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-revision 1.602 by jmc,
Thu Jan 26 01:57:44 2006 UTC
+revision 1.736 by heimbach,
Sun Oct 22 01:26:36 2006 UTC
 Line 4 
 $Name$
      Notes on tags used in MITgcmUV
      ==============================
+ o Adding some pkg/diagnostics capability to pkg/seaice
+   (will certainly be subject to changes)
+ checkpoint58q_post
+ o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
+/6-deg Southern Ocean configuration by 8% on IBM Datastar and
+   high_res_cube configuration by 4% on Columbia.
+ o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
+   add (in global_with_exf/code) a version of EXF_INTERP_READ without
+   dynamical allocation (seems to work in multi-threaded).
+ o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
+   single CPU io) so that TAF does not have to see EESUPPORT.h
+ o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
+ checkpoint58p_post
+ o obcs: stop if obcs is used with useCDscheme = .true.
+ o shelfice:
+  - fix a sign error so that no slip at shelfice interface works
+  - remove stop for combination non-hydrostatic code and shelfice. That does
+    not mean, that the results are correct, but at least they are numerically
+    stable
+ o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
+ o added adjoint exch routined for all exch*3d* routines
+   and updated flow directives
+ checkpoint58o_post
+ o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
+   remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
+ o change controling S/R for writing pickup file (new S/R do_write_pickup)
+   and clean-up reading/writing of pickup files.
+ o fix local version of read/write pickup (NH part) in rotating_tank/code
+ o simplify EXCH interface:
+  - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
+  - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
+ o added the regrid package
+ o shelfice:
+  - add a simple boundary layer scheme to reduce noise
+  - fix the indexing in shelfice_u/v_drag so that there will be actually drag
+ checkpoint58n_post
+ o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
+    local variable (not in common block).
+ o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
+   - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
+   - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
+     to work with SingleCpuIO.
+ o add "_d 0" to real constant of pkg/cfc subroutines ;
+    update exp. cfc_exemple & tutorial_cfc_offline output files.
+ o multi-threading and IO:
+   - all threads call READ_FLD S/R (needed if using SingleCpuIO):
+     (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
+   - barrier before and after reading.
+   - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
+   - avoid using MDS_WRITELOCAL for LAND pkg output.
+   - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
+     common-block variables ; Allows multi-threading with master-thread IO.
+ o change default MAX_NO_THREADS from 32 to 4 ;
+   and stop cleanly when MAX_NO_THREADS is too small.
+ o add S/R BAR_CHECK to check multi-threaded barrier synchronization
+ checkpoint58m_post
+ o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
+    and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
+ o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
+    keep global_ocean.90x40x15 (for AD testing) with former secondary test
+    (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
+ o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
+     add MITgcm_tutorials (= code + all the tutorials)
+ o ecco, option to compute cost for total ssh (mean+anom)
+ o consistent with addition of ptracer and ssh in pkg/profiles
+ o profiles: adding ptracer and ssh
+ o testreport: change multi-test output-file name
+   (from output.txt.{name} to output.{name}.txt)
+ o profiles: now ok for mutli-tiles case
+ o seaice: add 4 parameters for different advection schemes for area,
+   (effective) seaice thickness, enthalphy, and snow height. Their default
+   is the standard parameter SEAICEadvScheme
+ o calc_gw:
+  - add cosFacU in zonal viscous flux (harmonic.visc.).
+  - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
+    of tutorial_plume_on_slope.
+ o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
+ o calc_gw: true flux-form, account for horizontal grid spacing.
+   update rotating_tank results, but not plume_on_slope (affected at
+   truncation level, 11 digits).
+ checkpoint58l_post
+ o calc_gw:
+  - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
+  - remove side-drag for now (need to fix it); update plume_on_slope results.
+  - fix for partial-cell & non-uniform dz; update plume_on_slope results.
+ o commit code to make SST/SSS weights spatially variable
+   (based on either variable in-situ or variable initial T/S weights)
+ o pkg/ecco:
+   * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
+     now based on horizontally varying weights wthetaLev, wsaltLev
+   * cost_averagesflags now returns year indices in addition to day, month
+   * sflux balance is performed on annual basis
+     (sflxumm, sfluxmm2, bal_sfluxmm)
+   * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
+     including separate counting and multipliers
+ o pkg/rbcs
+   * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
+ checkpoint58k_post
+ o testreport:
+  - always build in dir. "build" (if not there, mkdir build instead of building
+    & running in input)
+  - run in dir run (if it exists), in build otherwise.
+  - call prepare_run (if input/prepare_run exists)
+  - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
+ o pkg/exf modifications to interpolation and rotation routines for more
+    reasonable treatment of North Pole singularity: for tracers North Pole
+    value is set to northernmost zonal-mean value, for zonal velocity it is
+    set to zero, and for meridional velocity it is set to northernmost value.
+ o pkg/exf/exf_check_range.F
+  - add tile index to diagnostics and move stop statement to the very
+    end of the routine.
+ o pkg/diagnostics: (diagnostics_main_init.F)
+   define title of isomorphic variables according to the current config.
+ o pkg/thsice with pkg/seaice dynamics:
+ - fix domain of computation (interior only, required for exf) and do exchanges
+ - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
+ o towards a standard way of dealing with multi-threading in MONITOR
+   and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
+ o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
+    to W momentum equation in nonhydrostatic and quasihydrostatic runs.
+ o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
+ o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
+ o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
+    (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
+ o tracer advection:
+  - clean-up and simplify calc_common_factors.F
+  - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
+    advection subroutine (but still not used within DST advection S/R)
+ o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
+ checkpoint58j_post
+ o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
+   from file (collects calls previously in FORWARD_STEP)
+ o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
+ o adjoint store dir. adjusted accordingly
+ o genmake2
+   replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
+ checkpoint58i_post
+ o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
+   on wind stress (SEAICEstressFactor defaults to 1.)
+ o Total number of Timers is finite (<=40): comment out 2 non-essential one
+   in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
+ o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
+   on CS-grid: no longer loosing mass.
+ o exf & curvilinear-grid: no longer modify longitude xC & xG.
+ o pkg/ggl90: fix sloppy output and fix a bug
+ o pkg/seaice: added SEAICEuseEVPpickup parameter
+   - Set to false in order to start EVP solver with
+     non-EVP pickup files when using SEAICEuseEVP
+   - fix sign error in diffusion in seaice_calc_rhs
+ checkpoint58h_post
+ * Modifications for bottom topography control
+   o replace hFacC by _hFacC at various places
+   o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
+   o add non-self-adjoint cg2d_nsa
+   o update autodiff support routines
+   o re-initialise hfac after ctrl_depth_ini
+   o works for 5x5 box, doesnt work for global_ocean.90x40x15
+ * Adding verification for 5x5 box (4-layer) bottom topography control
+ checkpoint58g_post
+ o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
+    used for mean seasonal cycle, mean diurnal cycle); add an example
+    in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
+ o pkg/ggl90:
+   - add parameter (minimum surface kinetic energy)
+   - fix bug (avoiding division by zero)
+ o couple pkg/thsice to pkg/seaice:
+   - modify advection in seaice to accomodate new scalar fields to be advected
+   - only muliDimAdection scheme work with seaice/thsice
+   - mapping of thsice-variables to seaice-variables, back and forth
+   - does not break the verification experiments, but does not give the
+     desired results either
+ o pkg/seaice
+   - make (default) second order advection a bit less confusing?
+ checkpoint58f_post
+ o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
+   to pkg/seaice):
+   - new routines thsice_map_exf and thsice_get_exf provide the interface
+   - add an additional formal parameter to thsice_solve4temp
+ o pkg/exf:
+   - add new fields wspeed, snowprecip (to be able to couple to thsice)
+   - correct Stefan-Boltzmann constant
+   - new parameter for longwave surface emittance
+   - separate some stuff from exf_bulkformulae into new routines
+     exf_radiation, exf_wind
+   - add new parameters and constants: longwave emissivity for ocean, ice
+     and snow, evaporation parameters over ice
+   - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
+     either wind from stress or stress from wind
+ o pkg/thSIce:
+ - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
+ - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
+    and THSICE_CALC_THICKN
+ - for now, call to THSICE_GET_BULKF remains inside i,j loops.
+ - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
+   to make debugging easier.
+ - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
+ o pkg/bulk_force:
+   - clean-up comments and parameters ;
+   - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
+ o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
+   generate new output for test-experiment: aim.5l_cs.thSI
+ o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
+   testreport accordingly
+ checkpoint58e_post
+ o SEAICE_CGRID adjoint done
+ o R_STAR adjoint implemented.
+   * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
+   * need to sort out init. of h0facc, etc.
+ o Make pkg/profile fully independent of ecco,cost, etc. stuff
+   to be able to use it in pure forward.
+ checkpoint58d_post
+ o upgrade simple test-experiment to tutorial example:
+  step.1: duplicate the experiment and (step.2) will remove the old copy.
+   tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
+   tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
+   tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
+   tutorial_global_oce_biogeo    <- copy of dic_example
+   tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
+   tutorial_plume_on_slope       <- copy of plume_on_slope
+   tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
+   tutorial_global_oce_optim     <- empty for now (David ?)
+   tutorial_global_oce_in_p      <- copy of global_ocean_pressure
+  some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
+ o correct a sign problem in cost_scat.F
+ o obcs and ptracers: fix boundary conditions for advections schemes
+   with larger stencil
+ o thsice adjoint: start
+ o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
+   completeness
+ o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
+   and COSINEMETH_III, add comments in default CPP_OPTIONS.h
+ o ptracers adjoint:
+   * avoid extensive recomputatations
+   * fix missing re-init. of gptr (missed by TAF)
+ o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
+   me to turn off the excessive output to STDOUT that this package produces
+ o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
+   and add those terms in Vector-Invariant formulation.
+ o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
+   if the control period (xx_hfluxperiod etc) is 0
+ o in profiles pkg, clean routines and fix details
+ o in ecco pkg, reading ssh data:
+   fix problem in case the model does not start at iter0=0
+ o fix mnc-pickup/restart for ptracers
+ o new package prifiles:
+   code to compute profile-based cost by Gael Forget
+   (modifs in ecco, ctrl, autodiff)
+ o Benign bug fix in initialization (spotted by M. Mazloff) of
+   ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
+ checkpoint58c_post
+ o adjoint: finish NLFS adjoint and provide reference output in
+   verification/global_ocean.90x40x15/results_ad_nlfs
+ o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
+   documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
+   SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
+   with SEAICE_CGRID defined.
+ o move calendarDumps from "data" to "data.cal" and clean-up the code
+   with a simple call to pkg/cal S/R: CAL_TIME2WRITE
+ o add useEXF & useCAL flags (for now, set in hard-coded way)
+ o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
+   (were missing in NH mode, and wrong in quasihydrostatic mode).
+   waiting for Chris updated version of calc_gw to add those CALLs.
+ o fix bug in quasihydrostatic S/R ;
+   add a test for this option: global_ocean.90x40x15.qshyd
+ o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
+   (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
+ o add on/off flag useOffLine for package OFFLINE
+ o seaice:
+   - modify advection so that it works also on the C-grid
+   - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
+     problem in multi-tile runs with C-grid
+   - add flags for clipping ice velocities and/or masking solver forcing
+   - fix drag (ocean on ice) formulation and a bug that caused noise in the
+     C-grid solver
+   - added a few comments to seaice_diffusion.F
+   - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
+     are now exclusive)
+   - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
+     required re-ordering the code a little:
+    + make DAIRN global variable (defined in SEAICE)
+    + move computation of the viscosities eta and zeta into a new separate
+      routine (because I need to recompute them in seaice_ocean_stress.F)
+ checkpoint58b_post
+ o AIM+thSIce: fix sign of Short-Wave through the Ice ;
+   update output.txt of exp. aim.5l_cs.thSI
+ o various mnc cleanups and improvements:
+   + shrink lookup tables by factor of ~4
+   + better error reporting when running out of lookup space
+   + able to handle longer path/file names (up to 500 chars)
+ o adjoint:
+   - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
+   - TBD: "hidden" mom_vecinv recomp. in dynamics
+ o change forcing_In_AB to affects both T,S forcing and Momentum forcing
+  (allow to differentiate between forcing components using new integer flags:
+   momForcingOutAB=1/0 & tracForcingOutAB=1/0)
+  and add new flag to put Dissipation tendency out of Adams-Bashforth.
+ o ecco
+   - enable trend removal from SSH anomaly obs.
+ o adjoint
+   - a fix for PmEpR when #undef EXACT_CONSERV
+   - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
+   - try to fix "hidden" recomp. in forward_step for NLFS
+     (NLFS seems broken sometimes after I checked it in)
+ o seaice:
+  - add c-grid version of the dynamic solver:
+    + three new routines that are the c-grid substitute lsr, dynsolver
+      and ostres
+    + put a few fields that were local to dynsolver into global common
+      blocks, so that I can move the computation of stresses etc into
+      seaice_lsr (saves coding but may break the adjoint).
+  - replace more hardwired parameters by runtime parameters
+  - add ice masks that mask the rhs of the implicit solvers where there
+    is no ice (commented out in seaice_dynsolver, because i am not sure
+    if this works properly), eventually this should replace the clipping
+    of ice velocities in seaice_dynsolver to +/-40cm/s.
+ o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
+   include it only where its needed
+ o move balancing of fluxes before the call of external_forcing_surf
+ o seaice:
+   - correct units of turning angles (now they are really in degrees)
+   - move computation of GWATX/Y out of main routine into dynsolver
+   - initialize GWATX/Y in seaice_init
+ o Apply mask on Fresh-Water flux (needed for SSH forcing).
+   update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
+ o seaice: add runtime flags for turning angles (default to zero)
+ o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
+   and trend from exf forcing and ctrl control adjustments
+ o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
+   (since checkpoint57x_post)
+ o change the default rotation period to 86164.s = the Earth rotation
+ o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
+   and based on a reference stratification. Tested within hs94.cs-32x32x5.
+ o seaice advection: add code for choosing between the default (2nd order
+   central differences) and multiDim advection schemes provided by
+   pkg/generic_advdiff
+ o seaice:
+   - removed all references to SEAICE_GRID.h fields from
+     dynsolver, advect, diffus, lsr, without changing the results of lab_sea
+     (cubed-sphere configuration will change a little)
+   - grid computations in seaice_init are obsolete now.
+   - cleaned up code a little so that is easier to read (hopefully).
+   - added new (better?) discretizations of default advection and diffusion
+     (turn on with SEAICEuseFluxForm)
+   - replace 1 in 3d global fields by kSurface in growth.F
+ checkpoint58a_post
+ o seaice:
+   - bug fix in advect.F
+ o shelfice:
+   - separate shelfice load anomaly from pload (breaks with time
+     dependent forcing), => introduce constant field shelficeLoadAnomaly.
+     Its default is 0., but it may be computed more cleverly from (unknown)
+     t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
+     done offline. A good approximation of the pressure load anomaly is
+     necessary to avoid large initial adjustment processes underneath
+     deep-reaching shelfice.
+   - small fix in ISOMIP shelfice_thermodynamics
+   - add more sophisticated thermodynamics of Hellmer (1989), this is
+     now the default
+   - give a few constants more intuitive names
+ o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
+   if bulk formulae are used in long integration (especially EmPmR). Turn
+   on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
+   if balancePrintMean, the imbalance that is substracted is printed to
+   STDOUT.
+ o fix bug (typo) in obcs_apply_eta.F
+ o add a new package shelfice which enables us to model the circulation
+   underneath shelf-ice with draughts of hundreds of meters.
+  - works
+  - to do: + include improved thermodynamics
+           + check whether kSurfC (from model/inc/SURFACE.h) can be used
+             instead of new field kTopC
+           + can we use topoFile, Ro_surf and existing code in ini_depth.F
+             instead of new field R_shelfIce and new code in ini_depth.F
+             and ini_mask_etc.F?
+           + adjust vertical mixing schemes?
+ o seaice pkg:
+  - add a cpp-flag to include a simple formula for a salinity dependent
+    freezing point of sea water at the surface
+  - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
+    meridional stresses are now different (and hopefully correct)
  o AIM pkg: change threshold on large-scale condensation to conserve Heat.
     update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
     and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)

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