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-revision 1.840 by dimitri,
Wed Jun 20 14:08:22 2007 UTC
+revision 1.1011 by jmc,
Tue Jul 29 21:17:45 2008 UTC
 Line 4 
 $Name$
      Notes on tags used in MITgcmUV
      ==============================
+ 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 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),
-Line 28 
 o pkg/profiles:
+Line 561 
 o pkg/profiles:
       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
-Line 162 
 o in FFIELDS.h:
+Line 694 
 o in FFIELDS.h:
       ATMOSPHERIC_LOADING is #define).
  o pkg/kpp: replaced _KPP_RL with _RL
  o bug fixes for vertical diffusivity computations when both KPP and
-D diffusivity arrays are used.
+D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
+     are no longer updating the vertical diffusivity array
+     (passed as argument) but are (re-) setting those arrays.
  o pkg/seaice: fix bug in evp solver, while doing that
    - change (improve?) discretization of stress computations for both
      cgrid-lsr and evp solver

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