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-revision 1.832 by mlosch,
Wed Jun  6 14:37:14 2007 UTC
+revision 1.1107 by jmc,
Tue May 26 23:28:40 2009 UTC
 Line 4 
 $Name$
      Notes on tags used in MITgcmUV
      ==============================
+ o eesupp:
+   new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg):
+   should be called before a "stop" if we know that all process are going
+   to stop; if one Proc does call this S/R, will hang in MPI_FINALISE.
+ checkpoint61o
+ o pkg/exch2: change check_depths to issue just a warning (instead of error+stop)
+ o model/src/ini_curvilinear_grid.F:
+    compute angleSin/CosC when they are not read from a file
  o pkg/seaice:
+    add pseudo time stepping for LSOR
+ o pkg/exch2:
+    temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW
+ o pkg/seaice:
+    Adding separate sea ice albedo, drag coefficients, and HO in Southern
+    Ocean from those in Arctic Ocean.  See *_south in SEAICE_PARAMS.h
+ o SingleCpuIO:
+    fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used.
+ o pkg/seaice:
+    put exchanged variable in (local) common block for MPI+Multi-Threads
+    to work (necessary with exch1, and for now with exch2 too).
+ o verification: to get more experiments tested with mpi, mth and mpi+mth,
+   change tiling of:
+    aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15,
+    hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope
+   update output of exp:
+    exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5),
+    tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod)
+   + ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU
+                    (note: output.txt generated on faulks using only 1 tile)
+ o eesupp & mdsio (SingleCpuIO):
+  - remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time
+    parameter "W2_useE2ioLayOut" (read from file "data.exch2").
+    Note: was not effective for globalFile & useSingleCpuIO=F; now fixed.
+  - move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc).
+  - fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same
+    gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array).
+ o pkg/exch2:
+  - new code to set-up W2-Exch2 topology (replace matlab-topology-generator):
+    read parameter file "data.exch2" if it exists; otherwise try default regular
+    cube without blank-tile; new header file "W2_EXCH2_SIZE.h";
+  - update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible
+    with new code (not to be used, just as a backup solution).
+  - add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2"
+    in utils/exch2/input.
+ checkpoint61n
+ o eesupp & mdsio (SingleCpuIO):
+   - move mapping to global io-buffer inside gather_2d/scater_2d: this save
+     memory (1 less 2D global RL array); skip 1 buffer copy; and only send/
+     receive real*4 array (instead of real*8) to read/write 32.bit files.
+     (new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S
+      and remove new mapping S/R)
+ o pkg/mdsio: in preparation for topology-generator within pkg/exch2:
+   - Change declaration of SingleCpuIO buffer, reduced to only 1 dim.:
+     xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h
+     when using exch2. Add S/R to map global io-buffer to global model array.
+   - uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt.
+ checkpoint61m
+ o write_utils : change WRITE_1D_R8 to WRITE_1D_RL
+   and add 3 other S/R for other types (R4,R8,RS).
+   Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument.
+ o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros):
+  - ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ;
+  - reduce number of macro definitions (keep only those which are used);
+    can always call directly the corrresponding S/R if needed.
+  - everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix
+    _R4/_R8 to _RS/_RL when applied to _RS/_RL variable.
+  Fixed wrong type of arg in:
+    atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F
+    ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F
+  To fix: global_sum of var in common block is wrong (multi-threaded) in:
+    dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F
+  To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops)
+ o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd
+   "nlfs" mpi test is going to stop when checking for unconnected tile egdes.
+ o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error
+ o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile
+   edges are closed (zero depth); might happen with "blank tiles";
+   for now, disabled if using OBCS.
+ o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi":
+   link *_mpi files from "MODS" dir) to return to a strait-forward behavior.
+ o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D)
+   to reduce length of 1.D array print in STDOUT.
+ o adjustment.cs-32x32x1: changed to oceanic test with 1 continent
+   + use 48 tiles (16x8): this will allow to test "blank tiles".
+ o start to test MPI + multi-threaded (change testreport to skip tests
+   where number of tiles do not match).
+ o genmake2: add option "-omp" to turn on Open-MP ;
+   passed to testreport (if using -mth) ; merge few (*+mth) optfiles.
+ o pkg/exch2 (+ utils/exch2): ignore blank tiles (instead of removing them)
+   and keep the original tile numbering. Note: compatible with old
+   W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files.
+ checkpoint61l
+ o Overlaps had been forgotten in calculating ijk keys : fixed
+ o fix cyrus makedepend for gcc 4.4
+ o experiment fizhi-cs-aqualev20:
+   switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE)
+   and generate new output. Note: new output is much closer to the old
+   one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from
+   the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007.
+ o pkg/fizhi:
+  - change to avoid indices going deliberately over array-bounds
+  - remove unnecessary MPI stuff
+  - perpetual spring equinox with "#define FIZHI_USE_FIXED_DAY"
+  - new version of S/R GETPWHERE available with #define TRY_NEW_GETPWHERE:
+    does not go over array-bounds and therefore returns reliable output.
+  - in fizhi_driver.F & fizhi_turb.F, fix "get_alarm" calls:
+    this S/R has 4 output arguments, which are used inside "get_alarm";
+    when it is called with the same variable "ndum" in place of several
+    output arguments, this produces weird side effect inside "get_alarm"
+   (e.g., datein=dates(n) is overwritten by timein=times(n) since both
+    datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum"
+    address) and produces error.
+ o tools/gemake2: (March 27-29 2009)
+   with option "-mpi": link *_mpi files from "MODS" dir (this is what
+   testreport does).
+ o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output
+ o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F:
+    update lab_sea.lsr & lab_sea.salt_plume results
+ o pkg/seaice:
+   Major overhaul of the LSOR solver: change discretization from original
+   finite differences to finite volume. The old routine is still in the
+   file seaice_lsr.F and can be turned on with the CPP-flag
+   SEAICE_OLD_AND_BAD_DISCRETIZATION
+   Along with this change, the discretization of the strain rates is changed.
+   The same flag turns on the old discretization in seaice_calc_strainrates.F
+   All verification experiments with seaice are affected (except for
+   seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old
+   results by setting the above flag.
+   Further changes involve changes in defaults:
+   - ALLOW_FLOODING is defined and turned on by default
+   - SEAICEadvSnow = .true. is now the default
+   - SEAICEadvSalt = .true. is now the default
+   - SEAICEadvAge  = .true. is now the default
+   - SEAICE_clipVelocities  = .false. is now the default
+                                      (as per J. Zhang's recommendation)
+   - B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE
+     is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS
+   - seaice_growth: replace computation of UG by a simple copy from wspeed
+ checkpoint61k
+ o pkg/seaice: a few bug fixes mostly concerning the metric terms:
+   seaice_lsr: fixed a few metric terms,
+               affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs
+               add more debugging diagnostics
+   seaice_evp: removed superfluous many metric terms of FV discretization
+               of stress divergence
+               affects lab_sea, lab_sea.hb87
+   seaice_ocean_stress: removed superfluous many metric terms of FV discretization
+               of stress divergence for non-evp solver
+               (this part is not tested anywhere)
+   seaice_calc_strainrates: fixed a bug in no-slip boundary conditions,
+               they were effectively only half slip
+               affects lab_sea.hb87
+   updated all relevant verification experiments (except lab_sea//output_adm.txt
+     which was left over, but fails at level 7 & 6)
+ checkpoint61j
+ o pkg/seaice: turn a few hard wired parameters into run time parameters
+ o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model
+   time in seconds as promised by the usints in seaice_monitor and exf_monitor
+ o pkg/mnc: fix the coordinate variables for multi-tile curvi-linear grids
+   that are not cubed-sphere grids
+ o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR
+ o pkg/ctrl:
+   fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low)
+ o non-hydrostatic (calc_gw.F):
+   fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec
+   update output of exp. global_ocean.cs32x15.viscA4
+ o remove backward compatibility for thetaMin,phiMin
+   (replaced by xgOrigin,ygOrigin on Jan 27, 2009)
+ o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the
+   interpolated wind field not only for curvilineargrid=.true., but also
+   for a rotated grid (rotateGrid=.true.)
+ o pkg/exf: add capability to bypass interpolation for runoff
+   by setting yet another CPP-flag
+ o eesupp/src, B-grid exchange:
+   add simple (6 tiles, non MPI) CS exch + standard interface S/R.
+ o autodiff
+   new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV
+   allows to switch to single-prec common blocks;
+   corresponding switch occurs in tamc.h, integer isbyte
+   TAF store directivs "byte" and "kind" seem equivalent;
+   Most tamc.h have been updated correspondingly.
+ checkpoint61i
+ o autodiff:
+   fix autodiff_sore/_restore indices for obcs
+   (spotted by I. Hoteit, M. Mazloff)
+ o pkg/autodiff, pkg/ctrl:
+   Add flag to reduce all tapelev I/O to single-prec.
+   In data.ctrl set
+     doSinglePrecTapelev = .TRUE.
+ o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2:
+   check in hack for SX8 compiler (for dxV, dyU); remove it afterwards.
+ o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for
+   real fresh water flux (not yet)
+ o pkg/mdsio & rw:
+  - add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta)
+  - add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX.
+ o pkg/flt:
+  - replace FLT_INIT by 3-steps standard initialization S/R: readparms,
+    init_fixed & ini_varia.
+  - clean-up & simplify linear interpolation S/R:
+    move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid.
+  - fix some indices (mainly vertical index) ; add IMPLICIT NONE.
+  - more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R.
+  - add vert. coordinate & horiz. indices to output files.
+  - change vertical position in initial condition, from index to depth [m].
+  - store horizontal (decimal) indices i,j in common block (instead of coord. x,y)
+    (easier to get to a curvilinear grid) ; delX,delY no longer used.
+ o pkg/ggl90: a few modifications:
+  - fix bottom boundary condition, and interpolation of KappaE
+    near top and bottom
+  - use same set of viscosity/diffusivity for TKE/momnetum/tracer
+  - add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH)
+  - add a few options for mixing-length upper limit (--> mxlMaxFlag)
+ o rename thetaMin,phiMin -> xgOrigin,ygOrigin
+   (maintain temporary backward compatibility, until next checkpoint)
+ checkpoint61h
+ o pkg/diagnostics with "periodic averaging diagnostics":
+   fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output.
+ o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82
+ o pkg/obcs: fix loop ranges for balancing code
+ o pkg/flt:
+  - improve criteria for finding which tile owns a float.
+  - fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case.
+ o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg
+   aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling
+   with ocean biogeo)
+ o pkg/flt:
+  - do some cleaning and fix the restart ;
+  - add output.txt in flt_example/results to get this pkg tested.
+ o genmake2: add an EXTENDED_SRC option and flag.
+    for now, cannot be turned on on command line (only through genmake_local)
+ o pkg/mdsio: read/write vector:
+  - singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS
+  - singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR
+    & MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS.
+  - affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO)
+   (drop to 4 digits matching for grad). But this test does not look very
+   reliable (was already failling on eddy, fc5, at 6.digits). Update output.
+ checkpoint61g
+ o pkg/flt:
+   - move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name)
+    + make OPTIONS file more standard.
+   - rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name)
+   - fix _BYTESWAPIO CPP-Flag
+   - standard reading of file-parameter "data.flt"
+   - fix argument list of S/R FLT_RESTART
+   still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F
+ o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell
+ o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to
+   a still unfixed compiler/optimization bug
+ checkpoint61f
+ o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ;
+   update results of global_ocean.cs32x15.icedyn test.
+ o move getcon.F from model/src to pkg/fizhi.
+ o pkg/exf: add parameter for extrapolation of temp up to the surface
+    and option to prevent negative evap (in bulk_largeyeager04 only).
+ o Prather Advection scheme: fix tracer conservation for divergent flow
+   (e.g., when using NonLin Free-Surface).
+ o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead
+ o gmredi (Visbeck-variable-K):
+  - add more parameters to Visbeck-variable-K.
+  - use a 5 points average for dSigmaR in Visbeck-K calculation
+    (more "homogenous": same stencil and same weights as in dSigmaH)
+  - update output of ideal_2D_oce experiment.
+ o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4
+   (#undef REAL4_IS_SLOW)
+  - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4
+    coordinate variable
+  - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables
+    (surface forcing fields), removes some of the functionality
+  - model/src/write_grid.F: write _RS variables as RS-netcdf variables
+  - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but
+    probably not all: copy _RS surface flux fields to RL field before
+    calling DIAGNOSTICS_FILL
+  - model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into
+    real*4 (CALL EXCH_*_RS) versions.
+  - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1
+    (generate new output).
+ checkpoint61e
+ o gmredi (Visbeck-variable-K):
+   - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
+   - change computation of Visbeck-K where Slope > Smax :
+     now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct)
+     previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output.
+ o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
+   to be the same as with Z-coord. (i.e., m/s & no-units respectively).
+ o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
+ o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
+   does not become too large (to avoid precision problems in implicit-diffusion
+   solver); update ideal_2D_oce output.
+ o pkg ggl90:
+   - in ggl90_cal.F: compute only one set of visc/diff, used to
+     step forward TKE/T/S/momentum
+   - default value of GGL90viscMax/GGL90diffMax larger and equal (to
+     have Prandlt =1)
+ o gmredi (fm07):
+   - add lower limit on Transition layer thickness + lower limit on 1/lambda
+   - allow to set few more params from data.gmredi
+ o pkg ggl90:
+       - add missing sqrt(2) factor in computation of mixing length
+         scale in ggl90_calc.F
+         (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
+ checkpoint61d
+ o adjoint modifs
+   - adapt to new field rhoInSitu
+   - allow to revert from StoreDynVars2D, StoreDynVars3D
+     to individual fields
+     (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
+ o store 3-D (in-situ) density in commom block (DYNVARS.h)
+  - save 1 rho computation.
+  - no longer modify T & S inland when using down_slope pkg.
+ o gad_som : allow to switch to SOM advection for T & S without corresponding
+   pickup files (using new S/R: MDS_CHECK4FILE).
+ o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
+   (for useSingleCpuIO to work in multi-threaded)
+ o pkg/shelfice:
+  - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
+    with SHELFICEtopoFile in data.shelfice
+  - move code for reading ice shelf topography and modifying hFacC into separate
+    subroutines of the shelfice package
+  - separate initialisation of "fixed" and "variable" variables
+  - kTopC is not (yet) replaced by kSurfC, although this is possible
+ o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
+ o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
+   and rename:
+   ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
+   ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
+ o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
+ checkpoint61c
+ o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
+   to add mass source/sink of fluid in the interior (3-D generalisation
+   of oceanic real-fresh water flux).
+ o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
+ o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
+ o new pkg: down_slope
+   density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
+   - presently, modify T & S inland (dwnslp_calc_rho.F).
+     can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
+   - implementation for ocean in P-coords not tested.
+   - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
+ o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
+   (to facilitate conversion of oceanic pkg to p-coordinate).
+ o change FIND_RHO to FIND_RHO_2D :
+   pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
+ o new pkg: cheapaml
+ checkpoint61b
+ o exch2:
+   change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
+   - no longer depend on the order sequence (N,S,E,W).
+   - 3rd exchange no longer needed (tested with 24 tiles).
+   - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
+   - exch_UV_A-grid readily available (but not yet tested).
+   comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
+   (both are no longer needed) in exch_uv: no effect in forward run; but
+    get truncation error differences with adjoint exch.
+ o exch2:
+  - change index-bounds storage (moved from target to local tile,
+    more intuitive this way) ; rename/remove some variables.
+  - change utils/exch2/matlab-topology-generator & code_mods accordingly.
+ checkpoint61a
+ o exch2/matlab-topology-generator:
+   fix bug in index bounds for N-S internal exchange (hard to tell if this
+   had any effect on the solution).
+ o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
+   is exceeded
+ o testreport: modify syntax of awk, so that it works also with
+   awk, and not only with nawk and gawk
+ checkpoint61
+ o autodiff
+   Change default for TAF usage by removing argument '-nonew_arg'
+   This changes TAF subroutine argument list (ordering of active var.)
+   Omission of this flag leads to incompatibility w.r.t. TAMC
+   To restore TAMC-compatibility, need following modifs:
+   * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
+   * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
+   Tested TAF version is 1.9.22
+   N.B.: exch2 hand-written adjoint code currently not TAMC compatible
+ checkpoint60
+ --->>> This is the last checkpoint for which generating the adjoint
+ --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
+ --->>> by default.
+ --->>> Future checkpoints will ommit this flag by default.
+ o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
+ o pkg/grdchk: Add gradient check to etan0 perturbations.
+ o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
+ o pkg/autodiff: more flexibility in zeroadj.
+   model/src: modifying do_oceanic_phys.F accordingly.
+ o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
+ o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
+   special setup of gmredi for which the adjoint is stable
+   enough for parameter optimization.
+ o bridging the gap between eddy stress and GM.
+   -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
+       along with a change in CPP option (now ALLOW_EDDYPSI).
+   -> when using GM w/ GM_AdvForm:
+       The total eddy streamfunction (Psi = eddyPsi + K x Slope)
+       is applied either in the tracer Eq. or in momentum Eq.
+       depending on data.gmredi (intro. GM_InMomAsStress).
+   -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
+   The key modifications are in model/src/taueddy_external_forcing.F
+   pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
+ checkpoint59r
+ o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
+   from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
+   fix option to read coriolis(@ cell-corner) from files with CS-grid.
+ o pkg/mnc: add some attributes to standard 1D-coordinate variables
+ o pkg/diagnostics: enforce missing_value attribute for scalar variables at
+   mass points, when using mnc for output
+   - add runtime parameter (missing_value, missing_value_int) to override
+     default (which is the value of getcon('UNDEF'))
+ o pkg/mnc: prepare mnc for the actual use of missing values with the
+   diagnostics package: small fix in mnc_cw_readwrite.template and more
+   initialisation of never used fields
+   - replace mnc_common.h and mnc_id_header.h with corresponding upper case
+   versions
+ o pkg/thsice/thsice_ini_vars.F added default initial values so that
+   thermodynamics sea ice solver does not blow up when some initial fields
+   are missing.
+ o move from external_forcing_surf.F to ini_forcing.F
+   the p-coord. hack consisting in using pLoad to set phi0surf ;
+   update output of tutorial_global_oce_in_p (affected @ truncation level).
+ o Freshen up a bit hs94.1x64x5, notably:
+   remove rotationPeriod and tRef=5*0. (adjoint only), and add
+   exactConserv=.TRUE.
+ o pkg/generic_advdiff:
+   change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
+   applies to files where Temperature & Salinity 2nd Order moments are used.
+ o pkg/ptracers: add second-order moment advection schemes (80 and 81);
+   this uses a dynamically allocated internal state data structure
+   (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
+   and requires a fortran 90 compiler
+ checkpoint59q
+ o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
+    (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
+ o Refresh tutorial_global_oce_biogeo, notably:
+   - change bathymetry (put back seamounts in ACC, use hFacs)
+   - change EOS (POLY3 --> JMD95Z)
+   - use Bryan-Lewis vertical diffusivity
+   - use multidimensional advection
+   - remove old virtual virtual in dic pkg, now done through ptracer pkg
+   - change a couple of parameters in dic pkg
+ o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
+ o pkg/obcs: change default to OBCSfixTopo = .true.,
+   - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
+   - replace "debugMode" with "debugLevel .GE. debLevB"
+ o implementation of TAF directives for gchem,cfc,dic
+ o remove "exp5" (replaced by tutorial_deep_convection).
+ o pkg/obcs: add code to fix topography gradients normal to open boundaries;
+   this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
+   the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
+   --> changes results in exp4, seaice_obcs
+ o tutorial_deep_convection :
+   update the set-up and increase resolution and domain size ; start
+   from pseudo initial conditions = output at t=120mn in order to see
+   something happening when running testreport.
+ o pkg/seaice: add os7mp as an advection scheme
+               add check for advection schemes
+               add a flag for restoring T and S underneath sea ice
+ o pkg/my82: add netcdf-support and diagnostics
+ o thsice pkg:
+   - Now hsMax limits snow height by turning it into ice following
+     flooding scheme (and now conserving energy)
+   - Slight rewriting of the formula in thsice_calc_thick.F
+   - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
+   --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
+ checkpoint59p
+ o gchem / dic / cfc :
+   - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
+   - add new parameter files: "data.dic" & "data.cfc" ;
+   - various re-arrangement in initialisation & header file ;
+   - fix tutorial_global_oce_biogeo for multi-threaded test.
+ o pkg/dic: test for "pickup_dic" file when restarting ;
+   if no pickup-file, can restart with a re-initialised pH (same as it did
+   before) providing pickupStrictlyMatch is set to False.
+ o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
+   + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
+ o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
+   and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
+ o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
+  & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
+    (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
+ o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
+    scheme to use for vorticty-term ;
+  - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
+    (with default selectVortScheme, return to original discretisation)
+  - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
+ o pkg/seaice: add a line to the summary to indicate grid type (B/C)
+ o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
+   bottom ; only used with variable horizontal viscosity and non-hydrostatic.
+   also fix diagnostics VISCAHW & VISCA4W.
+ checkpoint59o
+ o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
+ o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
+   move a few statemens out the main loop into separate loops
+ o pkg/shelfice:
+   - sort out freshwater flux; convert freshwater fluxes to mass fluxes
+     (kg/m^2/s), does not break tests, because in verification/isomip,
+     rhoConstFresh=rhoConst (by accident)
+   - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
+   - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
+     new file model/src/seawater.F, so that they are available for all pkgs.
+   - convert potential temperature into in-situ temperature. This changes the
+     isomip tests => update tests
+ o add a flag writePickupAtEnd (default=true) to be able to suppress
+   writing a pickup at the last timestep
+ o tools/mpack-1.6 :
+   - disable automake (not working) and autoconf (not needed).
+   - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
+     also cleaner with much less compilation warnings.
+ o pkg/profiles:
+   rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
+   (for "less than 32 characters name" compiler requirement)
+ o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
+   conditions that have a different sampling frequency than S/T/U/V obcs
+ o pkg/diagnostics (stats-diags):
+   - fix global Min/Max in case 1 processor get only empty tiles
+ o genmake2: replace (4 times)
+      make genmake_tc_1.o >> genmake_warnings 2>&1
+   with
+      COMM="$CC $CFLAGS -c genmake_tc_1.c"
+      echo $COMM >> genmake_warnings
+      $COMM >> genmake_warnings 2>&1
+   to make genmake2 always see the value of CC as specified in the optfile.
+ o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
+   - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
+   - modify verification advect_cs test to test SOM-advection on CS-grid.
+ o pkg/ctrl:
+   - Rewrite of ctrl_map_ini_ecco.F,
+     introducing a generic routine (ctrl_map_ini_gen.F).
+   - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
+ checkpoint59n
+ o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
+   number in dedicate array "hdiag":
+   - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
+     with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
+   - many small changes (integer format) for large number of diagnostics
+   - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
+     a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
+ o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
+   usingSphericalGrid, this allows to define the rotated grid coordinates
+   via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
+   geographical coordinates according to the inverse of the rotation defined
+   by the Euler angles, so that Coriolis parameter and online-interpolation by
+   exf works with the geographical coordinates on XC/YC/XG/YG.
+   Naturally, this feature does not work with all packages, so some
+   combinations are prohibited in config_summary (flt, flt_zonal, ecco,
+   profiles), because there the coordinates are assumed to be regular
+   spherical grid coordinates.
+ o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
+   - introduce isopycnal diffusion coefficient control.
+ o tools/adjoint_options:
+   - additional control vector components.
+ o pkg/mnc: have mnc create marginally meaning full coordinate variables
+   (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
+ o pkg/mypackage:
+   - add example of read/write pickup for state-var ;
+   - add entry points to the main code for state-vars diags & write-pickup.
+ o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
+   transitions for useExfYearlyFields
+   - add new subroutine that determines the file to read from for
+     use*YearlyFields = .TRUE. and .FALSE.
+   - add a verification experiment to global_with_exf that tests
+     useExfYearlyFields with USE_EXF_INTERPOLATION defined
+ o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
+   analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
+   subroutines (which could be generated from a template, because they are
+   almost identical), for now they are included in obcs_prescribe_read.F for
+   simplicity
+ o pkg/exf:
+   - add a little more diagnostic to exf_interp_read (in analogy to
+     mds_read_field, can be turned off with debugLevel < debugLevA=1)
+   - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
+     ugly but fast by unrolling short inner loops, inserting a unroll=8
+     directive in routine lagran, and splitting a loop and making do while the
+     outermost loop (the latter requires the intoduction of index arrays)
+ o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
+ o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
+   http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
+ o verification/seaice_obcs: updated for restart test and latest options
+ o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
+   ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
+   for now this is only available for the C-grid code and also within
+   #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
+ checkpoint59m
+ o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
+   and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
+ o gad_som : fix flux output (& diagnostics) to have same units as other
+   advection scheme fluxes (was previously multiplied by deltaT).
+ o added verification/seaice_obcs both to test seaice open boundaries
+   and to provide an example matlab scrpt for generating them
+ o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
+ o pkg/salt_plume: clean up salt_plume_frac.F to
+   remove redundancy in PlumeMethod 1 and 4
+ o pkg/kpp: added saltplume diagnostics
+ o pkg/obcs and pkg/seaice:
+   - do not set uice and vice to zero when OB*icefile are unspecified
+   - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
+   - moved seaice tracer obcs after call to seaice_growth
+ o pkg/salt_plume: added various options for salt plume depth
+   criterion and for vertical distribution of the salt
+ checkpoint59l
+ o pkg/ptracers: new version of ptracers pickup:
+   read meta file and write only fields which are needed to restart.
+   ( same logic as main pickup file ; also using pickupStrictlyMatch )
+ o pkg/seaice:
+   - add timescale for melting due to warm mixed layer as a means of
+     setting SEAICE_availHeatFrac more conveniently
+   - add a CPP-flag/runtime parameter check for flooding algorithm
+   - reformulated availHeat in seaice_growth.F to be independent of AREA
+ o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
+   unit changes
+ o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
+ o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
+   SX vector computer.
+ o pkg/seaice:
+   - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
+     seaice forcing fields can now be read only through pkg/exf
+   - removed some unused halos
+ o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
+ o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
+   or U/VICE from U/VWIND before computing U/VSTRESS
+ checkpoint59k
+ o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
+   dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
+ o fix un-initialised variable problem (in mom_vecinv & shap_filt):
+   all experiments pass when compile with un-initialised var. checking option.
+ o added pkg/salt_plume
+ o script to test restart (for now, in MITgcm_contrib/jmc_script)
+ o pkg/seaice: new read/write pickup version.
+   read meta file and write only fields which are needed to restart.
+   ( same logic as main pickup file ; also using pickupStrictlyMatch )
+ o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
+ o lab_sea.hb87: modify the domain & update output.hb87.txt :
+   lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
+   at j=1 & j=Ny+1 : this case is not treated correctly in the restart
+   process. Fixed here by closing the domain at the Northern boundary.
+ o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
+ o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
+   a set of consecutive levels in/from a 3-D array.
+ o pkg/ptracers:
+   use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
+   to-do: fix pkg/diagnostics when large number of diagnostics are defined.
+ checkpoint59j
+ o in pkgs: dic, obcs, offline, rbcs:
+   standard way to compute coeff. for time interpolation between 2 time reccords
+   which retains full precision (& make results less dependent on compiler).
+   update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
+ o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
+   packages instead of reading ice cover and wind speed separately
+ o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
+  (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
+   to allow to compile customized code before the update)
+ o cleaning-up:
+   - fix CPP instruction syntax in pkg/obcs
+   - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
+     add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
+   - fix some threads issue in IO parts.
+ o pkg/dic:
+   - add tons of "_d 0" (--> much better testreports !)
+    and then update outputs of tutorial_global_oce_biogeo
+ o pkg/mom_fluxform:
+   add a special version of momentum advection intended to conserve momentum
+   next to a bathymetry step or a coastline edge. (default = off = #undef)
+ o new read/write pickup version:
+   - for now, only implemented for main (mdsio) pickup file.
+   - write out only what is needed to restart; merge pickup_nh , pickup_ph
+     and main pickup together.
+   - read meta file; read only what is needed to restart; stop if a field
+     is missing (if pickupStrictlyMatch=T, = the default) or try to restart
+     if it make sense (even if the restart is not perfect).
+   - if no meta file, assume that pickup to read corresponds exactly to
+     a pickup that would currently be written.
+   - read pickup written in the old format (until checkpoint59i) if it
+     recognizes an old meta file (no field-list).
+   - add a meta file in exp. which starts from a pickup: 2 cases:
+     a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
+      e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
+     b) a meta file describing the content of the associated pickup file
+      e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
+ o pkg/mdsio & pkg/rw:
+   - new routine to read a meta file ; new set of routine to read
+     Multiple-fields file (with meta file).
+ o added open boundary conditions capability for seaice
+     HSNOW, HSALT, UICE, and VICE
+ checkpoint59i
+ o adjoint:
+   * fix multiDimAdvection adjoint
+     (partial recomputation problem by TAF for fVerT(:,:,kDown)
+     and comlev1 size definition (maxpass vs. max. number of tracers)
+   * verification/global_ocean.90x45x15 adjoint now tests
+     NLFS and multiDimAdvection using DST3 (=30)
+   * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
+ o pkg/kpp: add "_d 0" to real constant (if missing);
+   update output of exp: natl_box (10.digits); vermix (std, 7.digits)
+   and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
+ o prepare for "clever pickup" implementation: add new header file "RESTART.h"
+   for internal parameters related to restart process (formerly from PARAMS.h)
+   and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
+ o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
+   as argument. (only atm2d & obcs write_pickup have not yet been updated)
+ o pkg/monitor:
+   - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
+   - fix mon_stats_rs (statistics over the full domain, even where field is zero)
+   - account for deep Atmosphere factor and density factor (anelastic)
+ o added open boundary conditions capability for seaice HEFF and AREA
+ o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
+   thermodynamics
+   - requires a little reorganization, which affects the testreport results
+     of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
+     so that now the conservative form is tested
+   - add a few comments
+ o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
+ o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
+ o add new diagnostics to seaice: advective, diffusive fluxes (only for
+   multidim-advection, for scheme 2 they are not filled) and transports,
+   thermodynamic growth rates
+ o change units of EmPmR (inside the code, + within coupling interface)
+   from m/s to kg/m2/s (mass flux) but leave input file unchanged.
+   Affects results @ truncation level (cg2d match) and update output of
+    experiments: lab_sea(6), global_ocean.90x40x15(10),
+   global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
+   + adjoint results: global_ocean_ebm(11) and lab_sea (12).
+   Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
+   Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
+ checkpoint59h
+ o pkg/exf:
+   - improve vectorization by moving if-statement out of loops in
+     exf_mapfields, exf_radiation
+   - exf_bulkformulae.F: introduce 2D fields and vectorize code
+ o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
+ o testreport:
+   - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
+     monitor & update offline_exf_seaice exp. output.
+   - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
+ o pkg/seaice:
+   - bug fix in the evp solver: boundary conditions were affected be
+     masking of zMax/zMin (changes results)
+   - minor bug fix in boundary conditions in seaice_calc_strainrates
+     (changes results for no_slip)
+   - seaice_lsr.F: make interpolation of eta dependent on boundaries
+   - replace hardcoded lower limit for zeta (zMin) by runtime parameter
+   - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
+     stress formulation and no-slip boundary conditions
+ o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
+   in gad_calc_rhs.F ; add few safety stops in initialisation phase.
+ o pkg/seaice: a first HSALT time stepping equation has been checked in
+ o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
+   in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
+   without requiring DO-IF statements
+ o pkg/thsice:
+   use continuous power-law function for partition of energy between lateral
+   melting/freezing and thinning/thickening ; old code using step function
+   still available with #undef THSICE_FRACEN_POWERLAW
+   update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
+ o testreport: change AD testing : check against results/output_adm.txt
+   using same scripts as for forward test.
+ checkpoint59g
+ o adjoint testing: in preparation for changing testreport:
+   - output format: cost and grad written on separated lines
+   - ad output results in directory "results" (instead of "results_ad")
+ o pkg/seaice: adding ice salinity HSALT as a prognostic variable
+ o pkg/seaice: changes for using pkg/seaice with pkg/obcs
+ o pkg/ecco: allow user defined cost function contributions
+ o testreport:
+   Allow to choose (per experiment) the list of tested output variables
+    and the main variable (used to issue a pass/FAIL ) ;
+   - for now, done by adding the specific list in file: [exp]/input/tr_checklist
+   - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
+   Also modify printing of summary:
+    a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
+    b) echo the list of tested variables in the individual summary.txt of
+       each experiment.
+ o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
+   threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
+   (but still depend on the tile decompostion of the domain).
+ o pkg/seaice: change a discretization detail to make the B-grid code
+   "more symmetric". This change is likely to remove all "ridges/leads" that
+   where quasi-aligned with the grid in B-grid solutions. It may also be
+   the solution to the stress coupling issues with the B-grid.
+ o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
+   remove .cvsignore from input dir. (since testreport no longer run here).
+ o pkg/thsice:
+  - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
+  - fix reshaping of sea-ice just after advection:
+    melt all the ice only if ice-volume is too small.
+  - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
+    prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
+  and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
+ o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
+   tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
+ o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
+   forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
+   (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
+   and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
+   of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
+   -> update output.txt
+ o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
+  this affects truncation error: -> update output.txt of exp:
+   global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
+   ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
+ checkpoint59f
+ o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
+ o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
+   a bounded range (in forward mode)
+ o pkg/ecco, ctrl, autodiff and mom_common:
+  internal parameter controls, completements of implementations
+ o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
+ o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
+   (not seem any difference in testing results).
+ o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
+    at face corners.
+ o pkg/generic_advdiff:
+  - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
+   loop range indices for computing vertical advection tendency
+   and do the calculation in the interior only (no overlap) ;
+   for now, only implemented for SOM advection (to save CPU time).
+  - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
+ o exch2 adjoint
+   First set of changes:
+   - add exch2 hand-written adjoint templates
+   - exch2 hand-written no longer use TAF-flag 'nownew_arg'
+     This will require cleanup in pkg/autodiff/*.F
+     (changed routines currently kept separate in verif. code/)
+   - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
+     that used to hide exch2 or cubed-sphere specific code
+     (commented via 'cph-exch2')
+ o pkg/seaice
+   - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
+ o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
+    output of global_ocean.cs32x15.thsice .
+ checkpoint59e
+ o exch2: new S/R that only use the cube-tracer (center-position) exchange:
+   for B-grid vector (not yet tested) and C-grid vector (<- only used
+   when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
+ o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
+   (#ifdef ALLOW_SALT_PLUME)
+ o gather_2d/scatter_2d: removed halo regions
+ o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
+   scheme and the corresponding test case (under front_relax dir). For now,
+   only available with Skew-flux form and not yet tested in realistic set-up.
+   adjoint: store directives updated, but gradient checks deteriorated,
+   so maybe GM/Redi adjoint is now broken.
+ o seaice adjoint
+   * add AREA, HEFF, HSNOW as control variable
+     (should not change lab_sea results)
+   * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
+ o pkg/seaice:
+   * added computation of saltFlux in seaice_growth;
+     For time being, sea ice salinity is assumed constant
+     contribution of snow flooding to freshening of sea ice is neglected.
+     SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
+     defaults to 0.0 in order to maintain backward compatibility.
+     Typical values for SEAICE_salinity are 4 to 10 g/kg.
+   * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
+   * added SEAICE_availHeatFrac, which specifies fraction of surface level
+     heat content used to melt or grow ice
+   * commented out cap of HICE: it helps keep ice thinner
+   * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
+   * applied OBCS T/S mask to HEFFM sea ice mask
+ checkpoint59d
+ o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
+  for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
+  (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
+ o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
+  and change default value of parameter "GM_Small_Number";
+  update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
+    global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,
+    tutorial_global_oce_biogeo, tutorial_global_oce_latlon
+ o pkg/ecco: cost function when applying pkg/smooth to controls
+ o pkg/ctrl: add forcingPrecond run time parameter
+ o pkg/seaice:
+  - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
+  - fix bug in metric terms of u-equation in LSR solver (implicit part),
+    changes verification/lab_sea
+  - rearrange implicit part of u-equation in LSR solver to make it easier to
+    read, understand, and debug. This causes changes at the truncation level.
+  - fix (serious) bug in the boundary conditions (sign error in the implicit
+    part) of the LSR solver. Changes all LSR results.
+  - fixed problem with HSNOW initialization to avoid thick snow when AREA
+    is initilized with small values - does not change lab_sea results.
+  - added HsnowFile initialization capability
+ o pkg/smooth: addition to model/src and pkg/ctrl so allow
+  initialization of pkg/smooth and application to control vector
+ o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
+ o dependencies: pkg/profiles requires pkg/cal
+ o pkg/profiles:
+  - added option ALLOW_PROFILES_GENERICGRID
+      -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
+      that interpolation information (grid points and coefficients) is provided
+      within the netcdf input files.
+      -> sample matlab scripts can be found in MITgcm_contrib/gael
+      that allow you to prepare netcdf input files.
+  - also modified: cleaner include statements, cleaner error print statements,
+    cleaner stops when error, and more tests of the netcdf input files consistency.
+ o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
+ o pkg/seaice:
+  - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
+    requires a new routine: seaice_diagnostics_fill.F
   - make sure that seaice does not move if not forced (pressure replacement
     method, Hibler and Ip, 1995), changes results
   - and new damping criterion for EVP solver according to Hunke, JCP, 2001
-Line 134 
 o in FFIELDS.h:
+Line 1063 
 o in FFIELDS.h:
       ATMOSPHERIC_LOADING is #define).
  o pkg/kpp: replaced _KPP_RL with _RL
  o bug fixes for vertical diffusivity computations when both KPP and
-D diffusivity arrays are used.
+D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
+     are no longer updating the vertical diffusivity array
+     (passed as argument) but are (re-) setting those arrays.
  o pkg/seaice: fix bug in evp solver, while doing that
    - change (improve?) discretization of stress computations for both
      cgrid-lsr and evp solver
-Line 1616 
 o add two new packages
+Line 2547 
 o add two new packages
    - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
    - these scheme operate in a similar manner as KPP (without ghat, of
      course), however there is only one diffusivity that is used for both
-     temperature and salinity (and passive tracers)�
+     temperature and salinity (and passive tracers)
  o add offline package
  o add "verification/dic_example" which contains a dic-gchem-ptracer setup
    provided by Stephanie Dutkiewicz

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