--- MITgcm/doc/tag-index	2013/03/29 23:21:39	1.1844
+++ MITgcm/doc/tag-index	2014/02/06 01:34:01	1.1964
@@ -1,19 +1,661 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1844 2013/03/29 23:21:39 heimbach Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1964 2014/02/06 01:34:01 jmc Exp $
 $Name:  $
 
     Notes on tags used in MITgcmUV
     ==============================
 
-o verification/isomip, pkg/shelfic and OpenAD:
+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/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/offline_exf_seaice: replace adjoint experiment.
+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 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