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-revision 1.1445 by gforget,
Fri May 27 23:28:39 2011 UTC
+revision 1.1500 by jmc,
Fri Sep  2 18:34:27 2011 UTC
 Line 4 
 $Name$
      Notes on tags used in MITgcmUV
      ==============================
+ o pkg/obcs (seaice):
+   - add missing EXCH for uIce,vIce after applying OBCS;
+   - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
+     argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
+     EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
+   - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
+   - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
+     and eedata.mth for MPI and mutlti-threaded testing.
+ o pkg/flt:
+   - make FLT EXCH working with multi-threads (and MPI + multi-threads);
+   - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
+   - fix pickup and trajectories + profiles output with multi-threads;
+   - add parameter to select group of fields to write along trajectory and
+     profile (default unchanged);
+   - only call PORT_RAND* function when flt_noise <> 0;
+   - add multi-threaded test for verification exp. flt_example.
+ o eesupp/src:
+   - fix S/R ALL_PROC_DIE for MPI+multi-threads.
+   - USE_OMP_THREADING: check that number of threads (from eedata) matches
+     actual number (from env.var. setting).
+ o pkg/ebm:
+   - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
+   - add multi-threaded test for verification exp. global_ocean_ebm
+ checkpoint63b (2011/08/29)
+ o pkg/ebm:
+   - fix sign of runoff;
+   - update directly forcing fields (Qnet,EmPmR) to use standard
+     external_forcing_surf.F (remove ebm_forcing_surf.F);
+   - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
+   - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
+     and apply relaxation towards corresponding SST field (2-D map or ZonAver).
+   - update global_ocean_ebm parameters file data and update output (fwd+ad).
+ o verification/matrix_example:
+   - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
+     MPI and mutlti-threaded testing.
+ o pkg/matrix:
+   - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
+   - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
+   - fix for multi-threaded (remove DATA statement);
+   - use standard DIFFERENT_MULTIPLE function;
+   - add MATRIX_OPTIONS.h
+ o verification/matrix_example:
+    To allow to split the domain in several tiles, change the domain size
+     from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
+     Western side) of land points.
+ o (*_)write_pickup:
+   - fix few bugs in mypackage_read/write_pickup.F
+   - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
+     array of length 1 (was caught by compiler syntax-check).
+ o pkg/diagnostics (velocity potential solver):
+   - fix initialisation of main diagonal matrix (for overlap values)
+ o tools/build_options:
+   - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
+     into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
+   - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
+     * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
+     * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
+     and use "-devel" testreport option for standard testing on baudelaire.
+ o pkg/grdchk:
+   - Assume that all gradient-check position are within the same tile
+     corresponding to global indices (iGloTile,jGloTile) and that
+     positions (i,j indices or nbeg) are local to this tile;
+   - set tile local-indices and proc. number according to tile global-indices;
+   - remove grdchkwhichproc from namelist (retired param);
+   - send adjoint gradient to all procs so that all procs print it to STDOUT;
+   - switch on MPI test for global_ocean.90x40x15 AD test experiment.
+ o adding package bbl (Bottom Boundary Layer)
+   description in MITgcm/pkg/bbl/bbl_description.tex
+   example/test experiment in MITgcm_contrib/bbl
+ o adjoint verifications
+   - changed 5 experiments to multi-tiles
+     * global_ocean.90x40x15
+     * obcs_ctrl
+     * offline_exf_seaice
+     * tutorial_dic_adjoffline
+     * tutorial_tracer_adjsens
+     changed reference output for those that crossed tile boundaries
+     (changed choices of gradient check positions)
+   - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
+   - temporary bug fix in grdchk_loc.F for obcs
+ o genmake2 & testreport
+   - add target "obj" (just for OBJFILES files) to Makefile;
+   - add option to specify FEXTRAFLAGS on command line.
+ o pkg/mypackage:
+   - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
+ checkpoint63a (2011/08/02)
+ o pkg/diagnostics (velocity potential):
+   - fix velocity-potential calculation when using OBCS: balance net inflow
+     at each level (new S/R OBCS_DIAG_BALANCE).
+   - fix some of the problems with OBCS in stream-function calculation.
+ o pkg/exf/exf_readparms.F
+   - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
+     EXF_NML_OBCS) more consistent, so that you need not have these lists
+     in data.exf when they are not used.
+ o optim/optim_readdata.F:
+   - add some output about obcs variables that might help debugging
+   - add a check about nvarlength
+ o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
+ o pkg/diagnostics (velocity potential):
+   - fix mask for OBCS (still problems in stream-function with OBCS);
+   - add specific parameter (default = main code CG2D params) for solver;
+   - in case of poor convergence, use solution corresponding to lowest residual.
+ o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
+   adjoint code. In general statements like tmpscal=fld(i,j) are problematic
+   and should be avoided where possible.
+ o model/src (rStar):
+   - include r* effect on reference-state (PhiRef) in totPhiHyd
+     (so that it's really the potential anomaly at the cell center);
+     affect solution only if z* with full pressure in EOS.
+   - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
+     update output (because of z* in totPhiHyd and viscA4 changes);
+   - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
+     @ constant r) until interpolation at constant r is implemented.
+ o pkg/diagnostics
+   - fix RCENTER diagnostics in case cell center is not at interface middle
+ o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
+   this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
+   that THETA and SALT are "conservative temperature" and "absolute
+   salinity"
+ o pkg/ctrl
+   - fix computation of endrec in s/r ctrl_init_rec
+   - ctrl_pack/unpack_*: remove unused variables and some obsolete code
+ o pkg/seaice/seaice_growth.F
+   - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
+     remove then obsolete STORE directives
+   - fix STORE directives for tice and tices, so that only the
+     appropriate part of the fields are stored (and not the entire
+     field); update global_ocean.cs32x15.seaice AD output.
+   - cosmetic changes: adjust CPP flags and indentation for better
+     legibilty
+ o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
+   Chris Wilson)
+ o pkg/gmredi:
+    Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
+    and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
+ checkpoint63  (2011/07/11)
+ o pkg/exch2:
+  - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
+  - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
+    (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
+    increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
+ o pkg/diagnostics:
+  - deal with pairs of post-processed diags which are computed together; in
+    particular, re-order list of diags within 1 file to save 2nd computation.
+  - add S/R to compute velocity stream-function (called after velocity-potential
+    calculation) from divergence free transport -> new diagnostics "PsiVEL".
+  - add parameter to select grid-point location where PsiVEL == 0.
+ o eesupp/src:
+    new S/R to calculate cumulated sum on tiled array, corner grid-cell location
+    (specific S/R needed with exch2 topology - for now, just print an error msg)
+ o pkg/shelfice
+  - Implement friction velocity-dependent transfer coefficients following
+    Holland and Jenkins, JPO, 1999
+    Original code by M. Losch with small modifs.
+    Enable with CPP option SHI_ALLOW_GAMMAFRICT
+    and runtime flag SHELFICEuseGammaFrict
+ o verification lab_sea & global_ocean.cs32x15:
+  - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
+    does not miss some dependencies (but is slower) and also works with many files
+    (default makedepend limitation for AD built).
+  - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
+ o pkg/diagnostics:
+  - add run-time parameter "useMissingValue" (def=False) to fill land-point
+     (i.e., where mask=0) with MissingValue ; used only in MNC output file.
+    This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
+  - Extend the use of "missing_value" setting from data.diagnostics for the case
+    of counter-diagnostics (where fraction-weight is zero). This applies both to
+    MNC and MDS output files.
+ o pkg/seaice/seaice_growth.F:
+   - add 'a priori' cap of latent heat flux based on actual mass considerations
+     when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
+     non-legacy seaice_solve4temp.
+   - add diagnostic of the residual sublimation freshwater flux (the freshwater
+     flux taken from the ocean if the total actual latent heat fluxes exceed
+     the maximum)
+   - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
+    fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
+   - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
+    SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
+   - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
+   - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
+ o verification 1D_ocean_ice_column:
+    made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
+    update results
+ o pkg/diagnostics:
+  - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
+    which are not filled-up but computed from other diags ; In this case, the mate
+    diag points to the primary (filled-up) diag to used for post processing.
+  - Update Velocity-potential computation using post-processed diag framework.
+  ==> Change the ordering of fields and time-periods in MDS output file
+    when using periodic averaging: now writes one time record with the full set
+    of fields for this time period, then the next time reccord (it used to be
+    one field with the full set of time records then the next field).
+      Note: this is now similar to NetCDF (MNC) output file. <==
+ checkpoint62z (2011/06/21)
+ o adjoint monitor:
+  - Add adjoint monitor output for packages exf, seaice
+    and update relevant testreport output
+ o pkg/seaice:
+  - re-order diags inits so that they appear in order in available_diagnostics.log
+  - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
+    area/heff/hsnow preceeding thermodynamic growth/melt.
+  - modified diag: SIdA; output actual effect, as the description states.
+  - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
+  - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
+    (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
+     and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
+  - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
+  - added diagnostics for seaice generic tracers (SItr*).
+  - added SItrUnit and SItrNameLong run time param (for SItr* diags).
+  - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
+  I. Fenty: 18-Jun-2011:
+  Minor changes to seaice package:
+) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
+     added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
+    - Differentiated "regularization variables" from "floor variables"
+     * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
+     * hiceMin became SEAICE_hice_reg (old hiceMin)
+       (with _reg meaning regularization variable)
+    - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
+     so as to ensure energy conservation when going between phases
+   - A22 was not used anywhere
+) Changed regularization procedure for heffActual and hsnowActual to ensure
+     well-boundedness and smooth adjoint in seaice_growth.F
+) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
+     because the old regularization always set heffActual >= 0.05 cm
+) Changed the model so that the default behavior is to put a small (10^-5) "floor"
+     on AREA when HEFF > 0.
+   - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
+     requiring that DISABLE_AREA_FLOOR *not* be defined
+  Affected verifications:
+   - 1D_ocean_ice_column (output.txt output_adm.txt)
+   - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
+ o pkg/diagnostics:
+   - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
+   - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
+     (was _RL, now integer) with option = 0 to retrieve all levels.
+   - add pieces of code to compute velocity potential at each level (new diagnostics
+     PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
+     for now, using same params as CG2D (target-resisual, max Nb of iter ...).
+   - fix few issues with counter diagnostics in diagnostics_setdiag.F &
+     diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
+     and in diagnostics_fract_fill.F (do not need a valid pointer for the
+     diagnostics counter-mate); check that definition of counter-diagnostic
+     includes a valid counter-mate (in diagnostics_set_levels.F).
+ o model/src (rStar):
+   - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
+     affect solution only if z* with full pressure in EOS;
+     update output of test-exp global_ocean.90x40x15.
+ o pkg/seaice:
+   - introduce siEps=1e-5 parameter
+   - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
+   - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
+   - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
+     For now it covers, and was tested for, ice salinity and age (attached to HEFF),
+     as well as ice cover age and ridging index (attached to AREA).
+     For now the run time parameters (in data.seaice/SEAICE_PARM03) are
+     SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
+     Up to SItrMaxNum=3 tracers can be used simultaneously.
+ o pkg/salt_plume:
+   -introduce SPsalFRAC run time parameter that sets the fraction of the
+    salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
+    that gets vertically redistributed (fluxed down) by pkg/salt_plume.
+ o model debug options:
+   - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
+     in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
+   - Refine debug-msg printing selection (3 new levels):
+     debugMode  : controls printing of debug messages (sequence of S/R calls).
+     debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
+      debLevZero =  0 ; /* level of disabled aux. msg printing */
+      debLevA =  1 ; /* level of minimum  aux. msg printing */
+      debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
+      debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
+      debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
+      debLevE =  5 ; /* level of extensive debug printing */
+     New debugLevel default: with default debugMode value (=F),
+       = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
+       and if debugMode=T, default debugLevel = 4 (debLevD).
+     Relation with previous settings:
+      debLevB (=2) corresponds to former debLevA (=1)
+      debLevD (=4) corresponds to former debLevB (=2)
+     Note:
+      a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
+      b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
+         to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
+   - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
+     detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
+ o pkg/obcs:
+   - change OBCSfixTopo default from True to False (should not change the results);
+     keep OBCSfixTopo=T in verification-exp. seaice_obcs.
+ o pkg/thsice:
+   - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
+nd layer seaice sublimation (unlikely to happen)
+   - use Interior mask for OBCS in thsice_advection.F (similar to what is
+     done in gad_advection & seaice_advection).
+ o adjoint:
+   bug fix spotted by Gael Forget:
+   seaice_advection and thsice_advection still had
+   legacy CPP options to avoid CS corner updates for adjoint
+ o pkg/seaice:
+   => Change some of the defaults (2011/05/29):
+      - change SEAICEuseFluxForm default (from False to True)
+      - change DIFF1 default (from 0.004 m/s to 0. m/s)
+      And print warnings if DIFF1 is not set in data.seaice and centered
+       avection scheme is used without any diffusion.
+   also:
+   - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
+   - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
+   - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
+     other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
+     #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
+   update results of test exp.:
+      lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
+          output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
+          output_adm.noseaicedyn (SEAICEuseFluxForm=T)
+      offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
+      seaice_obcs: output (SEAICEuseFluxForm=T)
+   and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
+       for standard fwd & AD lab_sea tests (to keep the same output).
  o pkg/seaice/seaice_growth.F:
    - use Ian Fenty's capping formulas for actual ice
    thickness thoughout EVOLUTION branch.
    - put treatment pathological case #2) in CPP brackets
    (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
    - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
  o pkg/seaice:
    - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
-   pass the Laplacian diffusivity (in m/s2) diffKh as a parameter;
+   pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
    also pass fac as a param, which can be 1. (to update the tendency
    field) or the time step (to update the field itself).
    - seaice_advdiff.F: for multidim, call seaice_diffusion with
    e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
    seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
    - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
    hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
-   - note: if any of SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
-   is specified to be >0, then DIFF1 is set to 0.
  o pkg/seaice:
    diffusion with centered advection scheme (diffus.F & advect.F):
    - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)

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