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revision 1.1445 by gforget, Fri May 27 23:28:39 2011 UTC revision 1.1544 by jmc, Tue Dec 6 19:31:02 2011 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o pkg/ecco
8      - added IES cost term
9    o verification/advect_xz
10      - scale down the depth by 1/100 (from 200 km to just 2.km)
11      - add secondary test using divergent flow, r-star and implicit vertical advection.
12      - add note (check_conserve_TS.txt) and matlab script to check global
13        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
14    o pkg/rbcs:
15      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
16    o pkg/obcs (Stevens BCs):
17      - fix various problems in the phase speed computations of the Stevens
18        boundary conditions:
19        - sign error for western and southern boundaries,
20        - time tendencies were underestimated by factor of dTracerLev and some just
21          zero (for multidim advection schemes) -> now estimate time tendencies
22          from difference between previous (n) time level and the one before (n-1);
23          this requires storing a field per tracer per boundary, also in the pickup
24          files.
25        - replace deltaTmom in cflMer/Zon computation with dTracerLev
26        - set default phase velocity to cflMer/Zon
27      - update verification experiment exp4.stevens
28    o pkg/generic_advdiff (implicit_r):
29      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
30        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
31      - fix implicit vertical diffusion or advection with NonLin FreeSurf
32        (was using current recip_hFacC instead of future recip_hFacC): set future
33        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
34        solver S/R ;
35      - fill diagnostics of vertical advective fluxes (computed from tendency)
36        when using implicit vert. advection;
37      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
38         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
39         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
40         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
41    o pkg/diagnostics:
42      - add diags for T & S tendency which goes through Adams-Bashforth.
43    
44    checkpoint63f (2011/11/30)
45    o pkg/obcs/obcs_calc_stevens.F:
46      - join some loops to reduce number of if-statements
47      - fix a bug in code for northern and southern boundaries.
48    o pkg/seaice/seaice_init_varia.F
49      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
50        caused zero ice-velocities for the B-grid code
51    o pkg/seaice/seaice_init_fixed.F
52      - fix a bug in the initialisation of the second metric terms
53        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
54      - this affects all seaice configurations with useCurviLinearGrid = .true.
55        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
56        = .true. (default)
57      - the only verification experiment affected is global_ocean.cs32x15:
58        icedyn, seaice, and seaice_dynmix (AD)
59    o pkg/thsice/thsice_diagnostics_state.F
60      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
61        not contain garbage that can lead to surprises in diagstats_calc.F
62    o model/src:
63      - move bi,bj loops inside INTEGR_CONTINUITY ;
64      - call INTEGR_CONTINUITY directly from forward_step.F
65        (previously called from momentum_correction_step.F)
66      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
67        forward_step.F and pkg/ecco/the_main_loop.F
68    o model/src/do_oceanic_phys.F:
69      - reset addMass to zero only if useICEFRONT ;
70      - separated k-loop for rhoInSitu calculation ;
71      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
72        and at constant T,S (= WdRHOdP);
73      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
74        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
75        transport of locally-referenced potential density);
76        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
77    o gluemnc:
78      - replace ncrcat with ncks when adding variables to *.glob.nc
79      - change the way variables without record dimensions are handled so that
80        files that have variables with and without record variables can be glued:
81        add a record dimension with a new unique name to be able to differentiate
82        between variable with and without a-prior record dimensions. Remove
83        this record dimension before adding the variable to the *.glob.nc file.
84        This procedure automatically works also for grid.*.nc files that do not
85        have any record dimension.
86    o verification/cpl_aim+ocn:
87      - generate new reference output on baudelaire (gfortran, mpich2) (previously
88        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
89    o pkg/obcs/obcs_calc_stevens.F:
90      - add code for northern and southern boundaries.
91      - reorder some loops to save some operations and so that drFBar can be scalar
92    o model/src:
93      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
94        truncation) and add diagnostics for Adams-Bashforth tendency increment.
95      - update test-exp. AD output:
96        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
97      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
98        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
99        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
100        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
101        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
102        tutorial_plume_on_slope.
103    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
104      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
105      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
106      does not even come with an F77 compiler anymore, this should not be
107      a limitation
108    
109    checkpoint63e (2011/11/06)
110    o pkg/seaice adjoint of LSR:
111      - substantially rework STORE dirs.
112      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
113        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
114        and only perform SOLV_MAX_FIXED adjoint iters.
115        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
116        always goes to same record, meaning that the last forward field will be
117        the one used in the adjoint - an approximation.
118      - now produces non-zero LSR-related gradients, and acceptable gradients for
119        An's zonal (x-z) test case (to be checked in)
120      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
121        (but these are screwed up by the thermodynamics in the first place);
122        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
123        output_adm.txt also reflects changes to seaice_lsr
124      - global_ocean.cs32x15:
125        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
126          (output_adm.seaice.txt was updated)
127        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
128          (output_adm.seaice_dynmix.txt)
129    o test-exp. exp4+stevens:
130      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
131    o pkg/seaice (lsr solver):
132      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
133        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
134      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
135      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
136        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
137      - compute (with new S/R) and print initial (+ free-driff sol. if available)
138        and final residual of linearised system.
139    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
140      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
141    o pkg/obcs: Stevens BCs (still only for east and west)
142      - fix Stevens BCs by using intermediate velocities of previous
143        time step as "baroclinic" contribution rather velocity of one grid cell
144        inside the boundaries; more consistent but makes the entire treatment
145        more complicated, requires new pickup files and two new S/Rs:
146        obcs_copy_uv_n and obcs_save_uv_n
147        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
148        (undefined by default)
149      - silently move computation of some grid factors into separate loops to
150        save some recomputations
151      - add a hack for non-linear free surface
152      - add a verification experiment to exp4 that tests this code
153    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
154    
155    checkpoint63d (2011/10/25)
156    o pkg/obcs + seaice-dynamics:
157      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
158        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
159        values (consistent with an implicit method).
160      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
161        return to older implementation (same results as before); note that none of
162        the "experimental" OBCS_SEAICE options are implemented in the new version.
163      - switch test exp. seaice_obcs to use new version (update output).
164    o pkg/seaice:
165      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
166      - add parenthesis in Water-Ice drag calculations (evp & lsr);
167      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
168        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
169      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
170        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
171    o pkg/layers:
172      - Include potential density as new coordinate (Thanks to David Munday)
173    o pkg/dic:
174      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
175        carbonate computation/output to CALC_PCO2_APPROX
176    o pkg/generic_advdiff
177      - make TAF generate code that vectorizes:
178        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
179    o model/src:
180      - improve vectorization also for adjoint code of
181        solve_tridiagonal and solve_pentadiagonal. As this requires up to
182        5 new 3D-fields, this code is only turned on for the combination of
183        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
184        for singular matrix check (only for TARGET_NEC_SX).
185      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
186        ALLOW_AUTODIFF. This flag now needs to be set outside of
187        solve_tri/pentadiagonal.F
188    o pkg/exf:
189      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
190        optional namelist EXF_NML_OBCS).
191      - add many debug-print (to trace down where pkg/cal error msg comes from)
192    o pkg/mom_vecinv/mom_vi_hdissip.F
193      - rearrange loops so that vectorization is improved and in particular
194        the adjoint routine vectorizes. The code is a little longer now, but I
195        think easier to read.
196        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
197    o pkg/seaice:
198      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
199    o pkg/exch2:
200      - alternative code (without tile x tile matrix) for cumulated (global) sum;
201        used as default; keep using matrix version in adjustment.cs-32x32x1.
202    o tools/build_options:
203      - after merging some MPI and/or multi-threads specific optfiles so that
204        the modified default optfile support both built (using genmake2 -mpi
205        for the MPI built, using genmake2 -omp for OpenMP built),
206        move now obsolete optfiles to tools/build_options/unsupported/
207       (add copy of email sent to support list in doc/optfiles_changes.txt)
208    
209    checkpoint63c (2011/09/28)
210    o pkg/ebm:
211      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
212        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
213    o pkg/seaice (SItracer pickup)
214    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
215      To be done:
216      - thorough testing of missing fields in S/R seaice_read_pickup
217      - thorough matching between generic tracers and specific fields used
218        (e.g. volume-weighted age, area-weighted age, salinity, ...)
219    o pkg/grdchk:
220      - all procs calculate and print finite-difference gradient (for testreport)
221      - change description output used by testreport;
222      - AD testing: also compare and report Finite-difference gradient;
223        => update all output_adm*.txt
224    o test exp. global_ocean_ebm:
225      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
226        and turn on exactConserve; update (fwd) output.
227    o pkg/seaice (LSR):
228      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
229      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
230        * identical results with non-CS topology (but save up to half of EXCH calls)
231        * no much changes in cs-32 verification tests since no ice at face edges
232         (differences due to convergence criteria, since nb of iterations changed)
233        * expect some differences on lat-lon-cap grid.
234        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
235    o pkg/exch2:
236      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
237        many tiles); until alternative coding is added, just add a stop.
238    o pkg/kpp:
239      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
240        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
241    o optfiles:
242      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
243        into corresponding standard one, which now support different build:
244        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
245      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
246    o pkg/obcs (seaice):
247      - add missing EXCH for uIce,vIce after applying OBCS;
248      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
249        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
250        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
251      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
252      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
253        and eedata.mth for MPI and mutlti-threaded testing.
254    o pkg/flt:
255      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
256      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
257      - fix pickup and trajectories + profiles output with multi-threads;
258      - add parameter to select group of fields to write along trajectory and
259        profile (default unchanged);
260      - only call PORT_RAND* function when flt_noise <> 0;
261      - add multi-threaded test for verification exp. flt_example.
262    o eesupp/src:
263      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
264      - USE_OMP_THREADING: check that number of threads (from eedata) matches
265        actual number (from env.var. setting).
266    o pkg/ebm:
267      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
268      - add multi-threaded test for verification exp. global_ocean_ebm
269    
270    checkpoint63b (2011/08/29)
271    o pkg/ebm:
272      - fix sign of runoff;
273      - update directly forcing fields (Qnet,EmPmR) to use standard
274        external_forcing_surf.F (remove ebm_forcing_surf.F);
275      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
276      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
277        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
278      - update global_ocean_ebm parameters file data and update output (fwd+ad).
279    o verification/matrix_example:
280      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
281        MPI and mutlti-threaded testing.
282    o pkg/matrix:
283      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
284      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
285      - fix for multi-threaded (remove DATA statement);
286      - use standard DIFFERENT_MULTIPLE function;
287      - add MATRIX_OPTIONS.h
288    o verification/matrix_example:
289       To allow to split the domain in several tiles, change the domain size
290        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
291        Western side) of land points.
292    o (*_)write_pickup:
293      - fix few bugs in mypackage_read/write_pickup.F
294      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
295        array of length 1 (was caught by compiler syntax-check).
296    o pkg/diagnostics (velocity potential solver):
297      - fix initialisation of main diagonal matrix (for overlap values)
298    o tools/build_options:
299      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
300        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
301      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
302        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
303        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
304        and use "-devel" testreport option for standard testing on baudelaire.
305    o pkg/grdchk:
306      - Assume that all gradient-check position are within the same tile
307        corresponding to global indices (iGloTile,jGloTile) and that
308        positions (i,j indices or nbeg) are local to this tile;
309      - set tile local-indices and proc. number according to tile global-indices;
310      - remove grdchkwhichproc from namelist (retired param);
311      - send adjoint gradient to all procs so that all procs print it to STDOUT;
312      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
313    o adding package bbl (Bottom Boundary Layer)
314      description in MITgcm/pkg/bbl/bbl_description.tex
315      example/test experiment in MITgcm_contrib/bbl
316    o adjoint verifications
317      - changed 5 experiments to multi-tiles
318        * global_ocean.90x40x15
319        * obcs_ctrl
320        * offline_exf_seaice
321        * tutorial_dic_adjoffline
322        * tutorial_tracer_adjsens
323        changed reference output for those that crossed tile boundaries
324        (changed choices of gradient check positions)
325      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
326      - temporary bug fix in grdchk_loc.F for obcs
327    o genmake2 & testreport
328      - add target "obj" (just for OBJFILES files) to Makefile;
329      - add option to specify FEXTRAFLAGS on command line.
330    o pkg/mypackage:
331      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
332    
333    checkpoint63a (2011/08/02)
334    o pkg/diagnostics (velocity potential):
335      - fix velocity-potential calculation when using OBCS: balance net inflow
336        at each level (new S/R OBCS_DIAG_BALANCE).
337      - fix some of the problems with OBCS in stream-function calculation.
338    o pkg/exf/exf_readparms.F
339      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
340        EXF_NML_OBCS) more consistent, so that you need not have these lists
341        in data.exf when they are not used.
342    o optim/optim_readdata.F:
343      - add some output about obcs variables that might help debugging
344      - add a check about nvarlength
345    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
346    o pkg/diagnostics (velocity potential):
347      - fix mask for OBCS (still problems in stream-function with OBCS);
348      - add specific parameter (default = main code CG2D params) for solver;
349      - in case of poor convergence, use solution corresponding to lowest residual.
350    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
351      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
352      and should be avoided where possible.
353    o model/src (rStar):
354      - include r* effect on reference-state (PhiRef) in totPhiHyd
355        (so that it's really the potential anomaly at the cell center);
356        affect solution only if z* with full pressure in EOS.
357      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
358        update output (because of z* in totPhiHyd and viscA4 changes);
359      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
360        @ constant r) until interpolation at constant r is implemented.
361    o pkg/diagnostics
362      - fix RCENTER diagnostics in case cell center is not at interface middle
363    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
364      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
365      that THETA and SALT are "conservative temperature" and "absolute
366      salinity"
367    o pkg/ctrl
368      - fix computation of endrec in s/r ctrl_init_rec
369      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
370    o pkg/seaice/seaice_growth.F
371      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
372        remove then obsolete STORE directives
373      - fix STORE directives for tice and tices, so that only the
374        appropriate part of the fields are stored (and not the entire
375        field); update global_ocean.cs32x15.seaice AD output.
376      - cosmetic changes: adjust CPP flags and indentation for better
377        legibilty
378    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
379      Chris Wilson)
380    o pkg/gmredi:
381       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
382       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
383    
384    checkpoint63  (2011/07/11)
385    o pkg/exch2:
386     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
387     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
388       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
389       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
390    o pkg/diagnostics:
391     - deal with pairs of post-processed diags which are computed together; in
392       particular, re-order list of diags within 1 file to save 2nd computation.
393     - add S/R to compute velocity stream-function (called after velocity-potential
394       calculation) from divergence free transport -> new diagnostics "PsiVEL".
395     - add parameter to select grid-point location where PsiVEL == 0.
396    o eesupp/src:
397       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
398       (specific S/R needed with exch2 topology - for now, just print an error msg)
399    o pkg/shelfice
400     - Implement friction velocity-dependent transfer coefficients following
401       Holland and Jenkins, JPO, 1999
402       Original code by M. Losch with small modifs.
403       Enable with CPP option SHI_ALLOW_GAMMAFRICT
404       and runtime flag SHELFICEuseGammaFrict
405    o verification lab_sea & global_ocean.cs32x15:
406     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
407       does not miss some dependencies (but is slower) and also works with many files
408       (default makedepend limitation for AD built).
409     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
410    o pkg/diagnostics:
411     - add run-time parameter "useMissingValue" (def=False) to fill land-point
412        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
413       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
414     - Extend the use of "missing_value" setting from data.diagnostics for the case
415       of counter-diagnostics (where fraction-weight is zero). This applies both to
416       MNC and MDS output files.
417    o pkg/seaice/seaice_growth.F:
418      - add 'a priori' cap of latent heat flux based on actual mass considerations
419        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
420        non-legacy seaice_solve4temp.
421      - add diagnostic of the residual sublimation freshwater flux (the freshwater
422        flux taken from the ocean if the total actual latent heat fluxes exceed
423        the maximum)
424      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
425       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
426      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
427       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
428      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
429      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
430    o verification 1D_ocean_ice_column:
431       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
432       update results
433    o pkg/diagnostics:
434     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
435       which are not filled-up but computed from other diags ; In this case, the mate
436       diag points to the primary (filled-up) diag to used for post processing.
437     - Update Velocity-potential computation using post-processed diag framework.
438     ==> Change the ordering of fields and time-periods in MDS output file
439       when using periodic averaging: now writes one time record with the full set
440       of fields for this time period, then the next time reccord (it used to be
441       one field with the full set of time records then the next field).
442         Note: this is now similar to NetCDF (MNC) output file. <==
443    
444    checkpoint62z (2011/06/21)
445    o adjoint monitor:
446     - Add adjoint monitor output for packages exf, seaice
447       and update relevant testreport output
448    o pkg/seaice:
449     - re-order diags inits so that they appear in order in available_diagnostics.log
450     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
451       area/heff/hsnow preceeding thermodynamic growth/melt.
452     - modified diag: SIdA; output actual effect, as the description states.
453     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
454     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
455       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
456        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
457     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
458     - added diagnostics for seaice generic tracers (SItr*).
459     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
460     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
461     I. Fenty: 18-Jun-2011:
462     Minor changes to seaice package:
463     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
464        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
465       - Differentiated "regularization variables" from "floor variables"
466        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
467        * hiceMin became SEAICE_hice_reg (old hiceMin)
468          (with _reg meaning regularization variable)
469       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
470        so as to ensure energy conservation when going between phases
471      - A22 was not used anywhere
472     2) Changed regularization procedure for heffActual and hsnowActual to ensure
473        well-boundedness and smooth adjoint in seaice_growth.F
474     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
475        because the old regularization always set heffActual >= 0.05 cm
476     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
477        on AREA when HEFF > 0.
478      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
479        requiring that DISABLE_AREA_FLOOR *not* be defined
480     Affected verifications:
481      - 1D_ocean_ice_column (output.txt output_adm.txt)
482      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
483    o pkg/diagnostics:
484      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
485      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
486        (was _RL, now integer) with option = 0 to retrieve all levels.
487      - add pieces of code to compute velocity potential at each level (new diagnostics
488        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
489        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
490      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
491        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
492        and in diagnostics_fract_fill.F (do not need a valid pointer for the
493        diagnostics counter-mate); check that definition of counter-diagnostic
494        includes a valid counter-mate (in diagnostics_set_levels.F).
495    o model/src (rStar):
496      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
497        affect solution only if z* with full pressure in EOS;
498        update output of test-exp global_ocean.90x40x15.
499    o pkg/seaice:
500      - introduce siEps=1e-5 parameter
501      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
502      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
503      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
504        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
505        as well as ice cover age and ridging index (attached to AREA).
506        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
507        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
508        Up to SItrMaxNum=3 tracers can be used simultaneously.
509    o pkg/salt_plume:
510      -introduce SPsalFRAC run time parameter that sets the fraction of the
511       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
512       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
513    o model debug options:
514      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
515        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
516      - Refine debug-msg printing selection (3 new levels):
517        debugMode  : controls printing of debug messages (sequence of S/R calls).
518        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
519         debLevZero =  0 ; /* level of disabled aux. msg printing */
520         debLevA =  1 ; /* level of minimum  aux. msg printing */
521         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
522         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
523         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
524         debLevE =  5 ; /* level of extensive debug printing */
525        New debugLevel default: with default debugMode value (=F),
526          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
527          and if debugMode=T, default debugLevel = 4 (debLevD).
528        Relation with previous settings:
529         debLevB (=2) corresponds to former debLevA (=1)
530         debLevD (=4) corresponds to former debLevB (=2)
531        Note:
532         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
533         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
534            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
535      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
536        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
537    o pkg/obcs:
538      - change OBCSfixTopo default from True to False (should not change the results);
539        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
540    o pkg/thsice:
541      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
542        2nd layer seaice sublimation (unlikely to happen)
543      - use Interior mask for OBCS in thsice_advection.F (similar to what is
544        done in gad_advection & seaice_advection).
545    o adjoint:
546      bug fix spotted by Gael Forget:
547      seaice_advection and thsice_advection still had
548      legacy CPP options to avoid CS corner updates for adjoint
549    o pkg/seaice:
550      => Change some of the defaults (2011/05/29):
551         - change SEAICEuseFluxForm default (from False to True)
552         - change DIFF1 default (from 0.004 m/s to 0. m/s)
553         And print warnings if DIFF1 is not set in data.seaice and centered
554          avection scheme is used without any diffusion.
555      also:
556      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
557      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
558      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
559        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
560        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
561      update results of test exp.:
562         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
563             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
564             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
565         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
566         seaice_obcs: output (SEAICEuseFluxForm=T)
567      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
568          for standard fwd & AD lab_sea tests (to keep the same output).
569  o pkg/seaice/seaice_growth.F:  o pkg/seaice/seaice_growth.F:
570    - use Ian Fenty's capping formulas for actual ice    - use Ian Fenty's capping formulas for actual ice
571    thickness thoughout EVOLUTION branch.    thickness thoughout EVOLUTION branch.
572    - put treatment pathological case #2) in CPP brackets    - put treatment pathological case #2) in CPP brackets
573    (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).    (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
574    - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
575  o pkg/seaice:  o pkg/seaice:
576    - seaice_diffusion.F : remove the min(DX,DY) factor permanently;    - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
577    pass the Laplacian diffusivity (in m/s2) diffKh as a parameter;    pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
578    also pass fac as a param, which can be 1. (to update the tendency    also pass fac as a param, which can be 1. (to update the tendency
579    field) or the time step (to update the field itself).    field) or the time step (to update the field itself).
580    - seaice_advdiff.F: for multidim, call seaice_diffusion with    - seaice_advdiff.F: for multidim, call seaice_diffusion with
581    e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call    e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
582    seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.    seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
583    - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :    - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
584    hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.    hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
   - note: if any of SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.  
   is specified to be >0, then DIFF1 is set to 0.  
585  o pkg/seaice:  o pkg/seaice:
586    diffusion with centered advection scheme (diffus.F & advect.F):    diffusion with centered advection scheme (diffus.F & advect.F):
587    - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)    - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
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