--- MITgcm/doc/tag-index	2013/08/25 00:09:46	1.1917
+++ MITgcm/doc/tag-index	2014/06/06 21:17:12	1.2005
@@ -1,9 +1,485 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1917 2013/08/25 00:09:46 dgoldberg Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.2005 2014/06/06 21:17:12 jmc Exp $
 $Name:  $
 
     Notes on tags used in MITgcmUV
     ==============================
 
+o verification/global_with_exf:
+  - swith 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 reccord (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 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: