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-revision 1.53.2.32 by dimitri,
Thu Feb 27 22:29:13 2003 UTC
+revision 1.1237 by jmc,
Sat Mar 13 01:04:05 2010 UTC
 Line 1
  $Header$
+ $Name$
      Notes on tags used in MITgcmUV
      ==============================
- untagged
+ o pkg/seaice:
- o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F
+   fix seaice_model.F for adjoint (gael) and update AD results of experiments
- o Added SEAICE_initialHEFF to pkg/seaice
+    lab_sea (std + evp + noseaicedyn) and offline_exf_seaice.
- o SEAICE_WRITE_PICKUP needs to be called before WRITE_CHECKPOINT
+ o testreport:
+   add option '-runonly' (short: '-ro') to just do the run part (without make).
+ o eesupp: remove JAM communication code (obsolete).
+ o add option to genmake2 & testreport to switch "_RS" type to "real*4"
+   (if allowed in CPP_EEOPTIONS.h); update default CPP_EEOPTIONS.h and return
+   to default CPP_EEOPTIONS.h for exp. inverted_barometer & solid-body.cs-32x32x1
+   (update also the output).
+ checkpoint62c (2010/03/02)
+ o tools/build_options :
+    move (some) old optfiles from build_options/ to build_options/unsupported/
+ o model/src and pkg/exf
+    surface relaxation -- separating data and data.exf options
+    The point is to ensure that we specify the surface relaxation
+    either in data or in data.exf (but not half and half) and to
+    avoid an accidental relaxation to 0 (which happened if a time
+    scale was specified but the file name was left empty)
+ o model/src model/inc and pkg/mom_common
+    ALLOW_3D_VISCAH/ALLOW_3D_VISCA4 => 3D specification of Viscosity
+    => addition to the viscosity field as computed by others schemes
+ o tools/build_options:
+   - rename "_generic_mpi" -> "+mpi_generic" (like other "+mpi" optfile)
+     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
+   - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
+       the two options are complementary.
+ o pkg/smooth
+   - migration from contrib to the main repository
+ checkpoint62b (2010/01/26)
+ o pkg/monitor:
+   - change back mon_printstats_rl.F & mon_stats_rl.F and add a stop
+     (in case someone forgot to update customized pieces of code)
+ o nonHydrostatic:
+   - add Non-hydrostatic free-surface form (selectNHfreeSurf=1)(not fully tested);
+   - add a simple 2-D experiment (short_surf_wave) to test it.
+ o pkg/icefront:
+    adding the shell of, and the hooks to, a new package that
+    will model melting and freezing of vertical glacier ice fronts
+ o momentum:
+   add diagnostics of momentum tendency from Hydrostatic pressure gradient
+    (without surf.pressure term: would need a 2nd filling since implicit term).
+ o add 3 "_d 0"s so that fizhi compiles with xlf on iblade, and replace
+   two " &end" by " &" (in fizhi-cs-*) because S/R NML_SET_TERMINATOR
+   cannot deal with the former
+ o cleaning:
+   - remove all (except OpenAD) old TLM output from results_ad dirs.
+   - remove unused S/R (MDSWRITEMETA, DIAGNOSTICS_ADD2LIST, old DFILE IO S/R)
+   - comment out maskH definition (replaced by maskInC)
+ o pkg/monitor:
+   - change mon_printstats_rl.F & mon_stats_rl.F (were similar to mon_writestats_rl
+     & mon_calc_stats_rl) to be the RL equivalent of mon_printstats_rs & mon_stats_rs.
+ checkpoint62a (2010/01/15)
+ o model/src:
+   - bottom pressure diagnostic: correct for r* (when nonlinFreeSurf >= 4)
+ o pkg/diagnostics:
+   - add optional level number diagnostics (i.e., level number to be define
+     explictly with S/R DIAGNOSTICS_SETKLEV) with parser-code(10)="X".
+   - strictly check for valid parser-code(10) ;
+   - check if adding diag to the list from the right place.
+ o pkg/longstep:
+   - change parameters and fix tracer conservation with rstar/nonlinear free surface
+ o diagnostics:
+  - in all pkgs, replace remaining calls to old S/R DIAGNOSTICS_ADD2LIST with newer
+    S/R DIAGNOSTICS_ADDTOLIST ; fix seaice VICE diagnostics.
+ o pkg/diagnostics:
+  - Add option for writing vertical integral (sum of selected levels) of an output
+     field instead of writing output field levels. Activate this option on a per
+     output-file basis, by setting the 2nd character of fileflag to 'I'.
+  - Add field-specific information relative to level integral in 3rd postion
+     of parser diagnostics code (gdiag): " "=cumulate levels, "R"=integrate
+     vertically (x level-thickness x hFac), "r"=same but without hFac.
+ o do_the_model_io:
+   - pass end-of-model-run flag as argument, from forward_step to diagnostics_write:
+     in case useSIGREG, will write (averaged) diagnostics (if dumpAtLast) before
+     writing pickups and stopping.
+ o pkg/diagnostics (for now, only with mdsio):
+   - write time information to meta file (and modify accordingly rdmds.m) :
+     time-averaged diagnostics output: write starting and ending time of the
+     time-averaging interval ; snap-shot diagnostics output remains unchanged;
+ o pkg/timeave:
+   - S/R TIMEAVE_NORMALIZ: change size of cumulated-time array (was previously
+     always Nr), now assumed to be equal to number of levels of averaged field;
+     only used for DIC_COST monthly mean arrays: this fixes dic_aver_final.F
+ o pkg/sbo:
+   - fix ocean bottom pressure global-average & 2-D time-ave output (was
+     neither initialised nor filled).
+   - add starting iteration in suffix of global-average output file
+     (to avoid over-writing the file after a restart)
+   - use standard MDSIO pkg S/R instead of SBO_WRITEVECTOR (fix byte-swap Pb).
+ o time-average:
+   - use simple cumulative-time array (no k index) in all pkgs: {PKG}_timeAve(bi,bj)
+     (pkgs: aim_v23, bulk_force, dic, gmredi, kpp, land, ocn_compon_interf,
+      ggl90, my82, opps, pp81, ptracers, sbo, seaice, shelfice, thsice)
+     this fix DIC_COST cumulative-time array (previously: bi,bj,k)
+   - fix 1rst call (nIter0) snap-shot output and accumulation (pkg/shelfice)
+   - fix missing accumulation for pkg/opps.
+   - cumulate fields only if doing time-ave output ({PKG}_taveFreq > 0)
+      (pkgs: ptracers, kpp, ocn_compon_interf, ggl90, my82, pp81);
+   - fix initialisation of time-ave vars and do only full time-step increment
+     (i.e.: no first & last "half time-step") (pkgs: ggl90, my82, opps, pp81);
+ o pkg/layers:
+   - use standard RW pkg S/R to write the output
+     and remove local write_fld version (which had a problem).
+   - use simple cumulative-time array (no level index) to fix time-ave S/R calls.
+   - fix LAYERS_CALC argument list.
+ o pkg/timeave:
+   - store cumulative-time in a simple tiled array (drop the level index)
+   - add new S/R (TIMEAVE_NORMALIZE) which uses simple cumulative-time array.
+ o pkg/ocn,aim_compon_interf
+   - changes for multi-threaded coupled run. (tested with ifort-11 on danton)
+ checkpoint62  (2009/12/23)
+ o switch on useOBCSbalance in tutorial_plume_on_slope exp. and update output.
+     (was not previously tested in any other exp.)
+ o pkg/monitor:
+   - clean-up _RL/_RS version: add specific S/R for statistics with mask & volume:
+     mon_writestats_rl/s,F mon_calc_stats_rl/s.F ; will keep the old one
+     (mon_printstats_rl/s,F mon_stats_rl/s.F) just for bare statistics.
+   - use hFac & 2-D mask (instead of 3-D mask + hFac in previous mon_stats_rl.F).
+   - change del2 calculation.
+   - use interior masks (instead of maskH, <- to be remove).
+   - shorter monitor suffix for forcing stats ("forcing" instead of "extforcing").
+ o mask & obcs:
+   - define 2-D "interior" masks (i.e., zero beyond OB) at 3 locations (C, W & S).
+   - move global area computation from ini_masks_etc.F to ini_linear_phisurf.F
+     (called after packages_init_fixed)
+ o pkg/obcs:
+   - move bi,bj loops into obcs_calc, so obcs_prescribe_read is called only once.
+     Fixes bug in obcs+exf with nSx*nSy.GT.1
+   - fix multi-tile handling in obcs balance code
+ o nonHydrostatic:
+   - Implement AB-3 for non-hydrostatic vertical momentum ;
+     (change ordering of var. stored in pickup file when using NH)
+   - move NH code from solve_for_pressure.F to 2 new S/R: PRE_CG3D & POST_CG3D.
+   - add 2-D field to store Hydrostatic Surface Pressure adjusment from cg3d_x
+     (in prep. for new NH free surface form).
+ o pkg/obcs:
+   add files & OB-variables for wVel (Non-Hydrostatic) with useOBCSprescribe
+ o model/src:
+   fix 2-D solver initialisation for deep-atmosphere (p-coord) with topography
+ checkpoint61z (2009/12/01)
+ o nonHydrostatic:
+   Fix missing vertical flux of vert. momentum near surface (k=1). This fixes
+     a spurious source of energy in simple baroclinic adjusment test case.
+   Update all non-hydrostatic exp output.
+ o model/src (3-d solver):
+   Change again 3-D solver free-surface RHS term when exactConserv=T:
+     simpler, consistent with exactConserv, and works with implicDiv2Dflow < 1
+     (which was not the case with previous formulation).
+   To recover previous version, just reset "oldFreeSurfTerm" to previous value.
+   Affects results of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW.
+ o nonHydrostatic:
+   - compatible with implicDiv2Dflow < 1 ; + implement implicit factor
+     for Non-Hydrostatic pressure gradient (similar to implicSurfPress).
+   - change 3-D solver to work with r* (for now, only with linear free-surf.)
+   - add few debug diagnostics (cg3d_x, residual)
+ o model/src:
+   fix missing EmPmR in 3-D solver RHS (was in cg2d_b but missing in cg3d_b).
+     update output of exp. global_ocean.cs32x15.viscA4
+ o update output of exp. global_ocean.cs32x15.icedyn after removing
+   #define SEAICE_OLD_AND_BAD_DISCRETIZATION from SEAICE_OPTIONS.h
+ o add entry points for Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
+ o mnc: add horizontal grid coordinates (XC,YC) and (XG,YG) to netcdf output
+   for complex grids, for now only to "state", "adstate", "adexf", "adseaice"
+ o model: add Christopher Wolfe's implemetation of the single reduction cg2d
+   (d'Azevedo, Eijkhout, and Romine, 1999) with CPP-flag ALLOW_SRCG and
+   runtime flag useSRCGSolver. Modify verification experiment global_with_exf
+   to test this code
+ o pkg/cd_code:
+   Change defaut D-grid time-stepping to get the same for D-grid momentum as for
+    C-grid momentum. D-grid velocity used to be stepped forward in time with
+    Adams-Bashforth only on surface pressure term. Tests show that using AB on
+    D-grid coriolis term improves stability (as expected from CD-scheme paper).
+   To reproduce old results, add 2 options (in CD_CODE_OPTIONS.h).
+   Update results of exp: global_with_exf (x2), ideal_2D_oce, isomip (x2),
+    lab_sea (3 Fwd +3 AD), natl_box (x2), tutorial_global_oce_biogeo (Fwd+AD),
+    tutorial_global_oce_latlon, tutorial_global_oce_optim & tutorial_tracer_adjsens.
+   Keep old results by adding CD_CODE_OPTIONS.h in exp: cfc_example, exp2,
+        global_ocean.90x40x15(+AD), global_ocean_ebm(+AD) and OpenAD.
+ o pkg/obcs:
+  - fix bug in initialisation (broken since Oct 1rst modification)
+    for useOBCSprescribe without useEXF.
- release1_p12
+ checkpoint61y (2009/11/15)
- o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf,
+ o pkg/seaice
-   kpp_transport_t.F, forward_step.F, and the_main_loop.F
+  - change (once again) the discretization for the evp solver: rather than
+    squaring the averages of strain rates, average the squares to give
+    a better approximation to VP behavior (in simple test); this breaks
+    verification experiments that use EVP (lab_sea and lab_sea.hb87)
+     --> update outputs
+ o add CPP-flag (in mom_calc_visc.F) and TAF directive (in gmredi_slope_limit)
+   to improve vectorization of adjoint code on TARGET_NEC_SX
+ o verification/vermix:
+   - change vermix to a more "classical" 1d column with high vertical
+     resolution, seasonal heat flux forcing and constant wind forcing
+     --> update outputs
+ o pkg/seaice
+  - fix diagnostics of principal stress components for EVP
+  - add optional diagnostics of non-linear convergence for LSOR solver
+  - make maximum zeta a runtime parameter
+ o model/src (3-d solver):
+   Undo modif from Dec 12, 2005 (solve_for_pressure.F cvs version v.49),
+    which consisted in removing the Surf. Non-Hydrostatic pressure from the
+    whole column and adding it to Eta (inspired from Casualli, 1999):
+    Only affects 3-D solver initial guess and only if using ExactConserv,
+    but tests did show a degradation of solver convergence. For this reason,
+    decide to disable this piece of code.
+    to recover previous version, just set zeroPsNH = exactConserv (line 78).
+   Update output of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW
+ o pkg/ggl90:
+  - fix previous modif (unfortunatly has not been documented here).
+ o pkg/seaice/autodiff:
+  - add CPP flag to include clipping of zeta in EVP code;
+    although clipping of zeta is not necessary for EVP and not recommended
+    it was done by default, now clipping is disabled by default
+  - modify computation and store zetaC/Z in seaice_evp for TAF
+  - add CPP-flag SEAICE_ALLOW_CLIPVELS (undefined by default)
+  - change seaice_calc_viscosities/strainrates for better
+    vectorization after AD by TAF
+  - rearrange common blocks in SEAICE.h once again for easier dumps of
+    adjoint output, adjust adcommon.h and g_common.h
+  - change flux form of default advection scheme for better vectorization
+    of adjoint code
+  - modify lab_sea/input.lsr to test the flux form of default advection
+    scheme
+ o autodiff: fix seaice fields in g_common.h (left over from 3 to 1 level
+   transition in checkpoint61r)
+ checkpoint61x (2009/10/19)
+ o adjoint: adding two new verification experiments
+   * tutorial_global_biogeo: an online dic sensitivity experiment
+     (work with G. Forget)
+   * tutorial_dic_adjoffline: an offline dic sensitivity experiment
+     (an update of the Dutkiewicz et al., 2006 paper)
+   Both use the same CO2FLUX cost function, but different controls
+   Gradient checks look good, but some recomp. could still be traightened out
+   Should add xx_dic control variable to test at some point
+ o model/src:
+   add run-time parameters to check and/or mask initial Temp & Salt
+ o pkg/ptracers:
+   apply zonal filter (if used) to all passive tracers
+ checkpoint61w (2009/10/12)
+ o adjoint:
+   * update and finish work on adjoint of dic package (G. Forget)
+   * start adjoint of offline package
+   * bug fix for cube-sphere TLM code (active_file_g.F)
+ o tutorial_global_oce_optim:
+   now tested with 4 tiles (change data.grdchk and update output_adm.txt)
+   and add SIZE.h_mpi for MPI testing
+ o pkg autodiff
+  - fix bug in autodiff_restore
+  - make genmake2 remove comments and empty lines from ad_input_code.f in
+    order to reduce file size (new script file remove_comments_sed)
+ o allows to specify vertical profile of vertical viscosity (viscArNr)
+ o pkg autodiff
+   autodiff_ini_model_io: comment out writing of grid information to netcdf
+   files, because at this time the grid fields are a bunch of zeros
+   (this is analogous to ini_mnc_vars.F)
+ o pkg seaice/autodiff:
+  left-over from removing the 3-time-level fields:
+  - small rearrangement of common blocks (SEAICE.h)
+  - fix field declaration in order to get meaningful output in
+    adseaice.*.nc (adcommon.h)
+ o pkg obcs:
+  - go through NH code only if nonHydrostatic=T
+  - fix restart for Orlanski (Hydrostatic; still to fix NH+Orlanski restart)
+  - move call to OBCS_CALC before SEAICE_MODEL which needs seaice-obc fields
+    => Update output of experiment seaice_obcs
+  - useOBCSbalance: code is wrong with multi-tile / proc: add a stop.
+  - fix NH+Orlanski restart (add wvel OBC value in pickup file)
+  - fix restart for useOBCSprescribe + useEXF
+ o pkg ctrl
+  - make obcs as control parameter work also with useSingleCPUio
+  - replace a few sny and snx by Ny and Nx to be consistent with
+    ctrl_set_globfld_x/yz.F
+ o pkg seaice
+  - re-introduce global field frWtrAtm for the case of
+    ALLOW_MEAN_SFLUX_COST_CONTRIBUTION defined (SEAICE.h, seaice_growth.F)
+  - catch the case of an empty filename in seaice_cost_init_fixed.F
+ o pkg ecco:
+  - small bug fixes in the_main_loop
+   . fix order of monitor arguments
+   . change SEAICE_MULTILEVEL to SEAICE_MULTICATEGORY
+   . move include DYNVARS.h up outside the ALLOW_AUTODIFF_TAMC block so
+     that ALLOW_ECCO_FORWARD_RUN works with NONLIN_FRSURF
+  - replace cos(yc*deg2rad) by _rA in cost_mean_heat/saltflux.F, fix the
+    imbalance diagnostics for wmean_h/sflux = 0
+  - add actual values to f_obcsn/s/w/e in ecco_cost_final.F
+  - catch the case of empty filenames in ecco_cost_init_fixed.F
+    and ecco_readparms.F
+  - fix the logic of wsalt=0.and.wsalt2=0 to wsalt=0.or.wsalt2=0 (and theta)
+    to make this statement meaningfull in ecco_cost_weights.F
+ o pkg zonal_filt:
+   - change ZONAL_FILTER S/R interface (allows to filter 2-D fields)
+   - when using rStar, filter uVel*hFacW instead of uVel
+    (tested without topography: fix a Pb of growing instability with NLFS)
+ o pkg/aim/thsice:
+  -Add capacity to read a Q-Flux to be applied in slab-mixed layer thsice_slab_ocean.F
+   (works as SST restoring)
+ o pkg/thsice:
+  -add specific parameter for salt restoring in slab mixed-layer
+    (by default equal to the temperature restoring)
+ checkpoint61v (2009/09/21)
+ o pkg/kpp:
+  -add double diffusive contributions as a hack, turned off by default
+   for now, and the code can be excluded with a CPP-flag
+   EXCLUDE_KPP_DOUBLEDIFF just as EXCLUDE_KPP_SHEAR_MIX
+  -add a verification experiments to "vermix" to test this code
+ o pkg/mom_common:
+   Move computation of length scales to mom_init_fixed.F (avoid recomputation
+   at each time-steps*levels).
+ o pkg/layers:
+   Created a new package for computing volume fluxes in temperature or
+   [not yet implemented] density layers, e.g. for calculating residual
+   overturning circulations.
+ o pkg/diagnostics:
+   implement a RS type version for the set of DIAGNOSTICS-FILL subroutines
+ o fix few RS/RL type mismatch (check with ifort 11.1 "-warn all" option)
+ o pkg/mdsio (& pkg/rw): rework high level S/R interface:
+   To avoid mixing type (RS/RL) of input/output array argument,
+   replace single mixed-type array with a pair from each type (RS/RL).
+ o setting pickupSuff force to start from a pickup (even if nIter0=0): this
+   is now implemented for all pkgs (previously only done for the main pickup)
+ checkpoint61u (2009/08/25)
+ o pkg/obcs:
+   - change OB?eta from _RS to _RL and put them into a separate commen block
+   - add code to read OB?eta from a file via obcs_prescribe_read: the code
+     compiles and does not destroy any other experiments, the data is read
+     properly, but the code is not tested in actual applications
+ o ini_mnc_vars.F: if available (ALLOW_CAL), use startTime_1 and 2 to
+   create a meaningful unit attribute for the time coordinate variable
+ o pkg/ebm: add plenty of missing "_d 0" ;
+    update results of experiment global_ocean_ebm (fwd + adjoint tests)
+   Notes: several pieces of code only works for (very) specific set up
+    (domain size, lat range, etc ...); should be documented & stop if one
+    of those assumptions is not meet.
+ o pkg/seaice: add missing "_d 0" in HSNOW initialisation
+    update results of experiments: lab_sea (3 fwd tests + 2 adjoint tests)
+       and offline_exf_seaice (seaicetd + adjoint).
+ o add missing "_d 0" in ShortWave flux penetration (S/R SWFRAC):
+    update results of experiments: lab_sea (4 fwd tests + 3 adjoint),
+     seaice_obcs, global_ocean.cs32x15 (icedyn & thsice) and natl_box (x2).
+ o few changes to pass when compiling with strick checking of arguments
+    across S/R (allow to find few bugs in S/R calls).
  o pkg/seaice:
-   - adjoint-friendly modifications
+  - seaice_evp: move if-statement out of loop (TEM) at the cost of 11 new
-   - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
+d-fields, for slightly better performance
- release1_p12_pre
+ checkpoint61t (2009/07/22)
- o Updated useSingleCpuIO option in mdsio_writefield.F to
+ o pkg/seaice:
-   work with multi-field files, e.g., for single-file pickup.
+  - remove unused variables in seaice_evp
+  - reduce number of SQRT in seaice_evp and seaice_calc_viscosities
+ o eeset_parms.F, open_copy_data_file.F & ini_parms.F:
+    named file replacing SCRATCH files (for TARGET_BGL & TARGET_CRAYXT):
+    each processor opens a different file (a fix from Matt).
+ o cg2d:
+    use simple EXCH (overlap size = 1 and ignore corners), like in cg3d.F :
+    this reduces number of EXCH calls by 2 when using exch2.
+    For now, keep previous size array for gc2d_nsa.F to avoid Pb with store
+    directives and missing simple EXCH (exch_s3d_rx) adjoint code.
+ o pkg/thsice:
+    add code for Near Infra-Red albedo (from Jeff)
+    (turned on with run-time flag: thSIce_calc_albNIR, in data.ice).
+ o ini_model_io:
+    move (from packages_readparms.F & initialise_fixed.F) to ini_model_io.F
+    MNC & MONITOR initialisation calls; move MNC calls from {pkg}_readparms.F
+    to {pkg}_init_fixed.F for {pkg}= kpp, seaice & shelfice.
+ checkpoint61s (2009/06/30)
+ o pkg/exch2 (exch2_rxN_cube*):
+    remove last BARRIER (no need to synchronise after getting data from shared
+    buffer (get) as long as any change to buffer (put,recv) is between BARRIER)
+ o change tiling of natl_box (from 2 to 4 tiles) to get it tested with MPI+MTH
+   and generate new output (for the 2 tests) using default rotationPeriod.
+ o pkg/exch2:
+   - always call exch2_*_cube, not exch-1 anymore, if useCubedSphereExchange=F
+     (was already the case with AUTODIFF_EXCH2 defined)
+   - add bj in exch2 arrays and S/R.
+   - can now use pkg/exch2 for regular (non CS) set-up; switch test experiment
+     MLAdjust to exch2 (identical results except with MPI -> truncation diff);
+ o add pkg/longstep for ptracer timestep a multiple of U/V/T/S timestep
+   - adds deltaT argument to the subroutines TIMESTEP_TRACER DWNSLP_APPLY
+     GAD_ADVECTION GAD_CALC_RHS GAD_IMPLICIT_R GAD_SOM_ADVECT
+   - verification experiment natl_box.longstep
+ o build_options: ifort+mpi_aces optfile (following Constantinos advise):
+   allow different versions of ifort (8 or 9) and different versions
+    of mpi (mpich or mpich2) to be used with the same optfile.
+   requires to load a netcdf module and set MPI_INC_DIR (see comments inside
+    optfile). Change testing scripts (example_scripts/ACESgrid) accordingly.
+ o pkg/seaice:
+   fix previous modif (3-level field removed) for old-pickup reading
+ checkpoint61r (2009/06/25)
+ o pkg/seaice:
+  - clean up the 3-time levels of UICE,VICE,HEFF,AREA in three steps:
+. introduce fields for time step (N-1)
+. do not use levels 2 and 3 anymore (but keep them)
+. replace 3D versions of UICE,VICE,HEFF,AREA by 2D versions. This
+      includes changes to pkg/thsice/thsice_get_velocity.F,
+      model/src/external_forcing_surf.F, pkg/obcs/obcs_apply_seaice.F, and
+      pkg/obcs/obcs_apply_uvice.F.
+  - completely remove code for leap-frog time stepping for second order
+    advection
+  - adjusted adjoint accordingly;
+    gradient checks have improved by an order of magnitude!
+ checkpoint61q (2009/06/22)
+ o pkg/seaice: fix bug in free slip boundary conditons for LSOR solver
+  - the boundary conditions along open boundaries are unclear, because the
+    associated masks are set to zero and are thus treated as closed when
+    applying the slip-boundary conditions.
+  - move initialisation of grid variables from seaice_init_varia to _fixed
+ o adding doc/diags_changes.txt
+ o model/src:
+   do_the_model_io: rename few pkg S/R which are called from do_the_model_io,
+    to avoid "_diags" naming if no relation to pkg/diagnostics.
+   ini_theta,ini_salt: fix (at least compile the code) reading from NetCDF
+    file and only call PLOT_FIELD_XYZ if debugMode=T.
+   remove few PLOT_FIELD_XY calls outside initialisation.
+   remove few unnecessary BARRIER.
+ o pkg/salt_plume: add SaltPlumeSouthernOcean to allow disabling
+   of salt_plume package in Southern Ocean
+ o pkg/thsice:
+  - fix hOceMxL in overlap (needed for sea-ice advection);
+    update output of experiment global_ocean.cs32x15.icedyn.
+ o pkg/seaice:
+  - make the (placeholder-)tracer IceAge a little more meaningful
+   by avoiding ridging of age due to convergent ice flow
+  - add diagnostics for surface temperature, atmospheric and oceanic
+    heat flux, and atmospheric and oceanic ice growth
+ checkpoint61p (2009/06/10)
+ o eesupp (global_max & global_sum):
+  - add one more element to buffer (start at index 0) for GL_MAX/SUM output;
+  - remove starting & endding barrier (no longer needed)
+ o pkg/mdsio, writelocal:
+    works also in multi-threaded when LOCBIN_IO_THREAD_SAFE is undefined
+    (remove the STOP): uses shared buffer IO to store data from all threads
+    and then let master-thread write nThreads tiles.
+ o pkg/mdsio (read/write field):
+  - tiled IO done in 1 piece (all levels at a time);
+  - new header file "MDSIO_BUFF_3D.h" with 3-D buffers.
+  - multi-threaded: allow to read/write local (non-shared) array
+    (was already working with singleCpuIO ; now works also without);
+    => no longer needs barrier call after reading a file (added inside
+    mds_read/write field).
+  - move barrier calls outside gather/scatter_2d to mds_read/write_field
+ o pkg/obcs/exf
+   - exf_getffieldrec.F: add a few ". _d 0" and
+                         add code to catch the case fldperiod = 0.
+   - obcs_precribe_read.F: change if statements so that they match
+                           the variable type (_RL)
+   - add a separate exf_iprec_obcs to exf_set_obcs (by default equal to
+     exf_iprec) as part of namelist EXF_NML_01
+ o pkg/mdsio:
+   - read/write tiled (local) files: read/write 1-level tile chunk at a time
+     (instead of segment of length sNx); expected to speed up tiled IO.
+ o pkg/exch2:
+   - take buffer copy from/to array out of S/R exch2_send/recv into new
+     S/R exch2_put/get ; Exch of local variable now works with MPI+MTH
+     (tested by removing commom block statement in SOLVE_FOR_PRESSURE.h).
+   - ad version of send/recv no longer needed (but needs exch2_ad_put/ad_get)
+   - simplify argument list of S/R exch2_get_uv_bounds and exch2_get_scal_bounds
+     (which replaces exch2_get_recv_bounds & exch2_get_send_bounds) by
+     including Topology header file (and common blocks).
+   - implement EXCH_IGNORE_CORNERS in scalar exchange (rx1);
+     remove 2nd exch call in exch2_s3d_rx (no longer needed).
+   - document S/R arg. list (+ update some comments)
  o pkg/seaice:
-   - bug fix in growth.F: QNET for no shortwave case
+   - added SEAICE_CLIM_AIR code, which permits modulation of surface air
-   - added HeffFile for specifying initial sea-ice thickness
+     temperature and humidity over sea ice based on climatological values.
-   - changed SEAICE_EXTERNAL_FLUXES wind stress implementation
+   - clean up computation of Hibler+Bryan (1987) stress coupling for the case
+     of LSR (this change is expected to change the results slightly because now
+     it uses slightly difference moduli from the second last LSR solution, but
+     that is more consistent with the stress computations; this part of the code
+     is not tested in the verification experiments)
+   - fix diagnostics for flux of ice in case of B-grid
+   - turn strain rates eij and press into global fields within global
+     common block in SEAICE.h for more straighforward diagnostics
+   - fix diagnostics for principal stress components, press, zeta, eta
+     to give something meaning full
+ o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate
+   new output (all 4 tests) using default rotationPeriod.
+ o pkg KPP:
+   - add flag (LimitHblStable) to avoid limiting BL depth under stable conditions
+   - fix vertical indices in RI_IWMIX (match between KPP grid from 0 to Nr+1
+     and normal grid from 1 to Nr)
+ o Fix computations of L4rdt in mom_calc_visc.F
+ 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 (2009/05/26)
+ 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 (2009/05/12)
+ 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 (2009/04/29)
+ 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 (2009/04/07)
+ 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 (2009/03/18)
+ 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 (2009/03/17)
+ 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 (2009/02/13)
+ 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 (2009/01/27)
+ 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 (2008/12/29)
+ 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 (2008/11/21)
+ 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 (2008/10/23)
+ 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 (2008/09/25)
+ 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 (2008/08/30)
+ 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 (2008/08/05)
+ 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 (2008/07/29)
+ 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 (2008/06/24)
+ 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 (2008/06/19)
+ --->>> 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 (2008/05/29)
+ 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 (2008/05/06)
+ 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 (2008/04/10)
+ 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 (2008/03/07)
+ 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 (2008/02/09)
+ 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 (2008/01/14)
+ 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 (2007/12/18)
+ 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 (2007/11/30)
+ 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 (2007/11/09)
+ 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 (2007/10/21)
+ 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 (2007/09/29)
+ 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 (2007/09/17)
+ 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 (2007/08/21)
+ 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 (2007/07/26)
+ 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 (2007/06/21)
+ 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
+  - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
+    It is turned off by default (=-1.), because it changes the results.
+  - make it possible to read AREA from a file, too.
+ checkpoint59c (2007/06/04)
+ o add S/R and diagnostics for oceanic mixed-layer depth
+ o move GMRedi call after all vertical mixing schemes (including KPP)
+ o pkg/thsice:
+  - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
+   (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
+ o pkg/obcs:
+  - bug fix for balance code
+ o pkg/seaice:
+   - allow values of SEAICE_elasticParm > 1
+   - add new parameter SEAICE_evpTauRelax as an alternative
+     to SEAICE_elasticParm
+   - make lsr boundary conditions free slip (by default), changes result
+   - add code for no slip boundary conditions for lsr
+   - set minimum of zeta to zero (and not 4e8) (changes results)
+   - add a cap on AREA after advecting AREA if seaice_growth is not called
+ o change calculation of Visbeck K:
+   - no longer depend on tapering scheme; instead, compute slope (limited
+     by GM_maxSlope). this is equivalent to what was comuted before with
+     clipping or linear tappering.
+   - fix vertical averaging (wrong by 1/2 level)
+   - leave the old version (but will not be maintained) within
+     #ifdef OLD_VISBECK_CALC / #endif
+   - update output of exp. ideal_2D_oce
+ o change error catch in calc_r_star to improve vectorization
+ o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
+   add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
+ o adjoint:
+   Re-organized adjoint checkpointing according to Matt Mazloff
+   (but with modifs/completions/cleanups)
+   Storing is now bundled into large arrays to optimized I/O
+   (and second step in cleanup of the_main_loop)
+ checkpoint59b (2007/05/16)
+ o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
+   - export/import (between ocean & coupler) fields needed for ocean DIC.
+ o pkg/seaice:
+   - get rid of three more exchanges seaice_calc_viscosities (required
+     different loop boundaries in seaice_lsr and seaice_ocean_stress)
+   - bug fix in seaice_ocean_stress (update of lab_sea required)
+   - reduce loop boundaries to necessary minimum also in seaice_evp
+   - go back to the old way of computing deltaC/Z as the adjoint likes that
+     better
+ o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
+   passive tracer to an Age Tracer) + update output.txt
+ o pkg/exf:
+   - implement A-grid / C-grid selection for wind-stress input files.
+   - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
+   for now, in exf_bulk_largeyeager04.F only :
+   - change implementation for case where windspeed + 2. components wind-stress
+     are read-in. AND use rhoConstFresh to convert evap.
+ o pkg/seaice:
+   - use correct EXCH_UV for wind-forcing (on A-grid).
+   - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
+     SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
+ o pkg/exf:
+   - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
+   EXF_INTERPOLATION:
+   - merge global_with_exf/code version of exf_interp_read.F
+     to the main code ;
+   - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
+     reading the file ; Important: This options needs to be defined to recover
+     previous code.
+     otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
+   - no longer loose real*8 precision along the way when using exf_iprec=64.
+ o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
+   - change discretisation of evp-solver in order to avoid another exchange
+     (changes lab_sea) and clean up a little
+   - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
+     help the adjoint (this also changes the results slightly)
+   - add a few "_d 0" where they had been missing in seaice_evp.F
+   - cleaning up: remove unused seaice_calc_rhs.F
+ o pkg/exf: some cleaning-up:
+   - change various "constants" into runtime parameters
+   - cleaned-up Large&Yeager04 routine which should eventually
+     replace exf_bulkformulae.F (changed names of S/R and CPP)
+     and merged various ALLOW_ATM_WIND options
+  only used with thsice pkg (in thsice_get_exf.F):
+   - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
+     which are used when useStabilityFct_overIce=TRUE (= the default)
+   - change default values of ice & snow emissivity and scale downward LW
+     by ice & snow emissivity.
+ o pkg/thsice:
+  fix few little problems, in thsice_calc_thickn.F:
+   - growth vertically (and not laterally) if iceFrac == iceMaskMax
+   - melt only laterally if hIce < hThinIce (as the comments say)
+   and in thsice_extend.F:
+   - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
+   - start to form ice as soon as the minimum ice-volume is reachable.
+  update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
+   and cpl_aim+ocn
+ o pkg/kpp
+  - move computation of surface related input fields to KPP into a new
+    subroutine kpp_forcing_surf.F
+  - remove wrong (within bi,bj loops) EXCH calls.
+  - little cleaning (add argument myThid in last position, cvs header ...)
+  - for now, fix conservation problem by exchanging KPPviscAz (may not
+    be the best fix)
+ o pkg/seaice
+  - check for inconsistent evp parameter/cpp-flag combination
+  - remove leftover errIO flat for obsolete name list error handling
+ o OpenAD
+  - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
+ checkpoint59a (2007/05/01)
+ o pkg/seaice: some parameter clarifications and a little bit of clean up
+ o pkg/thsice: rename run-time parameters:
+    himin       -> hIceMin
+    himin0      -> hThinIce
+    hihig       -> hThickIce
+    i0          -> i0swFrac
+    transCoef   -> bMeltCoef
+    frac_energy -> fracMelting
+   add new parameters: hNewIceMax, fracFreezing, dhSnowLin
+    with default values (for now) that do not change the results.
+   remove old version of thsice vars advection in pkg/seaice.
+ o in FFIELDS.h:
+   - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
+   - make pLoad & sIceLoad always available (but still only used if
+      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; 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
+   - add a new routine to compute strain rates
+   - the above changes lab_sea results
+   - add no slip conditions for evp solver (off by default), lsr-version
+     may follow
+   - fix exchange for shear at Z-points (does not change lab_sea)
+   - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
+     (to force the user to pick a time step since there is not "safe" way
+     of choosing it)
+   - add principal stress diagnostics
+   - rearrange fields for evp a little to avoid having to call a: too many
+     exchanges and b: exchanges for stress trensor components which we do
+     not have.
+   - modify Hibler+Bryan (1987) stress coupling so that it reuses information
+     of evp, complete rewrite for lsr case (latter is does not yet work
+     in all cases)
+ o pkg/kpp: add code to have mixing in shelf ice caverns
+   - add myThid to all kpp routines (long overdue)
+ checkpoint59 (2007/04/19)
+ o pkg/exf:
+   - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
+     ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
+   - move exf header files from lower_case.h to UPPER_CASE.h ;
+     add missing cvs Header & Name
+   - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
+   - add namelist param. selectStressGridPosition, exf_monFreq
+   - retire many _CLIM routines, and remove data.exf_clim
+     + params moved to data.exf
+     + climsst, climsss now handled by exf_set_gen, i.e.
+       climss?period=0 refers to constant field,
+       climss?period=-12 to monthly forcing
+   - split up namelists in data.exf
+ o pkg/seaice:
+   - remove seaice_exch and seaice_exch_uv
+   - remove superfluous exchange of theta
+   - add myThid to seaice_budget_ocean/ice
+   - add new interface for atmospheric wind forcing (C-grid only)
+     + new routine
+     + two new field (taux, tauy for stress over ice)
+     + removed one global field (DAIRN) for C-grid case only
+ o pkg/thsise
+   - 2nd set of modifs for thsice adjoint in conjunction with exf
+ o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
+ checkpoint58y_post (2007/04/15)
+ o Added capability for latitudinal dependence of Bryan and Lewis, 1979
+   vertical diffusivity, similar to that in MOM4; turned on using
+   #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
+   diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
+ o Added capability for 3D specification of background vertical diffusion
+   coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
+   in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
+   "data" file that contains the 3D vertical diffusivity coefficients.
+ o ice dynamics (pkg/seaice) with thsice thermodynamics:
+   - add code within pkg thsice to advect & diffuse sea-ice fields
+   similar to (and will replace) what has been added in  seaice_advdiff.F,
+   but: - conserving Mass, Heat & Salt.
+        - better when using non-linear advection scheme (not yet fully tested)
+        - can also be used in atmospheric set-up (for now, only the diffusion).
+ checkpoint58x_post (2007/04/04)
+ o IO option for global-file compact format:
+   - add options when generating topology (utils/exch2/matlab-topology-generator)
+   - add I/O capability (pkg/mdsio).
+   - adapt utils/matlab/rdmds.m to read this format.
+   for now long-line format not yet supported by pkg/mdsio (& exch2).
+ o shelfice: add a few diagnostics
+ checkpoint58w_post (2007/03/13)
+ o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
+   rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
+   (and replace horiVertRatio in NH code).
+   Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
+                      and tutorial_plume_on_slope (sensitive to truncation)
+ o seaice: if ALLOW_ATM_WIND is undefined use wind stress
+   directly to drive seaice model (C-grid only)
+ o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
+  - reintroduce computation of wind from stress,
+  - compute tau (in exf_bulkformulae.F) from windstress averaged to
+    mass points to avoid tau = 0
+  - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
+ o rdmnc.m: make it work with "global" files created with gluemnc
+ o rdmnc.m : some improvements in dealing with singleton dimension
+   (tested on all testreport mnc output files).
+ o genmake2: disable pkg/profiles if netcdf test fails.
+ o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
+ o move call to cal_readparms up to make calendar parameters/variable available
+   to all packages
+ checkpoint58v_post (2007/02/08)
+ o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
+   useDynP_inEos_Zc tested.
+ o pkg/exf: changes to properly interpolate/mask/scale initial fields
+ o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
+   and portions thereof.  See read_cs.txt for description and examples.
+ o utils/matlab/cs_grid/bk_line: to compute transport through passages,
+   add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
+   following the great-circle arc between those 2 points.
+ o trap un-initialized variable with pathscale compiler on weddell.mit.edu
+   (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
+ o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
+  - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
+  - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
+  - still needs work (not working with some options ; efficiency to improve)
+    and serious testing.
+  - use this scheme for temperature & salinity in 2 advection test exp.:
+    advect_xy & advect_xz, respectively.
+ checkpoint58u_post (2007/01/12)
+ o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
+ o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
+ o testreport: add option "-skipdir" to skip some test.
+ o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
+   momentum calculation.
+ o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
+ o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
+   remove checkpoint.F and the_correction_step.F (no longer used);
+   do the k loop inside CYCLE_TRACER (supposed to be more efficient).
+ o add option (linFSConserveTr) to correct for tracer source/sink due to
+   Linear Free surface
+ o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
+ o pkg/thsice: fix reading mnc-pickups
+ checkpoint58t_post (2006/12/30)
+ o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
+ o pkg/mdsio:
+  - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
+    move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
+    mdsio_write_field.F (S/R MDS_WRITE_FIELD);
+  - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
+  - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
+    either MDS_READ_FIELD or MDS_WRITE_FIELD )
+  - new S/R (to replace MDSWRITEMETA), which allows to write more
+    informations (variable names, time ...) to meta files.
+  - modify rdmds.m to give back the meta file content.
+ o pkg/diagnostics: change vertical interpolation to be safer, and more
+    flexible (define p-levels to interpolate to in data.diagnostics);
+   add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
+    diagnostic pointer.
+ o pkg/seaice: more cleaning up of seaice_growth, added many comments
+ o pkg/exf: put runoff0 and runoff1 into the appropriate common block
+ o fix multi-category seaice:
+  - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
+    SEAICE_MULTICATEGORY
+  - fix short wave heat flux
+ o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
+    and allow to use EVP solver. Change forward lab_sea: test both EVP
+    solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
+ o Initial check-in of lab_sea adjoint
+   (very similar to natl_box_adjoint/code_seaice)
+   * used C-grid and EVP solver
+   * used KPP, GM/Redi
+   * uses inAdExact=.TRUE.
+   * gradient checks fail for both ADM and TLM
+     due to sensitive snow melt code in seaice_grwoth (look for "JZ")
+     f.d. gradients actually seem more problematic than ADM, TLM gradients;
+     issue is related to forward mismatch between g77 an ifort
+ o pkg/seaice: overhaul of thermodynamics
+  - growth.F and groatb.F are replaced by new routine seaice_growth.F
+  - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
+  - move a few global fields out of SEAICE.h into seaice_growth.F and
+    make them 2D (FICE/QNETO/ ...)
+  - remove FO (it is the same as QNETO)
+  - introduce a few local fields to avoid modifying external fields such
+    as atemp, etc.
+ checkpoint58s_post (2006/12/11)
+ o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
+   changed exf_set_gen.F so that
+     genperiod=0 means input file is one time-constant field and
+     genperiod=-12 means input file contains 12 monthly means
+ o CG2D: use pre-computed solver main-diagonal (stored in common block);
+   this affects truncation error ; generate new output file for exp. which
+   fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
+     global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
+     ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
+     MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
+     tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
+     vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
+ o start implementation of deep-atmosphere and anelastic formulation
+ o verification: remove 2nd copy of input files and use script "prepare_run"
+   to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
+ o mom_common/vecinv/fluxform: fix a few initialisation isssues
+ o profiles: fix for multithreaded case
+ o diagnostics: rename few diags:
+   s/'PRESSURE'/'RCENTER '/g
+   s/'TICE    '/'oceFreez'/g
+   s/'TAUX    '/'oceTAUX '/g
+   s/'TAUY    '/'oceTAUY '/g
+   s/'SWFLUX  '/'oceQsw  '/g
+   s/DIFx/DFxE/g
+   s/DIFy/DFyE/g
+   and add few ocean-forcing diagnostics:
+   atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
+ o modifications to pkg/seaice/growth.F and budget.F, which change results of
+   lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
+   as actual snow thickness.  It now refers everywhere to effective snow
+   thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
+ checkpoint58r_post (2006/11/17)
+ o modifications to pkg/seaice/growth.F, which change results of
+   lab_sea experiment: fixes pertain to melting snow over open water, to
+   masking EVAP under sea ice, and to using the correct AREA variable for
+   computations of EVAP, PRECIP, HSNOW, and GHEFF
+ o add ability to read bathy, salt, and theta using MNC (off by def)
+ o add flooding algorithm and advection of HSNOW for pkg/seaice;
+   both are turned off by default and do no change any results
+ o seaice advection with pkg/thsice: a step toward the use of non-linear
+   advection scheme, but #ifdef or commented out for now (requires more EXCH).
+ o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
+   (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
+   in natl_box (affects results @ truncation level: update output.txt)
+ o multi-threading and IO:
+   - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
+   - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
+     (needed to work with SingleCpuIO): tested in all verif. exp.
+ o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
+   affects the results (but none of the verification test uses this scheme).
+ o Adding some pkg/diagnostics capability to pkg/seaice
+   (will certainly be subject to changes)
+ o ctrl: adding new control variables:
+   lwflux, lwdown, evap, snowprecip, apressure, runoff
+ checkpoint58q_post (2006/10/20)
+ o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
+/6-deg Southern Ocean configuration by 8% on IBM Datastar and
+   high_res_cube configuration by 4% on Columbia.
+ o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
+   add (in global_with_exf/code) a version of EXF_INTERP_READ without
+   dynamical allocation (seems to work in multi-threaded).
+ o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
+   single CPU io) so that TAF does not have to see EESUPPORT.h
+ o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
+ checkpoint58p_post (2006/09/08)
+ o obcs: stop if obcs is used with useCDscheme = .true.
+ o shelfice:
+  - fix a sign error so that no slip at shelfice interface works
+  - remove stop for combination non-hydrostatic code and shelfice. That does
+    not mean, that the results are correct, but at least they are numerically
+    stable
+ o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
+ o added adjoint exch routined for all exch*3d* routines
+   and updated flow directives
+ checkpoint58o_post (2006/08/28)
+ o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
+   remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
+ o change controling S/R for writing pickup file (new S/R do_write_pickup)
+   and clean-up reading/writing of pickup files.
+ o fix local version of read/write pickup (NH part) in rotating_tank/code
+ o simplify EXCH interface:
+  - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
+  - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
+ o added the regrid package
+ o shelfice:
+  - add a simple boundary layer scheme to reduce noise
+  - fix the indexing in shelfice_u/v_drag so that there will be actually drag
+ checkpoint58n_post (2006/08/14)
+ o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
+    local variable (not in common block).
+ o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
+   - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
+   - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
+     to work with SingleCpuIO.
+ o add "_d 0" to real constant of pkg/cfc subroutines ;
+    update exp. cfc_exemple & tutorial_cfc_offline output files.
+ o multi-threading and IO:
+   - all threads call READ_FLD S/R (needed if using SingleCpuIO):
+     (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
+   - barrier before and after reading.
+   - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
+   - avoid using MDS_WRITELOCAL for LAND pkg output.
+   - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
+     common-block variables ; Allows multi-threading with master-thread IO.
+ o change default MAX_NO_THREADS from 32 to 4 ;
+   and stop cleanly when MAX_NO_THREADS is too small.
+ o add S/R BAR_CHECK to check multi-threaded barrier synchronization
+ checkpoint58m_post (2006/07/17)
+ o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
+    and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
+ o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
+    keep global_ocean.90x40x15 (for AD testing) with former secondary test
+    (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
+ o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
+     add MITgcm_tutorials (= code + all the tutorials)
+ o ecco, option to compute cost for total ssh (mean+anom)
+ o consistent with addition of ptracer and ssh in pkg/profiles
+ o profiles: adding ptracer and ssh
+ o testreport: change multi-test output-file name
+   (from output.txt.{name} to output.{name}.txt)
+ o profiles: now ok for mutli-tiles case
+ o seaice: add 4 parameters for different advection schemes for area,
+   (effective) seaice thickness, enthalphy, and snow height. Their default
+   is the standard parameter SEAICEadvScheme
+ o calc_gw:
+  - add cosFacU in zonal viscous flux (harmonic.visc.).
+  - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
+    of tutorial_plume_on_slope.
+ o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
+ o calc_gw: true flux-form, account for horizontal grid spacing.
+   update rotating_tank results, but not plume_on_slope (affected at
+   truncation level, 11 digits).
+ checkpoint58l_post (2006/07/12)
+ o calc_gw:
+  - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
+  - remove side-drag for now (need to fix it); update plume_on_slope results.
+  - fix for partial-cell & non-uniform dz; update plume_on_slope results.
+ o commit code to make SST/SSS weights spatially variable
+   (based on either variable in-situ or variable initial T/S weights)
+ o pkg/ecco:
+   * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
+     now based on horizontally varying weights wthetaLev, wsaltLev
+   * cost_averagesflags now returns year indices in addition to day, month
+   * sflux balance is performed on annual basis
+     (sflxumm, sfluxmm2, bal_sfluxmm)
+   * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
+     including separate counting and multipliers
+ o pkg/rbcs
+   * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
+ checkpoint58k_post (2006/07/06)
+ o testreport:
+  - always build in dir. "build" (if not there, mkdir build instead of building
+    & running in input)
+  - run in dir run (if it exists), in build otherwise.
+  - call prepare_run (if input/prepare_run exists)
+  - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
+ o pkg/exf modifications to interpolation and rotation routines for more
+    reasonable treatment of North Pole singularity: for tracers North Pole
+    value is set to northernmost zonal-mean value, for zonal velocity it is
+    set to zero, and for meridional velocity it is set to northernmost value.
+ o pkg/exf/exf_check_range.F
+  - add tile index to diagnostics and move stop statement to the very
+    end of the routine.
+ o pkg/diagnostics: (diagnostics_main_init.F)
+   define title of isomorphic variables according to the current config.
+ o pkg/thsice with pkg/seaice dynamics:
+ - fix domain of computation (interior only, required for exf) and do exchanges
+ - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
+ o towards a standard way of dealing with multi-threading in MONITOR
+   and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
+ o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
+    to W momentum equation in nonhydrostatic and quasihydrostatic runs.
+ o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
+ o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
+ o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
+    (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
+ o tracer advection:
+  - clean-up and simplify calc_common_factors.F
+  - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
+    advection subroutine (but still not used within DST advection S/R)
+ o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
+ checkpoint58j_post (2006/06/15)
+ o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
+   from file (collects calls previously in FORWARD_STEP)
+ o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
+ o adjoint store dir. adjusted accordingly
+ o genmake2
+   replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
+ checkpoint58i_post (2006/06/14)
+ o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
+   on wind stress (SEAICEstressFactor defaults to 1.)
+ o Total number of Timers is finite (<=40): comment out 2 non-essential one
+   in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
+ o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
+   on CS-grid: no longer loosing mass.
+ o exf & curvilinear-grid: no longer modify longitude xC & xG.
+ o pkg/ggl90: fix sloppy output and fix a bug
+ o pkg/seaice: added SEAICEuseEVPpickup parameter
+   - Set to false in order to start EVP solver with
+     non-EVP pickup files when using SEAICEuseEVP
+   - fix sign error in diffusion in seaice_calc_rhs
+ checkpoint58h_post (2006/06/07)
+ * Modifications for bottom topography control
+   o replace hFacC by _hFacC at various places
+   o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
+   o add non-self-adjoint cg2d_nsa
+   o update autodiff support routines
+   o re-initialise hfac after ctrl_depth_ini
+   o works for 5x5 box, doesnt work for global_ocean.90x40x15
+ * Adding verification for 5x5 box (4-layer) bottom topography control
+ checkpoint58g_post (2006/06/07)
+ o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
+    used for mean seasonal cycle, mean diurnal cycle); add an example
+    in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
+ o pkg/ggl90:
+   - add parameter (minimum surface kinetic energy)
+   - fix bug (avoiding division by zero)
+ o couple pkg/thsice to pkg/seaice:
+   - modify advection in seaice to accomodate new scalar fields to be advected
+   - only muliDimAdection scheme work with seaice/thsice
+   - mapping of thsice-variables to seaice-variables, back and forth
+   - does not break the verification experiments, but does not give the
+     desired results either
+ o pkg/seaice
+   - make (default) second order advection a bit less confusing?
+ checkpoint58f_post (2006/06/05)
+ o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
+   to pkg/seaice):
+   - new routines thsice_map_exf and thsice_get_exf provide the interface
+   - add an additional formal parameter to thsice_solve4temp
+ o pkg/exf:
+   - add new fields wspeed, snowprecip (to be able to couple to thsice)
+   - correct Stefan-Boltzmann constant
+   - new parameter for longwave surface emittance
+   - separate some stuff from exf_bulkformulae into new routines
+     exf_radiation, exf_wind
+   - add new parameters and constants: longwave emissivity for ocean, ice
+     and snow, evaporation parameters over ice
+   - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
+     either wind from stress or stress from wind
+ o pkg/thSIce:
+ - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
+ - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
+    and THSICE_CALC_THICKN
+ - for now, call to THSICE_GET_BULKF remains inside i,j loops.
+ - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
+   to make debugging easier.
+ - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
+ o pkg/bulk_force:
+   - clean-up comments and parameters ;
+   - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
+ o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
+   generate new output for test-experiment: aim.5l_cs.thSI
+ o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
+   testreport accordingly
+ checkpoint58e_post (2006/05/17)
+ o SEAICE_CGRID adjoint done
+ o R_STAR adjoint implemented.
+   * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
+   * need to sort out init. of h0facc, etc.
+ o Make pkg/profile fully independent of ecco,cost, etc. stuff
+   to be able to use it in pure forward.
+ checkpoint58d_post (2006/04/21)
+ o upgrade simple test-experiment to tutorial example:
+  step.1: duplicate the experiment and (step.2) will remove the old copy.
+   tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
+   tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
+   tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
+   tutorial_global_oce_biogeo    <- copy of dic_example
+   tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
+   tutorial_plume_on_slope       <- copy of plume_on_slope
+   tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
+   tutorial_global_oce_optim     <- empty for now (David ?)
+   tutorial_global_oce_in_p      <- copy of global_ocean_pressure
+  some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
+ o correct a sign problem in cost_scat.F
+ o obcs and ptracers: fix boundary conditions for advections schemes
+   with larger stencil
+ o thsice adjoint: start
+ o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
+   completeness
+ o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
+   and COSINEMETH_III, add comments in default CPP_OPTIONS.h
+ o ptracers adjoint:
+   * avoid extensive recomputatations
+   * fix missing re-init. of gptr (missed by TAF)
+ o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
+   me to turn off the excessive output to STDOUT that this package produces
+ o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
+   and add those terms in Vector-Invariant formulation.
+ o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
+   if the control period (xx_hfluxperiod etc) is 0
+ o in profiles pkg, clean routines and fix details
+ o in ecco pkg, reading ssh data:
+   fix problem in case the model does not start at iter0=0
+ o fix mnc-pickup/restart for ptracers
+ o new package prifiles:
+   code to compute profile-based cost by Gael Forget
+   (modifs in ecco, ctrl, autodiff)
+ o Benign bug fix in initialization (spotted by M. Mazloff) of
+   ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
+ checkpoint58c_post (2006/03/23)
+ o adjoint: finish NLFS adjoint and provide reference output in
+   verification/global_ocean.90x40x15/results_ad_nlfs
+ o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
+   documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
+   SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
+   with SEAICE_CGRID defined.
+ o move calendarDumps from "data" to "data.cal" and clean-up the code
+   with a simple call to pkg/cal S/R: CAL_TIME2WRITE
+ o add useEXF & useCAL flags (for now, set in hard-coded way)
+ o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
+   (were missing in NH mode, and wrong in quasihydrostatic mode).
+   waiting for Chris updated version of calc_gw to add those CALLs.
+ o fix bug in quasihydrostatic S/R ;
+   add a test for this option: global_ocean.90x40x15.qshyd
+ o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
+   (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
+ o add on/off flag useOffLine for package OFFLINE
+ o seaice:
+   - modify advection so that it works also on the C-grid
+   - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
+     problem in multi-tile runs with C-grid
+   - add flags for clipping ice velocities and/or masking solver forcing
+   - fix drag (ocean on ice) formulation and a bug that caused noise in the
+     C-grid solver
+   - added a few comments to seaice_diffusion.F
+   - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
+     are now exclusive)
+   - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
+     required re-ordering the code a little:
+    + make DAIRN global variable (defined in SEAICE)
+    + move computation of the viscosities eta and zeta into a new separate
+      routine (because I need to recompute them in seaice_ocean_stress.F)
+ checkpoint58b_post (2006/03/13)
+ o AIM+thSIce: fix sign of Short-Wave through the Ice ;
+   update output.txt of exp. aim.5l_cs.thSI
+ o various mnc cleanups and improvements:
+   + shrink lookup tables by factor of ~4
+   + better error reporting when running out of lookup space
+   + able to handle longer path/file names (up to 500 chars)
+ o adjoint:
+   - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
+   - TBD: "hidden" mom_vecinv recomp. in dynamics
+ o change forcing_In_AB to affects both T,S forcing and Momentum forcing
+  (allow to differentiate between forcing components using new integer flags:
+   momForcingOutAB=1/0 & tracForcingOutAB=1/0)
+  and add new flag to put Dissipation tendency out of Adams-Bashforth.
+ o ecco
+   - enable trend removal from SSH anomaly obs.
+ o adjoint
+   - a fix for PmEpR when #undef EXACT_CONSERV
+   - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
+   - try to fix "hidden" recomp. in forward_step for NLFS
+     (NLFS seems broken sometimes after I checked it in)
+ o seaice:
+  - add c-grid version of the dynamic solver:
+    + three new routines that are the c-grid substitute lsr, dynsolver
+      and ostres
+    + put a few fields that were local to dynsolver into global common
+      blocks, so that I can move the computation of stresses etc into
+      seaice_lsr (saves coding but may break the adjoint).
+  - replace more hardwired parameters by runtime parameters
+  - add ice masks that mask the rhs of the implicit solvers where there
+    is no ice (commented out in seaice_dynsolver, because i am not sure
+    if this works properly), eventually this should replace the clipping
+    of ice velocities in seaice_dynsolver to +/-40cm/s.
+ o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
+   include it only where its needed
+ o move balancing of fluxes before the call of external_forcing_surf
+ o seaice:
+   - correct units of turning angles (now they are really in degrees)
+   - move computation of GWATX/Y out of main routine into dynsolver
+   - initialize GWATX/Y in seaice_init
+ o Apply mask on Fresh-Water flux (needed for SSH forcing).
+   update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
+ o seaice: add runtime flags for turning angles (default to zero)
+ o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
+   and trend from exf forcing and ctrl control adjustments
+ o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
+   (since checkpoint57x_post)
+ o change the default rotation period to 86164.s = the Earth rotation
+ o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
+   and based on a reference stratification. Tested within hs94.cs-32x32x5.
+ o seaice advection: add code for choosing between the default (2nd order
+   central differences) and multiDim advection schemes provided by
+   pkg/generic_advdiff
+ o seaice:
+   - removed all references to SEAICE_GRID.h fields from
+     dynsolver, advect, diffus, lsr, without changing the results of lab_sea
+     (cubed-sphere configuration will change a little)
+   - grid computations in seaice_init are obsolete now.
+   - cleaned up code a little so that is easier to read (hopefully).
+   - added new (better?) discretizations of default advection and diffusion
+     (turn on with SEAICEuseFluxForm)
+   - replace 1 in 3d global fields by kSurface in growth.F
+ checkpoint58a_post (2006/02/13)
+ o seaice:
+   - bug fix in advect.F
+ o shelfice:
+   - separate shelfice load anomaly from pload (breaks with time
+     dependent forcing), => introduce constant field shelficeLoadAnomaly.
+     Its default is 0., but it may be computed more cleverly from (unknown)
+     t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
+     done offline. A good approximation of the pressure load anomaly is
+     necessary to avoid large initial adjustment processes underneath
+     deep-reaching shelfice.
+   - small fix in ISOMIP shelfice_thermodynamics
+   - add more sophisticated thermodynamics of Hellmer (1989), this is
+     now the default
+   - give a few constants more intuitive names
+ o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
+   if bulk formulae are used in long integration (especially EmPmR). Turn
+   on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
+   if balancePrintMean, the imbalance that is substracted is printed to
+   STDOUT.
+ o fix bug (typo) in obcs_apply_eta.F
+ o add a new package shelfice which enables us to model the circulation
+   underneath shelf-ice with draughts of hundreds of meters.
+  - works
+  - to do: + include improved thermodynamics
+           + check whether kSurfC (from model/inc/SURFACE.h) can be used
+             instead of new field kTopC
+           + can we use topoFile, Ro_surf and existing code in ini_depth.F
+             instead of new field R_shelfIce and new code in ini_depth.F
+             and ini_mask_etc.F?
+           + adjust vertical mixing schemes?
+ o seaice pkg:
+  - add a cpp-flag to include a simple formula for a salinity dependent
+    freezing point of sea water at the surface
+  - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
+    meridional stresses are now different (and hopefully correct)
+ o AIM pkg: change threshold on large-scale condensation to conserve Heat.
+    update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
+    and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
+ o pkg/diagnostics: add options and parameters for regional-statistics
+    diagnostics ; define regions by reading a region-mask from a file
+    (might add other options later)
+ o pkg/bulk_force:
+  - add option and parameters to use AIM surface-flux formulae.
+  - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
+    others forcing fields (defined in PARM05, parameter file "data") are loaded
+    from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
+  - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
+  - use the right EXCH call for uwind,vwind (to work on CS-grid).
+  - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
+    and parameters (note: calcWindStress replaces .NOT.readwindstress).
+  - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
+ checkpoint58 (2006/01/12)
+ o add "--embed-source" option to genmake2 which, when the supporting
+   tools can be compiled (as determined by genmake2) will turn on the
+   embed_files package which then embeds the entire MITgcm source code
+   (*.[fFhc] + Makefile) used for the build within the executable
+   - requested by CNH but off by default
+   - adds a paltry <9MB to the mitgcmuv executable in most cases
+   - only writes the output when useEMBEDSRC in eedata is true
+ o clean up 3-dim. relaxation codes:
+   * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
+   * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
+   * Thanks to Tom Haine for testing!
+ checkpoint57z_post (2005/12/31)
+ o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
+   affects output (@ truncation level) of exp. plume_on_slope ; updated.
+ o fix the pickup behavior for obcs in combination with ptracers
+ o fix a bug in ptracers_external_fields_load
+ o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
+   affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
+ o transfered surface NH pressure to eta field (if exactConserv).
+ o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
+      and update lab_sea output.txt file.
+ o completing 3-dim. relaxation code: additional term
+/tau*( theta(i,j,k) - thetaStar(i,j,k) )
+   in S/R EXTERNAL_FORCING_T (file external_forcing.F)
+   * At compile time, in "EXF_OPTIONS.h" set
+       #define  ALLOW_CLIMTEMP_RELAXATION
+       #define  ALLOW_CLIMSALT_RELAXATION
+   * At runtime in "data", under &PARM03 set (e.g., units in seconds)
+       tauThetaClimRelax3Dim = 15552000.0,
+       tauSaltClimRelax3Dim  = 15552000.0,
+   * 3 cases:
+) Use a constant-in-time 3-dim. field
+) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
+) Real-time relax. to time-evolving prescribed field
+ o Adding Laplacian-type smoothness constraint on
+   initial and boundary (forcing) controls (ic, bc)
+   * enable at compile-time via
+     ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
+   * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
+   * Absolute scale somewhat unclear so far
+   * no area weighting was included since no other cost term does so far
+ checkpoint57y_post (2005/12/08)
+ First step for a NLFS adjoint
+ o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
+ o new init. routines for calc_r_star, calc_surf_dr
+ o still need to deal with ini_masks_etc
+ o testreport seemed happy
+ checkpoint57y_pre (2005/12/08)
+ o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
+ o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
+ o add new offset feature to offline pkg (plus minor cleanup)
+ o cfc fixes for final year of integration
+ o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
+   be in GCHEM_OPTIONS).
+ checkpoint57x_post (2005/12/04)
+ o fix testreport Pb in multiple test experiment.
+ o cleanup our namelist syntax in verification:
+   - make it more F95 standards compliant (some work still needed)
+   - allows the vast majority of our tests to work with gfortran
+ o Non-Hydrostatic:
+  - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
+  - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
+ o Allow to apply AB on T,S rather than on AB(gT,gS):
+  - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
+  - use the same arrays (gtNm,gsNm) to hold tracer field at previous
+    time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
+  - need a "clever" read_pickup to restart from the other AB formulation
+ o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
+ o remove some unused variables (reduces number of compiler warnings)
+ o adjoint
+   * Disable useVariableViscosity for adjoint for time being
+     (there are a number of extensive recomputations)
+   * Initialize certain variables needed for adjoint
+ checkpoint57w_post (2005/11/03)
+ o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
+              fix the singleCpuIO RS version of MDSWRITEFIELD
+    and add a WARNING if using globalFiles=T with multi-processors.
+ o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
+   using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
+ o tracer advection scheme:
+   add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
+    those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
+    was not very convenient).
+   add implicit version for DST-3 & DST3_Flux_Limit vertical advection;
+    (further tests needed for the implicit DST & Flux-Limiter schemes).
+ o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
+   and sRef for convenience, handy, when you want to initialize
+   ptracers in a large domain with a constant non-zero value. Also,
+   untangle ptracers_init.F a little.
+ checkpoint57v_post (2005/10/13)
+ o change dome exp. to use variable viscosity in side-drag terms.
+ o remove all the files from the cfc_offline test since they are now
+   incorporated into tutorial_cfc_offline which has been producing
+   identical results for a few days of testing
+ o add new parameter: sideDragFactor to enable half-slip-side BC
+   and change side-drag S/R to use viscosity from mom_calc_visc
+   (can switch back by setting sideDragFactor=0.); affects results at
+   truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
+    global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
+ o vorticity & strain are now computed without masking, to account for
+   no-slip-side BC in variable viscosity calculation ; mask is applied
+   anyway later on, before computing advection/coriolis terms.
+ o modify exp4 to test new obcs support for reading from external files
+   and for passive tracers
+ o fix behavior of ptracers_monitor when monitor output is written to a
+   netcdf-file; still not independent of monitor.F (writes in the same
+   file).
+ o change default value of tRef (put a uniform, meaningful value for ocean
+   & atmos) and initialize sRef (was missing, as Martin mentioned).
+ o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
+   to be proportional to enstrophy dissipation length.  Thus,
+    viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
+   This is now consistent with Smagorinsky and with the manual.
+ checkpoint57u_post
+ o OBCS and PTRACERS: add open boundary support for passive tracers
+   - either use homogenous (pseudo) v.Neumann conditions or prescribe
+     OB-values from file; this is not different from the way theta and salinity
+     are treated
+   - however, Orlanski-radiation conditions are not supported, and the model
+     will stop if you use pTracers and Orlanski at the same time.
+   - beefed up the rountine obcs_external_fields_load: now only those open
+     boundary values are overwritten with values from files for which there
+     are really files, otherwise the OB-fields remain untouched. This makes
+     it possible to use different OBs at different ends of the domain (as
+     with EXF)
+ o reduce number of exch calls in shap_filt (s2).
+ o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
+   truncation level) 4/5 MLAdjust test results (11&12 digits match).
+ checkpoint57t_post (2005/10/03)
+ o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
+ o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
+   same truncation, independent of the face number: affects affects several
+   test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
+ o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
+   note that biharmonic viscosity + no-slip was not tested in any experiment.
+ o fix bug in non-linear free-surf side-drag ; generate new output for
+   global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
+ o make mnc honor the writeBinaryPrec flag for most kinds of output
+ o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
+ o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
+   error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
+ o add brackets in multi-terms sum to get same truncation, independent of
+   the face number (manage to get exactly same value of gU,gV at the cs-edge)
+   affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
+ o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
+   and viscA4Remax, which allow one to limit the minimum viscosity by specifying
+   a maximum grid-scale Reynolds number.  Also, changes all length calculations
+   in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
+   Suggested values of viscosity parameters found in mom_calc_visc.
+   Many new viscosity diagnostics available.
+ checkpoint57s_post (2005/09/20)
+ o Add clearing-house for viscosity calculations, mom_calc_visc and
+   correct numerous bugs in LeithD and Smagorinsky discretizations.
+   mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
+   used simultaneously, and to be used in mom_vecinv and mom_fluxform.
+   Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
+   and with Strain-Tension viscous term calculation (mom_hdissip.F).
+   The Strain-Tension form is now called with useStrainTensonVisc=.true.
+   ViscAhStrain and viscAhTension are now retired.
+ o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
+ o In response to JMC's bug report, genmake2 now ignores any soft-links
+   that it finds in the *current* directory when searching for files.
+   Soft-links found in any other source directories will still work as
+   they did before.
+ o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
+   a C routine to unlimit the stack size
+ o mnc-ify pkg/aim snapshot vars
+ o mnc-ify pkg/land as requested by Daniel
+ o various changes to mnc including:
+   - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
+   - output can now be grouped so that all files within a group
+       change the ITER portion of their names in lock-step together
+   - can now read ("global") PER-FACE (in addition to PER-TILE) files
+       and works with both EXCH1 and EXCH2 (but needs more testing)
+   - writing works for all verification test cases w/ g77 on Linux
+ checkpoint57r_post (2005/09/07)
+ o make MNC variable initialization happen earlier
+ o add diagnostics for (almost) each term of the momentum Eq.
+ o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
+ o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
+ o remove MINIMAL_TAVE_OUTPUT option ;
+   add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
+ o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
+   allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
+ o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
+ o add time-dependent SST, SSS control
+ o cost terms in ecco/ modularized (new cost_generic.F)
+ o cost_averages routines are modularized (new cost_averagesgeneric.F)
+ o new infrastructure for seaice model vs. obs misfits in seaice/
+   * driver from the_main_loop.F is seaice_cost_driver.F
+   * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
+   * gradient check in Exp. 6a of natl_box_adjoint/
+ o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
+   (see README file)
+ checkpoint57q_post (2005/08/19)
+ o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
+ o fix annoying months-old bug in mnc/mdsio output for seaice pkg
+   - bug was reported by Jean-Michel and Ian Fenty
+ o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
+   update exp. cpl_aim+ocn output.
+ o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
+   Needed for high-res. runs with large global files
+   to be able to limit tapelev size
+ o Changed some tests for adjoint:
+   * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
+   * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
+   * global_ocean.90x40x15/ back to default 3-level checkpointing
+ o Modifications to enable scripted COMMON to MODULE conversion
+   * verification/OpenAD/code/ has necessary scripts and description;
+   * converts, compiles and runs successfully;
+ checkpoint57p_post (2005/08/01)
+ o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
+ o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
+   (already the case for some pkgs, including recent MNC_init, e.g. thsice)
+ o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
+ o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
+   (was already the case for dissipation with mom_vecinv,
+    and also the case for grad.PhiHyd when staggered-timeStep)
+   This will allow to put dissipation out-off the AB time-stepping.
+  Unfortunately, affects truncation error. Update output of exp. that "fails"
+   (cg2d matching number) and leave the others for later: front_relax(10),
+   global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
+   matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
+ checkpoint57o_post (2005/07/30)
+ o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
+   (2) its ready to be documented during the 20050801 DocFest
+ o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
+   for ideal_2D_oce and lab_sea on linux_ia32_g77
+ o set to #undef CTRL_SET_OLD_MAXCVARS_30
+   in global1x1_tot/code_seaice_adj to access indices 32, 33
+   (worth another tag)
+ checkpoint57n_post (2005/07/29)
+ o adding precip control xx_precip 32
+ o adding swflux control xx_swflux 33
+ o Replacing 10 forcing penalty cost routines by 1 generic.
+ o Implementing partitioning in time-mean and variable adjustment
+   for atmos. state.
+ o Time-mean constant error is now read in data.ecco (instead of hard-coded)
+ o in natl_box_adjoint:
+   * updated exp 1 to 10
+     (but does not have time-mean vs. variable split results yet)
+ o updated global1x1/*_seaice_adj/
+   to incorporate latest changes
+ o enable useSingleCpuIO for mdsio vector routines
+   (applies in particular to tapelev I/O)
+ o removed inefficient K-loop in all active_file*control*.F
+ checkpoint57m_post (2005/07/28)
+ o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)
+   and advect_cs (use EXCH-2 and standard cs-32 grid files).
+ o pkg/exch2: filling of face-corner halo regions is optional
+   (ifdef W2_FILL_NULL_REGIONS) and is turned off by default.
+ checkpoint57l_post (2005/07/14)
+  tag before updating tutorials (pre-release-2)
+ o add cos & sin of grid-direction orientation angle (curvilinear grid only,
+    for output and interpolation of input fields onto model grid)
+ o fix radius in mom_v_metric_cylinder.F (wrong by dy/2).
+    Affects results of exp. rotating_tank ; update output.txt.
+ o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor
+       and taking the square quantity and/or using a fraction-weight field.
+ o fix aim_diagnostics_init.F mate numbers.
+ o add mnc output capability to diagnostics/diagstat and update
+   our cvsignore files for the ACSII output generated
+ checkpoint57k_post (2005/07/02)
+ o lab_sea now uses diagnostics package and provides a suite of
+   new EXF diagnostics output.
+ checkpoint57j_post (2005/06/30)
+ o exf
+   * bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton):
+     Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982);
+     terms -2*ATAN(x) + pi/2 were added to both stable and unstable case.
+   * extended diagnostics output
+     - now includes all EXF variables
+     - hs, hl moved to common block
+     - separate S/R for diagnostics, called after ctrl vector is added
+     - name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet
+     - EXFqnet contains true Qnet (i.e. includes qsw)
+   * updated verif. lab_sea, global_with_exf
+   * Rearranging hflux (exf_mapfields -> exf_getforcing)
+     to ensure that diagnostics sees a true EXFqnet
+ o add matlab scripts for CS-grid vectors (in utils/cs_grid)
+ o diagnostics pkg: change pointers so that 1 diagnostic can be used
+   several times with different frequencies.
+ o mnc-ify the thsice package as requested by Daniel Enderton
+   - the monitor--MNC output needs work
+   - many attributes need to be added (most are currently blank)
+ o mnc-ify theaim_v23 package as requested by Daniel Enderton
+   - many attributes need to be added (most are currently blank)
+ o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign)
+ o add Sadourny like discretization to the 4th.O vorticity advection scheme
+ o fix bug in rStar code (calc_r_star.F) when used with topo/bathy.
+   update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn,
+      fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice).
+ o fix few little things to avoid floating error with -ftrapuv (ifort v9)
+  (ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F)
+ checkpoint57i_post (2005/06/19)
+ o Diagnostics package was changed: diagnostic allocation is now deactivated
+   by setting an empty file name in the namelist (used to be by setting 0 frequency)
+ o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ;
+   add 1rst Order upwind vertical Shear.
+ o add a quick fix for A/B checkpointing in OFFLINE mode
+ o add IGNORE_TIME define and -ignore_time option to genmake2 as an
+   end-run around the C/Fortran linking horror in eesup/src/timers.F
+ o added pkg/runclock: allows user to terminate run based on wall clock
+ o added non-hydrostatic scaling parameter: nh_am2
+ o pkg/my82: futile attempt to make results compiler-independent by adding
+   some "_d 0", etc. no effect.
+ o for mnc output, fill the 'T' coordinate var with myTime and create a
+   separate 'iter' variable for iteration count
+ o pkg/diagnostics:
+   add new capability: output of Global/Regional & per-level statistics ;
+   tested against monitor output (including land & thSIce) on various exp.
+ o make seaice-pkg I/O type flags (MNC/MDS) more standard.
+ checkpoint57h_done (2005/05/19)
+   tag after changing user customized files (DIAGNOSTICS_SIZE.h,
+   data.diagnostics, data.gchem, data.ptracers) is done.
+ o pkg/diagnostics: prepare for Global/Regional statistics.
+   add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h
+ o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE
+   and rename it: DIFFERENT_MULTIPLE
+ checkpoint57h_post (2005/05/14)
+ o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers
+ o pkg/diagnostics: change output frequency, now in seconds (instead
+   of Nb of iterations). This requires to change data.diagnostics.
+ checkpoint57h_pre (2005/05/12)
+ o in mnc, let the user create the output dir if both mnc_outdir_date
+   and mnc_outdir_num are false
+ o add fflags() to pkg/diagnostics which allows one to specify, on a
+   per-file basis, the file precision [default behavior is unchanged]
+ o added diagnostics to pkg/kpp, including computation of mixed layer
+   depth based on a temperature/density criterion
+ o updated verification/natl_box to test the new pkg/kpp diagnostics
+ o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T)
+ o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4)
+ o fix mnc flags in pkg/seaice so that they are "owned" by seaice,
+   not mnc -- this mistake was found by JMC and is now corrected
+ checkpoint57g_post (2005/04/15)
+ o add Adams-Bashforth 3rd Order time stepping:
+   - default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3)
+   - not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ...
+ checkpoint57g_pre (2005/04/15)
+ o make lambda[Theta,Salt]ClimRelax spatially varying
+   (default remains spatially uniform constant based on tau)
+ o added new control variables
+   * init. uVel, vVel, etanN
+   * lambda[Theta,Salt]ClimRelax
+ o separate masks used for ctrl_pack/unpack 'from write_grid' output
+   (suggested by G. Forget)
+ checkpoint57f_post (2005/04/06)
+ o add parameter "baseTime" = model base time = time at iteration zero
+   new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to
+   account for baseTime shift
+ o move Coriolis arrays from PARAMS.h to GRID.h
+ checkpoint57f_pre (2005/04/06)
+ o mnc-ifying the seaice package
+ o introduced an alternative length scale calculation for use in the limiting
+   maximum viscosity (off by default, see mom_vi_hdissip.F for details)
+ o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S
+ o added modified Leith scheme with viscosity proportional to grad(Hdiv)
+   as well as grad(vort3).  Made it compatible with both approximate form
+   for the cubed sphere and full form of these gradients.  Added flag
+   useFullLeith to select between approximate and full form.
+ o add "d0" in getcon.F to reduce differences between compilers/platforms
+   update output.txt of exp. fizhi-gridalt-hs
+ o change port_rand funtion to allow to set the seed.
+ o fix obscure MNC bug involving conversion between reals and integers
+   - it caused no problems with certain (eg. gcc, ifc) compilers but the
+     new version is now more standards-compliant
+ o adjoint-related modifications
+   * gad_dst3_adv_?: to be able to use advscheme=30 in adjoint
+   * gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33
+   * mom_vi_hdissip: to be able to use Leith scheme in adjoint
+ checkpoint57e_post (2005/02/28)
+ o Adding eddy stress controls a la Ferreira et al.
+ checkpoint57e_pre (actually was tagged: eckpoint57e_pre)
+ o fizhi pkg: fix AtoC and CtoA when called with same input & output array
+   update output.txt of exp. fizhi-gridalt-hs
+ o add more "Z" dimensions and associated coordinate vars to MNC
+ o pkg/exf: added twoDigitYear capability for option useExfYearlyFields
+ o parameter calendarDumps: when set, approximate months (30-31 days) and years
+   (360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq,
+   KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar
+   months and years.  Requires pkg/cal.
+ o diagnostics: add pickup functionality
+   - off by default for backwards compatibility
+   - current version only uses MDSIO -- MNC will be added
+ o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies.
+ o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2)
+ checkpoint57d_post (2005/02/11)
+ o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing
+ o modify verification/ideal_2D_oce so that it tests the creation of mnc
+   output from the diagnostics package
+ o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up
+ o make genmake2 more portable by using ".$FS" instead of ".f" for more
+   of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys)
+ o add coordinate variables to the MNC output from the diagnostics package
+ o change MNC-flags default value: true when useMNC=TRUE
+ o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F
+   the ability (off by default) to read the grid information using MNC
+ o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt
+ o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging
+ o do snap-shot diagnostics at the middle of the time-interval (instead of
+   at the end).
+ o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add
+   new test for AIM with thSIce + slab-ocean
+ o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h)
+ o move state variable diagnostics to the beginning of the time step ;
+   (note: still needs some work specially for snap-shot diagnostics)
+   duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z
+ checkpoint57c_post (2005/01/27)
+ o Change testing option (-ieee) to get closer agreement between g77 & ifort
+ o generate new output.txt files on faulks with g77 & the new -ieee option
+ checkpoint57c_pre (2005/01/27)
+ o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF);
+   update output.txt of exp. global_ocean.90x40x15
+ o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer
+   results; update global_ocean_pressure & global_ocean.cs32x15 output.txt
+ o add saltFlux(+File) forcing capability with periodicExternalForcing
+ o allow to use pkg diagnostics for GM-Redi & ThSIce output
+ o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc.
+ o improvements for the MNC output from DIAGNOSTICS:
+   - correct handling of the unlimitied dimension
+   - all dims now have associated coordinate variables
+   - variables located at U, V, and Corner ("Z") points are now written
+     with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that
+     *all* data points are output
+ o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice
+ o added pkg/seaice/seaice_monitor.F
+ o mdsio_readfield.F can now read files visible only to master MPI process.
+ o pkg/seaice: some test code for ice-modified ocean stress
+ o exf_getffields interpolation defaults to bilinear for all scalar forcing
+   fields (remains bicubic for wind velocity and stress).  This avoids, e.g.,
+   spurious negative numbers for precipitation and humidity.  Will cause
+   some small numerical differences for integrations using pkg/exf/exf_interp.F.
+ o pkg/ctrl/
+   * Add ctrlvec diagnostics in pack/unpack for nondimensional I/O
+     May be enabled via doPackDiag
+   *  introduce z-scaling of
+      + gradient (doZscalePack) and
+      + control (doZscaleUnpack)
+ o pkg/mdsio/
+   * enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F
+   * N.B.: leave tiled I/O for tapelev (i.e. mds...vector)
+ checkpoint57b_post (2004/12/20)
+ o simplify options in diagnostics_fill arguments (remove weird combinations)
+ o fix MNC coordinate variables so that they now contain per-face index
+   values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in
+   general, EXCH2 grids are only aligned to a "local" coordinate system
+ o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput)
+ o Implement instantaneous output within pkg diagnostics:
+   setting a negative frequency in data.diagnostics produces
+  "snap-shot" output (as opposed to time-average if freq > 0)
+ o move out off EQUIVALENCE all diagnostics that fizhi does not use ;
+   NOTE: change ptracer diagnostics name: use 2 characters to work with
+         more than 9 tracers. Add also diagnostics of advect & diffus flux.
+ o more CF compliance: convert all MNC 'iter' variables to 'T' so that it
+   becomes the coordinate variable for the 'T' dimension
+ o add CF-style coordinate variables to MNC
+   - just a first cut:  numbers are meaningless on the cubesphere and
+     missing along the T axis but otherwise it works!
+ o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX
+ o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC.
+ o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon)
+   this is based directly on what the model compute, so that the content of
+   each diagnostics might be affected by switching options (e.g., implicitDiffusion)
+ o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F)
+ o clean up build options files for SunOS, in particular
+   - remove -traditional from xmakedepend
+   - change -xarch=v9 to -xarch=native for f77
+   - restore use of make (not gmake)
+   - add CC=gcc if using g77
+ o changes per discussion of AM, JMC, & EH3 today:
+   - move redundant "grid" variables out of "state" -- in preparation of
+     creating proper CF-style coordinate variables and in recognition
+     that any/all grid variables can be easily copied (eg. w/NCO) from
+     the grid files into any of the other NetCDF files
+   - *always* output grid variables with MDSIO (this will eventually be
+     changed)
+   - output MNC grid file if useMNC is true
+ o every instance of _END_MASTER() has been found and replaced with
+   _END_MASTER( myThid ) in order to satisfy certain picky Sun
+   preprocessors
+ o re-arrange diagnostics pkg initialisation:
+  - allow each package to extend the available diagnostics list
+  - add some checking and fix small problems (multi-threaded, ...)
+  - new S/R diagnostics_fill (replace fill_diagnostics):
+    look through the short list of active diag. (instead of the long list)
+    create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active
+ checkpoint57a_post (2004/12/10)
+ o this set of changes restores TAMC compatibility
+   tested for global_ocean.90x40x15 adjoint on trough
+   (what a pain)
+ checkpoint57a_pre (2004/12/10)
+ o some modifs in tools/build_options for sunos
+ o call ctrl_pack for ctrl at end for optimcycle=0
+ checkpoint57 (2004/12/09)
+ o add horizontal bi-harmonic viscosity for vertical velocity
+   - new parameter viscA4W (defaults to viscA4)
+   - affects only non-hydrostatic code
+   - to be done: no-slip lateral boundary conditions
+ o switch back to "sflux = sflux - runoff" in exf_getforcing.F
+ o implement Implicit Vertical advection for pTracers
+ o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k)
+   (implemented also for implicit vertical diffusion & advection)
+ o OBCS: extend application of tracer open boundary conditions
+   to a strip beyond the boundary of width Olx/Oly
+ o add call monitor to TAF set of required calls (flow directives)
+   and include in natl_box_adjoint
+ o untangle a few ifdefs related to cost, ctrl, autodiff
+   untangel a few ALLOW_ECCO_OPTIMIZATION
+ o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)
+   (theta2, salt2 in ecco_cost_weights)
+ checkpoint56c_post (2004/12/03)
+ o OBCS as control variables
+   - update ctrl_ad_diff.list, obcs_ad_diff.list
+   - remove balance of obcs controls from default
+   - fix index bug nobcs in ctrl_init
+   - fix dummy fields filen in ctrl_pack
+   - add dummy weights for obcs
+ o lsopt: comment out fort.94 output
+ o optim:
+   - remove unnecessary header files
+   - adjusted namelists
+   - add xerbla.F to Makefile
+ o exf:
+   - multiple modifications of exf_check_range
+   - unit change in exf_init_runoff from [m/year] to [m/s]
+ o mdsio:
+   - i/o-vector change debugLevel from debLevA to debLevB
+ checkpoint56b_post (2004/12/01)
+ o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that
+   is called from DO_THE_MODEL_IO
+   - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE
+   - introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq)
+   - clean up PTRACERS_WRITE_TIMEAVE a little
+ o add another verification experiment that tests both the cfc-pkg and
+   the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with
+   reactive tendencies treated inline with regular timestepping
+ o testreport previously did a lousy job of comparing small numbers, so
+   we (Ed and Martin) changed the  way the cut-off of 1.e-12 is
+   implemented in the little c-progam tmp_cmpnum.c which is embedded in
+   testreport.
+ o ptracers_monitor: bug fix for MPI
+ checkpoint56a_post (2004/11/28)
+ o GCHEM: finish reorganizating the package
+   - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency
+     (introduces another 3D-array for each passive tracer, but only if
+     GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING
+     gchemTendency is not needed because the timestep is done separately)
+   - gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY
+   - GCHEM is now---more or less cleanly---separate from PTRACERS
+   - to bo done: handling of surfaceForcingPtr that is needed for KPP not
+     so clear to me how that should be done in a general way.
+ o CFC: improve formatting of output in CFC_ATMOS
+ o PTRACERS:
+   - rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so
+     that ALL experiments with ptracers enable can be checked. This makes
+     GCHEM_MONITOR obsolete.
+   - include a runtime parameter PTRACERS_monitorFreq that defaults to
+     monitorFreq
+   - set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true
+ o add PTRACERS (PTR0[1-5]) to testreport output
+ o exf_check_range:
+   * default changed to .TRUE.
+   * will check values for niter0 if debLevA, every timestep if debLevB
+   * STOP in exf_check_range if 'out of range'
+   * range chosen generous to allow for potential extema
+   TBD: a version with stricter range
+        permitted range would be runtime parameters
+ o GMredi:
+   - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;
+   - change S/R GRAD_SIGMA to be valid in the overlap on CS-grid.
+   - change the default GMREDI_OPTIONS.h: compile everything except Visbeck
+ o GCHEM:
+   - move call to GCHEM_FORCING_SEP, so that it is now called before
+     the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP
+   - introduced a useGCHEM runtime flag and applied it everywhere.
+   - renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING;
+     this flag is now only visible within GCHEM-pkg routines.
+   - moved gchem_forcing_int temporarily into ptracers_forcing, this will
+     be replaced by a 3D array that is computed before thermodynamics; for
+     this, the tracer ID iTracer had to be included into the parameter list
+     of ptracers_forcing
+   - set up forward_step to call gchem_forcing, that will replace
+     gchem_forcing_int in ptracers_forcing
+   - cleaning up
+ o small cleaning of exch2: remove files that are also in eesupp/src
+ checkpoint56 (2004/11/17)
+ o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0
+ o mnc: cleanup "full" files--fixes out-of-memory problem
+ o ECCO-GODAE
+   * model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup
+   * fully merged and updated from SIO code
+     windstress sign change affects
+     - exf_inscal_[u/v]stress
+     - sign of xx_tau[u/v] adjustments
+     - signs in cost_scat
+   * ctrl_get_gen: avoid update of tau[u/v] for first few days
+   * natl_box_adjoint updated and compressed
+   * 2-level checkpoint switch added
+     (tested in EXP. 1 of natl_box_adjoint)
+   * new switch doInitXX to avoid init. of xx_... in optimcycle=0
+ o SVD
+   * first complete, non-hacked version for SVD calculations
+   * all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_...
+     performed via direct access files admtlm_vector.it????
+     (via ctrl_[un]pack)
+   * optimcycle is used for ARPACK iteration counter
+     (note: adxx_... is iterated, rather than xx_...; latter is constant!)
+   * EV problem ok w.r.t. L2-norm in tangent space; need to check other norms
+     and add linear transforms where necessary
+   * controls are initial/final SST, SSS (can be extended; need to check
+     ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F
+ o mdsio: filename info to both stderr, stdout
+ o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec]
+   from sign change
+ checkpoint55j_post (2004/11/10)
+ o isolate dissipation tendency (allow to keep it out off AB) in V.I form.
+   affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
+ o add consistent build directories and .cvsignore files to verification
+ o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity
+ o make all subroutines 30 or less characters in length for certain older
+   compilers to work (a thorough search only turns up two routines in
+   pkg/ptracers)
+ o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity;
+   affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
+ checkpoint55i_post (2004/10/28)
+ o change arrays for total vertical diffusivity (2.D if explicit,
+.D if implicit) ; each ptracer uses its own background value.
+ o added mnc/NetCDF output capability to ocn_compon_interf
+   - added bits to verification/cpl_aim+ocn so that it can run on
+     ITRDA and other clusters without the mpirun "-wd" option
+ o fixed wayward endif in mom_fluxform.F that messed up cyclindrical
+   configuration
+ o give MNC the ability to create additional files rather than
+   exceeding a specified file size limit "MNC_MAX_FILESIZE"
+   - the default is just less than 2GB which is a practical limit
+     on many systems
+ o Compute the non-local term using either KPP vertical diffusivity (=default)
+    or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T)
+ checkpoint55h_post (2004/10/20)
+ o add verification test "vermix"
+ o remove all the *_ioinc flags and replace with the single global
+   outputTypesInclusive flag
+ o allow to set a vertical profile of vertical diffusivity for T & S
+ o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS
+ o useMNC moved from data.mnc to data.pkg
+ checkpoint55g_post (2004/10/14)
+ o Renaming carbon AD experiments to comply with testreport conventions
+ o Updating adjoint of Held-Suarez hs94.1x64x5
+ o Fixing directives for non-ECCO forward_step, after ECCO directives
+   have been fixed to avoid recomp. of do_oceanic_phys
+   Works well for global_ocean.90x40x15,
+   but recomp. issue remains for carbon
+ o Updating adjoint output for natl_box_adjoint after
+   pkg/ecco has been modified (see taga c55d_post)
+ checkpoint55f_post (2004/10/13)
+ o rename to timeave_init_fixed
+ checkpoint55e_post (2004/10/13)
+ o some delicate re-shuffle of store directives to avoid one
+   extra call of do_oceanic_physics
+   affects ecco_the_main_loop.F, do_oceanic_physics.F
+   checkpoint_lev1_directives.h
+ o NB: this may break global_ocean adjoint temporarily,
+   but it is clear how to fix it. Will do later, need this now.
+ checkpoint55d_post (2004/10/11)
+ o ECCO specific cost function terms (up-to-date with 1x1 runs)
+ o ecco_cost_weights is modified to 1x1 runs
+ o modifs to allow observations to be read in as
+   single file or yearly files
+ o enable to read exf forcing fields as either
+   single file or yearly files (flag useExfYearlyFields)
+ checkpoint55d_pre (2004/10/08)
+ o switch between 2-level and 3-level checkpointing
+ o add ability of MNC to write local and "partial" (eg. 2D slices where
+   the full 3D field is never actually stored) arrays to NetCDF files
+   with the correct (that is, the complete multi-dimensional) set of
+   array indicies
+   - used in mom_vecinv() to write the diagFreq output
+   - tested (demonstrated) in verification/aim.5l_cs
+ o further mnc-ification
+   - add verification/lab_sea to the list with mnc setups
+   - fix undefined mnc v-names in cd_code
+   - add kpp to mnc output (both snapshot and timeave)
+ o non-hydrostatic code
+   - added horizontal viscosity parameter viscAhW for w, that replaces viscAh
+     in calc_gw.F
+   - defaults to viscAh
+   - this is useful, when I want to use viscAh=0 (e.g., only biharmonic
+     friction or Leith) in non-hydrostatic mode, as long as there is
+     no biharmonic friction and/or Leigth or equivalent for vertical velocity.
+ o pkg/cost
+   extend simple cost functions to treat time mean quantities
+   (T,U,V) via cost_accumulate_state from cost_tile
+ o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to
+     be 2 times larger than the minimum size the advection scheme requires.
+     now get a perfect conservation of salt in advect_cs test-exp (updated)
+ o GGL90 (Gaspar's TKE mixed layer)
+   - add horizontal diffusion of TKE, requires exchanges in
+     do_fields_blocking_exchanges, horizontal diffusivity is zero by
+     default. In OPA there is no horizontal diffusion of TKE but the
+     mixing coefficients are computed from a horizontal average of TKE of
+points or so. I think that diffusion has a little more physical
+     justification.
+   - clean up ggl90_calc in the hope of reducing memory usage (this hope
+     was in vain)
+   - mask tke-variable in ggl90_init
+ o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass)
+ o fix biharmonic diffusion on CS-grid.
+ o more obcs stuff
+   - added obcs_external_fields_load as an alternative to the EXF-pkg option
+     for reading boundary values. This routine is called from
+     obcs_prescribe_read
+   - updated obcs_check
+   - changed sponge layer relaxation parameter units for days to seconds
+   - turned off sponge layer by default
+   - changed argument list of OBCS_CALC to myTime+deltaTclock
+   - fixed about 35 bugs in obcs_external_fields_load
+ checkpoint55c_post (2004/09/23)
+ o obcs stuff
+   - new runtime flags useOBCSprescribe, useOBCSbalance
+   - re-arranged obcs_calc
+   - moved exf_getobcs to obcs_prescibe_read
+     obcs_prescibe_read is called after ORLANSKI stuff
+     and independent of it (executable can contain all).
+   - updated obcs_check
+   - added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE.
+     These may be necessary only if tangential velocities are
+     prescribed at OB, not sure, needs testing.
+ o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments
+   which simplifies the calls and passes the ifc check-bounds test
+ checkpoint55b_post (2004/09/22)
+ o add a 2D scalar, Z location, exchange_2 routine.
+ o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows
+   to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]
+   affects advect_cs results (for the wrong reason): update output.txt
+ o use a more standard discretization for biharmonic viscosity ;
+  (original version still available with #define MOM_VI_ORIGINAL_VISCA4 )
+   affects results of dome set-up: update output.txt
+ o fix gad_advection.F (CubedSphere part), back to version 1.23
+ o fix bug in mom_vi_del2uv.F (CubedSphere part).
+ checkpoint55a_post (2004/09/20)
+ o merged code to
+   * prescribe/read time-dependent open boundaries
+     (works in conjunction with exf, cal)
+   * sponge layer code for open boundaries
+   * each boundary N/S/E/W now has its own CPP option
+     (healthy for the adjoint)
+ checkpoint55 (2004/09/17)
+ o up-to-date adjoint of previous breaks
+   - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix
+   - global_ocean_ebm: adjoint still needs fix (TLM ok)
+   - global_ocean.90x40x15: extended GMREDI_OPTIONS.h
+   - carbon: * remove tr1-related adjoint verification
+             * add ptracer as control variable
+ o remove all tr1-related code (ALLOW_PASSIVE_TRACER)
+   (adjoint stuff still has some tr1 'names', but all use ptracer arrays)
+ checkpoint54f_post (2004/09/16)
+ o in verification/carbin/ remove experiment related to
+   ALLOW_PASSIVE_TRACER (array tr1 etc)
+   code_ad/ input_ad/ results_ad
+ o add two new packages
+   - ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993)
+     + subject to optimization (memory)
+   - opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997)
+     + subject to reordering (many GOTOs in the original code)
+     + so far opps is called for every (i,j) point, and then operates in
+       the vertical; one may want to reorder the scheme in order operate in
+       horizontal slabs at the cost of (a lot of) memory, at least ten new 3D
+       fields)
+ o overhaul of IO so that we now have flags for MDSIO and/or MNC
+   - all verification tests compile and run with linux_ia32_g77
+   - defaults are compatible with current input files--nothing
+     should change if you were not previously using MNC
+   - MNC output has been added in numerous places (eg. timeave)
+     but there are still a few writes not yet do-able with MNC
+     (this is in progress)
+   - flags now allow for either/or/both use of MDSIO and MNC and
+     documentation will soon follow
+   - numerous small formatting cleanups for ProTeX
+ o add version info (via BUILD_INFO.h) to MNC and stdout
+ checkpoint54e_post (2004/09/02)
+ o add two new packages
+   - pp81 (Packanowski and Philander, 1981), Richardson number and
+     stratification dependent mixing
+   - 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)
+ o add offline package
+ o add "verification/dic_example" which contains a dic-gchem-ptracer setup
+   provided by Stephanie Dutkiewicz
+ o genmake2: add ability to search for C compilers and cleanup test output
+   - fixes recent SX-6 problems and should help with others (eg. HP-UX)
+ checkpoint54d_post (2004/07/27)
+ o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed
+ o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,
+   leading to additional shift by 5 days each year of integration
+    (i.e. leading to considerable offset over the years)
+ o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep
+ o start with no AB and no initial filtering (staggerTimeStep):
+   change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5
+ o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F
+   (external loading & cpl import/export stay in forward_step.F)
+ o update coupling interface to work with new staggerTimeStep
+ o change MDSIO ptracers_pickup.
+ o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F);
+ o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")
+ o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)
+ checkpoint54c_post (2004/07/18)
+ o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr
+   this affects (truncation error) output.txt of test-exp:
+    global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box
+ o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array)
+ o change Qnet to always be the net heat flux, (+upward).
+   affects (truncation error) output of natl_box exp.: updated
+ o define the max number of passive tracers in PTRACERS_SIZE.h
+ o start to test mnc routinely in exp0
+ o add sea-ice loading (sIceLoad) as a new forcing field.
+ checkpoint54b_post (2004/07/08)
+ o add testreport "-j JOBS" option for parallel builds (tested and pretty
+    impressive on Altix and Opteron systems)
+ o diagnostics can now write NetCDF files through the mnc package
+ o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output
+ o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added
+ o staggerTimeStep & NLFS: rescale T & S surface tendencies.
+   affects (truncation error) output of lab_sea & natl_box exp.: updated
+ o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
+ checkpoint54a_post (2004/07/06)
+ o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).
+ o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)
+ o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)
+ o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)
+   + internal_wave (shift in writing cg2d_ini_res)
+ checkpoint54a_pre (2004/07/05)
+ o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice
+   - modified verification/lab_sea and natl_box_adjoint accordingly
+ checkpoint54 (2004/07/02)
+ checkpoint53g_post (2004/07/02)
+ o prepare splitting of thermodynamics: store convect.counter in common block
+ o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)
+   output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave
+ o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection
+ o new parameter "nShapS": allow to treat differently S from T (nShapT)
+ o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)
+ o restore adjointability
+ checkpoint53f_post (2004/06/25)
+ o modifications that affect AIM experiment results (update output.txt):
+   - no advection of S at top interface Nr (pkg/generic_advdiff)
+   - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)
+ o AIM pkg:
+   - include stability function into surf.Flux derivative relative to Tsurf
+   - calculate clear-sky radiation & surface temp. change (for diagnostics)
+ checkpoint53e_post
+ o merged cylindrical coord configuration
+ o added rotating_tank experiment
+ checkpoint53e_pre
+ checkpoint53d_post (2004/06/14)
+ o faulks upgraded: re-generate output.txt that have changed:
+    global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box
+ o Added Bryan and Lewis, 1979, vertical diffusivity profile
+ o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing.
+ o added Sadourny discretization of Coriolis
+   - moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h
+   - re-enabled use of omega3 (useAbsVorticity)
+ o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for
+   vector-invariant equations
+   - note: does *NOT* yet use same variable visc. for no-slip BC's.
+ o recoded the lateral boundary conditions for non-hydrostatic w, this time
+   hopefully without new bugs
+   - still to do: biharmonic friction for non-hydrostatic w
+ o bug fix for mom_*_sidedrag: rA -> rAs,rAw
+ o regenerated output for global_ocean_ebm (using -ieee)
+ o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation
+   of mom_common/
+   - simple re-arrangement of instructions within computing loop
+ checkpoint53d_pre (2004/05/21)
+ checkpoint53c_post (2004/05/21)
+ o new version of coupler for AIM+thSIce and Ocean models
+  - new fields (SSS,h_MixLayer ...) are exchanged through the coupler
+  - land: change Evaporation of snow
+  - aim with thSIce: fix bug in snow-precip.
+ o changes to calc_gw.F
+  - bug fix for w^2 term near the bottom boundary
+  - (hopefully) improve the lateral slip boundary condtions for use with
+     partial/looped cells
+   - because the bug fix changes two verification experiments anyway (exp5
+     and plume on slope), change the lateral boundary condition from half slip
+     to the value of no_slip_sides
+ o ebm package wasnt quite up to the parallel task. Fixed that.
+ o Adjoint of EBM package + verification
+   * TLM OK
+   * ADM not sufficient accuracy yet (needs further testing)
+ checkpoint53b_post (2004/05/14)
+ o Commiting new energy balance model to repository
+   * package is pkg/ebm
+   * verif. is verification/global_ocean_ebm
+   * references are in ebm_driver.F
+ C      * X. Wang, P. Stone and J. Marotzke, 1999:
+ C        Global thermohaline circulation. Part I:
+ C        Sensitivity to atmospheric moisture transport.
+ C        J. Climate 12(1), 71-82
+ C      * X. Wang, P. Stone and J. Marotzke, 1999:
+ C        Global thermohaline circulation. Part II:
+ C        Sensitivity with interactive transport.
+ C        J. Climate 12(1), 83-91
+ C      * M. Nakamura, P. Stone and J. Marotzke, 1994:
+ C        Destabilization of the thermohaline circulation
+ C        by atmospheric eddy transports.
+ C        J. Climate 7(12), 1870-1882
+ o Will need long integration testing.
+ checkpoint53b_pre (2004/05/14)
+ o created pkg/mom_common in preparation for variable viscosity code
+ o renamed and split ini_mnc_io
+ o pkg/land: only liquid water can diffuse or run-off
+ o AIM using land: soil wetness availability account for snow
+ o added printMapIncludesZeros to EEPARMS namelist
+ checkpoint53a_post (2004/05/11)
+ o restore TAMC compatiility for exf_constants.h
+   (no usage of _d in .h)
+ o Additional storing in KPP in an attempt to fix
+   TAMC problem with adjoint of KPP code.
+   (no success...)
+   Identical code works fine with TAF.
+ o Fixed verification/natl_box_adjoint experiments.
+   Initial conditions for Experiments 4 and 5 are now
+   set to "SEAICE_initialHEFF=0", which is more reasonable,
+   and hence gives results closer to that of Experiment 2.
+   Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.
+ checkpoint53 (2004/05/06)
+ o stable checkpoint with up to date adjoint
+   TLM tests only run for 1st grdchk at the moment. Its unclear if
+   this is a code problem or a problem with resetting code for g_
+   variables that is being autogenerated wrong.
+   Otherwise:
+    o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix.
+    o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ)
+      are both still in chaos following their security messes.
+ checkpoint52n_post (2004/05/06)
+ o various build (mostly genmake2) changes including:
+   - ability to build/run more easily within Cygwin and MacOS X
+   - more complicated Makefiles with a stronger dependence on Gnu Make
+ o pkg/seaice modifications
+   - added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost
+     of pkg/seaice.  For time being, SEAICE_deltaTtherm = deltaTtracer
+     and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm
+   - changed proxy for geostrophic velocity and updated
+     verification/lab_sea/results/* accordingly
+   - removed ADI dynamic solver from pkg/seaice
+   - replaced all occurrences of 1/CSTICE or 1/CSUICE
+     they caused a segmentation fault under certain circumstances
+   - removed unused field WATR
+ o bug fix in exf-package:
+   -  u/vwind are defined at tracer/pressure points. The values of u/vwindmask
+      now reflect that.
+ o small fixes in the cal-package:
+   - set reference date to first of January for the 'model'-calendar
+   - failing of cal_CheckDate in cal_FullDate now actually results in a
+     warning
+ o small modifications in exf-package to increase flexibility:
+   - change climtempfreeze from a constant to a runtime parameter that
+     is specified in data.exf_clim (default = -1.9)
+   - introduce runtime parameter windstressmax (default = 2.0) that is
+     specified in data.exf
+ o fix in pkg/thsice:
+   - update Evap (Tsf changes) to be consistent with Latent heat flux
+   - maintain snow precipitation unchanged (even if Tsf >=0).
+  both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice
+ checkpoint52m_post (2004/04/18)
+ o commented out call to cal_GetMonthsRec in swfrac.F and added some comments;
+   this does not change any of the results, because myIter=0 in swfrac always
+   lead to jwtype=2 (the default anyway), but the call makes little sense
+   as a default
+ o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated
+ o re-work pkg/thsice interface with ocean & bulk_force pkg to allow
+   atmospheric model (AIM) to use it ; add a "slab ocean" component.
+ o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice)
+ o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice
+ o extending useSingleCpuIO option to work with new exch2 I/O format
+   - old-style, missing-tile I/O is still accessible by defining CPP
+     option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h
+ o monitor package can write to NetCDF files and/or STDOUT
+ o fix re-definition bug in MNC_GRID_INIT_ALL()
+ o doc/api_reference added
+   - a framework for building an API Reference Manual using all
+     the "protex" comments embedded in the code
+   - see pkg/generic_advdiff, pkg/mnc for examples
+ o MNC:
+   - make myThid the last argument for all subroutines
+   - new default for the grid files: NO halos
+   - add useMNC and other run-time flags
+   - separate per-file-group handling of the unlimited dimension
+   - early initialization of MNC w/ flags read at the eeboot stage
+     and lookup tables set in initialize_fixed
+   - write all MNC output to a freshly-created directory
+ o thermodynamics sea-ice (thsice) is now tested with testreport.
+ o test exp. advect_cs: use the standard cs32 grid ; update output.
+ o Added functionality to grdchk:
+   pick global i,j,k position (or nearest wet) where to perform check.
+ checkpoint52l_post (2004/03/11)
+ o new land formulation:
+   a) use ground enthalpy as prognostic variable to ensure exact
+      energy conservation.
+   b) account for water temperature and for latent heat of freezing
+      in all processes (rain, run-off, ground storage)
+   c) compute surface and ground temperature implicitly.
+ o aim_v23 modification for new land model:
+   a) Treat separately land / ocean / sea-ice surface fluxes
+      to allow implicit computation of land & sea-ice surface temp.
+   b) add snow precipitation.
+ checkpoint52l_pre (2004/03/11)
+ o fix problem (when 1 tile is empty) in min/max monitor.
+ o fix bug in timeAve (u,vZetatave in common block)
+ o no restoring terms under ice for pkg/seaice
+ o moved SEAICE_DO_DIAGS to S/R do_the_model_io
+ o bug fix for pkg/seaice pickups
+ o change MNC call locations and add coordinate attributes
+ o mask vorticity at the corner ; affects global_ocean.cs output
+ o fix ini_curvilinear_grid ; test CS experiments with mpi
+ o aim.5l_cs: modify sea-ice fraction input file ; update output
+ o exf: Adding simple range check routine for exf fields after read
+ checkpoint52k_post (2004/02/23)
+ o removed top-level directory "diags"
+   - we migrated these functions to pkg/timeave a long time ago
+ o fixed bug introduced in pkg/monitor
+ o accuracy ctrlprec = 32 insuffient for gradient checks using
+   averaged fields (I/O via cost_averages)
+   -> use ctrl.h in active_file*.F to control I/O precision.
+ o paramter list of CALL ADTHE_MAIN_LOOP
+ o added initial do_the_model_io to ecco
+ o set all ...Freq to zero after cost_final
+   taveFreq, dumpFreq, pChkptFreq
+ o MAIN and ECCO differentiability restored
+ checkpoint52j_post (2004/02/18)
+ o fix nchklev in tamc.h for global_ocean...
+ o Bringing flow and store directives up-to-date
+ o Really weird thing!
+   call do_the_model_io from the_main_loop with parameters
+   starttime, niter0, instead of mytime, myiter, screws up the adjoint:
+   TAF places a faulty re-call of initialise_varia
+   after cost_final call which should not be there!
+ checkpoint52j_pre (2004/02/03)
+ o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and
+   error messages
+ o fix errorMessageUnit problem. remove old version of mdsio from eesup/src
+ o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating
+   debug output
+ o modfied mdsio_writefield.F to handle non-global files under exch2
+ o update AIM Cubed-Sphere exp (aim.5l_cs):
+   use land, p*, and Franco.M forcing fields with fractional land-sea mask.
+ o update AIM Equatorial Channel exp:
+   use standard aim_v23 pkg and change the SST fields to be more realistic.
+ o globalFile now works with exch2
+ o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and
+   mon_vort3.F to make exch2 friendly with >1 tile per cube face
+ o limit timeave output for hi-res integrations
+ checkpoint52i_post (2004/01/21)
+ o removed CPP_EEOPTIONS.h from verification/*/code
+ o updated the tiling for global_ocean_pressure
+ checkpoint52i_pre (2004/01/20)
+ o update aim.5l_LatLon using the standard aim_v23 pkg (instead of
+   the old pkg/aim).
+ checkpoint52h_pre (2004/01/20)
+ o shortened offending lines in exch2_send_rx?.template
+ o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator
+ o genmake2: add build & execute test for NetCDF code
+ o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed
+   old grid files, moved CPP_EEMACROS.h to pkg/exch2
+ o added useSingleCPUIO flag to monitor.F and mon_out.F
+ o added temporary hack for sea-ice dynamics on the cube:
+   metric terms are ignored and it is assumed that
+   there is no sea-ice on cube faces 1, 2, 4, and 5.
+ checkpoint52f_post (2004/01/09)
+ o added exch2 cube routines to pkg/exch2
+ o modified hs94.cs-32x32x5 to use it
+ o added new grid files to hs94.cs-32x32x5
+ checkpoint52f_pre (2004/01/07)
+ checkpoint52e_post (2004/01/07)
+ o first attempt to solve vertical advection (momemtum & T,S) Implicitly
+   for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom)
+ o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F)
+   to work with implicit vertical advection and AB ;
+ o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme.
+ o update output (gad_calc_rhs.F changes affect truncation error) of exp:
+  front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box
+ checkpoint52e_pre (2004/01/02)
+ o fix bug in impldiff when Nr=1 or Nr=2.
+ o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt
+ o little changes (fftpack, aim/phy_suflux ...) to pass the "checkbounds" test.
+ o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2
+   ocean exp. that use NLFS: global_ocean.cs32x15 & global_ocean_pressure
+ o added exf_offset_atemp for Celsius to Kelvin conversion of atemp
+ o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024
+ o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations
+ checkpoint52d_post (2003/12/16)
+ o re-tiled many expts to allow comparison in multi-processor mode
+   - updated output accordingly
+   - changed hs94.128x64x5 to use intial T from file rather than use the
+     random number generator
+ o add infrastructure in model routines for fizhi and gridalt packages
+ o change global_ocean.cs32x15 because of Pb with GM on CS-grid.
+ o changes to permit hi-res, cubed-sphere, configuration
+   - added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F
+   - added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F
+   - added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation
+     of surface winds for the cube
+   (A verification experiment, based on global_ocean.cs32x15, but with
+    pkg/seaice turned on and with on-the-fly interpolation from the NCEP
+    Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice,
+    complete with example surface forcing files and matlab scripts to look
+    at the output and compare it with that of global_ocean.cs32x15.)
+ o packages pickup: $PKG_write_pickup called from packages_write_pickup ;
+    but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code
+    to conform to the common rule.
+ o check-in the first version of the coupler + interfaces for multi-components
+    set-up (Chris's version, adapted to work on cubed-sphere grid); use MPI.
+    - imply modification in eesupp (MPI_COMM_MODEL < MPI_COMM_WORLD).
+    - atmosphere: use pkg aim_v23 ; no sea-ice for now.
+    - ocean and atmos. share the same horizontal grid (no interpolation).
+    - exchanges between component and coupler is done in forward_step
+ o new verification experiment, cpl_aim+ocn:
+    coupled ocean - AIM atmosphere on cs32 grid.
+ checkpoint52d_pre (2003/12/06)
+ o surface flux time-av diagnostic modified for NLFS & RealFreshWater
+ o add call to AIM pendant S/R in external_forcing & external_fields_load.F
+ checkpoint52c_post (2003/11/25)
+ o Fixing OPTIONS files for use of exf:
+   - ALLOW_ECCO not needed
+   - ECCO_CPPOPTIONS.h should not be included from
+     EXF_OPTIONS.h/CAL_OPTIONS.h, but from CPP_OPTIONS.h
+     as has been the case in the past
+   - All cal/exf related options are currently set in
+     single header file. Should remain so until we
+     agree on a consistent new policy.
+ o Removed all CPP options for cal package.
+   cal has no more CPP options.
+ o modified STOREs in GAD_ADVECTION
+ o corrected key comp. for passkey
+ checkpoint52b_post (2003/11/23)
+ o new version: "thsice" of thermodynamic sea-ice pkg:
+  - only 1 call from "forward_step"; conserve energy, fresh-water & salt.
+  - modify fluxes but do not change theta directly;
+  - light cleaning of bulk_force pkg (still needed with thsice).
+  - add forcing fields + data files in global_ocean.cs32x15/inp_thsice
+    + output_thsice.txt to test thsice & bulk_force pkgs.
+ o put back grid & coriolis monitor output.
+ checkpoint52b_pre (2003/11/23)
+ o call "do_the_model_io" at the beginning (=> dump initial state)
+ o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P)
+ o sort out interplay between tamc.h and PTRACERS_OPTIONS.h
+   (need info on NUMBER_OF_PTRACERS)
+ o missing PTRACERS headers in some routines
+ o default tamc.h in pkg/autodiff supposed to crash
+   to ensure proper customization
+ checkpoint52a_post (2003/11/17)
+ o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp
+   - moved surfaceTendencyTice from pkg/seaice to main code
+   - subroutine FREEZE_SURFACE now limits only surface temperature
+     and is called in FORWARD_STEP (if allowFreezing=.TRUE.)
+     => new output.txt for global_ocean.cs32x15 & global_with_exf
+   - keep the old version of FREEZE for backward compatibility;
+     global_ocean.90x40x15 left unchanged using useOldFreezing=.TRUE.
+   - corresponding modifs for TAF directives
+ o added surface flux output variables to TIMEAVE_STATVARS
+ o time-averaged output for pkg/ptracers
+ o fix problem with ECCO-related divided adjoint
+   snapshot file was missing some ad-variables,
+   but no warning issued by TAF
+ checkpoint52a_pre (2003/11/12)
+ o some bug fixes for #undef REAL4_IS_SLOW
+ checkpoint52 = ecco_c52_e35
+ o after testing adjoints of checkpoint51u_post
+ checkpoint51u_post (2003/11/06)
+ o this is the post-merge tag of the ecco-branch
+   (needs another clean checkout and re-testing)
+ o various natl_box_adjoint configs and results
+   but no input fields
+ o obcs adjoint not yet merged!
+ o adding ECCO global 1x1 and 2x2 degree configs
+ o updated/extended some store directives for seaice
+ o pkg/ecco now containes ecco-specific part of cost function
+ o top level routines the_main_loop, forward_step
+   supersede those in model/src/
+   previous input data.cost now in data.ecco
+   (new namelist ecco_cost_nml)
+ o in ctrl/ cleaned some cross-dependencies and updated CPP options
+ checkpoint51t_post (2003/11/04)
+ o this is the pre-merge tag of the ecco-branch
+ checkpoint51s_post (2003/11/04)
+ o cleanup: removed various obsolete #define-s
+ o pkg/grdchk
+   - renamed 'ph-grd 3' to 'grad-res'
+   - merged from ecco-branch
+     (remaining bug fixes for obcs gradient checks)
+   - additional high-precision output for testreport
+     (grep for 'precision_grdchk_result')
+ checkpoint51r_post (2003/11/03)
+ o cleaned up or removed CPP_OPTIONS.h files
+ o updated results for some of the tests to reflect the new
+   optfiles (-ieee: -O0 instead of -O3)
+ checkpoint51q_post (2003/10/30)
+ o cd_code:
+   - moved cd_scheme.F -> cd_code_scheme.F
+   - separate read_checkpoint from cd_code_ini_vars.F
+   - separated cd_code part from write_checkpoint
+   - updated AD_SOURCE, generated .flow
+   - added CD_CODE_VARS.h to the_main_loop
+   - Moving cd_code specific store dir.s to pkg/cd_code
+ o ctrl package totally restructured
+   - pack/unpack now optional and decoupled from
+     xx_/adxx_ I/O
+   - ctrl_pack/unpack cleaned
+     (new routines ctrl_init_ctrlvar.F, pkg/ctrl/ctrl_init_wet.F)
+   - confined inclusion of AD_CONFIG.h to where necessary.
+ o genmake2: changed AD dependencies from SRCFILES to AD_FILES
+ checkpoint51p_post (2003/10/30)
+ o create initial cd_code package
+   - WARNING: the initialization of fields within packages
+     is broken because INI_FIELDS (where READ_CHECKPOINT is
+     called) is called *before* PACKAGES_INIT_VARIABLES.
+     This seems to be backwards since
+) its important to initially zero the entire field including
+        the "halo" region
+) zeroing needs to be done *before* reading pickup info
+        and the pickup call might or might not happen in any
+        particular run
+   - this needs an overhaul for R2
+ o cleanup verification/*/code/GMREDI_OPTIONS.h
+ o cleanup testreport
+ checkpoint51o_post (2003/10/27)
+ o bringing AD-related verif's up to date with genmake2
+   - carbon/
+   - global_ocean.90x40x15/
+   - hs.94.1x64x5/
+   - (front_relax/ )
+ o (more) consistent directory structure for AD-related verif.'s
+ o cleaning ALLOW_GRADIENT_CHECK -> ALLOW_GRDCHK
+ o cleaning some ALLOW_TANGENTLINEAR_RUN -> ALLOW_AUTODIFF
+ o bug fix in find_alpha.F for MDJWF:
+   - modif. to alpha = 1/D*( dN/dT - rho*dD/Dt) to account for
+     change rho -> rho-rhoConst
+   - replace call find_rho to find_rhonum
+ o initialisation of rFlx extended to full array (required by TAF)
+   and shifted to thermodynamics
+ o removed PTRACERS.h in ptracers routine
+ o added surfacetendencyPtr to S/R parameter list pracers_forcing
+ o Correcting initialisations for fVerU, fVerV.
+ o helping TAF to recognize dependency on kUp for
+   fVerU, fVerV
+ o Replacing delZ by delR in pkg/ctrl/
+ checkpoint51o_pre (2003/10/24)
+ o undid all of cp51 pending some cleanups and discussion
+ o added the [#include "AD_CONFIG.h"] statement to all files that need
+    it for adjoint/tl #defines
+  o re-worked the build logic in genmake2 to support AD_CONFIG.h
+  o removed tools/genmake since it no longer works
+ checkpoint51n_post (2003/10/23)
+ o modifications to make FREEZE flux visible to pkg/kpp
+   - moved surfaceTendencyTice from pkg/seaice to main code
+   - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP
+   - subroutine FREEZE now limits only surface temperature
+     (this means new output.txt for global_ocean.90x40x15,
+      global_ocean.cs32x15, and global_with_exf)
+ o added surface flux output variables to TIMEAVE_STATVARS
+ checkpoint51n_pre (2003/10/23)
+ o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F
+ o added [#include "AD_CONFIG.h"] to all files that use the following
+   defines:
+   - ALLOW_ADJOINT_RUN
+   - ALLOW_TANGENTLINEAR_RUN
+   - ALLOW_ECCO_OPTIMIZATION
+ checkpoint51m_post (2003/10/21)
+ o incorporating changes to get TAMC/TAF working in genmake2
+   - added new TAMC/TAF targets to the Makefile
+   - various cleanups related to package handling
+   - these changes should have no impact on the forward model
+ checkpoint51l_post (2003/10/20)
+ o changes to pkg/cal and pkg/exf that allow and speed-up long integrations
+  - faster algorithm for cal_addtime.F
+  - higher precision arithmetic, where needed
+  - pkg/exf *startdate variables changed from calendar date to
+    model integration time
+ checkpoint51l_pre (2003/10/17)
+ o add salt flux to forcing fields (used when salty sea-ice forms or melts)
+ o enable to apply restoring on S & T only in a latitude band.
+ o update output (external_forcing_surf modif. change truncation errors)
+    global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box
+ checkpoint51k_post (2003/10/16)
+ o change default to: useNHMTerms=.FALSE.
+  - new output.txt for atmos. exp (NHMTerms were wrong but now turned off):
+    adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5
+  - new output.txt for idealized oceanic exp (NHMTerms are now turned off):
+     exp1, ideal_2D_oce
+  - change data file of oceanic exp (leave the results unchanged for now)
+    exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box
+ o set gravitySign automatically according to the vertical coordinate used
+   (and change sign: back to "logical" value: +1 when R increases downward)
+ o added an include barrier to the default CPP_OPTIONS.h and
+   removed the #include "PACKAGES_CONFIG.h" from it
+ o fix a bug in mom_fluxform (from chk51j_post)
+ checkpoint51j_post (2003/10/10)
+ o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/
+ o adjusted some flow directives (dynamics, thermodynamics)
+ o added cubed-sphere case to test cost function
+ o heckpoint_lev?_directives.h now include
+   pkg-specific directives, whenever those are enabled.
+ o Moving pkg-specific flow directives to corresponding pkg
+   Moving pkg-specific differentiation list to corresponding pkg
+   Moving pkg-specific checkpoint-lev storing to corresponding pkg
+   ---> conventions are
+        - pkg_ad.flow
+        - pkg_ad_diff.list
+        - pkg_ad_check_lev?_dir.h
+ checkpoint51i_post (2003/10/09)
+ o merge of the branch-genmake2
+   - knowingly breaks the older genmake
+   - automatic generation of all ALLOW_${PKG_NAME} defines
+   - new testreport supersedes older testscript
+ o large number of package inclusion and header cleanups
+ checkpoint51i_pre (2003/10/08)
+ o new output for adjoin of global ocean vector invariant
+ o fix for checkpoint of thermodynamic seaice and bulk_force
+ o Steph gchem various cleanups
+ checkpoint 51h_pre
+ o fixed some single quotes
+ o modify gchem pkg to be more versatile
+ o modifications to clean up dic pkg
+ o add pkg/cfc
+ checkpoint51g_post (2003/10/02)
+ o provide links for ARPACK and ADM*TLM
+ o start removing verification/vero/
+ o update AD-related stuff
+   (in particular some IF-statements in model/src/ routines)
+ o adding to verification/global_ocean.90x40x15/ adjoint of
+   vector invariant setup
+ checkpoint51f_post (2003/10/02)
+ o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif)
+ o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation
+   of tracer Green's fucntions for ocean inversion project.
+ checkpoint51f_pre (2003/08/07)
+ o Added on-the-fly spatial interpolation capability
+     "USE_EXF_INTERPOLATION" to pkg/exf.
+   - This is a temporary Cartesian-grid hack until
+     the super-duper ESMF coupler becomes available.
+   - See verification/global_with_exf/README for usage example.
+   - Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid
+     flags and modified pkg/seaice accordingly.
+ o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F,
+     and pkg/kpp/kpp_transport_ptr.F for dealing with tracer
+     non-local transport term.
+ checkpoint51e_post (2003/08/03)
+ o pkg/mom_vecinv:
+   - changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec)
+   - add time-ave diagnostic of vorticity advection.
+ o add diagnostic (instantaneous) of Shapiro Filter effect for T,S & UV.
+ o atmospheric geopotential: - include water vapor effect;
+                             - use p^kappa in p* scaling.
+ o land pkg: read initial state from files.
+ o AIM : add stratospheric drag in the upper level
+ checkpoint51d_post (2003/07/18)
+ o change function ILNBLNK (=> last non-blank char.) to return zero
+   (instead of the string length) when the string. char is empty
+ o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid)
+ o modif's to restore TAMC compatibility
+   - avoid "_d" constructs in PARAMETER declarations
+   - avoid interrupting lines by comment lines
+ o Use cluster local disks for purely local I/O
+   vs. globally visible disks needed for ctrl stuff
+   (merged from ecco-branch)
+   - new active_file_loc... and mdsio_..._loc routines
+   - affected packages: autodiff, ctrl, grdchk, mdsio
+ checkpoint51c_post (2003/07/08)
+ o introducing integer flag debugLevel
+   - debLevZero: suppress all output
+   - debLevA: standard
+   - debLevB: equivalent to current debugMode=.TRUE.
+ o introducing pathname variable mdsioLocalDir for mdsio
+   that can be specified at runtime
+   (relevant for cluster I/O to local disk)
+ `
+ >>>checkpoint51b_post
+ adjoint of ptracers
+ o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM
+ o extended state in checkpoint_lev?, etc.
+ o alternative ctrl/cost with tr1 or ptracer
+ o new comlev1_bibj_ptracers
+ o new ptracers.flow
+ o made ptracers_forcing same as external_forcing_s
+ o added verification for adjoint with ptracers
+   - adm. grdchk fail so far
+   - tlm. grdchk OK
+   - checked tapelev/comlev recomputations: OK
+ <<<checkpoint51b_pre
+ checkpoint51a_post (2003/06/25)
+ o added code for biogeochemistry package
+   - new pkgs: dic, gchem
+   - new subroutine in ptracers
+ o modify code for biogeo packages
+   - in model/src and pkg/ptracers
+ checkpoint51 (2003/06/24)
+ o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN
+   - autodiff, ctrl, exf, grdchk, seaice
+   kept separate packages
+   - cost, ecco, obcs
+ o updating verification/internal_wave, verification/lab_sea
+   (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)
+ checkpoint50i_post (2003/06/23)
+ o Preparing next differentiable checkpoint and sync
+   of MAIN vs. ecco-branch
+   - 1st step: this one is differentiable
+   - 2nd step: next(! not this) checkpoint will have updated packages
+               from ecco-branch)
+ checkpoint50h_post (2003/06/20)
+ o new package "land": provide surface BC for AIM.
+ o pkg/ptracers: apply exchange to all tracers after reading a pickup.
+ o AIM: use true log-P extrapolation for near surface temp (= as in
+     F.Molteni paper) ; update aim.5l_cs output.
+ o New variable in PARM03 for more flexible pickups
+ o somewhat cleaned package initialisation sequence for
+   ctrl/ cost/ ecco/ in packages_... routines
+ checkpoint50g_post (2003/05/23)
+ o merged with release1_p17 (pkg/seaice and verification/lab_sea)
+   - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics
+   - LSR sea-ice dynamic solver moved to SouthWest B-grid location and
+     made the default because of faster convergence than ADI
+ checkpoint50f_post (2003/05/23)
+ o exf totally restructured
+   - replaced all exf_set_ routines by one generic exf_set_gen.F
+     and made sure it's still differentiable
+   - split exf_getffields.F into new exf_bulkformulae.F
+   - exf_inscal_/exf_outscal_ suffixes consistent with field names
+   - updated adjoint/makefile and relevant verif. accordingly
+ checkpoint50f_pre (2003/05/23)
+  o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ;
+       + change Evap over land. (update aim.5l_cs output)
+  o added missing .cvsignores and made uniform across expts
+  o changed configuration of tidal_basin_2d expt
+  o added pkg/debug functions for tracing code in fatal crashes
+  o tidied pkg/monitor to use MONITOR_OPTIONS.h
+  o new fn in pkg/monitor to stop model if solution grows too big
+  o removed lots of single quotes from comments
+ checkpoint50e_post (2003/05/14)
+ o make KPP work with PTRACERS
+  - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is
+    nearly a copy of kpp_transport_s
+  - there is no analogue to SurfaceTendencyS, so I have to use
+    gPtr(of the surface layer) instead
+ o add a new platform SunFire+mpi (SunFire 15000) to genmake
+ checkpoint50e_pre (2003/05/13)
+ checkpoint50d_post (2003/05/13)
+ o change kpp output from multiple-record state files to single-record state
+   files analogous to write_state.F
+ o reduce the output frequency of cg3d-related stuff to the monitor frequency,
+   analogous to the cg2d-related output.
+ o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512,
+   so that writing to internal file fn (with length 512) fails.
+ checkpoint50d_pre (2003/05/12)
+ checkpoint50c_post (2003/05/12)
+ o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)
+ o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.
+ o add time-average diagnostic of U*V and vertical diffusive flux for theta.
+ o bug fixed in convective adjustment diagnostic (multi-tile set-up).
+ o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.
+ checkpoint50c_pre (2003/04/30)
+ Merging from release1_p13:
+ o bug fix for pkg/seaice dynamic solver
+ o Added SEAICE_initialHEFF to pkg/seaice
- release1_p11
+ checkpoint50b_post (2003/04/17)
+ o store u*,v* in gU,V instead of in guNm1,gvNm1
+ o in order to put the momForcing out of the Adams-Bashforth:
+   move forcing & CD-scheme calls from mom_fluxform & mom_vecinv
+   to timestep.F
+ o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays
+ o re-generate output for highly sensitive test-exp:
+    global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box
+ checkpoint50b_pre (2003/04/17)
+ o restore the use of momAdvection & useCoriolis flags (mom_vecinv)
+ o corrected CPP option mismatch in exf_Bulk... functions for case
+   #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP
+ checkpoint50a_post (2003/03/21)
+ o Bug fix for merging between c50 and KPP.
+   ikey was passed from thermodynamics to kpp_calc via
+   common block rather than being recomputed in kpp_calc,
+   in contradiction with new key itdkey.
+   New key ikppkey created, and tamc.h headers updated.
+ checkpoint50 (2003/03/08)
+ - 2nd step of merge with ecco-branch:
+   merge changes in ecco-branch back into main trunk
+ - bug fix in find_alpha
+ - more storing in gmredi_calc_tensor.F, kpp_routines.F
+ - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC
+ - merged some sliced AD support routines
+ checkpoint49 (2003/03/06)
+ merged from ecco-branch:
+ o exf:
+   - Enable initialisation of forcing fields to constant
+     (runtime) values.
+   - in exf_getffields.F
+     Reduce i-/j-loop to interior domain, discarding overlaps.
+     That also fixes wrong TAF-key computations for key_1, key_2
+     with bulf formulae.
+   - exf_init.F modify #ifdef for exf_init_evap
+   - exf_getffieldrec.F, ctrl_getrec.F
+     The following INT-usages are not safe:
+       fldsecs  = int(fldsecs/fldperiod)*fldperiod
+       fldcount = int(fldsecs/fldperiod) + 1
+     and were modified.
+ o autodiff: checkpoint_lev...
+   - updated storing for bulk formulae (some arrays were missing)
+   - added state for seaice package
+   - synchronized with main branch
+ o DIVA:
+   Modif.s in
+   - the_main_loop.F
+   - the_model_main.F
+   and added cost_final_restore.F cost_final_store.F
+   o With these changes, it is possible to fully separate
+     the first forward run to compute the cost function (mdthe_main_loop)
+     and adjoint runs over individual DIVA intervals (adthe_main_loop)
+     into separate model executions.
+     This enables better tuning of DIVA to given queue sizes.
+   o Loss of cost function value in consecutive DIVA runs is
+     fixed by storing to 'costfinal' file.
+   o Appropriate call of ctrl_unpack/_pack,grdchk_main at
+     beginning/end of adjoint integration is accounted for.
+   The current changes apply to TAF-1.4.26.
+   TAF has one remaining bug, requiring one manual change
+   (see MITgcm manual).
+ o cal: synchronized between MAIN and ecco-branch
+ checkpoint48i_post (2003/03/05)
+ o Changes to restore differentiability of code w.r.t. previous tag
+   (mostly adding new routines to make list and replacing
+   pressure by totPhiHyd).
+ o Updated and merged grdchk package
+   - has both ADM and TLM checks
+   - works for single- and multi-proc.
+   - output cleaned
+   - worked successfully for parallel DIVA
+ o genmake:
+   - Adding -platform=SP4
+   - Modif. for DEC Alpha (many don't have makedepend; use mkdep instead).
+ o Modif. for DIVA:
+   ctrl_unpack should not be called in intermediate DIVA interval.
+   (similar thing would apply for active files such as
+   tbar, sbar, psbar, which should not be reinitialised;
+   only relevant for ecco-branch)
+ checkpoint48h_post (2003/02/28)
+ o improve "ini_p_ground" when using finite difference form for calc_phi_hyd
+ o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F
+ o Added SEAICE_initialHEFF to pkg/seaice
+ o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT
+ checkpoint48g_post (2003/02/18)
+ --- EOS:
+ o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF
+   store total Potential in totPhyHyd for diagnostics & EOS.
+ o fix restart and overlap Pb when using Z-coord and EOS funct. of P
+ --- Pressure/geopotential gradient:
+ o use Ro_surf & R_low instead of hFac in cal_phi_hyd:
+ o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind
+   ( changes results of global_ocean_pressure )
+ o NLFS + z-coord.: add eta*Rho' contribution.
+ o accurate phiHyd when using interface-W at the middle between 2 centers
+  ( changes results of ideal_2D_oce )
+ o includes r* 2nd term in potential gradient.
+ checkpoint48f_post (2003/02/18)
+ Merging from release1_p12:
  o Modifications for using pkg/exf with pkg/seaice
    - improved description of the various forcing configurations
    - added basic radiation bulk formulae to pkg/exf
-Line 38 
 o Lower bound for viscosity/diffusivity
+Line 3918 
 o Lower bound for viscosity/diffusivity
    - updated verification/lab_sea/results/output.txt
  o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F
  o Added useSingleCpuIO option (see PARAMS.h).
+ o Updated useSingleCpuIO option in mdsio_writefield.F to
+   work with multi-field files, e.g., for single-file pickup.
+ o pkg/seaice:
+   - bug fix in growth.F: QNET for no shortwave case
+   - added HeffFile for specifying initial sea-ice thickness
+   - changed SEAICE_EXTERNAL_FLUXES wind stress implementation
+ o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf,
+   kpp_transport_t.F, forward_step.F, and the_main_loop.F
+ o pkg/seaice:
+   - adjoint-friendly modifications
+   - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
- release1_p10
+ checkpoint48e_post (2003/02/12)
+ o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post)
+ o dynamics: change definition of computational domain & adapt mom_fluxform
+   accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2.
+ o following exp works with Olx=Oly=2 (and pass through checkbounds option):
+     adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1
+     exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5
+     global_ocean.90x40x15 global_with_exf global_ocean_pressure
+     inverted_barometer solid-body.cs-32x32x1
+   (high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure)
+ checkpoint48d_post (2003/02/09)
+ o in preparation for r*:
+  a) use pre-computed gradient of hydrostatic potential:
+     changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce
+  b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd:
+     => affects results of glob_oce_pressure (different truncation error)
+   update output.txt of ideal_2D_oce & global_ocean_pressure
+ checkpoint48d_pre (2003/02/08)
+ o in preparation for r*:
+   new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient.
+   pass the 2 comp. of the grad. as arguments to momentum S/R.
+   but for the moment, only used if it does not change the results.
+ o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP
+ checkpoint48c_post (2003/02/06)
+ Modifications in treatment of initial flux forcing controls
+ to avoid extra storing of flux fields.
+ checkpoint48c_pre (2003/01/21)
+ o Added tidal_basin_2d experiment (currently 1D!)
+ o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented)
+ checkpoint48b_post (2003/01/27)
+ o r* coordinate added in #ifdef NONLIN_FRSURF block.
+  (modification to pressure gradient not yet implemented)
+ o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports
+   (for U & V) that are used for vertical advection of momentum.
+ checkpoint48a_post (2003/01/24)
+ o In preparation for r*, use temp. array to compute vertical transport
+    in flux-form momentum pkg. => change results of few test-exp.
+   Update output of: exp4, exp5, front_relax, global_ocean_pressure,
+                     lab_sea, natl_box & plume_on_slope
+ checkpoint48 (2003/01/23)
+ o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D')
+ checkpoint47j_post (2003/01/21)
+ o add new exp. (ideal_2D_oce) to test "exotic" parameters and options.
+ o moved adexch from forward_step to addummy_in_stepping
+ o added exch in ctrl_map_...
+ o aveFreq.=0. at end of cost_final to avoid overwrite in
+   reverse checkpointing loop
+ o Yet more changes in gmredi:
+   * adgmredi_calc_tensor
+     avoiding all recomputation of gmredi_slope_limit
+   * adgmredi_x/y/rtransport
+     added flag for excessive storing to avoid recomp. of
+     u/v/rtans, dTdx/y/z
+     -> this is not really necessary and very memory-consuming
+   * adgmredi_slope_psi:
+     consistency with gmredi_slope_limit in treatment of GM_slopeSqCutoff
+   * gmredi_slope_limit
+     re-activated full calculation of taperfct for case 'ac02'
+ o updating verification/ adjoints of carbon, global_ocean.90x40x15
+ checkpoint47i_post (2003/01/13)
+ o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled.
+ o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi)
+   default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post)
+ o cg2dTargetResWunit: define tolerance using deltaTmom (and not deltaTfreesurf)
+ o gmredi: fix few bugs.
+ checkpoint47h_post (duplicate tag for PH's c48 tag, in order to move c48)
+ This will be a good checkpoint to plug into the ecco-branch.
+ o few modif.'s to get latest version adjointed
+   (mainly kick out code in ini_linear_phisurf)
+ o modif's to run adjoint with exactConserv
+ o case GM_BOLUS_ADVEC should be cleaned
+   S/R gmredi_slope_psi should be cleaned
+ o verification/carbon now has exactConserv=.TRUE.
+ checkpoint47g_post (2003/01/10)
+ o time-average AIM output: becomes independent from statvars time-average
+   (can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH)
+ o After TAF bug fix:
+   Tested adjoint of gmredi package.
+   Tests were done with checkpoint47 rather than with latest
+   checkpoint47f_post since the latter is broken for the adjoint
+   verification/carbon/ contains both ADM and TLM gradient checks.
+ Here they are, before they get changed/lost/stolen.
+ Mostly modif.'s to fix numerical sensitivities.
+ Gradient checks OK for
+ - GM_taper_scheme:
+   * clipping
+   * ac02
+   * linear
+   * glw91
+   * dm95
+   * ldd97
+ - GMREDI_OPTIONS:
+   * GM_VISBECK_VARIABLE_K
+   * GM_NON_UNITY_DIAGONAL
+   * GM_EXTRA_DIAGONAL
+   * GM_BOLUS_ADVEC
+ in conjunction with data.gmredi parameters to be checked in
+ in a few minutes under verification/carbon/code/
+ checkpoint47f_post (2002/12/28)
+ Merging from release1_p10:
  o modifications for using pkg/exf with pkg/seaice
    - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING
      and SEAICE_EXTERNAL_FLUXES
-Line 50 
 o modifications for using pkg/exf with p
+Line 4052 
 o modifications for using pkg/exf with p
    - verification/lab_sea default experiment now uses
      pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf
- release1_p9
+ checkpoint47e_post (2002/12/27)
+ o created a tag prior to creating a branch
+ checkpoint47d_post (2002/12/16)
+ o fixed bug in the oceanic pressure coordinates code: vertical viscosity
+   at the bottom boundary had an erroneous half slip boundary condition
+ o added bottom drag and no slip boundary condition capabilities to
+   oceanic pressure coordinates code
+ o added new verification experiment global_ocean_pressure, this experiment is
+   also described in the tutorial section of the manual
+ checkpoint47d_pre (2002/12/16)
+ checkpoint47c_post (2002/12/16)
+ o Added a verification experiment for a global cubed-sphere ocean run
+   -  verification/global_ocean.cubed32x32x30
+   -  uses pkg/therm_seaice and pkg/bulk_forcing
+ o allow to run AIM physics with SPEEDY input files (from Franco Molteni)
+ o allow a more accurate definition of Ro_Surf (selectFindRoSurf=1)
+   when using P-coordinate; only implemented for atmospheric config.
+ o OCEANICP & realFreshWater: include P-E direct effect on wVel ;
+   NOTES: requires option NONLIN_FRSURF to be "#define".
+ o update advect_xz/results/output.txt (left from checkpoint44g_post)
+ checkpoint47b_post (2002/12/05)
+ Merging from release1_p9:
  o pkg/seaice
    - removed GOTO's and added taf directives
    - double precision constants to reduce the g77 (Linux)
-Line 66 
 o verification/lab_sea
+Line 4093 
 o verification/lab_sea
    - added missing matlab routines
    - added test of thermodynamics parallelization
- release1_p8
+ checkpoint47a_post (2002/11/23)
+ o new pkg: aim_v23
+  = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.
+    for now, keep the same surface forcing as before.
+  - Part-Cell implemented into AIM; check that Heat & Water are conserved
+  - aim.5l_cs: use new aim pkg (run 10yr & get better results than before)
+  - aim.5l_LatLon & aim.5l_Equatorial_Channel are still using old aim pkg
+ o add diagnostic of surface correction term in monitor output
+ o bulk_force and therm_seaice
+ - Two packages:  bulk_force (Bulk forcing)
+   and therm_seaice (thermodynamic_seaice) - adopted from LANL CICE.v2.0.2
+ - Earlier integration from Stephaine Dutkiewicz
+   and Patrick Heimbach.
+ - Two ifdef statements for compile time,
+    ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE
+ checkpoint47 (2002/11/15)
+ differentiable version of checkpoint46n_post
+ o bug fix in quasihydrostaticterms
+ o * "clean" adjoint code (in terms of extensive recomputations)
+     can now be obtained for all GMREDI options (i.e. for
+     - GM_VISBECK_VARIABLE_K
+     - GM_NON_UNITY_DIAGONAL
+     - GM_EXTRA_DIAGONAL
+     - GM_BOLUS_ADVEC )
+   * However, wrong gradient check problem remains unsolved.
+   * New CPP options have been introduced for different
+     tapering schemes
+ o external_fields_load now part of differentiation list
+ o pressure needs multiple storing;
+   would be nice to have store_pressure at beginning or
+   end of forward_step, e.g. by having phiHyd global (5-dim.)
+   (NB: pressure is needed for certain cases in find_rho,
+   which is also invoked through convective_adjustment).
+ o recomputations in find_rho for cases
+  'JMD95'/'UNESCO' or 'MDJWF' are OK.
+ o #define ATMOSPHERIC_LOADING should be differentiable
+ o ini_forcing shifted to begining of initialise_varia
+ o Incorporating QNVS line search routines into MITgcm
+   (this is separate code, and therefore not under pkg)
+   lsopt/, optim/
+ o Updated verification/carbon/
+   - #define GM_VISBECK_VARIABLE_K
+   - GM_taper_scheme    = 'ldd97'
+ checkpoint46n_post (2002/11/12)
+ Merging from release1_p8:
  o verification/natl_box:
    updating new external_fields_load routine
  o New package: pkg/seaice
-Line 93 
 o New package: pkg/seaice
+Line 4167 
 o New package: pkg/seaice
    g d e n  d  n  x  n  .  n  x  n  .  n  x  n  .  n  x  n  .
    Y Y Y Y  5  5  7  7  7  8 10  9  6  6  6  6  7  5  7  5  7 FAIL  lab_sea
- release1_p7
  o GAD:
    - generated new common blocks to account for call of
      same gad routines with differing traceridentities
-Line 121 
 o Adding new verification experiment glo
+Line 4193 
 o Adding new verification experiment glo
    the exf (and cal) package instead of the
    external_fields_load routine (cf README file).
- release1_p6
+ checkpoint46m_post (2002/11/07)
+ o modified testscript to return -- when there are no lines of "%MON" output
+ o added new flag "quasiHydrostatic" for QH mode
+   and new routine quasihydrostaticterms()
+ o added 2*Omega*Cos(phi)*W to u equations (non-hydrostatic Coriolis term)
+   New routine: mom_u_coriolis_nh()
+ o fixed sign of non-hydrostatic metric terms in u and v equations.
+   Depend on correct sign of gravitySign.
+ o added work.pc* to .cvsignore in aim directories using ifc
+ o introduced flag for controllin non-hydrostatic metric terms
+ o removed gravitySign from PARM04
+ o switched to g77/ifc from pgf77 in aim experiments
+ checkpoint46l_post (2002/11/01)
+ o made convective adjustment work with pressure coordinates:
+  - changed the direction of k-loop in convective_adjustment.F for the
+    case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)
+  - adjusted the reference pressure k-index in convective_adjustment.F
+  - adjusted the convection condition in convect.F (in analogy to
+    calc_ivdc.F)
+  - convective_adjustment no longer computes anything on the halos
+  - removed the warnings about negative salinity from find_rho.F and
+    find_alpha.F; instead the new routine look_for_neg_salinity, called
+    at the beginning of find_rho, find_alpha, and find_beta, does a
+    check of the entire slice, if CPP-option
+    CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined
+ checkpoint46l_pre (2002/10/23)
+ checkpoint46k_post (2002/10/23)
  o fixed the verification/global_ocean.90x40x15 experiment:
   - new bathymetry (the world according to A., JMC, and M.)
   - new initial fields and forcing fields (*.bin files)
   - new POLY3.COEFFS (for the next release one should switch to a full
-    equation of state)
+    equation of state: JMD95P or MDJWF)
   - fixed several errors and redundancies in the data file
   - experiment uses looped cells
   - added matlab directory with diagnostic scripts for plotting of output
- release1_p5
+ o S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F:
- o import recent fix from MAIN branch:
+  - read AIM physics parameters from a file (data.aimphys)
-   - use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S
+  - set defaults values = F.Molteni paper (Clim.Dyn., 2002)
-   - change phiMin in exp1 (to agree with documentation)
-  from checkpoint45 to checkpoint45a_post:
+ checkpoint46j_post (2002/10/07)
-   - specific exchange for X-slice domain (case Ny=1)
+ o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH
-   - argument futureIter of S/R obcs_calc missing in
+ o move wVel computation at the end of the time step, in S/R integr_continuity
-     exp4 & internal_wave /code
+ o create specific S/R to exchange T,S before DYNAMICS (for stagger time step)
-   - solve_for_pressure : set cg2d_x to zero where OBCS are applied
+ o update timeave pkg for wVel diagnostic.
-  from checkpoint44f_post to checkpoint44g_post:
+ checkpoint46j_pre (2002/09/27)
-   - fix surface correction term in multiDimAdvection
-     (affects plume_on_slope results
+ checkpoint46i_post (2002/09/25)
- o bug fix in packages_readparms (missing ALLOW_CALENDAR)
+ o Clean up AIM package (and keep the results unchanged):
- o bug fix in CG2D.h (correct array size for LETS_MAKE_JAM
+   include CPP_OPTION and use IMPLICT NONE in all routines ;
- o Adjoint-related bug fixes in kpp:
+   declare all the variables _RL ; use _d 0 for all numerical constants.
-   - kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix
+   use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 !
-   - kpp_routines: store of Rib avoids partial recomputation bug of TAF.
- o added Eliassen-Palm flux hooks (dynamics,ini_fields)
+ checkpoint46h_post (2002/09/25)
- o removed unused TAF keys iikey, idkey (dynamics,thermodynamics)
+ o cleaned up the use of rhoNil and rhoConst.
- o flow directives:
+   - rhoNil should only appear in the LINEAR equation of state, everywhere
-   - new for S/R do_the_model_io
+     else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst
-   - enhanced for S/R checkpoint
+     and the dynamical equations are all divided by rhoConst
- o added Eliassen Palm flux controls to gradient check package
+ o introduced new parameter rhoConstFresh, a reference density of fresh
+   water, to remove the fresh water flux's dependence on rhoNil. The default
+   value is 999.8 kg/m^3
+ o cleanup up external_forcing.F and external_forcing_surf.F
+   - can now be used by both OCEANIC and OCEANICP
+ checkpoint46h_pre (2002/09/18)
+  Added code to convert surface volume flux (fresh water) into
+  a mass flux when using P coordinates in the ocean (OCEANICP).
+  Note: It assumes you have set rho0=rhoConst=density of fresh water.
+ checkpoint46g_post (2002/09/18)
+ o Include a new diagnostic variable phiHydLow for the ocean model
+   - in z-coordinates, it is the bottom pressure anomaly
+   - in p-coordinates, it is the sea surface elevation
+   - in both cases, these variable have global drift, reflecting the mass
+     drift in z-coordinates and the volume drift in p-coordinates
+   - included time averaging for phiHydLow, be aware of the drift!
+ o depth-dependent computation of Bo_surf for pressure coordinates
+   in the ocean (buoyancyRelation='OCEANICP')
+   - requires a new routine (FIND_RHO_SCALAR) to compute density with only
+     Theta, Salinity, and Pressure in the parameter list. This routine is
+     presently contained in find_rho.F. This routine does not give the
+     correct density for 'POLY3', which would be a z-dependent reference
+     density.
+ o cleaned up find_rho
+   - removed obsolete 'eqn' from the parameter list.
+ o added two new verification experiments: gop and goz
+   (4x4 degree global ocean, 15 layers in pressure and height coordinates)
+ checkpoint46g_pre (2002/09/16)
+ checkpoint46f_post (2002/09/16)
+ o Enable tangent linear (forward mode) gradient checks:
+   - extended active file handling to g_... files
+   - added TANGENT_SIMULATION to theSimulationMode
+   - extended grdchk package accordingly
+ o added tangent linear setup in verification/carbon/code_ftl
+ o added adjoint setup in verification/front_relax/code_ad
+ checkpoint46e_post (2002/09/05)
+ o Added new equation of state -> MDJWF
+   - EOS of McDougall et al., 2002, JAOT, submitted
+   - caveat: the equation of state is only valid for a smaller (more
+     realistic?) range of values than JMD95P/Z and UNESCO
+   - added masks to the calculation of pressure in store_pressure
+   - added more check values for density in check_eos (ini_eos.F), some of
+     the old check values are out of the range of the MDJWF-eos, so don't
+     expect perfect matches for those
+ checkpoint46e_pre (2002/08/19)
+ checkpoint46d_post (2002/08/19)
+ o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and
+   'OCEANICP', also initialised field pressure correctly in ini_eos in the
+   case of pressure coordinates. eosType='JMD95Z' in
+   combination with buoyancyRelation='OCEANICP' now causes an error.
+ o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)
+   in find_alpha/beta.
+ checkpoint46d_pre (2002/08/15)
+ o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)
+   so that JMD95Z and JMD95P give approptiate static stability in find_rho.
+ checkpoint46c_post (2002/08/15)
+ o Changes necessary for ocean in p-coordinates
+  -  Added new buoyancy relation = 'OCEANICP'
+  -  Added new parameters = gravitySign (this used to be contained inside
+     the factor dRdZ which I added when we first switched to R coordinates).
+  X GM/Redi is not compatible (yet)
+  X bottom drag and no-slip need to be debugged.
+ checkpoint46c_pre (2002/08/07)
+ checkpoint46b_post (2002/08/07)
+ o Added new equation of state -> JMD95Z and JMD95P
+   - EOS of Jackett and McDougall, 1995, JAOT
+   - moved all EOS parameters into EOS.h
+   - new routines ini_eos.F, store_pressure.F
+ o Added UNESCO EOS, but not recommended because it requires
+   in-situ temperature (see JMD95)
+ o Modified formatting for knudsen2.f in utils/knudsen2 and added
+   unesco.f to be used with POLY3
+ checkpoint46b_pre (2002/07/31)
+ checkpoint46a_post (2002/07/31)
+ o Added (atmospheric) pressure loading
+   - new field in FFIELDS.h, etc...
+   - new cpp flag ATMOSPHERIC_LOADING
+ o Changed hFacC to _hFacC in calc_phi_hyd.F
+ o Added SHORTWAVE_HEATING to some files for consistency
+ checkpoint46a_pre (2002/07/13)
+ checkpoint46 (2002/07/13)
+ further merges from release1_p5
  o new ctrl package
    - adopted from ECCO environment to enable optimization
    - added Eliassen Palm fluxes to controls
-   - adjusted global_ocean.90x40x15/ and carbon/ accordingly
+ o added Eliassen Palm flux controls to gradient check package
+ o cost package
+   - Compatible with new ctrl package
+   - added Eliassen Palm cost hooks
+   - modif's of existing cost functions
+ o Adjoint-related bug fixes in kpp:
+   - kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix
+   - kpp_routines: store of Rib avoids partial recomputation bug of TAF.
+ o autodiff package
+   - flow directives:
+     + new for S/R do_the_model_io
+     + enhanced for S/R checkpoint
+     + new gmredi.flow
+   - Introduced CPP option ALLOW_AUTODIFF_MONITOR to
+     disable adcommon.h/g_common.h by default.
+   - fixed problem for adjoint of global_max
+ o modified verification/carbon/
+ o New setup for adjoint of global_ocean
+ o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F)
+ o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)
+ o incorporated hooks for sponge layer code (external_forcing.F)
+ checkpoint45d_post (2002/07/12)
+ o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)
+ o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S
+   (affects plume_on_slope "cg2d" output)
+ o add new parameter deltaTfreesurf for free-surface time stepping
+ o exchange gT,gS when using staggerTimeStep & GM & Oly<4
+ o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B
+ o change phiMin in exp1 (to agree with documentation)
+ o add new flags:
+  - T,S forcing inside/outside Adams-Bashforth
+  - turn off temp,salt advection and/or forcing
+  - for each tracer, define internal flag for multiDimAdvection & A-B
+ o monitor: change definition of KE to check conservation of Energy
- release1_p4
+ checkpoint45c_post (2002/05/30)
  o Removed f90 comments ("!")
  o Modified initialisations to enable exf package for MITgcm
    (without invoking ECCO_PACKAGE).
-Line 167 
 o modifications to gradient check packag
+Line 4392 
 o modifications to gradient check packag
    - enable centered differences
    - modified format of standard output
- release1_p3
+ checkpoint45b_post (2002/05/30)
- o added tangent linear setup to verification/carbon/
+ o cleaned exchange calls in cg2d
- o added adjoint sensitivity setup to verification/global_ocean...
+ o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step
- o moved packages_init_variables before convective_adjustment
+ o included CPP option SINGLE_LAYER_MODE in thermodynamics
- o output of verif. which use GMRedi brought up-to-date with
+   to configure barotropic setup (Martin Losch)
-   MAIN trunk (those were re-created after changes in GMRedi)
+ o moved some initialisations within bi,bj loop in dynamics
- o included CPP option SINGLE_LAYER_MODE
+   (TAF flow dependency)
-   to configure barotropic setup (Martin Losch).
+ o in initialise_varia, moved call packages_init_variables
- o Removed auxiliary variable in impldiff
+   before convective_adjustment_init
-   (caused numerical differences with MAIN trunk routine).
+   (corresponding adjustment of TAF tape initialisation).
- o Introduced CPP option ALLOW_AUTODIFF_MONITOR to
+ o in calc_diffusivity/calc_viscosity extended domain to full overlap.
-   disable adcommon.h/g_common.h by default.
- o Cleaned exchange calls in cg2d.
+ checkpoint45a_post (2002/05/01)
+ o compute Rho over the whole domain (extend iMin,jMin indices)
- release1_p2
+ o specific exchange for X-slice domain (case Ny=1)
- o fixed array boundary problem for adjoint
+ o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code
-   (related to partial recomputation within subroutine
+ o solve_for_pressure : set cg2d_x to zero where OBCS are applied
-   related to dynamics -> calc_viscosity -> mom_...
- o fixed recomputation in thermodynamics
+ checkpoint44h_post = checkpoint45
- o prepare (but not complete) recomputation problem in impldiff
+ o Fix to restore differentiability:
- o fixed problem for adjoint of global_max
+   place at which packages_init_variables is called in
- o switched off sponge layer code in external_forcing
+   initialise_varia is crucial for reverse control flow.
+ o modifications in GMRedi to enable stable adjoint
- release1_p1
+   (corresponding modif's in thermodynamics, dynamics)
- o merged necessary patches:
+ o added missing hook for sponge layer code in external_forcing
-   - AD-related changes for GMRedi
+ o modified test cost functions
-   - fixes i KPP (delZ -> drF)
+ o storing in gad_advection (plus removal of write(0,*)!
-   - hook to OBCS songe layer code in external_forcing
+ o missing headers TR1.h added in convective_adjustment routines
-   - errorMessageUnit non-zero in eeboot.F
+ o errorMessageUnit set non-equal zero in eeboot
-   - modified test cost function and carbon verif.
+   (conflict on some platforms, e.g. IBM SP3)
+ o modified carbon verif.
- release1_chkpt44d_post = chkpt44d_post
+ checkpoint44h_pre (2002/03/14)
+ o vertical grid option: allow to put the Interface at the middle between
+cell-centers ; replace delZ in pkg/kpp by drF.
+ o GM Advective form: Tracers are advected using the residual transport (=
+   Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.
+ checkpoint44g_post (2002/03/05)
+ o fix surface correction term in multiDimAdvection (affects plume_on_slope
+   results) ; ifdef missing in thermodynamics.F
+ checkpoint44f_pre,checkpoint44f_post
+ o added PTRACERS package
+   This allows an arbitrary number of passive tracers to be integrated
+   forward simultaneously with the dynamicaly model.
+   + Implemented so far:
+     - basic forward algorithm (time-stepping, advection, diffusion, convection)
+     - I/O and checkpointing
+     - GM/Redi  *but*  using the GM/Redi coefficient of Salt
+   + Not implemented so far:
+     - KPP
+     - OBCS
+   + No specific example supplied (yet) but global_ocean.90x40x15 has the
+     necessary data.ptracer file. Simply use -enable=ptracers and uncomment
+     line in data.pkg.
+   + This package is disabled by default since it increases storage.
+ o testscript: added -cleanup option
+ o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter
+              b) enable to filter 2D fields.
+ checkpoint44e_pre,post
+ o re-wrote convective adjustment to use pre-calculated weights
+   Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F
+   Adds:    model/src/convective_weights.F, convectively_mixtracer.F
+   Original calls to convect() still in place.
  chkpt44d_pre,post
  o added missing EXCLUDE_MONITOR flags
-Line 209 
 o in genmake added variable MAKEDEPEND
+Line 4470 
 o in genmake added variable MAKEDEPEND
    plus resetting for case SunOS
  o added timer_stats.c routine for IBM SP3
  o removed variables in dynamics
+ !!! I forgot to create tag chkpt44d_pre !!!
+ !!! But chkpt44d_pre = chkpt44c_post    !!!
  o real fresh water flux implemented with non-linear free-surface.
-Line 232 
 o merge of relevant stuff from the ecco-
+Line 4495 
 o merge of relevant stuff from the ecco-
  o check parameters & config (chkpt44a_pre,post)
  o OBC and NonLin_FrSurf.
- checkpoint44
+ checkpoint44 (2002/01/18)
  o fix bug in mom_vi_del2uv
  o select when filters are applied ; add options to zonal_filter (data.zonfilt)
  o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
-Line 240 
 o update AIM experiments (NCEP input fil
+Line 4503 
 o update AIM experiments (NCEP input fil
  o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
  o added some stuff for AD
- checkpoint43
+ checkpoint43 (2001/09/28)
  o added two new advection tests
  o added global 4x4 degree ocean test
  o added test of H&S94 with free surface on cube
  o some final mods for gradient check, adjoint,...
- checkpoint42
+ checkpoint42 (2001/09/27)
    Fixed AD-related problems:
  o Store directives up-to-date with re-arranged Adams-Bashforth
    (mainly thermodynamics.F)
-Line 258 
 o Modified store directives for split of
+Line 4521 
 o Modified store directives for split of
    for the case ALLOW_KPP
  o Cleaned argument list for timestep_tracer.F
- checkpoint41
+ checkpoint41 (2001/09/27)
  o re-formatted/added comments in prologues of key subroutines
    to work with protex
- checkpoint40
+ checkpoint40 (2001/09/27)
  o moved calc_gs, calc_gt and calc_tr1 back to model/src
  o added FLT (floats) package from Arne along with demo. experiment
  o re-arranged Adams-Bashforth scheme for tracers to allow easier
-Line 271 
 o more mods for non-linear free-surface
+Line 4534 
 o more mods for non-linear free-surface
  o modified multi-dim method to work on cube
  o bug fix in KPP (from DM)
- checkpoint40pre9
+ checkpoint40pre9 (2001/09/27)
  o added DST advection schemes
  o fix MPI bug on SGI's
  o modifications for non-linear free-surface
-Line 281 
 o changes to commenting of arguments for
+Line 4544 
 o changes to commenting of arguments for
  o added/updated many matlab scripts
  o added multi-dimensional advection method for tracers
- checkpoint40pre8
+ checkpoint40pre8 (2001/09/05)
  o new package rw/
    Added method for dumping intermediate local arrays:
    mdsio_writetile - same as mdsio_writefield except works from inside
-Line 300 
 o TAMC-related update to cope with mom_f
+Line 4563 
 o TAMC-related update to cope with mom_f
    currently nothing implemented to switch this storing off
    in case fluxform is used since no CPP flag available).
- checkpoint40pre7
+ checkpoint40pre7 (2001/08/14)
  o bug fix in dynamics.F
    calc_viscosity called before k=1,Nr loop.
  o added some #ifdef's ALLOW_PASSIVE_TRACER
  o cleaned initialisations in ctrl_map_ini
    related to TAF
- checkpoint40pre6
+ checkpoint40pre6 (2001/08/13)
  o split dynamics into thermodynamics & dynamics
  o corresponding split of calc_diffusivity into
    calc_diffusivity, calc_viscosity
-Line 315 
 o corresponding split of calc_diffusivit
+Line 4578 
 o corresponding split of calc_diffusivit
  o Added diffkr, kapgm to control variables
  o bug fix in gmredi_slope_limit for ldd97
- checkpoint40pre5
+ checkpoint40pre5 (2001/07/31)
  o proper initialization of Adams-Bashforth time stepping
    + uses forward step for very first step of model (iter=0)
  o re-generated *all* output since almost all output is modified by this
-Line 329 
 o added new expt "solid-body.cs-32x32x1"
+Line 4592 
 o added new expt "solid-body.cs-32x32x1"
    + this uses an alternative form of ini_curvilinear_grid.F which
      is not necessarily any better than the current one...
- checkpoint40pre4
+ checkpoint40pre4 (2001/07/30)
  o added re-initialisations of utrans,vtrans,rtrans in
    calc_common_factors which are crucial for TAF.
  o extended iMin,jMin range for calc_common_factors,
-Line 337 
 o extended iMin,jMin range for calc_comm
+Line 4600 
 o extended iMin,jMin range for calc_comm
  o added option ALLOW_PASSIVE_TRACER
  o a few minor updates and fixes
- checkpoint40pre3
+ checkpoint40pre3 (2001/07/13)
  o created calc_gtr1.F for gad package
  o split the_main_loop and re-introduced forward_step
  o some recomputations of nIter0 for TAMC
- checkpoint40pre2
+ checkpoint40pre2 (2001/07/13)
  o Updated to latest branch of AJA, JMC
  o Added gradient check package
  o Added routines for passive tracer handling
  o Added carbon sequestration sensitivity experiment
- checkpoint39
+ checkpoint39 (2001/05/14)
   o Modifications and fixes to support TAMC
     (mainly missing or wrong directives)
   o Corrected common blocks when fooling TAMC to produce adjoint I/O
-Line 362 
 checkpoint39
+Line 4625 
 checkpoint39
           (NB: this is not the full ECCO environment)
   o disabled some packages by default in genmake
- checkpoint38
+ checkpoint38 (2001/04/10)
   o see notes_c37_adj.txt
   o corrected wrong layer index in external_forcing_t
   o replaced the_main_loop/forward_step by the_main_loop
-Line 370 
 checkpoint38
+Line 4633 
 checkpoint38
     (replaced criteria for initial/final state)
   o added runtime flag for pre-C35 pickups: usePickupBeforeC35
- checkpoint37
+ checkpoint37 (2001/03/13)
   o mdsio.F routine split and packaged in pkg/mdsio
     (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
      used unless genmake -disable=mdsio)
-Line 387 
 checkpoint37
+Line 4650 
 checkpoint37
   o Non-Hydrostatic pickup file Pb fixed.
   o bug with Rigid-lid version (since c35) fixed.
- checkpoint36
+ checkpoint36 (2001/02/20)
   o implement Crank-Nickelson barotropic time-stepping
   o recover Time-Average diagnostics
   o fix Pb in checkpoint (PR#19)
   o AIM become a standard package ; clean unused CPP_kees
- checkpoint35
+ checkpoint35 (2001/02/08)
   o subtantial rewrite of dynamics.f
   o allows staggered time-stepping
   o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
   o added bottom drag (linear + quadratic)
- checkpoint34
+ checkpoint34 (2001/01/30)
   o Modified exchange routines for correct reverse simulation.
   o Added verification output to comply with bug fix in impldiff.F
     as of c33 (exp2, natl_box).
-Line 410 
 checkpoint34
+Line 4673 
 checkpoint34
   o Added routine GLOBAL_SUM_INT to global_sum.F
   o Added mdsio_gl.F for ECCO purposes.
- checkpoint33
+ checkpoint33 (2000/11/30)
   o Fixed bug in lower BC in impldiff.F
   o Fixed confusion about units of forcing arrays in FFIELDS.h
     namely Fu,Fv,Qnet,Qsw,EmPmR:
-Line 428 
 checkpoint33
+Line 4691 
 checkpoint33
       possibly use them.
   o Corrected genmake to delete a temporary file during configuration
- checkpoint32
+ checkpoint32 (2000/11/13)
   o Scaling of forcing fields moved from external_forcing.F to
     external_fields_scale.F, called directly after loading fields.
   o Surface relaxation terms added to surface tendency fields in
-Line 439 
 checkpoint32
+Line 4702 
 checkpoint32
   o Modifications and bug fixes in KPP package.
   o Verification experiment for KPP added (verification/nat_box/)
- checkpoint31
+ checkpoint31 (2000/09/11)
   o Packages interface brought in line with defined standard
     -> new routines packages_...F
     -> changes in initialise_fixed.F, initialise_varia.F
-Line 456 
 checkpoint31
+Line 4719 
 checkpoint31
     - not yet tested for GMRedi.
     - not yet tested for KPP.
- checkpoint30
+ checkpoint30 (2000/07/13)
   o Updates for OBCs
   o New experiment for test OBCs (internal_wave)
   o New output.txt in verification/exp4/results/
-Line 465 
 checkpoint30
+Line 4728 
 checkpoint30
   o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)
     and entry for T90 in genmake
- checkpoint29
+ checkpoint29 (2000/06/21)
   o packaged KPP and GM/Redi
- checkpoint28
+ checkpoint28 (2000/06/09)
   o Corrected initialization of hFacMin for difference vertical coordinates
   o Modified calculation of partial cell thickness to more robust algorithm
   o config_summary.F: replaced write_1D_... by write_0D_...
-Line 481 
 checkpoint28
+Line 4744 
 checkpoint28
     included store directives and tape key computations required for TAMC.
   o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
- checkpoint27
+ checkpoint27 (2000/04/10)
   o fixed calc_isoslopes() to so that cancellation of terms in tensor
     formulation works properly with variable resolution.
   o restructured the calling tree between the_model_main() and dynamics()
-Line 489 
 checkpoint27
+Line 4752 
 checkpoint27
   o introduced initialization file pSurfInitFile for free surface (cg2d_x)
     in new routine ini_psurf()
- checkpoint26
+ checkpoint26 (2000/04/05)
   o moved some #ifdef in optional routines to encompass everything
     except the argument declarations. This was using up some memory.
   o fixed macros like _ADT to work with both versions of Linux cpp
-Line 499 
 checkpoint26
+Line 4762 
 checkpoint26
     (macros are now in eesupp/inc/CPP_EEMACROS.h)
   o patch for 2 processor JAM mode
- checkpoint25
+ checkpoint25 (2000/03/15)
   o updates for OBCs and NH
   o dramatically reduced memory usage
   o added "JAM" routines for use on Artic network
-Line 510 
 checkpoint25
+Line 4773 
 checkpoint25
      an explicit free-surface option)
   o initial state input files for U and V
- checkpoint24
+ checkpoint24 (1999/08/02)
   o Removed some spurious "REAL"s
   o Updated KPP to latest version from JPL
   o Added a COS(latitude) in horizontal viscosity
- checkpoint23
+ checkpoint23 (1999/05/26)
   o Added del^4 diffusion for salt and temperature
   o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
- checkpoint22
+ checkpoint22 (1999/05/18)
   o Made many small changes: implicit none, format(i5), etc...
   o Introduced KPP mixing scheme (compiles and runs but *not* tested)
- checkpoint21
+ checkpoint21 (1999/05/18)
   o Introduced new I/O package that supports direct-access records (mdsio.F)
   o Split-up mid-level I/O routines
   o Updated input data for experiments 0,1,2,4 and 5
   o Finally removed the genmake.* scripts (everyone seems happy with genmake)
- checkpoint20
+ checkpoint20 (1999/03/22)
   o Tidied up open-boundaries some more
   o Added non-hydrostatic code
   o Fixed some input data
   o Modified MPI start-up to work in "coupled" context.
- checkpoint19
+ checkpoint19 (1998/12/15)
   o Tidied up directory structure for verification experiments.
   o Added new code for open boundaries.
   o Corrected advective terms near boundaries.
-Line 543 
 checkpoint19
+Line 4806 
 checkpoint19
   o Implemented free-slip/no-slip BCs and del^4 dissipation.
   o Split default parameters out of ini_parms.F into set_defaults.F.
- checkpoint18
+ checkpoint18 (1998/11/30)
   o Further changes for optional code generation with
     CPP - ugh!
- checkpoint17
+ checkpoint17 (1998/11/03)
   o Beginning to incorporating modularity
     for supporting atmos. and ocean configs.
   o Small changes for TAMC complinace
   o New ultra simple test case. Barotropic box
     configuration "exp0".
- checkpoint16
+ checkpoint16 (1998/10/28)
   o Minor changes to exchange routines to support
     accumulation in reverse mode. Adjoint of an
     assignment is an addition.
-Line 562 
 checkpoint16
+Line 4825 
 checkpoint16
     syntax) and by g77 under Linux ( 72 character
     limit ).
- checkpoint15
+ checkpoint15 (1998/09/29)
   Rewrote exchange routines to allow
   o General tile <-> tile connectivity.
   o TAMC reverse mode flag ( is this really needed? )
-Line 571 
 checkpoint15
+Line 4834 
 checkpoint15
     shmput/shmget, VIA, SYSV shmem and every other cool
     communication method.
- checkpoint14
+ checkpoint14 (1998/09/09)
   Consistent isomorphism chages made. These allow dynamical core
   to support both pressure and meters as a vertical coordinate.
- checkpoint13
+ checkpoint13 (1998/07/17)
   Release which corrects global_max problem and a couple
   of KGM time-averaging diagnostic errors. Also contains
   a double-gyre experiment setup as well as the baseline
-Line 590 
 branch-point-rdot
+Line 4853 
 branch-point-rdot
   I don't want to commit the rDot to the main-trunk until
   we've actually tested it...
- checkpoint12
+ checkpoint12 (1998/07/08)
   Tidy up and added generic genmake script (formerly
   configure script).
   Released to testers.
- checkpoint11
+ checkpoint11 (1998/07/02)
   Re-arranged initialise() and introduced ini_vertical_grid()
   and ini_masks_etc().
- checkpoint10
+ checkpoint10 (1998/07/01)
   Introduced the configure script.
   Separated out the diags package.
   Added template for writing time-averages of tile/intermediate quantities.
   Updated SIZE.h in exp2 and made the data big-endian.
- checkpoint9
+ checkpoint9 (1998/06/22)
   MPI fix. Filename changes (meta/data). salbin*y stuff.
   General tidy-up.
   SST.bin SSS.bin added to verification/exp2
- checkpoint8
+ checkpoint8 (1998/06/22)
   Inludes time-dependant forcing and time-averaging.
   Works at 4x4 and 2.8125x2.8125 global
-Line 620 
 checkpoint7-4degree-ref
+Line 4883 
 checkpoint7-4degree-ref
   model etc..
   Configured for verification/exp2 - 4 degree global, two process.
- checkpoint7
+ checkpoint7 (1998/06/15)
   Created by cnh
   Simple 4 degree global simulation
   configuration.
-Line 628 
 checkpoint7
+Line 4891 
 checkpoint7
   hydrography, bathymetry etc
   Does not include Heat Flux and E-P
- checkpoint6
+ checkpoint6 (1998/06/08)
   Created by cnh
   merged checkpoint5 with CD and
   spherical polar code.
   Still some problems with GM Redi
   abd full topography.
- checkpoint5
+ checkpoint5 (1998/06/08)
   Created by AJA
   contains updates to GM Redi
   and reordered timestepping loop
   for Implicit Diffusion.
- checkpoint4
+ checkpoint4 (1998/05/30)
   Created by cnh
   Contains memory saving macros ( _rdxc etc..) for when
   grid variations are limited.
   Contains polynomial coeffs for EOS and knudsen program
   for generation.
- checkpoint3
+ checkpoint3 (1998/05/26)
   Created by cnh
   Added extra flags for runtime options
   Added this file

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