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-revision 1.300 by heimbach,
Fri May 21 21:48:53 2004 UTC
+revision 1.685 by baylor,
Thu Jun 22 19:39:21 2006 UTC
 Line 1
  $Header$
+ $Name$
      Notes on tags used in MITgcmUV
      ==============================
+ 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.
+   - change the default GMREDI_OPTIONS.h: compile everything except Visbeck
+ o GCHEM:
+   - move call to GCHEM_FORCING_SEP, so that it is now called before
+     the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP
+   - introduced a useGCHEM runtime flag and applied it everywhere.
+   - renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING;
+     this flag is now only visible within GCHEM-pkg routines.
+   - moved gchem_forcing_int temporarily into ptracers_forcing, this will
+     be replaced by a 3D array that is computed before thermodynamics; for
+     this, the tracer ID iTracer had to be included into the parameter list
+     of ptracers_forcing
+   - set up forward_step to call gchem_forcing, that will replace
+     gchem_forcing_int in ptracers_forcing
+   - cleaning up
+ o small cleaning of exch2: remove files that are also in eesupp/src
+ checkpoint56
+ o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0
+ o mnc: cleanup "full" files--fixes out-of-memory problem
+ o ECCO-GODAE
+   * model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup
+   * fully merged and updated from SIO code
+     windstress sign change affects
+     - exf_inscal_[u/v]stress
+     - sign of xx_tau[u/v] adjustments
+     - signs in cost_scat
+   * ctrl_get_gen: avoid update of tau[u/v] for first few days
+   * natl_box_adjoint updated and compressed
+   * 2-level checkpoint switch added
+     (tested in EXP. 1 of natl_box_adjoint)
+   * new switch doInitXX to avoid init. of xx_... in optimcycle=0
+ o SVD
+   * first complete, non-hacked version for SVD calculations
+   * all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_...
+     performed via direct access files admtlm_vector.it????
+     (via ctrl_[un]pack)
+   * optimcycle is used for ARPACK iteration counter
+     (note: adxx_... is iterated, rather than xx_...; latter is constant!)
+   * EV problem ok w.r.t. L2-norm in tangent space; need to check other norms
+     and add linear transforms where necessary
+   * controls are initial/final SST, SSS (can be extended; need to check
+     ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F
+ o mdsio: filename info to both stderr, stdout
+ o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec]
+   from sign change
+ checkpoint55j_post
+ o isolate dissipation tendency (allow to keep it out off AB) in V.I form.
+   affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
+ o add consistent build directories and .cvsignore files to verification
+ o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity
+ o make all subroutines 30 or less characters in length for certain older
+   compilers to work (a thorough search only turns up two routines in
+   pkg/ptracers)
+ o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity;
+   affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
+ checkpoint55i_post
+ o change arrays for total vertical diffusivity (2.D if explicit,
+.D if implicit) ; each ptracer uses its own background value.
+ o added mnc/NetCDF output capability to ocn_compon_interf
+   - added bits to verification/cpl_aim+ocn so that it can run on
+     ITRDA and other clusters without the mpirun "-wd" option
+ o fixed wayward endif in mom_fluxform.F that messed up cyclindrical
+   configuration
+ o give MNC the ability to create additional files rather than
+   exceeding a specified file size limit "MNC_MAX_FILESIZE"
+   - the default is just less than 2GB which is a practical limit
+     on many systems
+ o Compute the non-local term using either KPP vertical diffusivity (=default)
+    or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T)
+ checkpoint55h_post
+ o add verification test "vermix"
+ o remove all the *_ioinc flags and replace with the single global
+   outputTypesInclusive flag
+ o allow to set a vertical profile of vertical diffusivity for T & S
+ o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS
+ o useMNC moved from data.mnc to data.pkg
+ checkpoint55g_post
+ o Renaming carbon AD experiments to comply with testreport conventions
+ o Updating adjoint of Held-Suarez hs94.1x64x5
+ o Fixing directives for non-ECCO forward_step, after ECCO directives
+   have been fixed to avoid recomp. of do_oceanic_phys
+   Works well for global_ocean.90x40x15,
+   but recomp. issue remains for carbon
+ o Updating adjoint output for natl_box_adjoint after
+   pkg/ecco has been modified (see taga c55d_post)
+ checkpoint55f_post
+ o rename to timeave_init_fixed
+ checkpoint55e_post
+ o some delicate re-shuffle of store directives to avoid one
+   extra call of do_oceanic_physics
+   affects ecco_the_main_loop.F, do_oceanic_physics.F
+   checkpoint_lev1_directives.h
+ o NB: this may break global_ocean adjoint temporarily,
+   but it is clear how to fix it. Will do later, need this now.
+ checkpoint55d_post
+ o ECCO specific cost function terms (up-to-date with 1x1 runs)
+ o ecco_cost_weights is modified to 1x1 runs
+ o modifs to allow observations to be read in as
+   single file or yearly files
+ o enable to read exf forcing fields as either
+   single file or yearly files (flag useExfYearlyFields)
+ checkpoint55d_pre
+ o switch between 2-level and 3-level checkpointing
+ o add ability of MNC to write local and "partial" (eg. 2D slices where
+   the full 3D field is never actually stored) arrays to NetCDF files
+   with the correct (that is, the complete multi-dimensional) set of
+   array indicies
+   - used in mom_vecinv() to write the diagFreq output
+   - tested (demonstrated) in verification/aim.5l_cs
+ o further mnc-ification
+   - add verification/lab_sea to the list with mnc setups
+   - fix undefined mnc v-names in cd_code
+   - add kpp to mnc output (both snapshot and timeave)
+ o non-hydrostatic code
+   - added horizontal viscosity parameter viscAhW for w, that replaces viscAh
+     in calc_gw.F
+   - defaults to viscAh
+   - this is useful, when I want to use viscAh=0 (e.g., only biharmonic
+     friction or Leith) in non-hydrostatic mode, as long as there is
+     no biharmonic friction and/or Leigth or equivalent for vertical velocity.
+ o pkg/cost
+   extend simple cost functions to treat time mean quantities
+   (T,U,V) via cost_accumulate_state from cost_tile
+ o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to
+     be 2 times larger than the minimum size the advection scheme requires.
+     now get a perfect conservation of salt in advect_cs test-exp (updated)
+ o GGL90 (Gaspar's TKE mixed layer)
+   - add horizontal diffusion of TKE, requires exchanges in
+     do_fields_blocking_exchanges, horizontal diffusivity is zero by
+     default. In OPA there is no horizontal diffusion of TKE but the
+     mixing coefficients are computed from a horizontal average of TKE of
+points or so. I think that diffusion has a little more physical
+     justification.
+   - clean up ggl90_calc in the hope of reducing memory usage (this hope
+     was in vain)
+   - mask tke-variable in ggl90_init
+ o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass)
+ o fix biharmonic diffusion on CS-grid.
+ o more obcs stuff
+   - added obcs_external_fields_load as an alternative to the EXF-pkg option
+     for reading boundary values. This routine is called from
+     obcs_prescribe_read
+   - updated obcs_check
+   - changed sponge layer relaxation parameter units for days to seconds
+   - turned off sponge layer by default
+   - changed argument list of OBCS_CALC to myTime+deltaTclock
+   - fixed about 35 bugs in obcs_external_fields_load
+ checkpoint55c_post
+ o obcs stuff
+   - new runtime flags useOBCSprescribe, useOBCSbalance
+   - re-arranged obcs_calc
+   - moved exf_getobcs to obcs_prescibe_read
+     obcs_prescibe_read is called after ORLANSKI stuff
+     and independent of it (executable can contain all).
+   - updated obcs_check
+   - added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE.
+     These may be necessary only if tangential velocities are
+     prescribed at OB, not sure, needs testing.
+ o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments
+   which simplifies the calls and passes the ifc check-bounds test
+ checkpoint55b_post
+ o add a 2D scalar, Z location, exchange_2 routine.
+ o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows
+   to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]
+   affects advect_cs results (for the wrong reason): update output.txt
+ o use a more standard discretization for biharmonic viscosity ;
+  (original version still available with #define MOM_VI_ORIGINAL_VISCA4 )
+   affects results of dome set-up: update output.txt
+ o fix gad_advection.F (CubedSphere part), back to version 1.23
+ o fix bug in mom_vi_del2uv.F (CubedSphere part).
+ checkpoint55a_post
+ o merged code to
+   * prescribe/read time-dependent open boundaries
+     (works in conjunction with exf, cal)
+   * sponge layer code for open boundaries
+   * each boundary N/S/E/W now has its own CPP option
+     (healthy for the adjoint)
+ checkpoint55
+ o up-to-date adjoint of previous breaks
+   - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix
+   - global_ocean_ebm: adjoint still needs fix (TLM ok)
+   - global_ocean.90x40x15: extended GMREDI_OPTIONS.h
+   - carbon: * remove tr1-related adjoint verification
+             * add ptracer as control variable
+ o remove all tr1-related code (ALLOW_PASSIVE_TRACER)
+   (adjoint stuff still has some tr1 'names', but all use ptracer arrays)
+ checkpoint54f_post
+ o in verification/carbin/ remove experiment related to
+   ALLOW_PASSIVE_TRACER (array tr1 etc)
+   code_ad/ input_ad/ results_ad
+ o add two new packages
+   - ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993)
+     + subject to optimization (memory)
+   - opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997)
+     + subject to reordering (many GOTOs in the original code)
+     + so far opps is called for every (i,j) point, and then operates in
+       the vertical; one may want to reorder the scheme in order operate in
+       horizontal slabs at the cost of (a lot of) memory, at least ten new 3D
+       fields)
+ o overhaul of IO so that we now have flags for MDSIO and/or MNC
+   - all verification tests compile and run with linux_ia32_g77
+   - defaults are compatible with current input files--nothing
+     should change if you were not previously using MNC
+   - MNC output has been added in numerous places (eg. timeave)
+     but there are still a few writes not yet do-able with MNC
+     (this is in progress)
+   - flags now allow for either/or/both use of MDSIO and MNC and
+     documentation will soon follow
+   - numerous small formatting cleanups for ProTeX
+ o add version info (via BUILD_INFO.h) to MNC and stdout
+ checkpoint54e_post
+ o add two new packages
+   - pp81 (Packanowski and Philander, 1981), Richardson number and
+     stratification dependent mixing
+   - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
+   - these scheme operate in a similar manner as KPP (without ghat, of
+     course), however there is only one diffusivity that is used for both
+     temperature and salinity (and passive tracers)�
+ o add offline package
+ o add "verification/dic_example" which contains a dic-gchem-ptracer setup
+   provided by Stephanie Dutkiewicz
+ o genmake2: add ability to search for C compilers and cleanup test output
+   - fixes recent SX-6 problems and should help with others (eg. HP-UX)
+ checkpoint54d_post
+ o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed
+ o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,
+   leading to additional shift by 5 days each year of integration
+    (i.e. leading to considerable offset over the years)
+ o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep
+ o start with no AB and no initial filtering (staggerTimeStep):
+   change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5
+ o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F
+   (external loading & cpl import/export stay in forward_step.F)
+ o update coupling interface to work with new staggerTimeStep
+ o change MDSIO ptracers_pickup.
+ o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F);
+ o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")
+ o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)
+ checkpoint54c_post
+ o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr
+   this affects (truncation error) output.txt of test-exp:
+    global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box
+ o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array)
+ o change Qnet to always be the net heat flux, (+upward).
+   affects (truncation error) output of natl_box exp.: updated
+ o define the max number of passive tracers in PTRACERS_SIZE.h
+ o start to test mnc routinely in exp0
+ o add sea-ice loading (sIceLoad) as a new forcing field.
+ checkpoint54b_post
+ o add testreport "-j JOBS" option for parallel builds (tested and pretty
+    impressive on Altix and Opteron systems)
+ o diagnostics can now write NetCDF files through the mnc package
+ o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output
+ o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added
+ o staggerTimeStep & NLFS: rescale T & S surface tendencies.
+   affects (truncation error) output of lab_sea & natl_box exp.: updated
+ o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
+ checkpoint54a_post
+ o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).
+ o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)
+ o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)
+ o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)
+   + internal_wave (shift in writing cg2d_ini_res)
+ checkpoint54a_pre
+ o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice
+   - modified verification/lab_sea and natl_box_adjoint accordingly
+ checkpoint54
+ checkpoint53g_post
+ o prepare splitting of thermodynamics: store convect.counter in common block
+ o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)
+   output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave
+ o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection
+ o new parameter "nShapS": allow to treat differently S from T (nShapT)
+ o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)
+ o restore adjointability
+ checkpoint53f_post
+ o modifications that affect AIM experiment results (update output.txt):
+   - no advection of S at top interface Nr (pkg/generic_advdiff)
+   - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)
+ o AIM pkg:
+   - include stability function into surf.Flux derivative relative to Tsurf
+   - calculate clear-sky radiation & surface temp. change (for diagnostics)
+ checkpoint53e_post
+ o merged cylindrical coord configuration
+ o added rotating_tank experiment
+ checkpoint53e_pre
+ checkpoint53d_post
+ o faulks upgraded: re-generate output.txt that have changed:
+    global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box
+ o Added Bryan and Lewis, 1979, vertical diffusivity profile
+ o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing.
+ o added Sadourny discretization of Coriolis
+   - moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h
+   - re-enabled use of omega3 (useAbsVorticity)
+ o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for
+   vector-invariant equations
+   - note: does *NOT* yet use same variable visc. for no-slip BC's.
+ o recoded the lateral boundary conditions for non-hydrostatic w, this time
+   hopefully without new bugs
+   - still to do: biharmonic friction for non-hydrostatic w
+ o bug fix for mom_*_sidedrag: rA -> rAs,rAw
+ o regenerated output for global_ocean_ebm (using -ieee)
+ o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation
+   of mom_common/
+   - simple re-arrangement of instructions within computing loop
+ checkpoint53d_pre
  checkpoint53c_post
  o new version of coupler for AIM+thSIce and Ocean models
   - new fields (SSS,h_MixLayer ...) are exchanged through the coupler

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