--- MITgcm/doc/tag-index	2012/12/27 23:16:48	1.1795
+++ MITgcm/doc/tag-index	2013/10/06 00:48:15	1.1928
@@ -1,16 +1,693 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1795 2012/12/27 23:16:48 gforget Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1928 2013/10/06 00:48:15 jmc Exp $
 $Name:  $
 
     Notes on tags used in MITgcmUV
     ==============================
 
+o pkg/exf:
+  - to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice:
+     rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION
+     and rename array obsSIce to exf_iceFraction.
+o tutorial_deep_convection:
+  - add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe),
+    for now all in this exp. code dir.
+  - add secondary test using Smag-3D viscosity (keep very low backgroud visc for
+    testing) and flux-limter advection scheme for Temp. (no explicit diffusion).
+o eesupp/src:
+  - added SINGLE_DISK_IO option because reading of parameter files on
+    very large number of processors did not work with existing set-up
+
+checkpoint64o (2013/09/25)
+o pkg/atm_phys & atm_compon_interf:
+  - allows for coupling of gray-atmosphere (atm_phys) with ocean.
+o tools/build_options:
+  - switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran
+    & linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also
+    remove CPP setting (was identical to genmake2 default).
+o pkg/gmredi & model/src: Some updating and work done on the residual model.
+  - created new file model/src/calc_eddy_stress.F to calculate the eddy stress.
+  - fixed up the calculation of the eddy stress and how it is added to the
+    external forcing via taueddy_external_forcing.F
+  - at the moment, it is very experimental and only works with the variable eddy
+    diffusivity calculated in gmredi_k3d.F
+o pkg/seaice/seaice_check.F: add a check to catch the case of specifying
+    lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice
+o testreport (& tools/do_tst_2+2):
+  - for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}'
+o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11:
+  - remove CPP='cpp -traditional -P' (this is genmake2 default)
+  - add switch (for big setups) to use 'medium' memory-model (but leave it
+    commented out for now). Note: needed with FC 19 to compile big setups.
+o pkg/atm_compon_interf:
+  - regroup per field origin (model & pkgs) the coupling storage routines
+     (which accumalate in time each coupling field)
+  - move bi,bj loops inside atm_store_my_data.F and store also wind-stress;
+    update accordingly + simplify aim_do_physics.F
+
+checkpoint64n (2013/08/26)
+o pkg/bbl:
+  - update formulation to reduce dispersion of tracer properties in bbl
+  - replaced horizontal and vertical transport parameters with velocities
+  - changes results for verification/global_with_exf.yearly
+o verification/halfpipe_streamice:
+  - change to matrix construction; update both Fwd & AD output.
+o verification/tutorial_tracer_adjsens:
+  - OpenAD test: switch to vector-invariant momentum since fluxform with
+    rStar causes problems with OpenAD; update output.
+o tools:
+  - genmake2: define a common prefix for all temp-file names ; move them
+    to local /tmp disk (but would be easy to move them back);
+  - xmakedepend: apply the same switch for temp-files.
+o pkg/offline:
+  - changes for use with rStar (NLFS): assume that we continue to provide
+    UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid
+    output files) and apply r* scaling at each time-step (function of the time
+    varying Eta field); use normal pickup files (needed for restart with NLFS).
+o adjoint with OpenAD:
+  - move OpenAD-specific files from verification/OpenAD/code_oad_all to a new
+    package openad.  This package has to be compiled for all runs with OpenAD
+    instead of specifying code_oad_all as a modification directory.
+  - link the fortran templates from tools/OAD_support to the build directory
+    for preprocessing to avoid conflicts between different setups compiled
+    simultaneously and simplify cleanup.
+o pkg/exf:
+  - in exf_getforcing.F: comment out most of the EXCH calls (fields used by
+    main model or other pkgs are exchanged in EXF_MAPFIELDS).
+o model/src:
+  - do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline
+    (similar to do_fields_blocking_exchanges.F).
+o tools/genmake2:
+  - remove TAF output src code just before calling staf (when not doing a fresh
+    built, will stop if things go wrong with staf).
+  - fix target "adobj" (left from TAF version-2 transition)
+o pkg/diagnostics:
+  - add a parameter to track the status of pkg/diagnostics activation;
+    this replace/extend the use of logical param "settingDiags" (to check
+    when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call.
+    New S/R to print error message and stop when pkgStatus is not right.
+  - to try: add a warning when "data.diagnostics" exist but useDiagnostics=F.
+
+checkpoint64m (2013/08/13)
+o model/inc:
+  - move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from
+    8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h)
+o pkg/kpp & aim_v23:
+  - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
+o pkg/seaice:
+  - restore (last time on 2011/12/24) ability to compile pkg/seaice with
+    undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options.
+  - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
+o eesupp/src:
+  - fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH)
+    in exch1_rx[_ad].template (thanks to Francois Lefeuvre report).
+o switch to TAF version-2:
+  - add flow directives to "freeze" naming convention for ad-routines that
+    are used in I/O routines of adjoint state and associated common blocks
+    that are used in adcommon.h (backward compatible with version-1)
+  - update all ad-optfiles (in tools/adjoint_options + few local to some
+    verification exp) to switch to latest TAF version (currently 2.5.5);
+    merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented
+    out except for diva).
+  - the major change with TAF version-2 is that both the differentiated
+    routines and the forward routines (new) are returned as part of the TAF
+    output source code. Update genmake2 accordingly.
+  - new output for AD experiment tutorial_global_oce_biogeo (better AD gradient
+    with version-2 when compared to TLM or FWD gradient); other experiments
+    output show minor changes (machine truncation level); update the few AD &
+    TLM output with 12 matching digits only (some prior to version-2 switch).
+
+checkpoint64l (2013/08/05)
+o model/src:
+  - in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F
+  - main_do_loop.F: no longer includes additional (AUTODIFF) header files
+    when using TAF but only if using OpenAD.
+o pkg/mom_common+fluxform+vecinv:
+  - always set horiz. viscosity arrays to background value before calling
+    MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC
+    only when using variable horiz. viscosity (useVariableVisc=T);
+  - simplify mom_vecinv.F (only 1 block for momViscosity).
+o pkg/mom_common: variable horiz. viscosity in NH code
+  - move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F)
+    from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h
+  - store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc,
+    useBiharmonicVisc & useVariableVisc.
+  - fix old bug (already in 1rst implementation of variable horizontal viscosity
+    in calc_gw.F, version 1.27, 2006/06/20):
+    horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0
+    even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero.
+  - change background horiz viscosity in vertical momentum (gW) to always be
+    viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using
+    any type of variable viscosity, e.g., viscAh/4Grid)
+  - change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of
+    viscAh,viscA4) which default to viscAh,viscA4 :  this avoid missing
+    horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since
+    default viscAh,viscA4 is zero).
+o model/src:
+  - extend length of drC & recip_drC from Nr to Nr+1.
+o Divided Adjoint (DIVA) with MPI:
+  - genmake2: do not create local ./mpi_headers dir when no file to copy into.
+  - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT
+    and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h.
+
+checkpoint64k (2013/07/23)
+o tools/OAD_support:
+  - avoid the need for file "oadtempflile" in insertTemplateDir.bash
+    and remove it from genmake2.
+o tools/build_options:
+  - remove MPI_HEADER_FILES_INC setting (no longer used) and comment out
+    MPI_HEADER_FILES list (let genmake2 find the missing headers)
+o verification/halfpipe_streamice:
+  - change to driving stress formulation; update both Fwd & AD output.
+o tools/genmake2 and Divided Adjoint with MPI:
+  - remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken);
+  - only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set;
+  - add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in
+    Makefile, which is set by genmake2, and check which mpi-headers are needed.
+    Note: need to update adjoint_options/adjoint_diva_mpi accordingly.
+  - update target "CLEAN" (to also remove ./mpi_headers/ dir).
+o testreport:
+  - changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present,
+    perform additional runs (number of additional runs is "add_DIVA_runs" taken
+    from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h").
+o verification/lab_sea (AD test):
+  - change to test Divided Adjoint Run in this set-up (both standard AD test
+    and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test.
+o pkg atm_ & ocn_compon_interf:
+  - remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old
+    staggerTimeStep implementation) and disable (retired) corresponding
+    parameter.
+o pkg/offline:
+  - comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01];
+  - add S/R OFFLINE_CHECK to print offline parameter summary
+    and stop if loading a file that is not used;
+  - enable to calculate GMRedi tensor, KPP mixing and convective index
+    when the corresponding file(s) is/are not specified (but pkg is used).
+  - comment out resetting of monitorFreq (to endTime) since it still useful
+    for monitoring CFL numbers and checking offline fields.
+o OpenAD:
+  - do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get
+    smaller standard output) and generate new (smaller) output (on baudelaire
+    using gfortran with -ieee) for exp. tutorial_tracer_adjsens
+o model/src:
+  - call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F),
+    (where external_forcing_adjust was called) and change list of arguments;
+  - merge external_forcing_adjust.F into external_forcing_surf.F
+  - put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F)
+    which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX,
+    previously in file "balance_relax.F", now removed); remove corresponding
+    arrays in FFIELDS.h.
+  - EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement
+    a hack for getting back surfaceForcingS (loaded from file) when using
+    ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up.
+  - update output of AD test experiment global_ocean.cs32x15.seaice_dynmix
+    (was getting only 11 digits for AD-grad, due to different truncation
+     error in AD code).
+
+checkpoint64j (2013/07/04)
+o pkg/offline:
+  - to enable the use of other features with pkg offline (e.g., obcs),
+    also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come.
+  - comment out "allowFreezing" (now active) in 2 offline testing exp.
+o pkg/exf ALLOW_RUNOFTEMP
+  - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL
+  - ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice
+  - changes verification/global_ocean.cs32x15/results/output.seaice.txt
+o pkg/atm_phys:
+  - allows to add some damping on uVel,vVel (strength only function of k).
+o verification, ad-tests:
+  - reduce length of the simulation for AD test: global_ocean.cs32x15.seaice,
+    global_ocean_ebm and offline_exf_seaice.thsice.
+o verification/halfpipe_streamice:
+  - found a bug in s/r pkg/streamice/streamice_advect_thickness which caused
+    flux input boundary conditions to be ignored; a fix for this bug changed
+    verification results for forward test.
+  - add adjoint test.
+o pkg/ptracers:
+  - allow to restart without SOM pickup (resetting SOM to zero).
+o pkg/gmredi:
+  - New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added.
+  - It uses mixing length theory and suppression by steering level effects to
+    calculate a diffusivity used in the Redi tensor (see Bates et al., submitted
+    to JPO, for more details).
+  - It also uses the diffusivity to calculate an eddy induced streamfunction
+    based on a PV closure (rather than a buoyancy closure as in GM).
+  - New files added to pkg/gmredi:
+    gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy
+      induced overturning streamfunction (called from gmredi_calc_tensor)
+    gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required
+      for use in gmredi_k3d
+    gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate
+      the eddy diffusivity
+
+checkpoint64i (2013/06/18)
+o pkg/cheapaml:
+  - take src files from MITgcm_contrib/verification_other/offline_cheapaml/code
+    that enable the use of seaice (pkg/thsice thermo & pkg/seaice dynamics)
+    with pkg/cheapaml.
+o utils/python: add subpackage for cubed sphere function, first example is
+    simple cs.pcol to plot 2D fields on a map
+o pkg/streamice:
+  - This is a new package in MITgcm, which solves dynamic equations for ice
+     sheets and ice streams
+  - At the moment it is independent of atmosphere/ocean dynamics, or any
+    other physical packages in MITgcm, even ShelfIce (although it is anticipat-
+    ed that this will change)
+  - There is a new verification exercise that tests it, halfpipe_streamice,
+    evolves a 40x80 km ice stream/ice shelf (at coarse resolution) in a
+    rectangular embayment
+  - halfpipe_streamice is forward-only for now, will have TAF test soon
+  - for questions, email dgoldber@mit.edu
+o pkg/thsice:
+  - fix filling of snow-precip diagnostic (SIsnwPrc) (left from the removing
+    of snowPrc from common bloc, on May 2nd, thsice_step_fwd.F revision 1.40);
+  - remove diagnostics 'SI_FrcFx' ( now identical to 'SI_Fract' with new
+     call sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect );
+  - allow precip from pkg/cheapaml to make snow over seaice.
+o pkg/cfc:
+  - move in separated header file (CFC_ATMOS.h) time-serie arrays of Atmos CFC
+  - remove atmos CFC 2-D arrays from common bloc (now local variables)
+  - change some hard-coded constant to run time parameter for reading and
+    and interpolating atmospheric CFC ; keep same default as previously.
+  - more flexible reading of Atmos CFC (number of records no longer hard-coded)
+  - put arguments in standard order: myTime, myIter, myThid
+  - use standard S/R GET_PERIODIC_INTERVAL for time interpolation of
+    atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.
+  - fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf
+  - new routine to print summary of CFC params and check for consistency.
+o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff,
+  similar to thsice_advdiff.
+  Note that for the B-grid case the routine parameters uc/vc are overwritten.
+o pkg/cfc:
+  - change time interpolation for atmospheric CFC-11 (now same as for CFC-12);
+    update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline.
+  - fix interpolation of atmphspheric CFC between Sorthern and Northern
+    hemisphere value.
+o pkg/seaice:
+  - allow to use seaice dynamics without pkg/exf (e.g., using pkg/cheapaml)
+o pkg/seaice: add Adams-Bashforth2 time discretization for ice dynamics;
+              so far only for JFNK-solver, turn on with SEAICEuseAB2 = .TRUE.
+  - requires an additional time level that is stored in the pickup
+  - you can start with AB2 from a pickup without this time level with
+    pickupStrictlyMatch = .false.
+
+checkpoint64h (2013/05/26)
+o pkg/cheapaml:
+  - replace one ()**.5 with SQRT + use temp var "cdu = tau/Du" (coare3_flux);
+    affect machine truncation (but exp cheapAML_box still pass with 13 digits).
+  - consistent treatment of uWind,vWind location: assume everywhere in
+    pkg/cheapaml that they are on C-grid (@ uVel,vVel location)
+    (Note: was already the case for Tair,Qair advection);
+    add option (INCONSISTENT_WIND_LOCATION) to recover old results.
+  - compute diabatic forcing only in the interior (excluding overlap regions)
+  - fill in array "Qsw" (for short-wave heating);
+  - add diagnostic for precip ; fill-in diagnostics for cheapAML state vars
+    before any update (consistent with MITgcm state var diagnostics);
+  - cheapaml_fields_load.F & cheapaml_init_varia.F : only fill outer edges if
+    non periodic ; + adjusted for uWind,vWind (C-grid).
+o pkg/seaice:
+  - remove dependence of pkg/seaice versus pkg/exf (file: pkg/pkg_depend) and
+    add explicitly pkg/exf in experiments that currently use pkg/seaice.
+  - allows to compile pkg/seaice without pkg/exf.
+o tools/OAD_support:
+  - use a local copy (ourRWCPinBd) to ensure index ourRWCP stays within bounds
+    of array "ourStepOf" in function rvNextAction (revolve.F90).
+o pkg/aim_compon_interf renamed to pkg/atm_compon_interf
+  - change pkg name (to be used with other atmospheric physics pkg)
+    but by-pass CVS when making the new pkg so that we keep the CVS history.
+o pkg/offline:
+  - call OFFLINE_FIELDS_LOAD from pkg/offline/offline_init_varia.F
+    (previously called from pkg/dic_surfforcing_init.F)
+o model/src:
+  - re-order sequence of calls within packages_init_variables.F, using
+    standard order, except for:
+     DIAGNOSTICS_INIT_VARIA and OFFLINE_INIT_VARIA (called @ the top),
+     CTRL_MAP_INI and OBCS_INIT_VARIABLES (called @ the bottom)
+o new pkg: atm_phys
+  - add entry point and source code (previously in contrib
+      verification_other/atm_gray/code_gray/) for new pkg "atm_phys"
+    (atmospheric physics pkg from P. O'Gorman and T. Schneider, JCl, 2008).
+  - re-order sequence of calls within packages_readparms.F,
+     packages_init_fixed.F and packages_write_pickup.F
+    (but skip packages_init_variables.F because of TAF issues).
+  - update contrib/*/atm_gray/ experiment.
+o pkg/seaice (ITD code):
+  - simplify and fix the writing of pickup-files for ITD case
+o pkg/seaice (ITD code):
+  - introduce floe size dependent lateral melt for ITD case;
+  - cleaning (avoid division by zero, change to f77 syntax, remove tabs)
+  - update seaice_itd experiment main output.
+o pkg/thsice:
+  - remove snowPrc from common block THSICE_FLUX, in THSICE_VARS.h and
+    declared it locally (without bi,bj) in thsice_main.F & aim_do_physics.F;
+    changed accordingly pkg/atm2d.
+
+checkpoint64g (2013/05/01)
+o pkg/exf ALLOW_RUNOFTEMP
+  - if defined,  river and glacier runoff temperature can be read-in from
+    runoftempfile; runoftempfile needs to have same format as runofffile
+o pkg/thsice (& pkg/bulk_force):
+  - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
+    for energy content of Precip + RunOff & Evap (like with pkg/exf).
+  - change computation domain to always be the interior (without overlap).
+  - fix bug (wrong overlap) when using EXF and stressReduction > 0.
+o verification/tutorial_global_oce_biogeo:
+  - add preliminary OpenAD setup (still has problems)
+o pkg/seaice:
+  - turn some parameters for choosing the convergence criterion of
+    the inexact Newton method (JFNK) into runtime parameters for convenience
+  - clean up seaice_calc_viscosities.F: remove/retire two options for
+    SEAICetaZmethod (1,2), introduce area weighting for method 3; this changes
+    the results of lab_sea/input because a division has been replaced by
+    a multiplication with the reciprocal (sumNorm)
+  - modify offline_exf_seaice/input.dyn_jfnk/data.seaice to improve
+    convergence of solver (changes results, of course), and to test some
+    new features
+o model/src:
+  - remove unused (since Aug 2006) S/R SET_WRITE_GLOBAL_PICKUP and its call.
+  - remove unused forcing field "dQdT" and associated parameter "dQdTFile".
+  - move forcing adjustment (balancing surface forcing) in specific S/R
+    where might also be applied exchanges (if needed) to forcing arrays.
+o pkg/shelfice:
+  - allow to specify the Ice-Shelf mass per unit area (instead of
+    shelficeLoadAnomaly) and do the conversion from one to the other
+  - move loading from file of shelficeLoadAnomaly from SHELFICE_INIT_VARIA
+    to SHELFICE_INIT_FIXED: (a) avoid some TAF recompution issues and
+    (b) will be loaded in time (before calling INI_PRESSURE) in case it is
+    needed in phi0surf for initial pressure calculation when useDynP_inEos_Zc
+  - update isomip experiment forward output (get machine truncation error
+    from conversion shelficeLoadAnomaly -> shelficeMass -> shelficeLoadAnomaly)
+o verification/offline_exf_seaice:
+  revise data.seaice in input.thermo and input_ad and update results accordingly
+    HO = 0.2, SEAICE_areaLossFormula = 2,
+    SEAICE_growMeltByConv = .TRUE.,
+    SEAICE_doOpenWaterMelt = .TRUE.,
+  Improve consistency with input.thsice and fix the spurious 500m ice corners
+o verification/global_ocean.cs32x15:
+  - set Energy Reference Level to liq. water @ 0 degC: temp_EvPrRn=0.,
+    in icedyn (thsice+seaice-dyn) test and update output.
+o verification/offline_exf_seaice:
+  - adjust list of tested variables (with testreport) and update
+    standard test output with better slection of monitored fields.
+o pkg/cd_code:
+  - swtich off Adams-Bashforth on the 1rst iteration. Update output of
+    experiment lab_sea.hb87
+o tools/genmake2:
+  - change default makedepend from the system default to tools/xmakedepend:
+    When no makedepend is specified, select tools/xmakedepend it the test pass,
+    otherwise select the system default (if exist and pass the test) or
+    try to build cyrus-makedepend ; stop if none of the 3 works.
+o pkg/exf & pkg/thsice:
+  - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
+    for energy content of Precip + RunOff & Evap. Assumes:
+   1) Rain has same temp as Air.
+   2) Snow has no heat capacity (consistent with seaice & thsice pkgs)
+   3) Run-Off comes at the temp of surface water (with same Cp)
+   4) Evap over ocean is released to the Atmos @ surf-temp (=SST); should be
+    put directly into Latent Heat flux & should use water-vapor heat capacity.
+   5) Evap over snow/seaice (pkg/thsice) assumes constant Lf+Lv (consistent
+    with snow having no Cp) => water vapor is released to Atmos @ 0^oC (=ERL).
+o pkg/seaice: simplify the use of CPP flags in JFNK-related files
+    (compile when SEAICE_ALLOW_JFNK is defined)
+o pkg/thsice:
+  - fix oceanic flux diagnostics & timeave (left from new sequence of calls
+    implementation): move THSICE_AVE call after the advection (called directly
+    from thsice_do_advect.F).
+o verification/global_ocean.90x40x15 and OpenAD:
+  New experiment for OpenAD is identical to the one in input_ad except that
+    multiDimAdvection=.FALSE.,
+  There is still an issue with this.
+o pkg/thsice:
+  - account for ice velocity (ocean relative velocity) in turbulent heat flux
+    at the base of the ice; update output of global_ocean.cs32x15 (icedyn)
+    and offline_exf_seaice (main test).
+
+checkpoint64f (2013/03/31)
+o verification/OpenAD:
+  - new (smaller, without OAD_DEBUG) output_oadm.txt generated using gfortran.
+o verification/isomip, pkg/shelfice and OpenAD:
+  - add OpenAD setup to this exp and make shelfice package work with OpenAD
+o verification/tutorial_global_oce_biogeo:
+  - update AD and TLM output after turning off ALLOW_FE (in DIC_OPTIONS.h)
+o verification/offline_exf_seaice:
+  - replace adjoint experiment (now similar to fwd input.thermo/ setup).
+o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD:
+  - add OpenAD setup to this exp and make ptracers package work with OpenAD
+o pkg/seaice/seaice_evp.F:
+   mask the asymmetric contribution of the ice-ocean stress (when
+   the turningAngle is non-zero) over open water to avoid stripes
+   in the EVP-solutions after many EVP-substeps. This does not change
+   the verification experiment (because turningAngle=0 in that experiment),
+   but will affect other EVP solutions with turningAngle.ne.0
+o verification, AD & TLM output:
+  - new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple
+    additions and multiplications which affect results at machine truncation
+    level. Update few AD output (1D_ocean_ice_column, bottom_ctrl_5x5,
+    lab_sea.noseaicedyn & offline_exf_seaice) and TLM output
+    (1D_ocean_ice_column & tutorial_tracer_adjsens.som81) which had only 12
+    digits of matching.
+o pkg/seaice:
+   modify lsr-algorithm so that it vectorizes AND converges by using a
+   "zebra" method: split vector loop into two with step size 2; this
+   solves a general convergence problem for the JFNK solver on a vector
+   computer. It has the potential to even improve convergence for
+   non-vector machines, but it does change the results so it is turned
+   off by default. To turn on define CPP-flags SEAICE_VECTORIZE_LSR and
+   SEAICE_VECTORIZE_LSR_ZEBRA in SEAICE_OPTIONS.h
+
+checkpoint64e (2013/03/05)
+o pkg/ecco and several verification experiments:
+   Remove special versions of the_model_main.F, the_main_loop.F, forward_step.F
+   from ecco package, and revert to unified routine in model/src/
+   Adjust verification experiments accordingly, especially gloal_oce_llc90
+   Should conclude long-standing work by Gael to reconsile the_main_loop with
+   ECCO and will enable OpenAD's revolve loop in ECCO setup.
+o pkg/generic_advdiff:
+  - implement compressible flow method for multi-dim advection (similar to
+    gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since
+    TAF generates many recomputations) to use it; no yet coded with implicit
+    vertical advection.
+  - change experiment advect_cs (new output) and advect_xy (same output)
+    to test compressible flow multi-dim advection.
+o pkg/generic_advdiff:
+  - fix SOM advection for unusual cases (linear Free-Surf in r*, other
+    cases where linear Free-Surf is not @ k=1, e.g., useShelfIce)
+o pkg/seaice:
+  - fix bug in the no-slip implementation in seaice_calc_strainrates.F, this
+    bug affects two verification experiments (lab_sea and lab_sea.hb87),
+    recover old (wrong) results by setting noSlipFac = 2. in
+    seaice_calc_strainrates.F;
+  - add another averaging method for etaZ (etaZmethod=3), a mix of 2 and 0
+  - add runtime parameter SEAICE_JFNKepsilon for that finite difference
+    gradient in the Jacobian times vector operation (s/r seaice_jacvec)
+  - fix line search in seaice_jfnk.F (s/r seaice_jfnk_update)
+o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code:
+  - new subroutines seaice_lsr_tridiagu/v
+  - introduce loop bounds i/jmin/max to be able to use a restricted
+    additive Schwarz method, but not used for now.
+  - rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS
+  - use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner
+o OpenAD support
+   Reorganize S/R call for overall time-stepping loop to facilitate
+   OpenAD revolve loop replacement
+   (new S/R main_do_loop.F)
+o model/src:
+  - add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3;
+  - pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R
+    ADAMS_BASHFORTH2.
+o pkg/cheapaml:
+  - add new parameter (default=F, same as before) to disable full domain
+    (including land) periodicity in X & Y dir.
+  - new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of
+    prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer
+    into single S/R CHEAPAML_TIMESTEP.
+
+checkpoint64d (2013/02/17)
+o pkg/monitor (angular momentum):
+  - do not add Eta contribution to the total AM if using rigid-lid;
+  - correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta).
+  - horizontal discretisation: compute Zonal wind contribution separately for
+    each component (instead of from cell centered averaged) and use the 4
+    grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part.
+  - Check that AM is conserved with linear dynamics (momAdvection=F and linear
+    FreeSurf) if using vectorInvariant momentum.
+o model/src (horizontal grid):
+  - move initialisation of all horizontal grid arrays to null value
+    from specific horizontal grid S/R to main S/R INI_GRID;
+  - add 2 new arrays to project model C-grid velocity on to zonal direction
+    (similar to AngleCosC & -AngleSinC but at U and V point location) and
+    compute them in S/R CALC_GRID_ANGLES.
+o pkg/seaice: replace a hard coded parameter by a runtime parameter
+    SEAICE_JFNK_tolIter
+o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in
+    preconditioner for JFNK (run LSR into the overlaps as far as possible,
+    i.e OLx/y-2, but overwrite the solution in the overlaps)
+  - extend loop range in seaice_calc_viscosity
+  - add new parameters SEAICE_OLx/y (default = OLx/y-2)
+  - add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs
+  - slightly modify loops in tridiagonal solver lsr-preconditioner
+  - by default remove the extra exchange in seaice_preconditioner with a
+    replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE
+  - modify offline_exf_seaice so that old results without RAS are reproduced
+    for output.dyn_jfnk.txt
+  in seaice_fgmres.F (unrelated to RAS)
+  - add a cpp-flag option for a re-ordered mapping (potentially more
+    efficient), but because this changes the results, turn it off by
+    default
+  - replace the save statement by local common blocks
+o utils/matlab:
+  - fix tile-offset in rdmnc.m when output was produced using EXCH2.
+  - update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab)
+    instead of local script "load_cs.m".
+o pkg/seaice:
+  - fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected
+    to the scalarProductMetric and the unrolling. By chance this does not
+    change the verification experiment, because of the particular domain
+    decomposition
+o pkg/diagnostics:
+  - change default missing_value from UNSET_RL to -999.
+o pkg/layers: improve vectorization of layers_fluxcalc.F
+  - step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu
+    time spent in this routine by more than a factor of 3 on an NEC-SX8
+  - step 2: replace search algorithm by a bisection algorithm found in
+    Press et al. Numerical Recipes in Fortran. This algorithm can be
+    vectorized and finds the correct bin in approx. log2(Nlayers) steps.
+    For now, use this algorithm only for TARGET_NEC_SX defined.
+  - moved the search algorithm into a separate subroutine, that is kept
+    within the same file for automatic inlining.
+  - modified catching potential errors
+o pkg/ecco:
+  - add compile switches ALLOW_SHALLOW_ALTIMETRY and ALLOW_HIGHLAT_ALTIMETRY.
+o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk :
+  - modifications for ALLOW_GENTIM2D_CONTROL
+  -- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes.
+  -- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid )
+  -- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc
+  -- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F
+o model/src:
+  - account for moist thermodynamics in (dry) potential temperature equation;
+    update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev)
+    and cpl_aim+ocn.
+  - also switch to standard compiler (gfortran, was using ifort previously)
+    for fizhi-cs experiments reference output.
+o pkg/ctrl:
+  - 1st step toward generic time-varying control variable (2D) via CPP option
+    ALLOW_GENTIM2D_CONTROL
+  - note new namelist ctrl_nml_genarr in data.ctrl
+o verification/global_ocean.cs32x15:
+  - switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new
+    thsice calling sequence and update "output.icedyn.txt" output file.
+o pkg/ptracers:
+  - from Ryan A.: code to allow to restart a tracer at regular time interval
+    specifying a reset frequency and a reset-phase (for each tracers).
+o pkg/thsice:
+  - implement new sequence of calls for thsice+seaice:
+      previously:   ice-Dyn,ice-Advect,ice-Thermo(thsice)
+      new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect
+  - allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE"
+    in CPP_OPTIONS.h) to recover old sequence;
+  - update diagnostics for Intermediate State thsice diagnostics: now filled
+    just before advection (instead of just after advection in old sequence);
+  - update output of experiment offline_exf_seaice (standard test);
+  - in global_ocean.cs32x15 exp., postpone output.icedyn.txt update
+    by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h
+o pkg/aim_v23:
+  - use tiled array for aim_CO2 and surface wind speed for export to coupler;
+  - use standard pkg/mdsio routines to read & write CO2 pickup file;
+  - in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F;
+  - Implement new sequence of calls for seaice advection (with thsice and
+    seaice diffusion): do ice advection after ice-Thermodynamic (previously
+    was done before); change aim_do_physics.F (split the bi,bj loops block);
+  - use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence;
+o pkg/thsice:
+  - add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case
+    where just seaice diffusion is used without seaice-dynamics.
+
+checkpoint64c (2013/01/18)
+o pkg/seaice:
+  - add a parameter JFNKres_tFac that can replace JFNKres_t
+    (= JFNKres_tFac*JFNKresidual before JFNK solver)
+  - add a line search option to the JFNK solver
+  - move update of u/vIce and computation of initial residual into a separate
+    routine (same file); makes the code a little easier to read (?)
+  - the line search requires computation of the residual and for some reason
+    I cannot do the update of u/vIce at the beginning of the Newton loop
+    without changing the results, so we move computation of the new residual
+    also to the end of the Newton loop, even without the line search
+o pkg/mdsio:
+  - write missing value (corresponding to undefined array value) to meta files;
+    skip this if missing value is one (UNSET_RL would be a better value for the
+    case of undefined missing value but it's current the default missing-value);
+    Also update mdsio_read_meta.F (reading timeInterval & missing-value).
+o pkg/exf & thsice:
+  - for diagnostics purpose, fill-up and update Qsw array (+ fill the
+    diagnostics) even when SHORTWAVE_HEATING is #undef;
+o verification/cfc_example:
+  - turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to
+    illustrate how to use it).
+o verification/offline_exf_seaice:
+  in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing
+    files to only one time-record.
+  in input.thermo: narrow the 2 bands of low initial ice-concentration near
+    N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for
+    snapshot output; same mcPheePiston value as in thsice with
+    surf-current=0.2m/s.
+  in input.thsice: similar set-up as in input.thermo (channel with same seaice
+    initial conditions).
+o verification/cfc_example:
+  - update file "data" with more standard choice (default rotationPeriod,
+    exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F,
+    set deltaTFreeSurf to deltaTtracer) and update the output.
+o pkg/layers:
+  - fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC;
+  - ensure that "layers_bolus" is switched to False when useGMRedi=False.
+o verification/offline_exf_seaice:
+  - set all {field}period to zero for constant-in-time forcing (not tested
+    anywhere else).
+o verification/offline_exf_seaice:
+  - dyn_lsr  : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice;
+  - dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice.
+o model/src:
+  - implement Finite-Volume method for (hydrostatic) presure gradient
+    from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate.
+o pkg/seaice: implement EVP* by Lemieux et al. (2012).
+  - In order to be compatible with the default EVP code, this requires changing
+    the EVP code around a little; and because any small change immediately
+    breaks the lab_sea.hb87 verification experiment, the reference output is
+    updated two times (each time the remaining aggrement was only 2 digits):
+    - after replacing 1/dt by 1*recip_dt with a precomputed recip_dt
+    - after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt
+    The adjoint test lab_sea.evp also needed to be updated.
+  - Turn on EVP* by setting SEAICE_deltaTevp as before, and setting
+    SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be
+    a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps
+    explicitly with SEAICEnEVPstarSteps (thereby overriding the default of
+    INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately
+    kept obscure, because I need to test it a little more.
+o pkg/cheapaml:
+  - fix few incorrect type (_RL/_RS) in subroutine calls.
+o pkg/seaice:
+  - new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays
+    to _RL vector; this fixes JFNK code when compiling with "-use_r4" option.
+o model/src:
+  - add a warning if using select_rStar=2 with nonlinFreeSurf <> 4;
+    change (in input_ad*/data) select_rStar from 2 to 1 for AD verification
+    experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output)
+o pkg/cheapaml:
+  - replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and
+    update output of experiment cheapAML_box.
+  - store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity,
+    and set them only in one place (cheapaml_readparms.F).
+  - replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI"
+  - remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms)
+    and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia).
 o model/src/the_main_loop.F:
   - fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION.
 o pkg/seaice:
   - remove legacy branch code.
   - retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly.
 o verification/*/code*/SEAICE_OPTIONS.h:
-  - remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY, SEAICE_CAP_HEFF).
+  - 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.