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-revision 1.1687 by gforget,
Wed Jul 11 21:51:27 2012 UTC
+revision 1.1961 by heimbach,
Thu Jan 30 21:07:20 2014 UTC
 Line 4 
 $Name$
      Notes on tags used in MITgcmUV
      ==============================
+ o pkg/thsice
+   - corrected store directive fixes thsice adjoint gradient checks
+ o genmake2 & testreport:
+   - add genmake2 option "-oad" to generate a Makefile for OpenAD built and
+     in this case, use tools/adjoint_options/adjoint_oad as default AD optfile.
+     Update testreport accordingly. No need to set "export OPENAD=true"
+     in adjoint_options/adjoint_oad anymore (will be removed later).
+ o pkg/shelfice:
+   - put T & S shelfice forcing into model surfaceForcing_T,_S (for now,
+     only if SHELFICEboundaryLayer=F); Change model/src/external_forcing.F
+     so that surface forcing applies to k=kSurf if using pkg/shelfice.
+ o pkg/ctrl, pkg/grdchk, pkg/ecco:
+   - Changes to make GENARR more modular (i.e. invisible if not used)
+ o model/src/temp_integrate.F and salt_integrate.F
+   - re-include store directives that were removed on Dec 27th.
+ o model/src/external_forcing_surf.F
+   - add storage directives for EmPmR and PmEpR to avoid recomputation of
+     seaice_model in the adjoint that is problematic when seaice_model is
+     turned off in the adjoint. The resolved issue dated back to July when
+     EXTERNAL_FORCING_SURF call was moved.
+     Update global_ocean.cs32x15/*/output_adm.seaice_dynmix.txt accordingly.
+ o pkg/exf/exf_check.F
+   - fix a small bug again (originally found by Wentao Liu, now found again)
+   - streamline error output
+ o pkg/streamice and aim_v23:
+   - replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that
+     Apple's /usr/bin/cpp knows what to do:
+     Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
+     Target: x86_64-apple-darwin13.0.0
+ checkpoint64s (2014/01/05)
+ o tools/adjoint_options:
+   - switch to fastopt.net TAF server (instead of default fastopt.de) for
+     AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default).
+ o model/src:
+   - remove some unnecessary TAF storage directives in forward_step.F and
+     in dynamics.F (note: not always removed by TAF, e.g., double storage
+     of kappaRU,kappaRV in former version of dynamics.F).
+ o model/src & pkg/ptracers:
+   - call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F
+     salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F)
+     and remove ptracers_dwnslp_apply.F & ptracers_implicit.F
+   - call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F)
+   - add fZon & fMer as output argument of S/R GAD_CALC_RHS.
+   - update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad).
+ o useSingleCpuInput separates single-CPU input from single-CPU output;
+     for now only implemented for in exf_interp_read.F
+ o verification/advect_xy:
+   - fix missing EXCH call in local version of ini_salt.F and update output.
+ o momentum diagnostics:
+   - fix which deltaT is used in Total-Tendency diagnostics.
+   - fix typo in diagnostics for momentum tendency from AB.
+ o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the
+     SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8
+ checkpoint64r (2013/12/08)
+ o verification/*/results:
+   - Update reference output of experiments that were passing with just 13 digits
+      (make it easier to detect future changes in results)
+ o model/src & pkg/ptracers:
+   - move calls to GAD_ADVECTION (Multi-Dim advection) from thermodynamics.F to
+     inside temp_integrate.F and salt_integrate.F and from ptracers_advection.F
+     to inside ptracers_integrate.F ; remove ptracers_advection.F
+ o coupling interface pkgs:
+     [atm_compon_interf, ocn_compon_interf & atm_ocn_coupler]
+   - change the config check to test the agreement of Ocean Depth
+     with ATM land/sea mask (instead of ATM orography);
+   - send to coupler the number of coupler time-steps to do for this run:
+     this allows to check for consistency and don't need anymore to be
+     specified in parameter file "data";
+   in coupler:
+   - check consistency of RunOff map versus Ocean Depth and ATM land/sea mask.
+   - improve report to log-file of config setting (pass log-file unit to few S/R)
+ o pkg/compon_communic:
+   - add coupling send/receive for non-tiled integer vector;
+   - add S/R to check and stop if any proc has an error (similar to
+     eesupp/src/stop_if_error.F but single thread and across Comm_World).
+ o pkg/exch2:
+   - in exch2*_get_rx[1,2]: use new list "W2_tileIndex" to replace search
+     through list of all tiles my proc owns.
+ o model/src:
+   - AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying
+     from rTrans) to simplify dependencies (no need to store rTrans anymore in
+     calling S/R); this affects AD results at machine truncation level:
+     update AD-output (TAF) of experiments: 1D_ocean_ice_column,
+     bottom_ctrl_5x5 & obcs_ctrl (12 digits for AD grad, same FWD grad).
+ o tools/build_options:
+   - simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran
+ o coupling interface pkgs:
+     [compon_communic, atm_compon_interf & ocn_compon_interf]
+   - move declaration of local array "ibuf" out of header file "CPLR_SIG.h"
+     to each S/R that needs it; remove un-used variables.
+   - change component tile registration (cpl_register.F in both compon_interf
+     and mitcomponent_tile_register.F) to pass the full list of tiles
+     information (including bi,bj) in 1 vector (instead of in a bi,bj matrix).
+   - with pkg/exch2: adopt the same convention used for I/O to define mapping
+     towards coupler global array (unless W2_useE2ioLayOut=F):
+      a) can now use different tiling between atm & ocn comp.
+      b) no needs to modify the run-Off map when changing tiling (was needed
+         even if using the same tiling between atm & ocn).
+      c) will allow to run with blank-tiles in 1 component (e.g., for ocean
+         full land tiles); not yet tested.
+   - check for valid mapping from comp. tile to coupler global array
+   - improve report of tile registration results to log file.
+ o pkg/exch2:
+   - in eesupp/src/eeboot.F: move call to W2_EEBOOT before Coupler
+     tile-registration (CPL_REGISTER);
+   - activate (un-comment) definition and setting of "W2_tileIndex" list to
+     store the local bi,bj indices of each tile;
+   - also print bi,bj in local report to log file;
+   - fix pkg/debug/debug_cs_corner_uv.F for the case nSy > 1 (left from
+     Jun 2009 modif of pkg/exch2).
+ o testing on baudelaire:
+   - run 2 tests at a time: no significant slow down (since enough cpu) and
+     get the full set of test done earlier
+   - switch the ifort test to "-devel" ; run the OpenAD test everyday.
+ o model/src/thermodynamics.F and routines called from it:
+   - pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F &
+     gmredi_calc_wflow.F) to update eulerian velocity (input) into residual
+     velocity (outp) by adding bolus velocity.
+   - model/src: calc_adv_flow.F (replacing calc_common_factors.F) to compute
+     mass transport from velocity + lateral grid cell area
+   - rename calc_gt.F to temp_integrate.F (includes call to TIMESTEP_TRACER)
+   - rename calc_gs.F to salt_integrate.F (includes call to TIMESTEP_TRACER)
+  in thermodynamics.F
+   - remove k from thermodynamics.F and move it to temp_integrate.F
+     salt_integrate.F and ptracers_integrate.F (now done inside the tracer
+     loop).
+   - compute locally (in thermodynamics.F) 3-D velocity field that is used to
+     advect tracers; pass it as argument to GAD_ADVECTION, GAD_SOM_ADVECT,
+     PTRACERS_ADVECTION, TEMP_INTEGRATE, SALT_INTEGRATE, PTRACERS_INTEGRATE,
+     GAD_IMPLICIT_R and PTRACERS_IMPLICIT
+   - update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column,
+     global_ocean.90x40x15, tutorial_global_oce_biogeo and
+     tutorial_tracer_adjsens (+ TLM output).
+ o tools/OAD_support and (verification/*/) code_oad:
+   - OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to
+     module conversion ; remove unneeded CPP_EEOPTIONS.h.
+   - code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard
+     version (closer to model/inc/CPP_OPTIONS.h).
+ o model/src:
+   - remove parameter "useOldFreezing" from PARAMS.h and push it to the
+     retired list of parameters (routine FREEZE has been replace by surface
+     freezing (10.yrs ago) and by pkg/frazil (interior freezing).
+ o pkg/gmredi:
+   - add option (GM_CALC_TRANSP_FROM_VEL) to compute transport directly from
+     velocity (same scheme but affects machine truncation) for GM_AdvForm.
+   - update output of FWD experiments: front_relax.bvp,
+     global_ocean.90x40x15.dwnslp, global_ocean.cs32x15 and ideal_2D_oce.
+ checkpoint64q (2013/11/17)
+ o verification:
+   - generate new output on baudelaire (gfortran, -ieee) for OpenAD experiments
+     tutorial_global_oce_biogeo and global_ocean.90x40x15.
+   - generate new output (growth & melt) for seaice_itd experiment after
+     updating the input pickup_seaice files (previously wrong).
+ o pkg/cost:
+   - define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL
+     (instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads:
+     o this fixes global-sum value if multi-threads (since GLOBAL_SUM_RL
+       cannot be applied to var in common block).
+     o allows to get results independent of tile-per-proc setting (if using
+       slower GLOBAL_SUM_SEND_RECV option).
+   - update accordingly: seaice_cost_final.F, shelfice_cost_final.F,
+     thsice_cost_final.F and ecco_cost_final.F (this one affects lab_sea
+     forward gradients: update output).
+   - update */code_oad/externalDummies.F by adding dummy GLOBAL_SUM_TILE_RL
+     S/R and, for most exp., also comment out GLOBAL_SUM_R8.
+ o pkg/mom_common:
+   - move to pkg/mom_common and model/src (previously in tutorial_deep_convection
+     code) 2nd version of isotropic 3-D Smagorinsky code interface: strain and
+     viscosity are locally declared in dynmics.F and pass as argument to CALC_GW;
+     ensure that all field value that are used are set.
+ o tutorial_deep_convection (smag3d):
+   - add missing scaling in mom_calc_smag_3d.F;
+   - set smag3D_coeff in input.smag3d such that results do not change.
+ o pkg/dic:
+   - change dic_cost.F to compute cost on each tile first and then apply
+     GLOBAL_SUM_TILE_RL: this affects forward gradient of AD experiments
+     tutorial_dic_adjoffline & tutorial_global_oce_biogeo; update output.
+   - remove kLev argument and use GLOBAL_SUM_TILE_RL in tracer_meanarea.
+ o eesupp/src & pkg/mdsio:
+   - remove gather/scatter_vector.F (from eesupp) and mdsio_read/writevector.F
+     (from pkg/mdsio) since they are no longer used for tape IO.
+   - move simple C subroutine "setdir.c" from pkg/compon_communic to eesupp/src
+     (+ keep a copy in pkg/atm_ocn_coupler).
+ o verification/isomip:
+   - split domain in 8 squared tiles (instead of just 2) for FWD, AD & OAD tests.
+ o tools/build_options:
+   - optfile linux_amd64_ifort11, fast (no ieee) case:
+     to get a working restart for all experiments, add "-fp-model source"
+     to FOPTIM (also remove "-opt-streaming-stores auto" <- this is the default).
+ checkpoint64p (2013/10/20)
+ o pkg/autodiff:
+   - adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO
+     criteria, return to simple (default) tape IO format.
+ o pkg/mdsio (+ eesupp/src):
+   - rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace
+     previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8);
+   - fix globalFile and singleCpuIO options using simpler global mapping.
+   - new pairs of scatter/gather vector S/R (one for each type, generated from
+     template) corresponding to simpler global mapping.
+   - adread_write.F: switch to new S/R (but leave old calls commented) and write
+     to globalFile when parameter globalFiles is set to True.
+   - switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip.
+ o pkg/autodiff:
+   - adread_adwrite.F: add a hack for RS arrays (when RS=real*4);
+     with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is
+     missing, just add a STOP if array type do not match.
+ o pkg/exf:
+   - to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice:
+      rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION
+      and rename array obsSIce to exf_iceFraction.
+ o tutorial_deep_convection:
+   - add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe),
+     for now all in this exp. code dir.
+   - add secondary test using Smag-3D viscosity (keep very low backgroud visc for
+     testing) and flux-limter advection scheme for Temp. (no explicit diffusion).
+ o eesupp/src:
+   - added SINGLE_DISK_IO option because reading of parameter files on
+     very large number of processors did not work with existing set-up
+ checkpoint64o (2013/09/25)
+ o pkg/atm_phys & atm_compon_interf:
+   - allows for coupling of gray-atmosphere (atm_phys) with ocean.
+ o tools/build_options:
+   - switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran
+     & linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also
+     remove CPP setting (was identical to genmake2 default).
+ o pkg/gmredi & model/src: Some updating and work done on the residual model.
+   - created new file model/src/calc_eddy_stress.F to calculate the eddy stress.
+   - fixed up the calculation of the eddy stress and how it is added to the
+     external forcing via taueddy_external_forcing.F
+   - at the moment, it is very experimental and only works with the variable eddy
+     diffusivity calculated in gmredi_k3d.F
+ o pkg/seaice/seaice_check.F: add a check to catch the case of specifying
+     lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice
+ o testreport (& tools/do_tst_2+2):
+   - for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}'
+ o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11:
+   - remove CPP='cpp -traditional -P' (this is genmake2 default)
+   - add switch (for big setups) to use 'medium' memory-model (but leave it
+     commented out for now). Note: needed with FC 19 to compile big setups.
+ o pkg/atm_compon_interf:
+   - regroup per field origin (model & pkgs) the coupling storage routines
+      (which accumalate in time each coupling field)
+   - move bi,bj loops inside atm_store_my_data.F and store also wind-stress;
+     update accordingly + simplify aim_do_physics.F
+ checkpoint64n (2013/08/26)
+ o pkg/bbl:
+   - update formulation to reduce dispersion of tracer properties in bbl
+   - replaced horizontal and vertical transport parameters with velocities
+   - changes results for verification/global_with_exf.yearly
+ o verification/halfpipe_streamice:
+   - change to matrix construction; update both Fwd & AD output.
+ o verification/tutorial_tracer_adjsens:
+   - OpenAD test: switch to vector-invariant momentum since fluxform with
+     rStar causes problems with OpenAD; update output.
+ o tools:
+   - genmake2: define a common prefix for all temp-file names ; move them
+     to local /tmp disk (but would be easy to move them back);
+   - xmakedepend: apply the same switch for temp-files.
+ o pkg/offline:
+   - changes for use with rStar (NLFS): assume that we continue to provide
+     UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid
+     output files) and apply r* scaling at each time-step (function of the time
+     varying Eta field); use normal pickup files (needed for restart with NLFS).
+ o adjoint with OpenAD:
+   - move OpenAD-specific files from verification/OpenAD/code_oad_all to a new
+     package openad.  This package has to be compiled for all runs with OpenAD
+     instead of specifying code_oad_all as a modification directory.
+   - link the fortran templates from tools/OAD_support to the build directory
+     for preprocessing to avoid conflicts between different setups compiled
+     simultaneously and simplify cleanup.
+ o pkg/exf:
+   - in exf_getforcing.F: comment out most of the EXCH calls (fields used by
+     main model or other pkgs are exchanged in EXF_MAPFIELDS).
+ o model/src:
+   - do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline
+     (similar to do_fields_blocking_exchanges.F).
+ o tools/genmake2:
+   - remove TAF output src code just before calling staf (when not doing a fresh
+     built, will stop if things go wrong with staf).
+   - fix target "adobj" (left from TAF version-2 transition)
+ o pkg/diagnostics:
+   - add a parameter to track the status of pkg/diagnostics activation;
+     this replace/extend the use of logical param "settingDiags" (to check
+     when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call.
+     New S/R to print error message and stop when pkgStatus is not right.
+   - to try: add a warning when "data.diagnostics" exist but useDiagnostics=F.
+ checkpoint64m (2013/08/13)
+ o model/inc:
+   - move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from
+yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h)
+ o pkg/kpp & aim_v23:
+   - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
+ o pkg/seaice:
+   - restore (last time on 2011/12/24) ability to compile pkg/seaice with
+     undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options.
+   - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
+ o eesupp/src:
+   - fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH)
+     in exch1_rx[_ad].template (thanks to Francois Lefeuvre report).
+ o switch to TAF version-2:
+   - add flow directives to "freeze" naming convention for ad-routines that
+     are used in I/O routines of adjoint state and associated common blocks
+     that are used in adcommon.h (backward compatible with version-1)
+   - update all ad-optfiles (in tools/adjoint_options + few local to some
+     verification exp) to switch to latest TAF version (currently 2.5.5);
+     merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented
+     out except for diva).
+   - the major change with TAF version-2 is that both the differentiated
+     routines and the forward routines (new) are returned as part of the TAF
+     output source code. Update genmake2 accordingly.
+   - new output for AD experiment tutorial_global_oce_biogeo (better AD gradient
+     with version-2 when compared to TLM or FWD gradient); other experiments
+     output show minor changes (machine truncation level); update the few AD &
+     TLM output with 12 matching digits only (some prior to version-2 switch).
+ checkpoint64l (2013/08/05)
+ o model/src:
+   - in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F
+   - main_do_loop.F: no longer includes additional (AUTODIFF) header files
+     when using TAF but only if using OpenAD.
+ o pkg/mom_common+fluxform+vecinv:
+   - always set horiz. viscosity arrays to background value before calling
+     MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC
+     only when using variable horiz. viscosity (useVariableVisc=T);
+   - simplify mom_vecinv.F (only 1 block for momViscosity).
+ o pkg/mom_common: variable horiz. viscosity in NH code
+   - move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F)
+     from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h
+   - store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc,
+     useBiharmonicVisc & useVariableVisc.
+   - fix old bug (already in 1rst implementation of variable horizontal viscosity
+     in calc_gw.F, version 1.27, 2006/06/20):
+     horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0
+     even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero.
+   - change background horiz viscosity in vertical momentum (gW) to always be
+     viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using
+     any type of variable viscosity, e.g., viscAh/4Grid)
+   - change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of
+     viscAh,viscA4) which default to viscAh,viscA4 :  this avoid missing
+     horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since
+     default viscAh,viscA4 is zero).
+ o model/src:
+   - extend length of drC & recip_drC from Nr to Nr+1.
+ o Divided Adjoint (DIVA) with MPI:
+   - genmake2: do not create local ./mpi_headers dir when no file to copy into.
+   - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT
+     and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h.
+ checkpoint64k (2013/07/23)
+ o tools/OAD_support:
+   - avoid the need for file "oadtempflile" in insertTemplateDir.bash
+     and remove it from genmake2.
+ o tools/build_options:
+   - remove MPI_HEADER_FILES_INC setting (no longer used) and comment out
+     MPI_HEADER_FILES list (let genmake2 find the missing headers)
+ o verification/halfpipe_streamice:
+   - change to driving stress formulation; update both Fwd & AD output.
+ o tools/genmake2 and Divided Adjoint with MPI:
+   - remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken);
+   - only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set;
+   - add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in
+     Makefile, which is set by genmake2, and check which mpi-headers are needed.
+     Note: need to update adjoint_options/adjoint_diva_mpi accordingly.
+   - update target "CLEAN" (to also remove ./mpi_headers/ dir).
+ o testreport:
+   - changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present,
+     perform additional runs (number of additional runs is "add_DIVA_runs" taken
+     from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h").
+ o verification/lab_sea (AD test):
+   - change to test Divided Adjoint Run in this set-up (both standard AD test
+     and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test.
+ o pkg atm_ & ocn_compon_interf:
+   - remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old
+     staggerTimeStep implementation) and disable (retired) corresponding
+     parameter.
+ o pkg/offline:
+   - comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01];
+   - add S/R OFFLINE_CHECK to print offline parameter summary
+     and stop if loading a file that is not used;
+   - enable to calculate GMRedi tensor, KPP mixing and convective index
+     when the corresponding file(s) is/are not specified (but pkg is used).
+   - comment out resetting of monitorFreq (to endTime) since it still useful
+     for monitoring CFL numbers and checking offline fields.
+ o OpenAD:
+   - do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get
+     smaller standard output) and generate new (smaller) output (on baudelaire
+     using gfortran with -ieee) for exp. tutorial_tracer_adjsens
+ o model/src:
+   - call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F),
+     (where external_forcing_adjust was called) and change list of arguments;
+   - merge external_forcing_adjust.F into external_forcing_surf.F
+   - put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F)
+     which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX,
+     previously in file "balance_relax.F", now removed); remove corresponding
+     arrays in FFIELDS.h.
+   - EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement
+     a hack for getting back surfaceForcingS (loaded from file) when using
+     ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up.
+   - update output of AD test experiment global_ocean.cs32x15.seaice_dynmix
+     (was getting only 11 digits for AD-grad, due to different truncation
+      error in AD code).
+ checkpoint64j (2013/07/04)
+ o pkg/offline:
+   - to enable the use of other features with pkg offline (e.g., obcs),
+     also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come.
+   - comment out "allowFreezing" (now active) in 2 offline testing exp.
+ o pkg/exf ALLOW_RUNOFTEMP
+   - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL
+   - ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice
+   - changes verification/global_ocean.cs32x15/results/output.seaice.txt
+ o pkg/atm_phys:
+   - allows to add some damping on uVel,vVel (strength only function of k).
+ o verification, ad-tests:
+   - reduce length of the simulation for AD test: global_ocean.cs32x15.seaice,
+     global_ocean_ebm and offline_exf_seaice.thsice.
+ o verification/halfpipe_streamice:
+   - found a bug in s/r pkg/streamice/streamice_advect_thickness which caused
+     flux input boundary conditions to be ignored; a fix for this bug changed
+     verification results for forward test.
+   - add adjoint test.
+ o pkg/ptracers:
+   - allow to restart without SOM pickup (resetting SOM to zero).
+ o pkg/gmredi:
+   - New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added.
+   - It uses mixing length theory and suppression by steering level effects to
+     calculate a diffusivity used in the Redi tensor (see Bates et al., submitted
+     to JPO, for more details).
+   - It also uses the diffusivity to calculate an eddy induced streamfunction
+     based on a PV closure (rather than a buoyancy closure as in GM).
+   - New files added to pkg/gmredi:
+     gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy
+       induced overturning streamfunction (called from gmredi_calc_tensor)
+     gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required
+       for use in gmredi_k3d
+     gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate
+       the eddy diffusivity
+ checkpoint64i (2013/06/18)
+ o pkg/cheapaml:
+   - take src files from MITgcm_contrib/verification_other/offline_cheapaml/code
+     that enable the use of seaice (pkg/thsice thermo & pkg/seaice dynamics)
+     with pkg/cheapaml.
+ o utils/python: add subpackage for cubed sphere function, first example is
+     simple cs.pcol to plot 2D fields on a map
+ o pkg/streamice:
+   - This is a new package in MITgcm, which solves dynamic equations for ice
+      sheets and ice streams
+   - At the moment it is independent of atmosphere/ocean dynamics, or any
+     other physical packages in MITgcm, even ShelfIce (although it is anticipat-
+     ed that this will change)
+   - There is a new verification exercise that tests it, halfpipe_streamice,
+     evolves a 40x80 km ice stream/ice shelf (at coarse resolution) in a
+     rectangular embayment
+   - halfpipe_streamice is forward-only for now, will have TAF test soon
+   - for questions, email dgoldber@mit.edu
+ o pkg/thsice:
+   - fix filling of snow-precip diagnostic (SIsnwPrc) (left from the removing
+     of snowPrc from common bloc, on May 2nd, thsice_step_fwd.F revision 1.40);
+   - remove diagnostics 'SI_FrcFx' ( now identical to 'SI_Fract' with new
+      call sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect );
+   - allow precip from pkg/cheapaml to make snow over seaice.
+ o pkg/cfc:
+   - move in separated header file (CFC_ATMOS.h) time-serie arrays of Atmos CFC
+   - remove atmos CFC 2-D arrays from common bloc (now local variables)
+   - change some hard-coded constant to run time parameter for reading and
+     and interpolating atmospheric CFC ; keep same default as previously.
+   - more flexible reading of Atmos CFC (number of records no longer hard-coded)
+   - put arguments in standard order: myTime, myIter, myThid
+   - use standard S/R GET_PERIODIC_INTERVAL for time interpolation of
+     atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.
+   - fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf
+   - new routine to print summary of CFC params and check for consistency.
+ o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff,
+   similar to thsice_advdiff.
+   Note that for the B-grid case the routine parameters uc/vc are overwritten.
+ o pkg/cfc:
+   - change time interpolation for atmospheric CFC-11 (now same as for CFC-12);
+     update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline.
+   - fix interpolation of atmphspheric CFC between Sorthern and Northern
+     hemisphere value.
+ o pkg/seaice:
+   - allow to use seaice dynamics without pkg/exf (e.g., using pkg/cheapaml)
+ o pkg/seaice: add Adams-Bashforth2 time discretization for ice dynamics;
+               so far only for JFNK-solver, turn on with SEAICEuseAB2 = .TRUE.
+   - requires an additional time level that is stored in the pickup
+   - you can start with AB2 from a pickup without this time level with
+     pickupStrictlyMatch = .false.
+ checkpoint64h (2013/05/26)
+ o pkg/cheapaml:
+   - replace one ()**.5 with SQRT + use temp var "cdu = tau/Du" (coare3_flux);
+     affect machine truncation (but exp cheapAML_box still pass with 13 digits).
+   - consistent treatment of uWind,vWind location: assume everywhere in
+     pkg/cheapaml that they are on C-grid (@ uVel,vVel location)
+     (Note: was already the case for Tair,Qair advection);
+     add option (INCONSISTENT_WIND_LOCATION) to recover old results.
+   - compute diabatic forcing only in the interior (excluding overlap regions)
+   - fill in array "Qsw" (for short-wave heating);
+   - add diagnostic for precip ; fill-in diagnostics for cheapAML state vars
+     before any update (consistent with MITgcm state var diagnostics);
+   - cheapaml_fields_load.F & cheapaml_init_varia.F : only fill outer edges if
+     non periodic ; + adjusted for uWind,vWind (C-grid).
+ o pkg/seaice:
+   - remove dependence of pkg/seaice versus pkg/exf (file: pkg/pkg_depend) and
+     add explicitly pkg/exf in experiments that currently use pkg/seaice.
+   - allows to compile pkg/seaice without pkg/exf.
+ o tools/OAD_support:
+   - use a local copy (ourRWCPinBd) to ensure index ourRWCP stays within bounds
+     of array "ourStepOf" in function rvNextAction (revolve.F90).
+ o pkg/aim_compon_interf renamed to pkg/atm_compon_interf
+   - change pkg name (to be used with other atmospheric physics pkg)
+     but by-pass CVS when making the new pkg so that we keep the CVS history.
+ o pkg/offline:
+   - call OFFLINE_FIELDS_LOAD from pkg/offline/offline_init_varia.F
+     (previously called from pkg/dic_surfforcing_init.F)
+ o model/src:
+   - re-order sequence of calls within packages_init_variables.F, using
+     standard order, except for:
+      DIAGNOSTICS_INIT_VARIA and OFFLINE_INIT_VARIA (called @ the top),
+      CTRL_MAP_INI and OBCS_INIT_VARIABLES (called @ the bottom)
+ o new pkg: atm_phys
+   - add entry point and source code (previously in contrib
+       verification_other/atm_gray/code_gray/) for new pkg "atm_phys"
+     (atmospheric physics pkg from P. O'Gorman and T. Schneider, JCl, 2008).
+   - re-order sequence of calls within packages_readparms.F,
+      packages_init_fixed.F and packages_write_pickup.F
+     (but skip packages_init_variables.F because of TAF issues).
+   - update contrib/*/atm_gray/ experiment.
+ o pkg/seaice (ITD code):
+   - simplify and fix the writing of pickup-files for ITD case
+ o pkg/seaice (ITD code):
+   - introduce floe size dependent lateral melt for ITD case;
+   - cleaning (avoid division by zero, change to f77 syntax, remove tabs)
+   - update seaice_itd experiment main output.
+ o pkg/thsice:
+   - remove snowPrc from common block THSICE_FLUX, in THSICE_VARS.h and
+     declared it locally (without bi,bj) in thsice_main.F & aim_do_physics.F;
+     changed accordingly pkg/atm2d.
+ checkpoint64g (2013/05/01)
+ o pkg/exf ALLOW_RUNOFTEMP
+   - if defined,  river and glacier runoff temperature can be read-in from
+     runoftempfile; runoftempfile needs to have same format as runofffile
+ o pkg/thsice (& pkg/bulk_force):
+   - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
+     for energy content of Precip + RunOff & Evap (like with pkg/exf).
+   - change computation domain to always be the interior (without overlap).
+   - fix bug (wrong overlap) when using EXF and stressReduction > 0.
+ o verification/tutorial_global_oce_biogeo:
+   - add preliminary OpenAD setup (still has problems)
+ o pkg/seaice:
+   - turn some parameters for choosing the convergence criterion of
+     the inexact Newton method (JFNK) into runtime parameters for convenience
+   - clean up seaice_calc_viscosities.F: remove/retire two options for
+     SEAICetaZmethod (1,2), introduce area weighting for method 3; this changes
+     the results of lab_sea/input because a division has been replaced by
+     a multiplication with the reciprocal (sumNorm)
+   - modify offline_exf_seaice/input.dyn_jfnk/data.seaice to improve
+     convergence of solver (changes results, of course), and to test some
+     new features
+ o model/src:
+   - remove unused (since Aug 2006) S/R SET_WRITE_GLOBAL_PICKUP and its call.
+   - remove unused forcing field "dQdT" and associated parameter "dQdTFile".
+   - move forcing adjustment (balancing surface forcing) in specific S/R
+     where might also be applied exchanges (if needed) to forcing arrays.
+ o pkg/shelfice:
+   - allow to specify the Ice-Shelf mass per unit area (instead of
+     shelficeLoadAnomaly) and do the conversion from one to the other
+   - move loading from file of shelficeLoadAnomaly from SHELFICE_INIT_VARIA
+     to SHELFICE_INIT_FIXED: (a) avoid some TAF recompution issues and
+     (b) will be loaded in time (before calling INI_PRESSURE) in case it is
+     needed in phi0surf for initial pressure calculation when useDynP_inEos_Zc
+   - update isomip experiment forward output (get machine truncation error
+     from conversion shelficeLoadAnomaly -> shelficeMass -> shelficeLoadAnomaly)
+ o verification/offline_exf_seaice:
+   revise data.seaice in input.thermo and input_ad and update results accordingly
+     HO = 0.2, SEAICE_areaLossFormula = 2,
+     SEAICE_growMeltByConv = .TRUE.,
+     SEAICE_doOpenWaterMelt = .TRUE.,
+   Improve consistency with input.thsice and fix the spurious 500m ice corners
+ o verification/global_ocean.cs32x15:
+   - set Energy Reference Level to liq. water @ 0 degC: temp_EvPrRn=0.,
+     in icedyn (thsice+seaice-dyn) test and update output.
+ o verification/offline_exf_seaice:
+   - adjust list of tested variables (with testreport) and update
+     standard test output with better slection of monitored fields.
+ o pkg/cd_code:
+   - swtich off Adams-Bashforth on the 1rst iteration. Update output of
+     experiment lab_sea.hb87
+ o tools/genmake2:
+   - change default makedepend from the system default to tools/xmakedepend:
+     When no makedepend is specified, select tools/xmakedepend it the test pass,
+     otherwise select the system default (if exist and pass the test) or
+     try to build cyrus-makedepend ; stop if none of the 3 works.
+ o pkg/exf & pkg/thsice:
+   - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
+     for energy content of Precip + RunOff & Evap. Assumes:
+) Rain has same temp as Air.
+) Snow has no heat capacity (consistent with seaice & thsice pkgs)
+) Run-Off comes at the temp of surface water (with same Cp)
+) Evap over ocean is released to the Atmos @ surf-temp (=SST); should be
+     put directly into Latent Heat flux & should use water-vapor heat capacity.
+) Evap over snow/seaice (pkg/thsice) assumes constant Lf+Lv (consistent
+     with snow having no Cp) => water vapor is released to Atmos @ 0^oC (=ERL).
+ o pkg/seaice: simplify the use of CPP flags in JFNK-related files
+     (compile when SEAICE_ALLOW_JFNK is defined)
+ o pkg/thsice:
+   - fix oceanic flux diagnostics & timeave (left from new sequence of calls
+     implementation): move THSICE_AVE call after the advection (called directly
+     from thsice_do_advect.F).
+ o verification/global_ocean.90x40x15 and OpenAD:
+   New experiment for OpenAD is identical to the one in input_ad except that
+     multiDimAdvection=.FALSE.,
+   There is still an issue with this.
+ o pkg/thsice:
+   - account for ice velocity (ocean relative velocity) in turbulent heat flux
+     at the base of the ice; update output of global_ocean.cs32x15 (icedyn)
+     and offline_exf_seaice (main test).
+ checkpoint64f (2013/03/31)
+ o verification/OpenAD:
+   - new (smaller, without OAD_DEBUG) output_oadm.txt generated using gfortran.
+ o verification/isomip, pkg/shelfice and OpenAD:
+   - add OpenAD setup to this exp and make shelfice package work with OpenAD
+ o verification/tutorial_global_oce_biogeo:
+   - update AD and TLM output after turning off ALLOW_FE (in DIC_OPTIONS.h)
+ o verification/offline_exf_seaice:
+   - replace adjoint experiment (now similar to fwd input.thermo/ setup).
+ o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD:
+   - add OpenAD setup to this exp and make ptracers package work with OpenAD
+ o pkg/seaice/seaice_evp.F:
+    mask the asymmetric contribution of the ice-ocean stress (when
+    the turningAngle is non-zero) over open water to avoid stripes
+    in the EVP-solutions after many EVP-substeps. This does not change
+    the verification experiment (because turningAngle=0 in that experiment),
+    but will affect other EVP solutions with turningAngle.ne.0
+ o verification, AD & TLM output:
+   - new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple
+     additions and multiplications which affect results at machine truncation
+     level. Update few AD output (1D_ocean_ice_column, bottom_ctrl_5x5,
+     lab_sea.noseaicedyn & offline_exf_seaice) and TLM output
+     (1D_ocean_ice_column & tutorial_tracer_adjsens.som81) which had only 12
+     digits of matching.
+ o pkg/seaice:
+    modify lsr-algorithm so that it vectorizes AND converges by using a
+    "zebra" method: split vector loop into two with step size 2; this
+    solves a general convergence problem for the JFNK solver on a vector
+    computer. It has the potential to even improve convergence for
+    non-vector machines, but it does change the results so it is turned
+    off by default. To turn on define CPP-flags SEAICE_VECTORIZE_LSR and
+    SEAICE_VECTORIZE_LSR_ZEBRA in SEAICE_OPTIONS.h
+ checkpoint64e (2013/03/05)
+ o pkg/ecco and several verification experiments:
+    Remove special versions of the_model_main.F, the_main_loop.F, forward_step.F
+    from ecco package, and revert to unified routine in model/src/
+    Adjust verification experiments accordingly, especially gloal_oce_llc90
+    Should conclude long-standing work by Gael to reconsile the_main_loop with
+    ECCO and will enable OpenAD's revolve loop in ECCO setup.
+ o pkg/generic_advdiff:
+   - implement compressible flow method for multi-dim advection (similar to
+     gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since
+     TAF generates many recomputations) to use it; no yet coded with implicit
+     vertical advection.
+   - change experiment advect_cs (new output) and advect_xy (same output)
+     to test compressible flow multi-dim advection.
+ o pkg/generic_advdiff:
+   - fix SOM advection for unusual cases (linear Free-Surf in r*, other
+     cases where linear Free-Surf is not @ k=1, e.g., useShelfIce)
+ o pkg/seaice:
+   - fix bug in the no-slip implementation in seaice_calc_strainrates.F, this
+     bug affects two verification experiments (lab_sea and lab_sea.hb87),
+     recover old (wrong) results by setting noSlipFac = 2. in
+     seaice_calc_strainrates.F;
+   - add another averaging method for etaZ (etaZmethod=3), a mix of 2 and 0
+   - add runtime parameter SEAICE_JFNKepsilon for that finite difference
+     gradient in the Jacobian times vector operation (s/r seaice_jacvec)
+   - fix line search in seaice_jfnk.F (s/r seaice_jfnk_update)
+ o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code:
+   - new subroutines seaice_lsr_tridiagu/v
+   - introduce loop bounds i/jmin/max to be able to use a restricted
+     additive Schwarz method, but not used for now.
+   - rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS
+   - use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner
+ o OpenAD support
+    Reorganize S/R call for overall time-stepping loop to facilitate
+    OpenAD revolve loop replacement
+    (new S/R main_do_loop.F)
+ o model/src:
+   - add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3;
+   - pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R
+     ADAMS_BASHFORTH2.
+ o pkg/cheapaml:
+   - add new parameter (default=F, same as before) to disable full domain
+     (including land) periodicity in X & Y dir.
+   - new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of
+     prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer
+     into single S/R CHEAPAML_TIMESTEP.
+ checkpoint64d (2013/02/17)
+ o pkg/monitor (angular momentum):
+   - do not add Eta contribution to the total AM if using rigid-lid;
+   - correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta).
+   - horizontal discretisation: compute Zonal wind contribution separately for
+     each component (instead of from cell centered averaged) and use the 4
+     grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part.
+   - Check that AM is conserved with linear dynamics (momAdvection=F and linear
+     FreeSurf) if using vectorInvariant momentum.
+ o model/src (horizontal grid):
+   - move initialisation of all horizontal grid arrays to null value
+     from specific horizontal grid S/R to main S/R INI_GRID;
+   - add 2 new arrays to project model C-grid velocity on to zonal direction
+     (similar to AngleCosC & -AngleSinC but at U and V point location) and
+     compute them in S/R CALC_GRID_ANGLES.
+ o pkg/seaice: replace a hard coded parameter by a runtime parameter
+     SEAICE_JFNK_tolIter
+ o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in
+     preconditioner for JFNK (run LSR into the overlaps as far as possible,
+     i.e OLx/y-2, but overwrite the solution in the overlaps)
+   - extend loop range in seaice_calc_viscosity
+   - add new parameters SEAICE_OLx/y (default = OLx/y-2)
+   - add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs
+   - slightly modify loops in tridiagonal solver lsr-preconditioner
+   - by default remove the extra exchange in seaice_preconditioner with a
+     replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE
+   - modify offline_exf_seaice so that old results without RAS are reproduced
+     for output.dyn_jfnk.txt
+   in seaice_fgmres.F (unrelated to RAS)
+   - add a cpp-flag option for a re-ordered mapping (potentially more
+     efficient), but because this changes the results, turn it off by
+     default
+   - replace the save statement by local common blocks
+ o utils/matlab:
+   - fix tile-offset in rdmnc.m when output was produced using EXCH2.
+   - update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab)
+     instead of local script "load_cs.m".
+ o pkg/seaice:
+   - fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected
+     to the scalarProductMetric and the unrolling. By chance this does not
+     change the verification experiment, because of the particular domain
+     decomposition
+ o pkg/diagnostics:
+   - change default missing_value from UNSET_RL to -999.
+ o pkg/layers: improve vectorization of layers_fluxcalc.F
+   - step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu
+     time spent in this routine by more than a factor of 3 on an NEC-SX8
+   - step 2: replace search algorithm by a bisection algorithm found in
+     Press et al. Numerical Recipes in Fortran. This algorithm can be
+     vectorized and finds the correct bin in approx. log2(Nlayers) steps.
+     For now, use this algorithm only for TARGET_NEC_SX defined.
+   - moved the search algorithm into a separate subroutine, that is kept
+     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.
+) 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,
+) 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
+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 SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget.
-  - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces).
+   - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces).
-  - update results (output.seaice.txt) accordingly.
+   - update results (output.seaice.txt) accordingly.
  o verification/lab_sea/input/data.seaice :
-  - remove SEAICEheatConsFix, which is now be tested
+   - remove SEAICEheatConsFix, which is now be tested
-    in global_ocean.cs32x15. The presently coded fix
+     in global_ocean.cs32x15. The presently coded fix
-    is only consistent with real fresh water + nlfs.
+     is only consistent with real fresh water + nlfs.
-  - update results (output.txt) accordingly.
+   - 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;
+   - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;
-  - remove #include "AD_CONFIG.h" from all included OPTIONS files and
+   - remove #include "AD_CONFIG.h" from all included OPTIONS files and
-    add it explicitly in each fortran src file where it is needed.
+     add it explicitly in each fortran src file where it is needed.
-    motivation: header file AD_CONFIG.h is generated/modified after "make depend"
+     motivation: header file AD_CONFIG.h is generated/modified after "make depend"
-    thus introducing potentially wrong dependency; therefore, better to include
+     thus introducing potentially wrong dependency; therefore, better to include
-    it only where it's really needed, and after any other included OPTIONS file
+     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
+     (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN
-    or ALLOW_TANGENTLINEAR_RUN).
+     or ALLOW_TANGENTLINEAR_RUN).
  checkpoint63p (2012/07/06)
  o pkg/autodiff:

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