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-revision 1.390 by jmc,
Sun Nov 21 22:22:31 2004 UTC
+revision 1.1043 by jmc,
Fri Nov 21 16:47:29 2008 UTC
 Line 1
  $Header$
+ $Name$
      Notes on tags used in MITgcmUV
      ==============================
+ checkpoint61f
+ o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ;
+   update results of global_ocean.cs32x15.icedyn test.
+ o move getcon.F from model/src to pkg/fizhi.
+ o pkg/exf: add parameter for extrapolation of temp up to the surface
+    and option to prevent negative evap (in bulk_largeyeager04 only).
+ o Prather Advection scheme: fix tracer conservation for divergent flow
+   (e.g., when using NonLin Free-Surface).
+ o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead
+ o gmredi (Visbeck-variable-K):
+  - add more parameters to Visbeck-variable-K.
+  - use a 5 points average for dSigmaR in Visbeck-K calculation
+    (more "homogenous": same stencil and same weights as in dSigmaH)
+  - update output of ideal_2D_oce experiment.
+ o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4
+   (#undef REAL4_IS_SLOW)
+  - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4
+    coordinate variable
+  - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables
+    (surface forcing fields), removes some of the functionality
+  - model/src/write_grid.F: write _RS variables as RS-netcdf variables
+  - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but
+    probably not all: copy _RS surface flux fields to RL field before
+    calling DIAGNOSTICS_FILL
+  - model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into
+    real*4 (CALL EXCH_*_RS) versions.
+  - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1
+    (generate new output).
+ checkpoint61e
+ o gmredi (Visbeck-variable-K):
+   - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
+   - change computation of Visbeck-K where Slope > Smax :
+     now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct)
+     previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output.
+ o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
+   to be the same as with Z-coord. (i.e., m/s & no-units respectively).
+ o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
+ o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
+   does not become too large (to avoid precision problems in implicit-diffusion
+   solver); update ideal_2D_oce output.
+ o pkg ggl90:
+   - in ggl90_cal.F: compute only one set of visc/diff, used to
+     step forward TKE/T/S/momentum
+   - default value of GGL90viscMax/GGL90diffMax larger and equal (to
+     have Prandlt =1)
+ o gmredi (fm07):
+   - add lower limit on Transition layer thickness + lower limit on 1/lambda
+   - allow to set few more params from data.gmredi
+ o pkg ggl90:
+       - add missing sqrt(2) factor in computation of mixing length
+         scale in ggl90_calc.F
+         (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
+ checkpoint61d
+ o adjoint modifs
+   - adapt to new field rhoInSitu
+   - allow to revert from StoreDynVars2D, StoreDynVars3D
+     to individual fields
+     (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
+ o store 3-D (in-situ) density in commom block (DYNVARS.h)
+  - save 1 rho computation.
+  - no longer modify T & S inland when using down_slope pkg.
+ o gad_som : allow to switch to SOM advection for T & S without corresponding
+   pickup files (using new S/R: MDS_CHECK4FILE).
+ o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
+   (for useSingleCpuIO to work in multi-threaded)
+ o pkg/shelfice:
+  - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
+    with SHELFICEtopoFile in data.shelfice
+  - move code for reading ice shelf topography and modifying hFacC into separate
+    subroutines of the shelfice package
+  - separate initialisation of "fixed" and "variable" variables
+  - kTopC is not (yet) replaced by kSurfC, although this is possible
+ o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
+ o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
+   and rename:
+   ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
+   ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
+ o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
+ checkpoint61c
+ o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
+   to add mass source/sink of fluid in the interior (3-D generalisation
+   of oceanic real-fresh water flux).
+ o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
+ o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
+ o new pkg: down_slope
+   density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
+   - presently, modify T & S inland (dwnslp_calc_rho.F).
+     can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
+   - implementation for ocean in P-coords not tested.
+   - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
+ o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
+   (to facilitate conversion of oceanic pkg to p-coordinate).
+ o change FIND_RHO to FIND_RHO_2D :
+   pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
+ o new pkg: cheapaml
+ checkpoint61b
+ o exch2:
+   change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
+   - no longer depend on the order sequence (N,S,E,W).
+   - 3rd exchange no longer needed (tested with 24 tiles).
+   - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
+   - exch_UV_A-grid readily available (but not yet tested).
+   comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
+   (both are no longer needed) in exch_uv: no effect in forward run; but
+    get truncation error differences with adjoint exch.
+ o exch2:
+  - change index-bounds storage (moved from target to local tile,
+    more intuitive this way) ; rename/remove some variables.
+  - change utils/exch2/matlab-topology-generator & code_mods accordingly.
+ checkpoint61a
+ o exch2/matlab-topology-generator:
+   fix bug in index bounds for N-S internal exchange (hard to tell if this
+   had any effect on the solution).
+ o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
+   is exceeded
+ o testreport: modify syntax of awk, so that it works also with
+   awk, and not only with nawk and gawk
+ checkpoint61
+ o autodiff
+   Change default for TAF usage by removing argument '-nonew_arg'
+   This changes TAF subroutine argument list (ordering of active var.)
+   Omission of this flag leads to incompatibility w.r.t. TAMC
+   To restore TAMC-compatibility, need following modifs:
+   * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
+   * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
+   Tested TAF version is 1.9.22
+   N.B.: exch2 hand-written adjoint code currently not TAMC compatible
+ checkpoint60
+ --->>> This is the last checkpoint for which generating the adjoint
+ --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
+ --->>> by default.
+ --->>> Future checkpoints will ommit this flag by default.
+ o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
+ o pkg/grdchk: Add gradient check to etan0 perturbations.
+ o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
+ o pkg/autodiff: more flexibility in zeroadj.
+   model/src: modifying do_oceanic_phys.F accordingly.
+ o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
+ o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
+   special setup of gmredi for which the adjoint is stable
+   enough for parameter optimization.
+ o bridging the gap between eddy stress and GM.
+   -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
+       along with a change in CPP option (now ALLOW_EDDYPSI).
+   -> when using GM w/ GM_AdvForm:
+       The total eddy streamfunction (Psi = eddyPsi + K x Slope)
+       is applied either in the tracer Eq. or in momentum Eq.
+       depending on data.gmredi (intro. GM_InMomAsStress).
+   -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
+   The key modifications are in model/src/taueddy_external_forcing.F
+   pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
+ checkpoint59r
+ o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
+   from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
+   fix option to read coriolis(@ cell-corner) from files with CS-grid.
+ o pkg/mnc: add some attributes to standard 1D-coordinate variables
+ o pkg/diagnostics: enforce missing_value attribute for scalar variables at
+   mass points, when using mnc for output
+   - add runtime parameter (missing_value, missing_value_int) to override
+     default (which is the value of getcon('UNDEF'))
+ o pkg/mnc: prepare mnc for the actual use of missing values with the
+   diagnostics package: small fix in mnc_cw_readwrite.template and more
+   initialisation of never used fields
+   - replace mnc_common.h and mnc_id_header.h with corresponding upper case
+   versions
+ o pkg/thsice/thsice_ini_vars.F added default initial values so that
+   thermodynamics sea ice solver does not blow up when some initial fields
+   are missing.
+ o move from external_forcing_surf.F to ini_forcing.F
+   the p-coord. hack consisting in using pLoad to set phi0surf ;
+   update output of tutorial_global_oce_in_p (affected @ truncation level).
+ o Freshen up a bit hs94.1x64x5, notably:
+   remove rotationPeriod and tRef=5*0. (adjoint only), and add
+   exactConserv=.TRUE.
+ o pkg/generic_advdiff:
+   change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
+   applies to files where Temperature & Salinity 2nd Order moments are used.
+ o pkg/ptracers: add second-order moment advection schemes (80 and 81);
+   this uses a dynamically allocated internal state data structure
+   (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
+   and requires a fortran 90 compiler
+ checkpoint59q
+ o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
+    (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
+ o Refresh tutorial_global_oce_biogeo, notably:
+   - change bathymetry (put back seamounts in ACC, use hFacs)
+   - change EOS (POLY3 --> JMD95Z)
+   - use Bryan-Lewis vertical diffusivity
+   - use multidimensional advection
+   - remove old virtual virtual in dic pkg, now done through ptracer pkg
+   - change a couple of parameters in dic pkg
+ o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
+ o pkg/obcs: change default to OBCSfixTopo = .true.,
+   - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
+   - replace "debugMode" with "debugLevel .GE. debLevB"
+ o implementation of TAF directives for gchem,cfc,dic
+ o remove "exp5" (replaced by tutorial_deep_convection).
+ o pkg/obcs: add code to fix topography gradients normal to open boundaries;
+   this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
+   the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
+   --> changes results in exp4, seaice_obcs
+ o tutorial_deep_convection :
+   update the set-up and increase resolution and domain size ; start
+   from pseudo initial conditions = output at t=120mn in order to see
+   something happening when running testreport.
+ o pkg/seaice: add os7mp as an advection scheme
+               add check for advection schemes
+               add a flag for restoring T and S underneath sea ice
+ o pkg/my82: add netcdf-support and diagnostics
+ o thsice pkg:
+   - Now hsMax limits snow height by turning it into ice following
+     flooding scheme (and now conserving energy)
+   - Slight rewriting of the formula in thsice_calc_thick.F
+   - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
+   --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
+ checkpoint59p
+ o gchem / dic / cfc :
+   - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
+   - add new parameter files: "data.dic" & "data.cfc" ;
+   - various re-arrangement in initialisation & header file ;
+   - fix tutorial_global_oce_biogeo for multi-threaded test.
+ o pkg/dic: test for "pickup_dic" file when restarting ;
+   if no pickup-file, can restart with a re-initialised pH (same as it did
+   before) providing pickupStrictlyMatch is set to False.
+ o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
+   + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
+ o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
+   and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
+ o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
+  & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
+    (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
+ o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
+    scheme to use for vorticty-term ;
+  - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
+    (with default selectVortScheme, return to original discretisation)
+  - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
+ o pkg/seaice: add a line to the summary to indicate grid type (B/C)
+ o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
+   bottom ; only used with variable horizontal viscosity and non-hydrostatic.
+   also fix diagnostics VISCAHW & VISCA4W.
+ checkpoint59o
+ o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
+ o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
+   move a few statemens out the main loop into separate loops
+ o pkg/shelfice:
+   - sort out freshwater flux; convert freshwater fluxes to mass fluxes
+     (kg/m^2/s), does not break tests, because in verification/isomip,
+     rhoConstFresh=rhoConst (by accident)
+   - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
+   - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
+     new file model/src/seawater.F, so that they are available for all pkgs.
+   - convert potential temperature into in-situ temperature. This changes the
+     isomip tests => update tests
+ o add a flag writePickupAtEnd (default=true) to be able to suppress
+   writing a pickup at the last timestep
+ o tools/mpack-1.6 :
+   - disable automake (not working) and autoconf (not needed).
+   - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
+     also cleaner with much less compilation warnings.
+ o pkg/profiles:
+   rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
+   (for "less than 32 characters name" compiler requirement)
+ o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
+   conditions that have a different sampling frequency than S/T/U/V obcs
+ o pkg/diagnostics (stats-diags):
+   - fix global Min/Max in case 1 processor get only empty tiles
+ o genmake2: replace (4 times)
+      make genmake_tc_1.o >> genmake_warnings 2>&1
+   with
+      COMM="$CC $CFLAGS -c genmake_tc_1.c"
+      echo $COMM >> genmake_warnings
+      $COMM >> genmake_warnings 2>&1
+   to make genmake2 always see the value of CC as specified in the optfile.
+ o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
+   - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
+   - modify verification advect_cs test to test SOM-advection on CS-grid.
+ o pkg/ctrl:
+   - Rewrite of ctrl_map_ini_ecco.F,
+     introducing a generic routine (ctrl_map_ini_gen.F).
+   - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
+ checkpoint59n
+ o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
+   number in dedicate array "hdiag":
+   - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
+     with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
+   - many small changes (integer format) for large number of diagnostics
+   - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
+     a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
+ o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
+   usingSphericalGrid, this allows to define the rotated grid coordinates
+   via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
+   geographical coordinates according to the inverse of the rotation defined
+   by the Euler angles, so that Coriolis parameter and online-interpolation by
+   exf works with the geographical coordinates on XC/YC/XG/YG.
+   Naturally, this feature does not work with all packages, so some
+   combinations are prohibited in config_summary (flt, flt_zonal, ecco,
+   profiles), because there the coordinates are assumed to be regular
+   spherical grid coordinates.
+ o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
+   - introduce isopycnal diffusion coefficient control.
+ o tools/adjoint_options:
+   - additional control vector components.
+ o pkg/mnc: have mnc create marginally meaning full coordinate variables
+   (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
+ o pkg/mypackage:
+   - add example of read/write pickup for state-var ;
+   - add entry points to the main code for state-vars diags & write-pickup.
+ o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
+   transitions for useExfYearlyFields
+   - add new subroutine that determines the file to read from for
+     use*YearlyFields = .TRUE. and .FALSE.
+   - add a verification experiment to global_with_exf that tests
+     useExfYearlyFields with USE_EXF_INTERPOLATION defined
+ o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
+   analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
+   subroutines (which could be generated from a template, because they are
+   almost identical), for now they are included in obcs_prescribe_read.F for
+   simplicity
+ o pkg/exf:
+   - add a little more diagnostic to exf_interp_read (in analogy to
+     mds_read_field, can be turned off with debugLevel < debugLevA=1)
+   - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
+     ugly but fast by unrolling short inner loops, inserting a unroll=8
+     directive in routine lagran, and splitting a loop and making do while the
+     outermost loop (the latter requires the intoduction of index arrays)
+ o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
+ o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
+   http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
+ o verification/seaice_obcs: updated for restart test and latest options
+ o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
+   ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
+   for now this is only available for the C-grid code and also within
+   #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
+ checkpoint59m
+ o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
+   and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
+ o gad_som : fix flux output (& diagnostics) to have same units as other
+   advection scheme fluxes (was previously multiplied by deltaT).
+ o added verification/seaice_obcs both to test seaice open boundaries
+   and to provide an example matlab scrpt for generating them
+ o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
+ o pkg/salt_plume: clean up salt_plume_frac.F to
+   remove redundancy in PlumeMethod 1 and 4
+ o pkg/kpp: added saltplume diagnostics
+ o pkg/obcs and pkg/seaice:
+   - do not set uice and vice to zero when OB*icefile are unspecified
+   - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
+   - moved seaice tracer obcs after call to seaice_growth
+ o pkg/salt_plume: added various options for salt plume depth
+   criterion and for vertical distribution of the salt
+ checkpoint59l
+ o pkg/ptracers: new version of ptracers pickup:
+   read meta file and write only fields which are needed to restart.
+   ( same logic as main pickup file ; also using pickupStrictlyMatch )
+ o pkg/seaice:
+   - add timescale for melting due to warm mixed layer as a means of
+     setting SEAICE_availHeatFrac more conveniently
+   - add a CPP-flag/runtime parameter check for flooding algorithm
+   - reformulated availHeat in seaice_growth.F to be independent of AREA
+ o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
+   unit changes
+ o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
+ o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
+   SX vector computer.
+ o pkg/seaice:
+   - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
+     seaice forcing fields can now be read only through pkg/exf
+   - removed some unused halos
+ o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
+ o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
+   or U/VICE from U/VWIND before computing U/VSTRESS
+ checkpoint59k
+ o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
+   dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
+ o fix un-initialised variable problem (in mom_vecinv & shap_filt):
+   all experiments pass when compile with un-initialised var. checking option.
+ o added pkg/salt_plume
+ o script to test restart (for now, in MITgcm_contrib/jmc_script)
+ o pkg/seaice: new read/write pickup version.
+   read meta file and write only fields which are needed to restart.
+   ( same logic as main pickup file ; also using pickupStrictlyMatch )
+ o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
+ o lab_sea.hb87: modify the domain & update output.hb87.txt :
+   lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
+   at j=1 & j=Ny+1 : this case is not treated correctly in the restart
+   process. Fixed here by closing the domain at the Northern boundary.
+ o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
+ o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
+   a set of consecutive levels in/from a 3-D array.
+ o pkg/ptracers:
+   use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
+   to-do: fix pkg/diagnostics when large number of diagnostics are defined.
+ checkpoint59j
+ o in pkgs: dic, obcs, offline, rbcs:
+   standard way to compute coeff. for time interpolation between 2 time reccords
+   which retains full precision (& make results less dependent on compiler).
+   update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
+ o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
+   packages instead of reading ice cover and wind speed separately
+ o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
+  (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
+   to allow to compile customized code before the update)
+ o cleaning-up:
+   - fix CPP instruction syntax in pkg/obcs
+   - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
+     add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
+   - fix some threads issue in IO parts.
+ o pkg/dic:
+   - add tons of "_d 0" (--> much better testreports !)
+    and then update outputs of tutorial_global_oce_biogeo
+ o pkg/mom_fluxform:
+   add a special version of momentum advection intended to conserve momentum
+   next to a bathymetry step or a coastline edge. (default = off = #undef)
+ o new read/write pickup version:
+   - for now, only implemented for main (mdsio) pickup file.
+   - write out only what is needed to restart; merge pickup_nh , pickup_ph
+     and main pickup together.
+   - read meta file; read only what is needed to restart; stop if a field
+     is missing (if pickupStrictlyMatch=T, = the default) or try to restart
+     if it make sense (even if the restart is not perfect).
+   - if no meta file, assume that pickup to read corresponds exactly to
+     a pickup that would currently be written.
+   - read pickup written in the old format (until checkpoint59i) if it
+     recognizes an old meta file (no field-list).
+   - add a meta file in exp. which starts from a pickup: 2 cases:
+     a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
+      e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
+     b) a meta file describing the content of the associated pickup file
+      e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
+ o pkg/mdsio & pkg/rw:
+   - new routine to read a meta file ; new set of routine to read
+     Multiple-fields file (with meta file).
+ o added open boundary conditions capability for seaice
+     HSNOW, HSALT, UICE, and VICE
+ checkpoint59i
+ o adjoint:
+   * fix multiDimAdvection adjoint
+     (partial recomputation problem by TAF for fVerT(:,:,kDown)
+     and comlev1 size definition (maxpass vs. max. number of tracers)
+   * verification/global_ocean.90x45x15 adjoint now tests
+     NLFS and multiDimAdvection using DST3 (=30)
+   * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
+ o pkg/kpp: add "_d 0" to real constant (if missing);
+   update output of exp: natl_box (10.digits); vermix (std, 7.digits)
+   and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
+ o prepare for "clever pickup" implementation: add new header file "RESTART.h"
+   for internal parameters related to restart process (formerly from PARAMS.h)
+   and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
+ o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
+   as argument. (only atm2d & obcs write_pickup have not yet been updated)
+ o pkg/monitor:
+   - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
+   - fix mon_stats_rs (statistics over the full domain, even where field is zero)
+   - account for deep Atmosphere factor and density factor (anelastic)
+ o added open boundary conditions capability for seaice HEFF and AREA
+ o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
+   thermodynamics
+   - requires a little reorganization, which affects the testreport results
+     of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
+     so that now the conservative form is tested
+   - add a few comments
+ o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
+ o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
+ o add new diagnostics to seaice: advective, diffusive fluxes (only for
+   multidim-advection, for scheme 2 they are not filled) and transports,
+   thermodynamic growth rates
+ o change units of EmPmR (inside the code, + within coupling interface)
+   from m/s to kg/m2/s (mass flux) but leave input file unchanged.
+   Affects results @ truncation level (cg2d match) and update output of
+    experiments: lab_sea(6), global_ocean.90x40x15(10),
+   global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
+   + adjoint results: global_ocean_ebm(11) and lab_sea (12).
+   Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
+   Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
+ checkpoint59h
+ o pkg/exf:
+   - improve vectorization by moving if-statement out of loops in
+     exf_mapfields, exf_radiation
+   - exf_bulkformulae.F: introduce 2D fields and vectorize code
+ o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
+ o testreport:
+   - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
+     monitor & update offline_exf_seaice exp. output.
+   - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
+ o pkg/seaice:
+   - bug fix in the evp solver: boundary conditions were affected be
+     masking of zMax/zMin (changes results)
+   - minor bug fix in boundary conditions in seaice_calc_strainrates
+     (changes results for no_slip)
+   - seaice_lsr.F: make interpolation of eta dependent on boundaries
+   - replace hardcoded lower limit for zeta (zMin) by runtime parameter
+   - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
+     stress formulation and no-slip boundary conditions
+ o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
+   in gad_calc_rhs.F ; add few safety stops in initialisation phase.
+ o pkg/seaice: a first HSALT time stepping equation has been checked in
+ o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
+   in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
+   without requiring DO-IF statements
+ o pkg/thsice:
+   use continuous power-law function for partition of energy between lateral
+   melting/freezing and thinning/thickening ; old code using step function
+   still available with #undef THSICE_FRACEN_POWERLAW
+   update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
+ o testreport: change AD testing : check against results/output_adm.txt
+   using same scripts as for forward test.
+ checkpoint59g
+ o adjoint testing: in preparation for changing testreport:
+   - output format: cost and grad written on separated lines
+   - ad output results in directory "results" (instead of "results_ad")
+ o pkg/seaice: adding ice salinity HSALT as a prognostic variable
+ o pkg/seaice: changes for using pkg/seaice with pkg/obcs
+ o pkg/ecco: allow user defined cost function contributions
+ o testreport:
+   Allow to choose (per experiment) the list of tested output variables
+    and the main variable (used to issue a pass/FAIL ) ;
+   - for now, done by adding the specific list in file: [exp]/input/tr_checklist
+   - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
+   Also modify printing of summary:
+    a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
+    b) echo the list of tested variables in the individual summary.txt of
+       each experiment.
+ o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
+   threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
+   (but still depend on the tile decompostion of the domain).
+ o pkg/seaice: change a discretization detail to make the B-grid code
+   "more symmetric". This change is likely to remove all "ridges/leads" that
+   where quasi-aligned with the grid in B-grid solutions. It may also be
+   the solution to the stress coupling issues with the B-grid.
+ o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
+   remove .cvsignore from input dir. (since testreport no longer run here).
+ o pkg/thsice:
+  - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
+  - fix reshaping of sea-ice just after advection:
+    melt all the ice only if ice-volume is too small.
+  - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
+    prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
+  and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
+ o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
+   tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
+ o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
+   forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
+   (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
+   and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
+   of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
+   -> update output.txt
+ o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
+  this affects truncation error: -> update output.txt of exp:
+   global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
+   ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
+ checkpoint59f
+ o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
+ o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
+   a bounded range (in forward mode)
+ o pkg/ecco, ctrl, autodiff and mom_common:
+  internal parameter controls, completements of implementations
+ o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
+ o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
+   (not seem any difference in testing results).
+ o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
+    at face corners.
+ o pkg/generic_advdiff:
+  - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
+   loop range indices for computing vertical advection tendency
+   and do the calculation in the interior only (no overlap) ;
+   for now, only implemented for SOM advection (to save CPU time).
+  - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
+ o exch2 adjoint
+   First set of changes:
+   - add exch2 hand-written adjoint templates
+   - exch2 hand-written no longer use TAF-flag 'nownew_arg'
+     This will require cleanup in pkg/autodiff/*.F
+     (changed routines currently kept separate in verif. code/)
+   - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
+     that used to hide exch2 or cubed-sphere specific code
+     (commented via 'cph-exch2')
+ o pkg/seaice
+   - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
+ o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
+    output of global_ocean.cs32x15.thsice .
+ checkpoint59e
+ o exch2: new S/R that only use the cube-tracer (center-position) exchange:
+   for B-grid vector (not yet tested) and C-grid vector (<- only used
+   when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
+ o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
+   (#ifdef ALLOW_SALT_PLUME)
+ o gather_2d/scatter_2d: removed halo regions
+ o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
+   scheme and the corresponding test case (under front_relax dir). For now,
+   only available with Skew-flux form and not yet tested in realistic set-up.
+   adjoint: store directives updated, but gradient checks deteriorated,
+   so maybe GM/Redi adjoint is now broken.
+ o seaice adjoint
+   * add AREA, HEFF, HSNOW as control variable
+     (should not change lab_sea results)
+   * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
+ o pkg/seaice:
+   * added computation of saltFlux in seaice_growth;
+     For time being, sea ice salinity is assumed constant
+     contribution of snow flooding to freshening of sea ice is neglected.
+     SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
+     defaults to 0.0 in order to maintain backward compatibility.
+     Typical values for SEAICE_salinity are 4 to 10 g/kg.
+   * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
+   * added SEAICE_availHeatFrac, which specifies fraction of surface level
+     heat content used to melt or grow ice
+   * commented out cap of HICE: it helps keep ice thinner
+   * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
+   * applied OBCS T/S mask to HEFFM sea ice mask
+ checkpoint59d
+ o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
+  for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
+  (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
+ o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
+  and change default value of parameter "GM_Small_Number";
+  update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
+    global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,
+    tutorial_global_oce_biogeo, tutorial_global_oce_latlon
+ o pkg/ecco: cost function when applying pkg/smooth to controls
+ o pkg/ctrl: add forcingPrecond run time parameter
+ o pkg/seaice:
+  - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
+  - fix bug in metric terms of u-equation in LSR solver (implicit part),
+    changes verification/lab_sea
+  - rearrange implicit part of u-equation in LSR solver to make it easier to
+    read, understand, and debug. This causes changes at the truncation level.
+  - fix (serious) bug in the boundary conditions (sign error in the implicit
+    part) of the LSR solver. Changes all LSR results.
+  - fixed problem with HSNOW initialization to avoid thick snow when AREA
+    is initilized with small values - does not change lab_sea results.
+  - added HsnowFile initialization capability
+ o pkg/smooth: addition to model/src and pkg/ctrl so allow
+  initialization of pkg/smooth and application to control vector
+ o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
+ o dependencies: pkg/profiles requires pkg/cal
+ o pkg/profiles:
+  - added option ALLOW_PROFILES_GENERICGRID
+      -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
+      that interpolation information (grid points and coefficients) is provided
+      within the netcdf input files.
+      -> sample matlab scripts can be found in MITgcm_contrib/gael
+      that allow you to prepare netcdf input files.
+  - also modified: cleaner include statements, cleaner error print statements,
+    cleaner stops when error, and more tests of the netcdf input files consistency.
+ o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
+ o pkg/seaice:
+  - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
+    requires a new routine: seaice_diagnostics_fill.F
+  - make sure that seaice does not move if not forced (pressure replacement
+    method, Hibler and Ip, 1995), changes results
+  - and new damping criterion for EVP solver according to Hunke, JCP, 2001
+  - 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
+ 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
+ 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
+ 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
+ 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
+ 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
+ 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
+ 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
+ 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
+ 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
+ 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
+ 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
+ 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
+ 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
+ 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
+ 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
+ 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
+ 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
+ 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
+ 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
+ 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
+ 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
+ * 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
+ 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
+ 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
+ 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
+ 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
+ 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
+ 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
+ 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
+ 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
+ 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
+ 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
+ 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
+ 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
+ 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
+ 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
+ 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
+ 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
+ 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
+ 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
+ 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
+ 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
+ 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
+ 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
+  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
+ o lab_sea now uses diagnostics package and provides a suite of
+   new EXF diagnostics output.
+ checkpoint57j_post
+ 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
+ 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
+   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
+ 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
+ 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
+ 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
+ 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
+ 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
+ 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
+ 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
+ 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
+ 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
+ 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
+ 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
+ o this set of changes restores TAMC compatibility
+   tested for global_ocean.90x40x15 adjoint on trough
+   (what a pain)
+ checkpoint57a_pre
+ o some modifs in tools/build_options for sunos
+ o call ctrl_pack for ctrl at end for optimcycle=0
+ checkpoint57
+ 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
+ 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
+ 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
+ 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.
-Line 11 
 o GCHEM:
+Line 2060 
 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

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Removed from v.1.390
 


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-Removed from v.1.390
+Added in v.1.1043

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