the tilt term in seaice dynamics.
 - Fix free drift calculation.
o pkg/shelfice:
  When initializing SHELFICEDragQuadratic, set default to be
  consistent with shiCdrag in case SHELFICEuseGammaFrict is used,
  but retain option to set it independently
  (inconsistenty spotted by Veronique Dansereau)
o eesupp/inc:
  - in EEPARAMS.h, add real-type constant for some frequently used simple number
     (0,1,2,1/2), with name explicitly referring to RS/RL type.
o model/src:
  - move balancing of relaxation terms to new S/R balance_relax.F.
o pkg/autodiff:
  re-write active I/O high-level (control) S/R:
  - rename  S/R ACTIVE_READ/WRITE_RL to ACTIVE_READ/WRITE_3D_RL
  - add 1 more argument (useCurrentDir) to replace the "_LOC" 2nd set of S/R.
  - use standard pkg/mdsio I/O routines (MDS_READ/WRITE_SEC_XZ/YZ  and
    MDS_READ/WRITE_FIELD); change loops to multi-threads.
  - update and merge active_file_control_slice.flow into active_file_control.flow
  - update the calls in lower level S/R (active_file.F, active_file_g.F and
    active_file_ad.F) keeping the argument list and function unchanged.
  - also update lower-level "_LOC" version (call same S/R with "useCurrentDir
    =.TRUE.") and remove high-level (control) _loc version (not called anymore).
  - new low-level active I/O routines, one for each type (RL/RS), for active var
    of various (XY,XZ,YZ) shape and level number (arguments: arrShape, myNr);
    fix ctrl_init_wet.F & ecco_cost_weights.F by calling the new S/R with the
    right type.
o autodiff and RS=real*4:
  - call the right type (_RS instead of _RL) of S/R in few output S/R (pkg/exf
    ad-monitor and snapshots); disable arrType='RS' in mdsio_gl*.F ;
  - change argument type of 3-D mask argument to _RS to match type in the call
    (in seaice_cost*.F, ctrl_*_gen.F and *ctrl_bound.F); to be continued.
o pkg/thsice:
  - re-anable balanceEmPmR when useSEAICE=T with useThSIce=T.
  - option to correct ocean fresh-water flux for imbalance of Atmos+Land
    fresh-water flux: uniform correction or proportional to local precip.
o pkg/ctrl:
  - new header file CTRL_SIZE.h for parameters maxCtrlArr2D, maxCtrlArr3D
  - redefine CPP option ALLOW_BOTTOMDRAG_CONTROL to
                        ALLOW_BOTTOMDRAG_CONTROL_NONGENERIC
  - verification/hs94.1x64x5/ tests ALLOW_GENARR{2D,3D}_CONTROL

checkpoint63q (2012/07/30)
o pkg/autodiff:
  note about monitor and snap-shot of ad-variables:
  a) need to apply ADEXCH before monitor or output of ad-vars to include
   overlap contributions (was done for adjDump but missing for monitor).
  b) since ADEXCH implies adding overlap values to interior array, machine
   truncation error is expected when adding an ADEXCH call in the middle of
   the time-stepping (although mathematically identical).
  modifs:
  - fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars
    declaration (adEddyPsiX,adEddyPsiY in adcommon.h).
  - add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how  to
    apply ADEXCH before monitor or snap-shot of ad-variables:
       =0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy.
  - implement new method (copy+adexch) for snap-shot and monitor of main model
    ad-vars (initially not used by default -> output unchanged).
  - change default (set to 2) to use new method and update few output_adm.txt
    with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo
    and both tutorial_tracer_adjsens tests).
  - switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice)
    and turn off momDissip_In_AB in the 2 other (needed for stable AB-3).
o pkg/ctrl:
  enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of
  generic control variables via
  #define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL
  Only required customization should be S/R ctrl_map_ini_genarr.F
  (routine in repository contains example)
o pkg/exf:
  - fix and refine checking of surface-relaxation setting when using EXF
o verification (adjoint exp):
  - reduce length of simulation by half for experiment global_ocean.cs32x15
    (std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output.
o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag)
  - replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers
    of KE that can occur with aggressive optimization
  + put quadratic bottom drag calculation in separated loops (only done if
    using bottomDragQuadratic)
o model/src: CG2D_NSA
  - clean-up:  stop if cg2dNormaliseRHS=T and AUTODIFF
     and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE.
  - in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens),
     change cg2d residual target to be expressed in Wunits (=> do not normalise
     RHS ; this fix global_max Pb with TAF); update output.
o verification/tutorial_tracer_adjsens:
   improve parameter consistency (and get rid of warnings):
   - use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf);
   - switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical)
   - use staggerTimeStep (for stability) in som81; use default rotation period.
o pkg/exch2:
  - with empty facet: fix compact-format (W2_mapIO=1) definition (was previously
    reset to 0 = 1 long line in X)
o pkg/mdsio:
  - fix reading of dimensions from meta file for large-size domain
o model/src:
  - fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long);
  - to refine CS-grid check, add logical flag "hasWetCSCorners": true if using
    Cubed-Sphere Exch with CS-corners inside the domain;
    make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate
    globalArea and to set hasWetCSCorners.
  - add warning if usingCurvilinearGrid and momAdvection in flux-form (missing
    metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form.
  - re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if
    useCDscheme and useCubedSphereExchange).
o pkg/seaice/seaice_growth.F :
  - compute the SEAICE_DISABLE_HEATCONSFIX term accordingly
    for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0)
    when the previous code was not correct.
  - in all cases diagnoze the boundary condition mismatch to SIaaflux
  - in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add
    that term to QNET (essentially to set the melt/freeze water to 0degC).
    when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed.
o verification/global_ocean.cs32x15/input.seaice :
  - add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget.
  - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces).
  - update results (output.seaice.txt) accordingly.
o verification/lab_sea/input/data.seaice :
  - remove SEAICEheatConsFix, which is now be tested
    in global_ocean.cs32x15. The presently coded fix
    is only consistent with real fresh water + nlfs.
  - update results (output.txt) accordingly.
o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd).
o AD_CONFIG.h file:
  - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;
  - remove #include "AD_CONFIG.h" from all included OPTIONS files and
    add it explicitly in each fortran src file where it is needed.
    motivation: header file AD_CONFIG.h is generated/modified after "make depend"
    thus introducing potentially wrong dependency; therefore, better to include
    it only where it's really needed, and after any other included OPTIONS file
    (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN
    or ALLOW_TANGENTLINEAR_RUN).

checkpoint63p (2012/07/06)
o pkg/autodiff:
  - rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ;
  - create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters
    which are now read from new parameter file "data.autodiff" (inAdExact
    previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg)
  - add file "data.autodiff" in all verification/*/input_ad/ directories.
  - add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward
    mode (used in global_ocean.cs32x15.seaice_dynmix test exp.)
o verification/tutorial_tracer_adjsens/
  - add extra sub-verification which uses "SOM" advection scheme
    (2nd Order-Moment Advection Scheme, Prather Limiter) with
      #define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h
    and in data:
      multiDimAdvection=.TRUE.,
      tempAdvScheme=81,
      saltAdvScheme=81,
o model/src:
  - introduce ALLOW_BALANCE_RELAX which allow the removal
   of the global mean of relaxation terms by setting
   balanceThetaClimRelax and balanceSaltClimRelax
  - disable balanceEmPmR and balanceQnet in the case when useSeaice.
   This case is now treated appropriately in seaice_growth.F
o pkg/seaice:
  - do balanceEmPmR and balanceQnet based on the net fluxes
    (SItflux) that enter the ocean+ice system rather than QNET
    and EMPMR. Works best in real fresh water.
  - SIatmFW, SIatmQnet, and SItflux computations had to be moved
    out of the diagnotics bloc, and stored in global arrays.

checkpoint63o (2012/06/29)
o vertical mixing schemes:
  - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging)
  - replace computation of density (in Function STATE1, opps_calc.F) by a call
    to S/R FIND_RHO_SCALAR
  - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC
    and use it for N^2 calculation in ggl90_calc.F (save 2 density computations);
    affects output (vermix.ggl90) at truncation level.
o testreport:
  - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles
    (nSx,nSy) for the number of threads (from eedata.mth)
o model/src:
  - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part)
    related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary).
o verification/tutorial_tracer_adjsens/
  - compile with ALLOW_CG2D_NSA
  - run with nonlinFreeSurf=3
  - update reference output_adm.txt
o tools/genmake2:
  - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
    refine usePROFILES switching off (only when NetCDF is not available).
o verification (atmospheric set-up):
  - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
o pkg/profiles : refine profiles and files handling.
o model/src and pkg/ecco : introduce run-time switch usePROFILES.
o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
  - changes to use model/src/the_main_loop.F rather than the ecco version
    in ecco type adjoint runs.
o model/src:
  - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
  - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
  - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
o model/src:
  - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
    update output of test experiment bottom_ctrl_5x5.
o pkg/generic_advdiff:
  - implement vertical bi-harmonic diffusion (for now, only for T & S and
    only explicitly).
o verification/bottom_ctrl_5x5/
  update reference output (results changed quite some time ago,
  not sure when; but new reference results look ok in terms of grdchk)
o verification/1D_ocean_ice_column/
  For verification purposes, the exact adjoint rather than an approx.
  should be used (e.g., to comare against F.D. or TLM).
  removed autodiff_inadmode*_ad.F routines in code_ad/
  Update results/ accordingly.
o pkg/cal:
  - change cal_getdate.F so that output date is function of input time only
    (less ambiguous, not mixed up with input iteration number).
  - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
o pkg/diagnostics:
  - implement calendarDumps also for stats-diags
  - implement calendarDumps also for snap-shot output (negative freq)
  - for now, ignores calendarDumps if non-zero phase-lag.

checkpoint63n (2012/06/04)
o model/src:
  - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
    between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
  - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
    similar to calc_r_star.F); update results of experiment internal_wave and
    tutorial_global_oce_in_p (affected @ truncation level).
o pkg/shelfice:
  - add parameterisation of advective-diffusive flux into the ice shelf
    according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
  - simply eps3/3a computation
o eesupp:
 - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
   between tiles, just fill-in edges assuming locally periodic subdomain) and
   add corresponding exchange subroutines (EXCH0);
 - new CG-solver version (_EX0) for disconnected-tiles special case.
o model/src (CG-solvers):
 - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
   (similar final residual output and max-Iter number as with standard version);
 - allows to store and use lowest-residual solution (standard & _SR versions);
 - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
 - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
o eesup/src:
 - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
   ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn

checkpoint63m (2012/04/27)
o pkg/shelfice:
 - account for partical cells in surface level below ice-shelf for hydrostatic
   pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
o ad test experiments:
 - update and rename to "ad_optfile.local" local AD-optfile specific to a
   particular adjoint verification experiment (in verification/*/code_ad/)
o pkg/seaice & pkg/exf:
 - Part two of ECCO-CLIVAR code merges.
   Completes merge of seaice area relax. code.
   Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
   to be set in EXF_OPTIONS.h since this pkg controls its I/O
   (and avoids second CPP option in SEAICE_OPTIONS.h)
 - change default value of costIceStart & costIceEnd to a valid date.
 - add snowPrecip to HSNOW in seaice_growth
o pkg/ptracers:
 - move ptracers summary and setup check into separated S/R ; add a check for
   valid PTRACERS_Iter0 value (error+stop or just warning).
o pkg/cal (+ pkg/ecco):
 - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
   as input; and for AD, unless both are not differentiable (e.g., k index)).
o model/src:
 - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
   is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
   temporary set to usingZCoords value (to be changed to F when using shelfice).
 - hydrostatic pressure: implement partial cell near the surface also for
   Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
   usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
o pkg/ctrl/ctrl_init.F:
 - add a formal parameter to s/r ctrl_init_rec to print
   xx_$(ctrl_valiable)_file for easier debugging
 - move call of cal_* routines into the if-block where they are really
   needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
   to specify a startdate
o pkg/seaice:
 - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
   global_ocean.cs32x15/code versions).
 - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
   verification experiment global_ocean.cs32x15.seaice and update results.
o pkg/exf:
 - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
   (according to useExfYearlyFields).
o pkg/cal:
 - move calendar setting & summary (previously in cal_readparams.F) into new
   S/R CAL_INIT_FIXED to be called later in the initialisation process, once
   length of the simulation is set (after SET_PARMS call); This is an attempt
   to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
 - For safety: keep a record of pkg/cal parameter settings status
           to allow to STOP if one pkg/cal S/R is called too early.
 - add a stop in all basic pkg/cal subroutines if called before setting is done.
 - modify cal_getdate.F: stop when nothing was returned;
   if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
   this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.

checkpoint63l (2012/04/04)
o pkg/bbl:
  - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
    update global_with_exf output.yearly.txt file.
o pkg/cal:
  - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
  - remove 2 unsused and very short (1 line only) functions ;
  - remove unsused subroutines from AD-Diff list.
o model/src:
  - start to implement clean wait to stop in initialization S/R (config_check.F,
     packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
o folowing PRINT_MESSAGE changes:
  - remove reminder multiple print to the same file (STDOUT) when multi-threads.
o pkg/bbl:
  - modification so it can work with z*
  - replace deltaT with dTtracerLev(k) for asynchronous time stepping
  - global_with_exf/input.yearly verification; changes output.yearly.txt
o eesupp/src:
  - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
    writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
  - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
    # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
  - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
  - when using MPI, always set usingMPI=T ; set default accordingly and stop
    if not consistent.
  - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
    argument is zero (in case called within single-thread section).
o pkg/fizhi:
    clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
    in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
o pkg/exch2:
  - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
    activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
  - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
    but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
    with bad ones coming from a not-yet-updated halo.
    This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
o pkg/frazil:
    move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
    http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
o verification/lab_sea
  * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
  * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
  * nTimeSteps 3 -> 4
  * changed reference output accordingly
o pkg/ctrl:
  * fix ctrl_get_gen for xx_sst, xx_sss
o pkg/fizhi:
  - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
    update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
  - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
    fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
    clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
o pkg/gmredi:
  - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
o pkg/fizhi:
  - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
    (old)aces open64 tuv test.
o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
o pkg/mom_vecinv:
  - fix 1 loop range in mom_vecinv.F to be like all the other loops which
    set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
    with non-lin free-surf).
o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
  in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
  some compilers (gfortran 4.6.0 on MacOS)
o momentum:
  - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
    & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
    fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.

checkpoint63k (2012/03/17)
o model/src:
   - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
     flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
   - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
     (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
o model/src: solve_*diagonal.F
   - replace division with multiplication by inverse (similar to original version)
     update output of AD exp. global_ocean.90x40x15.
   - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
     to enable the use of the vectorized & differentiable solve_tridiagonal.F
   - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
     vertical advection (to get solve_tridiagonal tested in AD mode).
o pkg/seaice: ECCO-CLIVAR merge:
  1. seaice AREA relaxation
     * CPP option: SEAICE_ALLOW_AREA_RELAXATION
     * runtime flag: SEAICE_tauAreaObsRelax
  2. modified global mean cost imbalance code: CPP option
      ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
o another iteration on solve_*diagonal.F
   Make choices independent of AUTODIFF
   Default will be the adjoinable vectorized version.
   Alternative choices are:
   * non-adjoinable original version with low memory footprint:
     #define SOLVE_DIAGONAL_LOWMEMORY
   * still adjoinable but does not vectorize (k as inner-most loop):
     #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
o testreport
 - add option to use a home made wrapper around "make"
 - remove MITGCM_IEEE env. variable (no longer active)
o pkg/shelfice
 - improve computation of friction velocity for velocity dependent
   exchange coefficients: include velocities into SHELFICEBoundaryLayer
   block to average velocities vertically
 - add TAF store directives for SHI_ALLOW_GAMMAFRICT
o Modify diagonal solvers, now three versions (upon request):
  #ifndef SOLVE_DIAGONAL_AUTODIFF
    1. default version (dating back a while ago)
  #else /* def SOLVE_DIAGONAL_AUTODIFF */
  # ifdef SOLVE_DIAGONAL_KINNER
    2. adjoinable version with k-innermost loop (G. Forget)
  # else
    3. adjoinable vectorized version of 2.
  # endif
  #endif /* SOLVE_DIAGONAL_AUTODIFF */
  All flags are currently set within routines, but could/should be moved to CPP-options.
  Array bounds for 1. are as before, for 2.,3. cover the entire domain
  (could be changed for 1. too).
o verification/lab_sea (fwd):
  - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
    use 7 categories (except hb87), new solve4temp params (except salt_plume),
    constant salinity (=4) or variable salinity (salt_plume) done through
    SItracer.
o pkg/seaice:
  - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
  - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
     SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
    from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
    SEAICE_freeze got retired) but already better than previously with
    SEAICE_freeze=123456.7 deg.C;
  - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
    (safer multi-threaded setting); always set SEAICEuseEVP;
  - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
    SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
    stop if multiple specifications for the same coeff; make sure default
    SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
o pkg/obcs:
  - allow to switch to upwind 1rst order advection scheme for the advective
    flux computation at the open-boundary; disabled for adjoint built.
o pkg/ptracers:
  - rename PTRACERS_RESTART.h -> PTRACERS_START.h
  - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
  - add parameter to decide when to start a tracer; use internal flag to
    know which tracer to step-forward; switch this internal flag at the top
    of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
    for adjoint built.
o pkg/seaice:
  - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
  - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
  - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
o pkg/ecco:
  - fix writing of output file DiagnosCost_ClimSalt/Theta
    and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
o pkg/seaice:
  - add missing initialisation of COR_ICE array in dynsolver.F
  - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
    compiled either way, and is tested in all exps (multidim was only tested
    in lab_sea ad before).
  - cosmetic change to prepare for future addition of ITD. no change to results.
    no defaults change.
  - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
  - by lack of adequate verification experiments, I further used custom versions
    of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
    should be correct.
  - avoid recomputations in ad.
o array initialisation in adjoint mode:
  1) pkg/mom_common/mom_calc_ke.F:
    add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
    The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
    part this initialisation is gone, resulting in Floating Point Exception
    (caught by open64 compiler with debug option).
  2) model/src/convective_weights.F
    set output convectCount over the full array range (instead of doing
    an update): this fix a similar issue when called within recomputation (adjoint)
    which could by-pass the initialisation (normally done in the caller S/R).
o pkg/seaice:
  - final version of turbulent flux params, as agreed at MIT ice meet:
       SEAICE_mcPheePiston (default is ~ 0.000875)
       SEAICE_mcPheeTaper (default is 0.)
       SEAICE_frazilFrac (defualt is 1.)
       SEAICE_mcPheeStepFunc (default is false)
  - changes results at trunction error level
  - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
o added pkg/frazil:
  - see frazil_description.tex for details
  - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
o pkg/shelfice/shelfice_thermodynamics.F
  - fix exponents for velocity dependent exchange coefficients: change
    from 2/3(=0) to 0.66666666666666667
  - move computation of velocity dependent exchange coefficients into
    separate loop, so that it applies to both thermodynamics
  - move some divisions by constants out of loops

checkpoint63j (2012/02/16)
o pkg/seaice:
  - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
  - SItracer:  added run time params, and allow coupling to ocn salinity.
o pkg/seaice: remove (almost) all divisions by constants within loops
  in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
  results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
  those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
  output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
o pkg/seaice :
  - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
    = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
  - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
  - add permanent SItflux diag that corresponds to TFLUX but includes
    ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
  - allow activation/testing of a fix for suspected missing term in
    ocn-ice heat budget (to be confirmed). To test this, you want to
    undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
    SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
  - no change in results, fwd or ad.
o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
  - switch to variable freezing point.
       Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
  - bug fix : the sublimation term that was missing is now activated.
       Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
  - bug fix : flooding sign term for SIsal0.NE.0.
       Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
o pkg/seaice:
  - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
    is now the default, and the old default constant freezing point is recovered
    with SEAICE_tempFrz0    = -1.96,
         SEAICE_dTempFrz_dS = 0.,
  - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
  - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
  - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
    activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
  - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
    was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
  - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
    seaice_growth r149 for legacy branch (no results change).
  - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
    from I. Fenty).
  - results did not change except for global_ocean.cs32x15, mostly due to the
    switch to variable freezing point (see above item for detail).
o pkg/thsice:
  - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
    seawater freezing in thsice_calc_thickn (not used).
o pkg/seaice: turbulent flux term specification via run time params.
  - replace CPP switches with run time switches to facilitate testing
  - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
                   GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
  - added runtime parameter : SEAICEturbFluxFormula
  - move Mcphee constants to SEAICE_PARAMS.h
  - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
             SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
             remove seaice_summary call (moved to seaice_init_fixed)
  - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
    SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
  - seaice_summary.F : add missing report of read turbulent flux term set up
                       and SITRACER.
  - seaice_check.F : check range; inform and stop if retired CPPs are used
                     (incl. SEAICE_AGE).
  - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
         CPP switch, same computation as before for the different options.
  - change results at the truncation level.
o pkg/seaice:
  - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
    useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
    SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
  - update verification/*/input*/data.seaice:
    to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
    code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
    and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
    set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
  - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
    algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
    difference in results only due to machine truncation.
  - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
    MaykutPolySatVap; keep MIN_LWDOWN.
  - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
  - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
    + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
o pkg/salt_plume:
  - isolate saltPlumeFlux array exch into a specific S/R called from
    do_oceanic_phys.F
  - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
o verification:
  - move untested set-up to MITgcm_contrib/verification_other.
o pkg/seaice:
  - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
o pkg/seaice:
  - seaice_solve4temp.F (keeping results unchanged):
    * add 2 future run-time params to select which saturation vapor pressure
      formula is used and how post-iteration fluxes are set.
      Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
    * New piece of code (not used) to update surf. atmos. heat flux F_ia using
      the linearized expression to stay consistent with tsurf finding.
  - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
    can be < 0.
o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
  - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
    conductive heat flux F_c , and add it explicitly when updating tsurf as
    solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
    so that now F_ia has a consistent meaning through the entire routine.
    This causes differences at truncation level: update output of fwd exp.
    global_ocean.cs32x15.seaice.
o pkg/seaice:
  - lots of editing/cleaning in seaice_solve4temp.F + better documentation
    of arrays, sign/direction of fluxes; no effect on results.
  - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
    in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
    note: this should have been done before changing celsius2K default.
  - to keep results unchanged, add back old value of celsius2K in verification
    exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
  - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
    SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
    value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
    freezing temp is consistent with value in seaice_growth.F ; this causes
    differences at machine truncation level: update lab_sea AD output (3/4).
o pkg/seaice:
  - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
    and climsst/sss even when using seaice (to prevent calculation that might
    use SST on land); does not affect any verification exp.
  - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
    of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
  over land (non-legacy code)
o vectorize salt_plume package:
  - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
  - this code computes plumebk everywhere (also over land), thus requires
    code to avoid divisions by zero and catch the case of kLev=Nr.
  - efficiency of salt_plume_frac is still sub-optimal
o tools (genmake2):
  - fix makefile NAME specification (option: -makefile NAME) by adding
    "-f $MAKEFILE" in few places where it was missing including makedepend
    command (contribution from Paul).

checkpoint63i (2012/01/24)
o model/src:
  - add factorized versions of some EOS code to find_rho.F,
    define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
o model/src:
  - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
  - change default celsius2K from 273.16 to 273.15
  - to keep results unchanged, add back old value of celsius2K in verification
    exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
     global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
  to make TAF generate vectorizable code
o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
   Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
   have flags that do this more efficiently.
o pkg/diagnostics/diagstats_calc.F
  - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
o pkg/obcs (with exch2):
  - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
    and remove code (in obcs_readparms.F) which was based on EXCH of indices
    (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
o pkg/exf and seaice exp:
  - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
    so that switching off area & heff advection flags does not affect results.
  - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
  - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
    EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
    results of verification experiments: 1D_ocean_ice_column(fwd),
    global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
    and offline_exf_seaice (all 4).
o pkg/seaice:
  - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
    remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
  - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
    but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
    not multi-dim advection;
  - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
    SHORTWAVE_HEATING #undef.
o optim: make Makefile more robust (?)
o pkg/obcs:
  * fix treatment of obcs_read_pickup for TAF
o pkg/shelfice:
  * add missing initialisation of num_shifwflx
  * new adjoint verification exp. for isomip
  * change Prandtl and Schmidt numbers from generic formulations
    (in terms of model diffus. and visc.) to separate runtime
    parameters, with Holland and Jenkins (1999) default values.
o pkg/exf (interpolation):
  - extended input field (2 rows) near the N & S poles:
    * fill in with the symetric value (when even Nb of data in longitude)
    * add average value at the poles only for scalar quantities ; for vector
      component interpolation, skip the averaging and keep duplicated values,
      unless the 2 components have same location (uvInterp=T) in which case
      interpolate the 2 components together using S/R EXF_INTERP_UV.
  - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
    together: this allows to account properly for local orientation when
    averaging at N & S pole.
  - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
    exf-interpolation near N & S poles. Undef by default.
  - add debug check/print on 1rst iter if debugLevel >=2.
o pkg/exf:
  - change masking flags definition (no longer "parameter"), put them in
    common block and set them in S/R EXF_INIT_FIXED.
  - change recognized masking flag from s,u,v to c,w,s since the mask
    to use (maskC,W,S) depends on position on model grid and has little to
    do with scalar/vector difference; fix masking if using P-coordinates.
  - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
    and update results of exp. global_with_exf (x2).
  - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
o pkg/obcs
  - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
o pkg/exf (interpolation):
  - assume periodicity in X only if input field cover full longitude range.
  - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
    and should vectorise).
  - fix input lat of the 2 added row (in case we provide N.pole data).

checkpoint63h (2011/12/30)
o pkg/seaice:
  - change declaration of UVM from _RL to _RS in order to get B-grid
    uIce,vIce monitor when _RS = real*4
o pkg/offline:
  - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
  - compute vertical velocity if not read from file (switch on exactConserv
    & staggerTimeStep);
  - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
o verification:
  - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
    with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
    fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
  - update output of exp. global_ocean.cs32x15.viscA4 after changing
    grid-file angles (used here for coriolis-3d);
  - remove (or gzip) few files not needed to run fizhi-cs experiments.
o pkg/exf (vector interpolation):
  - rotate vector component toward local grid-axis orientation using grid-angles
    (stored in GRID.h) instead of locally computed rotation angle; keep old code
    available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
o pkg/seaice:
  - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
    undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
o pkg/PKG_OPTIONS.h files:
  - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
    outside of the #ifdef ALLOW_THISPKG / #endif block.
  - update verification/*/code/PKG_OPTIONS.h files.
o add a verification experiment (offline_exf_seaice/input.seaice) that test
  the B-grid LSOR solver
o pkg/seaice: sort out emissivity and long wave radiation step 2:
  - add emissivity for snow and ice as new run-time parameters
    (unfortunately) that default to the corresponding exf values; this
    changes results in most verification experiments so that for backward
    compatibility these parameter have to be set explicitly to inconsistent
    values (ugly);
  - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
    emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
    until we agree how to handle this bug properly
o pkg/exf (interpolation):
  - add a set of run-time param ({inputfield}_interpMethod), one for
    each interpolated input field, to select the interpolation method
    with a value of zero switching off the interpolation;
  - print interpolation parameters to standard output;
  - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
    (to use instead runoff_interpMethod=0 in data.exf).
  - simplify default setting of interpolation parameters (for all fields,
    set position to match model grid cell-center position, leading to trivial
    interpolation in case of regular Lat-Lon grid) and fix for the case of
    non-uniform delY.
o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
   within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
   this factor is absolutely required, because the lw exitance (= out-going
   long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
   where the reflectivity rho = 1-emissivity for conservation reasons. Once
   this is established, we can remove the CPP-Flag (if we want to).
o pkg/seaice:
  - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
    ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
  - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
    what the name implies (and not emissivity*BoltzmannConstant), this means
    the old default value of 5.5e-8 now means
    5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
    S/R exf_readparms
  - FV-discretization of the B-grid LSOR solver, turn on with
    SEAICE_LSRBNEW. This new solver also involves a slight re-organization
    of the calling routine dynsolver, so that B and C-grid code look a
    little more alike.
  - fix index bugs in ostres.F (B-grid code)
o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
  default for SEAICE_emissivity, if useEXF; requires setting a wrong
  parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
  backward compatiblity
o model/src: use sigmaR in calc_ivdc

checkpoint63g (2011/12/16)
o pkg/seaice/seaice_growth.F:
  fix heat conservation of the coupled ocean-seaice system.
  when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
  solid vs liquid water treatment is resolved via QNET.
o pkg/seaice/seaice_growth.F:
  add missing term for sublimation in saltFlux, which was breaking conservation.
o pkg/seaice/seaice_model.F:
  Remove this patholigical case treatment in evolution branch,
  where it is un-necessary and breaks conservation.
  Update global_ocean.cs32x15/results accordingly for
  output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
o model/src:
  useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
  external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
o pkg/obcs:
  modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
  tendency for temperature and salinity that is then applied to update
  theta and salt in S/R obcs_apply_ts; this requires proper masking of all
  horizontal advection and diffusion contributions on the boundary (in
  S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
  removing the mask in S/R timestep_tracer. The advantage of this approach is
  that the updated tracer values include contributions from the surface
  forcing and vertical diffusion.
  This modification changes exp4.stevens because of vertical diffusion.
o model/src:
  change non-curvilinear grid setting to also work with exch2 + blank tiles:
  - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
    face dimensions.
  - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
    as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
    and INI_SPHERICAL_POLAR_GRID.
  change test-experiment global_ocean.90x40x15:
  - split the domain in many more tiles (9x4 tiles of 10x10 each);
  - switch to exch2 and remove 1 blank-tile (but only for MPI test).
  - update results of both test (std & dwnslp).
o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
   tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
o model/src:
  - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
    and fix initialisation when using sigma-coords.
o model/src:
 - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
   to their current value at the beginning of forward_step.F": add a new run-time
   switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
 - set doResetHFactors=T in the following test exp:
    global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
    global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
    and tutorial_global_oce_in_p (nonLinFS in p)
o pkg/ecco
  - added IES cost term
o verification/advect_xz
  - scale down the depth by 1/100 (from 200 km to just 2.km)
  - add secondary test using divergent flow, r-star and implicit vertical advection.
  - add note (check_conserve_TS.txt) and matlab script to check global
    conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
o pkg/rbcs:
  - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
o pkg/obcs (Stevens BCs):
  - fix various problems in the phase speed computations of the Stevens
    boundary conditions:
    - sign error for western and southern boundaries,
    - time tendencies were underestimated by factor of dTracerLev and some just
      zero (for multidim advection schemes) -> now estimate time tendencies
      from difference between previous (n) time level and the one before (n-1);
      this requires storing a field per tracer per boundary, also in the pickup
      files.
    - replace deltaTmom in cflMer/Zon computation with dTracerLev
    - set default phase velocity to cflMer/Zon
  - update verification experiment exp4.stevens
o pkg/generic_advdiff (implicit_r):
  - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
    (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
  - fix implicit vertical diffusion or advection with NonLin FreeSurf
    (was using current recip_hFacC instead of future recip_hFacC): set future
    recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
    solver S/R ;
  - fill diagnostics of vertical advective fluxes (computed from tendency)
    when using implicit vert. advection;
  - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
     global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
     tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
     and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
o pkg/diagnostics:
  - add diags for T & S tendency which goes through Adams-Bashforth.

checkpoint63f (2011/11/30)
o pkg/obcs/obcs_calc_stevens.F:
  - join some loops to reduce number of if-statements
  - fix a bug in code for northern and southern boundaries.
o pkg/seaice/seaice_init_varia.F
  - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
    caused zero ice-velocities for the B-grid code
o pkg/seaice/seaice_init_fixed.F
  - fix a bug in the initialisation of the second metric terms
    k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
  - this affects all seaice configurations with useCurviLinearGrid = .true.
    and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
    = .true. (default)
  - the only verification experiment affected is global_ocean.cs32x15:
    icedyn, seaice, and seaice_dynmix (AD)
o pkg/thsice/thsice_diagnostics_state.F
  - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
    not contain garbage that can lead to surprises in diagstats_calc.F
o model/src:
  - move bi,bj loops inside INTEGR_CONTINUITY ;
  - call INTEGR_CONTINUITY directly from forward_step.F
    (previously called from momentum_correction_step.F)
  - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
    forward_step.F and pkg/ecco/the_main_loop.F
o model/src/do_oceanic_phys.F:
  - reset addMass to zero only if useICEFRONT ;
  - separated k-loop for rhoInSitu calculation ;
  - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
    and at constant T,S (= WdRHOdP);
  NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
    of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
    transport of locally-referenced potential density);
    to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
o gluemnc:
  - replace ncrcat with ncks when adding variables to *.glob.nc
  - change the way variables without record dimensions are handled so that
    files that have variables with and without record variables can be glued:
    add a record dimension with a new unique name to be able to differentiate
    between variable with and without a-prior record dimensions. Remove
    this record dimension before adding the variable to the *.glob.nc file.
    This procedure automatically works also for grid.*.nc files that do not
    have any record dimension.
o verification/cpl_aim+ocn:
  - generate new reference output on baudelaire (gfortran, mpich2) (previously
    from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
o pkg/obcs/obcs_calc_stevens.F:
  - add code for northern and southern boundaries.
  - reorder some loops to save some operations and so that drFBar can be scalar
o model/src:
  - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
    truncation) and add diagnostics for Adams-Bashforth tendency increment.
  - update test-exp. AD output:
    1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
  and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
    front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
    global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
    matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
    tutorial_global_oce_in_p, tutorial_global_oce_latlon and
    tutorial_plume_on_slope.
o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
  that vectorises. This code uses 3 extra 2D fields, F90 array assignments
  and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
  does not even come with an F77 compiler anymore, this should not be
  a limitation

checkpoint63e (2011/11/06)
o pkg/seaice adjoint of LSR:
  - substantially rework STORE dirs.
  - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
    this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
    and only perform SOLV_MAX_FIXED adjoint iters.
    If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
    always goes to same record, meaning that the last forward field will be
    the one used in the adjoint - an approximation.
  - now produces non-zero LSR-related gradients, and acceptable gradients for
    An's zonal (x-z) test case (to be checked in)
  - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
    (but these are screwed up by the thermodynamics in the first place);
    reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
    output_adm.txt also reflects changes to seaice_lsr
  - global_ocean.cs32x15:
    * the "default" input_ad.seaice has been re-defined to always exclude dynamics
      (output_adm.seaice.txt was updated)
    * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
      (output_adm.seaice_dynmix.txt)
o test-exp. exp4+stevens:
  - switch off pTracers and nonHydrostatic (restart problems with NH); update output
o pkg/seaice (lsr solver):
  - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
    update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
  - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
  - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
    into initial guess for linearised solver; use weight ~ (1/err)^2,4.
  - compute (with new S/R) and print initial (+ free-driff sol. if available)
    and final residual of linearised system.
o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
  (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
o pkg/obcs: Stevens BCs (still only for east and west)
  - fix Stevens BCs by using intermediate velocities of previous
    time step as "baroclinic" contribution rather velocity of one grid cell
    inside the boundaries; more consistent but makes the entire treatment
    more complicated, requires new pickup files and two new S/Rs:
    obcs_copy_uv_n and obcs_save_uv_n
    keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
    (undefined by default)
  - silently move computation of some grid factors into separate loops to
    save some recomputations
  - add a hack for non-linear free surface
  - add a verification experiment to exp4 that tests this code
o make gluemnc/xplodemnc work with (moron) non-GNU shell tools

checkpoint63d (2011/10/25)
o pkg/obcs + seaice-dynamics:
  - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
    solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
    values (consistent with an implicit method).
  - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
    return to older implementation (same results as before); note that none of
    the "experimental" OBCS_SEAICE options are implemented in the new version.
  - switch test exp. seaice_obcs to use new version (update output).
o pkg/seaice:
  - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
  - add parenthesis in Water-Ice drag calculations (evp & lsr);
  - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
    and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
  - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
    and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
o pkg/layers:
  - Include potential density as new coordinate (Thanks to David Munday)
o pkg/dic:
  - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
    carbonate computation/output to CALC_PCO2_APPROX
o pkg/generic_advdiff
  - make TAF generate code that vectorizes:
    gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
o model/src:
  - improve vectorization also for adjoint code of
    solve_tridiagonal and solve_pentadiagonal. As this requires up to
    5 new 3D-fields, this code is only turned on for the combination of
    ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
    for singular matrix check (only for TARGET_NEC_SX).
  - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
    ALLOW_AUTODIFF. This flag now needs to be set outside of
    solve_tri/pentadiagonal.F
o pkg/exf:
  - fix previous modif in exf_readparms.F (revision 1.66: treatment of
    optional namelist EXF_NML_OBCS).
  - add many debug-print (to trace down where pkg/cal error msg comes from)
o pkg/mom_vecinv/mom_vi_hdissip.F
  - rearrange loops so that vectorization is improved and in particular
    the adjoint routine vectorizes. The code is a little longer now, but I
    think easier to read.
    Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
o pkg/seaice:
  - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
o pkg/exch2:
  - alternative code (without tile x tile matrix) for cumulated (global) sum;
    used as default; keep using matrix version in adjustment.cs-32x32x1.
o tools/build_options:
  - after merging some MPI and/or multi-threads specific optfiles so that
    the modified default optfile support both built (using genmake2 -mpi
    for the MPI built, using genmake2 -omp for OpenMP built),
    move now obsolete optfiles to tools/build_options/unsupported/
   (add copy of email sent to support list in doc/optfiles_changes.txt)

checkpoint63c (2011/09/28)
o pkg/ebm:
  - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
    test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
o pkg/seaice (SItracer pickup)
* Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
  To be done:
  - thorough testing of missing fields in S/R seaice_read_pickup
  - thorough matching between generic tracers and specific fields used
    (e.g. volume-weighted age, area-weighted age, salinity, ...)
o pkg/grdchk:
  - all procs calculate and print finite-difference gradient (for testreport)
  - change description output used by testreport;
  - AD testing: also compare and report Finite-difference gradient;
    => update all output_adm*.txt
o test exp. global_ocean_ebm:
  - switch back useRealFreshWaterFlux (no problem anymore with run-off);
    and turn on exactConserve; update (fwd) output.
o pkg/seaice (LSR):
  - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
  - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
    * identical results with non-CS topology (but save up to half of EXCH calls)
    * no much changes in cs-32 verification tests since no ice at face edges
     (differences due to convergence criteria, since nb of iterations changed)
    * expect some differences on lat-lon-cap grid.
    update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
o pkg/exch2:
  - add new CPP option to disable Cumul-Sum matrix (to save storage when using
    many tiles); until alternative coding is added, just add a stop.
o pkg/kpp:
  - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
    to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
o optfiles:
  - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
    into corresponding standard one, which now support different build:
    (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
  - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
o pkg/obcs (seaice):
  - add missing EXCH for uIce,vIce after applying OBCS;
  - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
    argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
    EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
  - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
  - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
    and eedata.mth for MPI and mutlti-threaded testing.
o pkg/flt:
  - make FLT EXCH working with multi-threads (and MPI + multi-threads);
  - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
  - fix pickup and trajectories + profiles output with multi-threads;
  - add parameter to select group of fields to write along trajectory and
    profile (default unchanged);
  - only call PORT_RAND* function when flt_noise <> 0;
  - add multi-threaded test for verification exp. flt_example.
o eesupp/src:
  - fix S/R ALL_PROC_DIE for MPI+multi-threads.
  - USE_OMP_THREADING: check that number of threads (from eedata) matches
    actual number (from env.var. setting).
o pkg/ebm:
  - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
  - add multi-threaded test for verification exp. global_ocean_ebm

checkpoint63b (2011/08/29)
o pkg/ebm:
  - fix sign of runoff;
  - update directly forcing fields (Qnet,EmPmR) to use standard
    external_forcing_surf.F (remove ebm_forcing_surf.F);
  - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
  - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
    and apply relaxation towards corresponding SST field (2-D map or ZonAver).
  - update global_ocean_ebm parameters file data and update output (fwd+ad).
o verification/matrix_example:
  - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
    MPI and mutlti-threaded testing.
o pkg/matrix:
  - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
  - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
  - fix for multi-threaded (remove DATA statement);
  - use standard DIFFERENT_MULTIPLE function;
  - add MATRIX_OPTIONS.h
o verification/matrix_example:
   To allow to split the domain in several tiles, change the domain size
    from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
    Western side) of land points.
o (*_)write_pickup:
  - fix few bugs in mypackage_read/write_pickup.F
  - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
    array of length 1 (was caught by compiler syntax-check).
o pkg/diagnostics (velocity potential solver):
  - fix initialisation of main diagonal matrix (for overlap values)
o tools/build_options:
  - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
    into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
  - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
    * move IEEE flags to DEVEL section; take I