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-revision 1.1738 by jmc,
Mon Sep 17 22:32:32 2012 UTC
+revision 1.1937 by jmc,
Wed Nov  6 22:18:19 2013 UTC
 Line 4 
 $Name$
      Notes on tags used in MITgcmUV
      ==============================
+ 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_TILE_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.
+ 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:

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