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revision 1.1445 by gforget, Fri May 27 23:28:39 2011 UTC revision 1.1529 by jmc, Mon Nov 7 22:28:38 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 model/src:
8      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
9        truncation) and add diagnostics for Adams-Bashforth tendency increment.
10      - update test-exp. AD output:
11        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
12      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
13        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
14        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
15        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
16        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
17        tutorial_plume_on_slope.
18    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
19      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
20      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
21      does not even come with an F77 compiler anymore, this should not be
22      a limitation
23    
24    checkpoint63e (2011/11/06)
25    o pkg/seaice adjoint of LSR:
26      - substantially rework STORE dirs.
27      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
28        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
29        and only perform SOLV_MAX_FIXED adjoint iters.
30        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
31        always goes to same record, meaning that the last forward field will be
32        the one used in the adjoint - an approximation.
33      - now produces non-zero LSR-related gradients, and acceptable gradients for
34        An's zonal (x-z) test case (to be checked in)
35      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
36        (but these are screwed up by the thermodynamics in the first place);
37        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
38        output_adm.txt also reflects changes to seaice_lsr
39      - global_ocean.cs32x15:
40        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
41          (output_adm.seaice.txt was updated)
42        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
43          (output_adm.seaice_dynmix.txt)
44    o test-exp. exp4+stevens:
45      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
46    o pkg/seaice (lsr solver):
47      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
48        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
49      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
50      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
51        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
52      - compute (with new S/R) and print initial (+ free-driff sol. if available)
53        and final residual of linearised system.
54    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
55      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
56    o pkg/obcs: Stevens BCs (still only for east and west)
57      - fix Stevens BCs by using intermediate velocities of previous
58        time step as "baroclinic" contribution rather velocity of one grid cell
59        inside the boundaries; more consistent but makes the entire treatment
60        more complicated, requires new pickup files and two new S/Rs:
61        obcs_copy_uv_n and obcs_save_uv_n
62        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
63        (undefined by default)
64      - silently move computation of some grid factors into separate loops to
65        save some recomputations
66      - add a hack for non-linear free surface
67      - add a verification experiment to exp4 that tests this code
68    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
69    
70    checkpoint63d (2011/10/25)
71    o pkg/obcs + seaice-dynamics:
72      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
73        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
74        values (consistent with an implicit method).
75      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
76        return to older implementation (same results as before); note that none of
77        the "experimental" OBCS_SEAICE options are implemented in the new version.
78      - switch test exp. seaice_obcs to use new version (update output).
79    o pkg/seaice:
80      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
81      - add parenthesis in Water-Ice drag calculations (evp & lsr);
82      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
83        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
84      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
85        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
86    o pkg/layers:
87      - Include potential density as new coordinate (Thanks to David Munday)
88    o pkg/dic:
89      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
90        carbonate computation/output to CALC_PCO2_APPROX
91    o pkg/generic_advdiff
92      - make TAF generate code that vectorizes:
93        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
94    o model/src:
95      - improve vectorization also for adjoint code of
96        solve_tridiagonal and solve_pentadiagonal. As this requires up to
97        5 new 3D-fields, this code is only turned on for the combination of
98        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
99        for singular matrix check (only for TARGET_NEC_SX).
100      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
101        ALLOW_AUTODIFF. This flag now needs to be set outside of
102        solve_tri/pentadiagonal.F
103    o pkg/exf:
104      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
105        optional namelist EXF_NML_OBCS).
106      - add many debug-print (to trace down where pkg/cal error msg comes from)
107    o pkg/mom_vecinv/mom_vi_hdissip.F
108      - rearrange loops so that vectorization is improved and in particular
109        the adjoint routine vectorizes. The code is a little longer now, but I
110        think easier to read.
111        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
112    o pkg/seaice:
113      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
114    o pkg/exch2:
115      - alternative code (without tile x tile matrix) for cumulated (global) sum;
116        used as default; keep using matrix version in adjustment.cs-32x32x1.
117    o tools/build_options:
118      - after merging some MPI and/or multi-threads specific optfiles so that
119        the modified default optfile support both built (using genmake2 -mpi
120        for the MPI built, using genmake2 -omp for OpenMP built),
121        move now obsolete optfiles to tools/build_options/unsupported/
122       (add copy of email sent to support list in doc/optfiles_changes.txt)
123    
124    checkpoint63c (2011/09/28)
125    o pkg/ebm:
126      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
127        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
128    o pkg/seaice (SItracer pickup)
129    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
130      To be done:
131      - thorough testing of missing fields in S/R seaice_read_pickup
132      - thorough matching between generic tracers and specific fields used
133        (e.g. volume-weighted age, area-weighted age, salinity, ...)
134    o pkg/grdchk:
135      - all procs calculate and print finite-difference gradient (for testreport)
136      - change description output used by testreport;
137      - AD testing: also compare and report Finite-difference gradient;
138        => update all output_adm*.txt
139    o test exp. global_ocean_ebm:
140      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
141        and turn on exactConserve; update (fwd) output.
142    o pkg/seaice (LSR):
143      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
144      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
145        * identical results with non-CS topology (but save up to half of EXCH calls)
146        * no much changes in cs-32 verification tests since no ice at face edges
147         (differences due to convergence criteria, since nb of iterations changed)
148        * expect some differences on lat-lon-cap grid.
149        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
150    o pkg/exch2:
151      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
152        many tiles); until alternative coding is added, just add a stop.
153    o pkg/kpp:
154      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
155        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
156    o optfiles:
157      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
158        into corresponding standard one, which now support different build:
159        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
160      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
161    o pkg/obcs (seaice):
162      - add missing EXCH for uIce,vIce after applying OBCS;
163      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
164        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
165        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
166      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
167      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
168        and eedata.mth for MPI and mutlti-threaded testing.
169    o pkg/flt:
170      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
171      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
172      - fix pickup and trajectories + profiles output with multi-threads;
173      - add parameter to select group of fields to write along trajectory and
174        profile (default unchanged);
175      - only call PORT_RAND* function when flt_noise <> 0;
176      - add multi-threaded test for verification exp. flt_example.
177    o eesupp/src:
178      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
179      - USE_OMP_THREADING: check that number of threads (from eedata) matches
180        actual number (from env.var. setting).
181    o pkg/ebm:
182      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
183      - add multi-threaded test for verification exp. global_ocean_ebm
184    
185    checkpoint63b (2011/08/29)
186    o pkg/ebm:
187      - fix sign of runoff;
188      - update directly forcing fields (Qnet,EmPmR) to use standard
189        external_forcing_surf.F (remove ebm_forcing_surf.F);
190      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
191      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
192        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
193      - update global_ocean_ebm parameters file data and update output (fwd+ad).
194    o verification/matrix_example:
195      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
196        MPI and mutlti-threaded testing.
197    o pkg/matrix:
198      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
199      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
200      - fix for multi-threaded (remove DATA statement);
201      - use standard DIFFERENT_MULTIPLE function;
202      - add MATRIX_OPTIONS.h
203    o verification/matrix_example:
204       To allow to split the domain in several tiles, change the domain size
205        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
206        Western side) of land points.
207    o (*_)write_pickup:
208      - fix few bugs in mypackage_read/write_pickup.F
209      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
210        array of length 1 (was caught by compiler syntax-check).
211    o pkg/diagnostics (velocity potential solver):
212      - fix initialisation of main diagonal matrix (for overlap values)
213    o tools/build_options:
214      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
215        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
216      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
217        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
218        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
219        and use "-devel" testreport option for standard testing on baudelaire.
220    o pkg/grdchk:
221      - Assume that all gradient-check position are within the same tile
222        corresponding to global indices (iGloTile,jGloTile) and that
223        positions (i,j indices or nbeg) are local to this tile;
224      - set tile local-indices and proc. number according to tile global-indices;
225      - remove grdchkwhichproc from namelist (retired param);
226      - send adjoint gradient to all procs so that all procs print it to STDOUT;
227      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
228    o adding package bbl (Bottom Boundary Layer)
229      description in MITgcm/pkg/bbl/bbl_description.tex
230      example/test experiment in MITgcm_contrib/bbl
231    o adjoint verifications
232      - changed 5 experiments to multi-tiles
233        * global_ocean.90x40x15
234        * obcs_ctrl
235        * offline_exf_seaice
236        * tutorial_dic_adjoffline
237        * tutorial_tracer_adjsens
238        changed reference output for those that crossed tile boundaries
239        (changed choices of gradient check positions)
240      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
241      - temporary bug fix in grdchk_loc.F for obcs
242    o genmake2 & testreport
243      - add target "obj" (just for OBJFILES files) to Makefile;
244      - add option to specify FEXTRAFLAGS on command line.
245    o pkg/mypackage:
246      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
247    
248    checkpoint63a (2011/08/02)
249    o pkg/diagnostics (velocity potential):
250      - fix velocity-potential calculation when using OBCS: balance net inflow
251        at each level (new S/R OBCS_DIAG_BALANCE).
252      - fix some of the problems with OBCS in stream-function calculation.
253    o pkg/exf/exf_readparms.F
254      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
255        EXF_NML_OBCS) more consistent, so that you need not have these lists
256        in data.exf when they are not used.
257    o optim/optim_readdata.F:
258      - add some output about obcs variables that might help debugging
259      - add a check about nvarlength
260    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
261    o pkg/diagnostics (velocity potential):
262      - fix mask for OBCS (still problems in stream-function with OBCS);
263      - add specific parameter (default = main code CG2D params) for solver;
264      - in case of poor convergence, use solution corresponding to lowest residual.
265    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
266      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
267      and should be avoided where possible.
268    o model/src (rStar):
269      - include r* effect on reference-state (PhiRef) in totPhiHyd
270        (so that it's really the potential anomaly at the cell center);
271        affect solution only if z* with full pressure in EOS.
272      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
273        update output (because of z* in totPhiHyd and viscA4 changes);
274      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
275        @ constant r) until interpolation at constant r is implemented.
276    o pkg/diagnostics
277      - fix RCENTER diagnostics in case cell center is not at interface middle
278    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
279      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
280      that THETA and SALT are "conservative temperature" and "absolute
281      salinity"
282    o pkg/ctrl
283      - fix computation of endrec in s/r ctrl_init_rec
284      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
285    o pkg/seaice/seaice_growth.F
286      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
287        remove then obsolete STORE directives
288      - fix STORE directives for tice and tices, so that only the
289        appropriate part of the fields are stored (and not the entire
290        field); update global_ocean.cs32x15.seaice AD output.
291      - cosmetic changes: adjust CPP flags and indentation for better
292        legibilty
293    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
294      Chris Wilson)
295    o pkg/gmredi:
296       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
297       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
298    
299    checkpoint63  (2011/07/11)
300    o pkg/exch2:
301     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
302     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
303       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
304       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
305    o pkg/diagnostics:
306     - deal with pairs of post-processed diags which are computed together; in
307       particular, re-order list of diags within 1 file to save 2nd computation.
308     - add S/R to compute velocity stream-function (called after velocity-potential
309       calculation) from divergence free transport -> new diagnostics "PsiVEL".
310     - add parameter to select grid-point location where PsiVEL == 0.
311    o eesupp/src:
312       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
313       (specific S/R needed with exch2 topology - for now, just print an error msg)
314    o pkg/shelfice
315     - Implement friction velocity-dependent transfer coefficients following
316       Holland and Jenkins, JPO, 1999
317       Original code by M. Losch with small modifs.
318       Enable with CPP option SHI_ALLOW_GAMMAFRICT
319       and runtime flag SHELFICEuseGammaFrict
320    o verification lab_sea & global_ocean.cs32x15:
321     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
322       does not miss some dependencies (but is slower) and also works with many files
323       (default makedepend limitation for AD built).
324     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
325    o pkg/diagnostics:
326     - add run-time parameter "useMissingValue" (def=False) to fill land-point
327        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
328       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
329     - Extend the use of "missing_value" setting from data.diagnostics for the case
330       of counter-diagnostics (where fraction-weight is zero). This applies both to
331       MNC and MDS output files.
332    o pkg/seaice/seaice_growth.F:
333      - add 'a priori' cap of latent heat flux based on actual mass considerations
334        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
335        non-legacy seaice_solve4temp.
336      - add diagnostic of the residual sublimation freshwater flux (the freshwater
337        flux taken from the ocean if the total actual latent heat fluxes exceed
338        the maximum)
339      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
340       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
341      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
342       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
343      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
344      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
345    o verification 1D_ocean_ice_column:
346       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
347       update results
348    o pkg/diagnostics:
349     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
350       which are not filled-up but computed from other diags ; In this case, the mate
351       diag points to the primary (filled-up) diag to used for post processing.
352     - Update Velocity-potential computation using post-processed diag framework.
353     ==> Change the ordering of fields and time-periods in MDS output file
354       when using periodic averaging: now writes one time record with the full set
355       of fields for this time period, then the next time reccord (it used to be
356       one field with the full set of time records then the next field).
357         Note: this is now similar to NetCDF (MNC) output file. <==
358    
359    checkpoint62z (2011/06/21)
360    o adjoint monitor:
361     - Add adjoint monitor output for packages exf, seaice
362       and update relevant testreport output
363    o pkg/seaice:
364     - re-order diags inits so that they appear in order in available_diagnostics.log
365     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
366       area/heff/hsnow preceeding thermodynamic growth/melt.
367     - modified diag: SIdA; output actual effect, as the description states.
368     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
369     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
370       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
371        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
372     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
373     - added diagnostics for seaice generic tracers (SItr*).
374     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
375     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
376     I. Fenty: 18-Jun-2011:
377     Minor changes to seaice package:
378     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
379        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
380       - Differentiated "regularization variables" from "floor variables"
381        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
382        * hiceMin became SEAICE_hice_reg (old hiceMin)
383          (with _reg meaning regularization variable)
384       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
385        so as to ensure energy conservation when going between phases
386      - A22 was not used anywhere
387     2) Changed regularization procedure for heffActual and hsnowActual to ensure
388        well-boundedness and smooth adjoint in seaice_growth.F
389     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
390        because the old regularization always set heffActual >= 0.05 cm
391     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
392        on AREA when HEFF > 0.
393      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
394        requiring that DISABLE_AREA_FLOOR *not* be defined
395     Affected verifications:
396      - 1D_ocean_ice_column (output.txt output_adm.txt)
397      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
398    o pkg/diagnostics:
399      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
400      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
401        (was _RL, now integer) with option = 0 to retrieve all levels.
402      - add pieces of code to compute velocity potential at each level (new diagnostics
403        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
404        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
405      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
406        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
407        and in diagnostics_fract_fill.F (do not need a valid pointer for the
408        diagnostics counter-mate); check that definition of counter-diagnostic
409        includes a valid counter-mate (in diagnostics_set_levels.F).
410    o model/src (rStar):
411      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
412        affect solution only if z* with full pressure in EOS;
413        update output of test-exp global_ocean.90x40x15.
414    o pkg/seaice:
415      - introduce siEps=1e-5 parameter
416      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
417      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
418      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
419        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
420        as well as ice cover age and ridging index (attached to AREA).
421        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
422        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
423        Up to SItrMaxNum=3 tracers can be used simultaneously.
424    o pkg/salt_plume:
425      -introduce SPsalFRAC run time parameter that sets the fraction of the
426       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
427       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
428    o model debug options:
429      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
430        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
431      - Refine debug-msg printing selection (3 new levels):
432        debugMode  : controls printing of debug messages (sequence of S/R calls).
433        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
434         debLevZero =  0 ; /* level of disabled aux. msg printing */
435         debLevA =  1 ; /* level of minimum  aux. msg printing */
436         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
437         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
438         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
439         debLevE =  5 ; /* level of extensive debug printing */
440        New debugLevel default: with default debugMode value (=F),
441          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
442          and if debugMode=T, default debugLevel = 4 (debLevD).
443        Relation with previous settings:
444         debLevB (=2) corresponds to former debLevA (=1)
445         debLevD (=4) corresponds to former debLevB (=2)
446        Note:
447         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
448         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
449            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
450      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
451        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
452    o pkg/obcs:
453      - change OBCSfixTopo default from True to False (should not change the results);
454        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
455    o pkg/thsice:
456      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
457        2nd layer seaice sublimation (unlikely to happen)
458      - use Interior mask for OBCS in thsice_advection.F (similar to what is
459        done in gad_advection & seaice_advection).
460    o adjoint:
461      bug fix spotted by Gael Forget:
462      seaice_advection and thsice_advection still had
463      legacy CPP options to avoid CS corner updates for adjoint
464    o pkg/seaice:
465      => Change some of the defaults (2011/05/29):
466         - change SEAICEuseFluxForm default (from False to True)
467         - change DIFF1 default (from 0.004 m/s to 0. m/s)
468         And print warnings if DIFF1 is not set in data.seaice and centered
469          avection scheme is used without any diffusion.
470      also:
471      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
472      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
473      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
474        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
475        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
476      update results of test exp.:
477         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
478             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
479             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
480         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
481         seaice_obcs: output (SEAICEuseFluxForm=T)
482      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
483          for standard fwd & AD lab_sea tests (to keep the same output).
484  o pkg/seaice/seaice_growth.F:  o pkg/seaice/seaice_growth.F:
485    - use Ian Fenty's capping formulas for actual ice    - use Ian Fenty's capping formulas for actual ice
486    thickness thoughout EVOLUTION branch.    thickness thoughout EVOLUTION branch.
487    - put treatment pathological case #2) in CPP brackets    - put treatment pathological case #2) in CPP brackets
488    (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).    (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
489    - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
490  o pkg/seaice:  o pkg/seaice:
491    - seaice_diffusion.F : remove the min(DX,DY) factor permanently;    - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
492    pass the Laplacian diffusivity (in m/s2) diffKh as a parameter;    pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
493    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
494    field) or the time step (to update the field itself).    field) or the time step (to update the field itself).
495    - seaice_advdiff.F: for multidim, call seaice_diffusion with    - seaice_advdiff.F: for multidim, call seaice_diffusion with
496    e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call    e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
497    seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.    seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
498    - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :    - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
499    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.  
500  o pkg/seaice:  o pkg/seaice:
501    diffusion with centered advection scheme (diffus.F & advect.F):    diffusion with centered advection scheme (diffus.F & advect.F):
502    - 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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