--- MITgcm/doc/tag-index	2010/05/07 18:37:44	1.1264
+++ MITgcm/doc/tag-index	2010/12/16 08:34:01	1.1349
@@ -1,19 +1,449 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1264 2010/05/07 18:37:44 gforget Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1349 2010/12/16 08:34:01 mlosch Exp $
 $Name:  $
 
     Notes on tags used in MITgcmUV
     ==============================
 
+o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
+  - first attempt to close budgets by taking into account the freshwater
+    flux implied by the sublimation of snow and ice. So far only the 
+    volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
+    SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
+o eesupp/src:
+  new S/R with new option (NML_EXTENDED_F77) to change array specification
+  from F95 standard to commonly accepted extended F77 form.
+  This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
+  and to revert back to the original syntax (with -DNML_EXTENDED_F77)
+  for less tolerant f77 compiler (e.g., pgf77, g77).
+o globalFiles:
+  commented out in parameter file "data" since it's not safe with MPI
+  (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
+  in this case); no longer commented out in restart test (tst_2+2).
+o add adTapeDir to specify a special directory where adjoint tapes are
+  written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
+  and cannot be used together with mdsioLocalDir.
+o nesting pkgs:
+  - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
+  - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
+  - add parameter files + utils dir + output from short run on beagle.
+o pkg/seaice:
+    fix seaice_growth.F store directives; update results of exp. lab_sea.ad
+o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
+  unnecessary copying in adjoint code, requires new parameter NMAX_ITER
+
+checkpoint62o (2010/11/25)
+o pkg/exf:
+  - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
+o pkg/seaice:
+  - seaice_ocean_stress: split a loop for better vectorization of the
+    adjoint code
+  - seaice_growth.F: fix bug in conservation of freshwater connected to
+    capping of heff, put contribution into d_HEFFbyNEG
+  - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
+    by something more sensible (parameters that are what their name implies)
+  - change some defaults, so that by default exf-parameters are used for
+    things like rhoAir, cpAir,latent/sensible heat parameters, in order
+    to reproduce the old results, many data.seaice now contain funny values
+    for cpAir and latent heat of sublimation
+o packages_readparms.F: move exf_readparms up in line so that
+    exf-parameters are visible for other packages (e.g. seaice)
+o debugMode & debugLevel=2:
+  - differentiate between debugMode & debugLevel=2:
+    debugMode: controls printing of debug messages (sequence of S/R calls).
+    debugLevel: controls printing of algorithm intermediate results and stats.
+  - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
+    => allows to print debug-stats without all sequence of call messages.
+  - switch control of debug print from debugLevel to debugMode in many S/R.
+o pkg/obcs (obcs-sponge):
+    fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
+    call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
+o pkg/generic_advdiff:
+  - record overlap minimum size for each advection scheme;
+  - refine criteria on overlap minimum size;
+  - check and stop (in gad_check) if overlap size is too small.
+o pkg/obcs:
+  - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
+    once, in ptracers_implicit.F)
+  - with seaice: remove test on empty file name in obcs_apply_seaice (always
+    apply OB values when tile has OB)
+o model/src, coriolis setting:
+  - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
+    useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
+    files (selectCoriMap=3) with any grid.
+  - add parameter "fPrime" for constant second Coriolis coeff (default=0).
+o pkg/seaice/seaice_growth.F:
+    a few cosmetic changes that reduce the number of lines of code
+o pkg/obcs: add boundary conditions following Stevens (1990)
+  - the code follows old MOM/NAOSIM code
+  - so far it is only implemented for the eastern and western boundaries
+    and NOT for pTracers
+o pkg/rbcs:
+  - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
+    beginning of the first rbcs forcing period.
+  - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
+    offline package, i.e., one file per time, labeled by iteration number;
+    deltaTrbcs sets the timestep with which the data was generated;
+    rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
+  - rbcsForcingCycle=0 makes forcing non-cyclic.
+  - make arithmetic safe for negative times and odd forcing periods.
+
+checkpoint62n (2010/11/09)
+o pkg/seaice:
+    fix masking in free-drift S/R ; update results of exp. lab_sea.fd
+o pkg/obcs:
+   New S/R to copy tracer value from the OB location to narrow band region
+    (width = same as overlap) beyond the OB: preserve OB value (needed for
+    high-order scheme) which were overwritten by EXCH call if in overlap
+    region. Applied to theta, salt, ptracer and advected seaice variables.
+   With seaice: use maskInC in similar way as in gad_advection.F,
+    in seaice_advection.F and advect.F.
+   Update output of experiment seaice_obcs and change exp4 to test OBCS with
+    4th order Adv.Scheme. for pasive salt and ptracer.
+o tools/genmake2:
+  - when looking for an optfile (not specified), only search for Fortran compiler
+    (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
+  - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
+    (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
+  - set default for CPP to "cpp -traditional -P" (was the case without specifying
+    an optfile, but otherwise default was just "cpp".
+  - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
+  - when "CC" is not set in the optfile, look for possible C compiler
+    (instead of just setting CC=cc)
+  - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
+    => add a ".F" to ".o" rule for source files with no "#include" (such as
+       port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
+  - move gfortran before g77 in list of possible Fortran compiler (consistent
+    with reference compiler switch from g77 to gfortran)
+o pkg/seaice:
+  o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
+    seaice_check that stops the model, when the CPP flag is used.
+  o seaice_growth.F: make capping of ice volume conserving by returning the
+    capped ice as freshwater to EmPmR. This does not change the verification
+    experiments but will change runs where the capping is acutally active
+o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
+  (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
+     global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
+     lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
+o tools/genmake2:
+  - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
+  - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
+  - clean previous genmake log files before anything else.
+  - change Makefile to remove testreport log files (*.tr_log) and genmake log
+    files only with "CLEAN" target (instead of "Clean");
+o pkg/generic_advdiff:
+  Change OBCS in multiDim advection (gad_advection.F):
+   Use maskInC to prevent intermediate update of tracer-field in OB regions,
+   thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
+   which were applying future time-step OB values.
+  This way, all explicit calculations use current-time-step OB values
+   (simpler and more consistent).
+  Affects results when set-up uses time-varying OBC and multi-dim advection;
+   update output of experiment seaice_obcs.
+o pkg/seaice:
+  move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
+   this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
+     SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
+  Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
+   but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
+   unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
+o pkg aim (2010/10/26):
+  - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
+    formulation with obliquity, eccentricity, ... as run-time parameters,
+  - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
+    upward shortwave radition at the surface (all-sky and clear-sky).
+o pkg/obcs:
+  - writing sections with globalFiles=T does not work: switch to tiled-files
+    when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
+  - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
+  - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
+
+checkpoint62m (2010/10/21)
+o pkg/seaice: vectorize seaice_solve4temp.F
+  - move iterations loops outside of i/j-loops
+  - requires 2D arrays for TB and effConduct
+  - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
+    modified in this routine
+  - a little bit of clean up, adjusting indentation, etc.
+  - replaced a few TEN**a by exp(a*log(10.)) in new code for better
+    performance and '**TWO' by '**2' (because TWO is a float),
+    replaced ONE, ZERO
+o eesupp/src:
+   fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
+o pkg/seaice/seaice_growth.F
+  Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
+  merging process. The merged routine has two branches, and one activates the 'evolution'
+  branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
+  In summary, here is what the '10/10 revision' did consist of
+    part 1: seaice_growth.F revisions 1.71 to 1.75
+      - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
+        The emphasis here was on improving readability (e.g. by trying to use meaningful
+        variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
+    part 1.5:
+      - revising the lab_sea experiment to make it a more useful (i.e. stable
+        and representative of an actual model run). This was done by generating a
+        (winter) pickup to start from, switching back the main experiment dynamic
+        solver from evp to lsr, having one of the experiments use the free drift solution.
+    part 2: seaice_growth.F revisions 1.76 to 1.85
+      - Sorting out hard-coded constants that prevented heat and fresh water conservation.
+      - Sorting out the various fields units and sign (set early on and reset at the end)
+        to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
+        fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
+      - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
+        and simplifying logical expressions to further improve readibility.
+    part 3: seaice_growth.F revisions 1.86 to 1.89
+      - Re-organize the blocks of code more logically.
+      - Merging the '_if.F' pieces that add something new.
+o pkg/thsice:
+  - vectorize thsice_solve4temp and thsice_get_exf.
+    Problem: thsice_solve4temp has an unvectorizable statement that
+    might also be problematic for TAF
+  - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
+    does not change the verifcation experiment, but will change all
+    experiments that have this flag undefined (not tested in verification);
+    a little reorganization to save a few 2D fields and recomputations
+  - 1st step of revisiting thsice adjoint (major recomp. sorted out)
+  - 2nd step:  fix some store dirs
+    o seems to work somewhat, i.e. using ifort but not g77
+    o likely cause are incomplete init. or recomputation
+    o start verification/global_ocean.cs32x15/input_ad.thsice
+o pkg/obcs: add support for exch2
+  - the position of the boundary and prescribed values are specified using
+    a global domain with exch2 facets stacked
+    - in x for N,S boundaries (like W2_mapIO=-1)
+    - in y for E,W boundaries (so E,W boundaries do not overlap)
+o pkg/mdsio: add support for writing global sections with exch2
+    file layout is as for obcs described above:
+    - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
+    - for y-z sections, facets are stacked in y
+o pkg/thsice:
+   - change a few routines for better vectorization: thsice_albedo.F,
+     thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
+     not affected, but in particular the latter routine has changed
+     dramatically (not necessarily easier to read now).
+   - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
+   iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
+o verification/lab_sea:
+  - overhaul of the forward model experiments. The main motivation
+    for this revision is that lab_sea has proven quite fragile (when
+    changing the sea-ice code, and switching platforms) to a point
+    when failures were very hard to attribute to specific code problems.
+  - the suspected reason for this fragility is noise amplification by evp so,
+    to start with, we decided to replace evp with lsr in the main experiment.
+  - the input.lsr experiment thus became obsolete and was removed.
+  - it was replaced with the input.fd experiment that uses an
+    analytical "free drift" solution as the ice velocity field.
+  - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
+    will hopefully allow us to discriminate problems due to dynamic solvers
+    from problems due to the thermodynamic code. input.salt_plume (lsr) allows
+    us to test additional options, along with the salt plume package.
+  - Finally a pickup was generated (at the end of a one year run) to
+    make the tests more representative of an actual model run. Previously
+    the tests starting point was a 1m thickness of ice everywhere.
+o pkg/seaice:
+  - introducing S\R seaice_freedrift.F that compute the
+    analytical solution to an approximate ice momentum
+    equation (i.e. the simple stress/coriolis balance).
+  - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
+    of the free drift velocity field, and enable its use.
+    To actually use the free drift solution as the model ice
+    velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
+o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
+
+checkpoint62l (2010/10/04)
+o pkg/seaice:
+  -fix the USE_ORIGINAL_SBI version (for variable freezing point);
+  -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
+   version (with USE_ORIGINAL_SBI undef);
+o add hooks for new packages OASIS, the package will follow
+  (hooks exclude the seaice pkg for now)
+o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
+  Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
+  rather than mdsio_readvector.F/mdsio_writevector.F, within
+  adread_adwrite.F to read/write adjoint-related tapes to disk.
+o eesupp and pkg/mdsio: ALLOW_WHIO
+  Option to write/read 2D fields to files including tiles halos.
+  The main purpose is for adjoint related "tape I/O".
+  The secondary purpose is for debugging phases.
+  A word on those rather specifically intended purposes.
+  The code was meant to be stripped down to the bare minimum.
+  Typically, there is a unique and basic mapping to the global
+  buffer (tile by tile, then proc by proc, then level by level), and
+  byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
+  meant to generate user friendly outputs of various shapes and forms.
+  Rather it is intended, for the knowledgeabale developers,
+  to be largely independent of the many mdsio options, to allow
+  outputs of tiles+halos in debugging phases and in adjoint runs,
+  and to allow some flexibility in tuning (adoint) I/O depending on each
+  file system behavior. With regard to tuning, most of the potential knobs
+  (to leave files open, to allocate the I/O indep. of usesinglecpuio,
+  to specify directories, to specify the typical size of I/O calls, etc.)
+  are not yet included, and will be added if they prove useful.
+o pkg/seaice:
+   fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
+o pkg/seaice:
+   new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
+   code (seaice_budget_ice_if.F) which enable to recover old standard
+   code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
+   temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
+o model/src (rStar):
+   use simple average (not area weighted) of rStarFac at U,V point when using
+   vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
+   update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
+
+checkpoint62k (2010/09/17)
+o adjoint
+   * changed verification/global_ocean.cs32x15 ; adjoint now tests
+     Adams-Bashforth 3 + NLFS + RSTAR
+   * some more modifs required for ECCO-GODAE v4
+o pkg/seaice
+   add SEAICE_AGE_VOL option to use volume instead of area for
+   integrating SEAICE_AGE
+o model/src:
+   first check-in of sigma & hybrid-sigma coordinate code ; also includes
+   non-linear free-surface parts ; but pressure-gradient not yet coded.
+o pkg/ptracers:
+   option for ptracer to convert Salt Relax into additional EmP.
+    tested in exp. global_ocean.90x40x15.dwnslp (update output)
+
+checkpoint62j (2010/08/25)
+o pkg/ggl90:
+   other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
+o pkg/dic: car_flux.F, phos_flux.F
+  - reduce number of exp-calls in order to improve performance
+  - clean up a little (replace fields by their macros, etc., fix
+    typo in CPP-flag)
+o pkg/ggl90: minor changes
+  - GGL90diffKrS was removed --> always use GGL90diffKr
+  - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
+  - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
+    (commented out for now)
+  - change in max/min operations to ensure that smoothing is ok
+  - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
+  - always use diffKrNrT as background profile (i.e. never use diffKr field)
+o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
+o pkg/dic:
+  - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
+    vectorization
+  - small bug fix in insol for the unlikely case of a cartesian grid
+  - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
+    + now vectorize, which also removes adjoint recomputations;
+    + replace integer maksp1 by _RL maskp1
+    + replace a**x by exp(x*log(a)) in phos_flux.F for speed
+
+checkpoint62i (2010/07/21)
+o pkg/flt:
+  - with OBCS: stop floats which enter the OB region
+o model/src:
+  - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
+    for implicit vertical advection.
+o pkg/seaice:
+ - account for melting in seaice age evolution.
+ - remove double counting of seaice ridging effect on seaice age.
+
+checkpoint62h (2010/06/18)
+o pkg/exch2:
+ - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
+o tools/genmake2
+  - remove "-pdefault" option: redundant with the use of "packages.conf";
+  - remove file pkg/pkg_default : set the default as a pkg group
+    ("default_pkg_list") defined in pkg/pkg_groups;
+  - fix for case pkg/pkg_depend is missing (was hanging before);
+  - add option "-pgroups" to specify a different pkg_groups than the default.
+o verification/adjustment.cs-32x32x1:
+   add a "minimal" set-up test (code_min & input_min) which only compiles
+   eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
+o tools/genmake2
+  - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
+  - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
+o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
+  files are nearly the same anyway.
+  Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
+   - redefinition of tau(i,i) (by a factor of ustar)
+   - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
+   - replace rhonil by rhoConstFresh in computation of evap (bug fix)
+   - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
+   - replace
+     rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
+     shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
+     by
+     shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
+     (changes results)
+   -> exf_bulkformulae v1.22,
+      update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
+      (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
+                output.txt 1.63
+       offline_exf_seaice: output.seaicetd.txt 1.7
+       seaice_obcs: output.txt 1.10)
+  Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
+   -> exf_bulkformulae v1.23,
+      unfortunately requires updating lab_sea.salt_plume (6 matching digits),
+      and global_ocean.cs32x15.icedyn (only 11 matching digits)
+  Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
+o adjoint of exch-1:
+ - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
+   (note: was already like this when using EXCH-2) and remove flow dir
+   and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
+ - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
+ - update pkg/exch2 diff list.
+
+checkpoint62g (2010/05/19)
+o eesupp/src (exch-1):
+ - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
+   and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
+   (renamed to exch1_*rx_cube.F).
+ - change accordingly exch_*_rx.template and AD version in pkg/autodiff
+   to call new exch1 S/R ; update Makefile and .cvsignore.
+ - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
+   exch2_xy_rx later)
+  Note: after updating your code, need to run "make clean" in eesupp/src
+o test experiment bottom_ctrl_5x5:
+   new output_adm.txt with fewer grdchk & less monitor output.
+o model/src:
+  remove the call to ini_cori in initialise_varia.F (just keep the usual one
+   in initialise_fixed.F). More consistent with coriolis & horizontal grid
+   beeing treated in the same way (ini_grid is not called a 2nd time).
+o pkg/exf:
+  - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
+  global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
+  - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
+  - cosmetic changes to exf_bulkformulae.F to make it look more like 
+    exf_bulk_largeyeager04.F 
+o eesupp/src (exch-1):
+  - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
+  - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
+    array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
+    (even without using MPI).
+  - Message mode: move RecvAck setting (indicator of buffer being ready)
+    from send_put to recv_get S/R (was useless before, but not sure if
+    it's much more useful now);
+  - Switch the order of sync: MPI-proc 1rst and then threads;
+  - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
+  - fix AD code for communication mode ='get' (but not used).
+o model/src:
+  initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
+  not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
+o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
+o pkg/ctrl: require a specific set of control variables and exf-flags for
+  adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
+o model/src:
+ a) 1rst version of a new driver S/R to turn-off output freq and flags after the
+   1rst forward sweep, to avoid over-writing output files during recomputations
+   recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
+ b) 2nd version:
+  - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
+  - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
+     writePickupAtEnd) + seaice & ptracers output;
+  - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
 o model/src:
   - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
 o pkg/exch2:
-  - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ; 
+  - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
   - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
 o pkg/autodiff & exch2:
   process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
   (for now, only if ALLOW_EXCH2 is defined).
 o pkg/autodiff:
-  - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F 
+  - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
     (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
    + clean-up comments (_RS is not always real*4)
   - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
@@ -137,8 +567,8 @@
     but keep the former optfile for few weeks for smooth transition
 o pkg/ecco
   - allow user defined cost function contributions
-	CPP: ALLOW_USERCOST_CONTRIBUTION
-	USAGE: compute contributions in cost_usercost_all.F
+     CPP: ALLOW_USERCOST_CONTRIBUTION
+     USAGE: compute contributions in cost_usercost_all.F
   - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
       the two options are complementary.
 o pkg/smooth