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revision 1.1445 by gforget, Fri May 27 23:28:39 2011 UTC revision 1.1678 by jmc, Thu Jun 28 15:36:41 2012 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o vertical mixing schemes:
8      - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging)
9      - replace computation of density (in Function STATE1, opps_calc.F) by a call
10        to S/R FIND_RHO_SCALAR
11      - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC
12        and use it for N^2 calculation in ggl90_calc.F (save 2 density computations);
13        affects output (vermix.ggl90) at truncation level.
14    o testreport:
15      - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles
16        (nSx,nSy) for the number of threads (from eedata.mth)
17    o model/src:
18      - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part)
19        related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary).
20    o verification/tutorial_tracer_adjsens/
21      - compile with ALLOW_CG2D_NSA
22      - run with nonlinFreeSurf=3
23      - update reference output_adm.txt
24    o tools/genmake2:
25      - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
26        refine usePROFILES switching off (only when NetCDF is not available).
27    o verification (atmospheric set-up):
28      - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
29    o pkg/profiles : refine profiles and files handling.
30    o model/src and pkg/ecco : introduce run-time switch usePROFILES.
31    o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
32      - changes to use model/src/the_main_loop.F rather than the ecco version
33        in ecco type adjoint runs.
34    o model/src:
35      - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
36      - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
37      - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
38    o model/src:
39      - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
40        update output of test experiment bottom_ctrl_5x5.
41    o pkg/generic_advdiff:
42      - implement vertical bi-harmonic diffusion (for now, only for T & S and
43        only explicitly).
44    o verification/bottom_ctrl_5x5/
45      update reference output (results changed quite some time ago,
46      not sure when; but new reference results look ok in terms of grdchk)
47    o verification/1D_ocean_ice_column/
48      For verification purposes, the exact adjoint rather than an approx.
49      should be used (e.g., to comare against F.D. or TLM).
50      removed autodiff_inadmode*_ad.F routines in code_ad/
51      Update results/ accordingly.
52    o pkg/cal:
53      - change cal_getdate.F so that output date is function of input time only
54        (less ambiguous, not mixed up with input iteration number).
55      - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
56    o pkg/diagnostics:
57      - implement calendarDumps also for stats-diags
58      - implement calendarDumps also for snap-shot output (negative freq)
59      - for now, ignores calendarDumps if non-zero phase-lag.
60    
61    checkpoint63n (2012/06/04)
62    o model/src:
63      - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
64        between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
65      - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
66        similar to calc_r_star.F); update results of experiment internal_wave and
67        tutorial_global_oce_in_p (affected @ truncation level).
68    o pkg/shelfice:
69      - add parameterisation of advective-diffusive flux into the ice shelf
70        according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
71      - simply eps3/3a computation
72    o eesupp:
73     - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
74       between tiles, just fill-in edges assuming locally periodic subdomain) and
75       add corresponding exchange subroutines (EXCH0);
76     - new CG-solver version (_EX0) for disconnected-tiles special case.
77    o model/src (CG-solvers):
78     - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
79       (similar final residual output and max-Iter number as with standard version);
80     - allows to store and use lowest-residual solution (standard & _SR versions);
81     - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
82     - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
83    o eesup/src:
84     - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
85       ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
86    o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
87    
88    checkpoint63m (2012/04/27)
89    o pkg/shelfice:
90     - account for partical cells in surface level below ice-shelf for hydrostatic
91       pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
92    o ad test experiments:
93     - update and rename to "ad_optfile.local" local AD-optfile specific to a
94       particular adjoint verification experiment (in verification/*/code_ad/)
95    o pkg/seaice & pkg/exf:
96     - Part two of ECCO-CLIVAR code merges.
97       Completes merge of seaice area relax. code.
98       Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
99       to be set in EXF_OPTIONS.h since this pkg controls its I/O
100       (and avoids second CPP option in SEAICE_OPTIONS.h)
101     - change default value of costIceStart & costIceEnd to a valid date.
102     - add snowPrecip to HSNOW in seaice_growth
103    o pkg/ptracers:
104     - move ptracers summary and setup check into separated S/R ; add a check for
105       valid PTRACERS_Iter0 value (error+stop or just warning).
106    o pkg/cal (+ pkg/ecco):
107     - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
108       as input; and for AD, unless both are not differentiable (e.g., k index)).
109    o model/src:
110     - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
111       is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
112       temporary set to usingZCoords value (to be changed to F when using shelfice).
113     - hydrostatic pressure: implement partial cell near the surface also for
114       Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
115       usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
116    o pkg/ctrl/ctrl_init.F:
117     - add a formal parameter to s/r ctrl_init_rec to print
118       xx_$(ctrl_valiable)_file for easier debugging
119     - move call of cal_* routines into the if-block where they are really
120       needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
121       to specify a startdate
122    o pkg/seaice:
123     - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
124       global_ocean.cs32x15/code versions).
125     - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
126       verification experiment global_ocean.cs32x15.seaice and update results.
127    o pkg/exf:
128     - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
129       (according to useExfYearlyFields).
130    o pkg/cal:
131     - move calendar setting & summary (previously in cal_readparams.F) into new
132       S/R CAL_INIT_FIXED to be called later in the initialisation process, once
133       length of the simulation is set (after SET_PARMS call); This is an attempt
134       to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
135     - For safety: keep a record of pkg/cal parameter settings status
136               to allow to STOP if one pkg/cal S/R is called too early.
137     - add a stop in all basic pkg/cal subroutines if called before setting is done.
138     - modify cal_getdate.F: stop when nothing was returned;
139       if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
140       this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
141    
142    checkpoint63l (2012/04/04)
143    o pkg/bbl:
144      - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
145        update global_with_exf output.yearly.txt file.
146    o pkg/cal:
147      - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
148      - remove 2 unsused and very short (1 line only) functions ;
149      - remove unsused subroutines from AD-Diff list.
150    o model/src:
151      - start to implement clean wait to stop in initialization S/R (config_check.F,
152         packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
153    o folowing PRINT_MESSAGE changes:
154      - remove reminder multiple print to the same file (STDOUT) when multi-threads.
155    o pkg/bbl:
156      - modification so it can work with z*
157      - replace deltaT with dTtracerLev(k) for asynchronous time stepping
158      - global_with_exf/input.yearly verification; changes output.yearly.txt
159    o eesupp/src:
160      - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
161        writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
162      - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
163        # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
164      - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
165      - when using MPI, always set usingMPI=T ; set default accordingly and stop
166        if not consistent.
167      - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
168        argument is zero (in case called within single-thread section).
169    o pkg/fizhi:
170        clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
171        in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
172    o pkg/exch2:
173      - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
174        activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
175      - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
176        but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
177        with bad ones coming from a not-yet-updated halo.
178        This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
179    o pkg/frazil:
180        move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
181        http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
182    o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
183    o verification/lab_sea
184      * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
185      * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
186      * nTimeSteps 3 -> 4
187      * changed reference output accordingly
188    o pkg/ctrl:
189      * fix ctrl_get_gen for xx_sst, xx_sss
190    o pkg/fizhi:
191      - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
192        update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
193      - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
194        fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
195        clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
196    o pkg/gmredi:
197      - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
198    o pkg/fizhi:
199      - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
200        (old)aces open64 tuv test.
201    o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
202    o pkg/mom_vecinv:
203      - fix 1 loop range in mom_vecinv.F to be like all the other loops which
204        set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
205        with non-lin free-surf).
206    o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
207      in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
208      some compilers (gfortran 4.6.0 on MacOS)
209    o momentum:
210      - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
211        & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
212        fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
213    
214    checkpoint63k (2012/03/17)
215    o model/src:
216       - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
217         flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
218       - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
219         (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
220    o model/src: solve_*diagonal.F
221       - replace division with multiplication by inverse (similar to original version)
222         update output of AD exp. global_ocean.90x40x15.
223       - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
224         to enable the use of the vectorized & differentiable solve_tridiagonal.F
225       - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
226         vertical advection (to get solve_tridiagonal tested in AD mode).
227    o pkg/seaice: ECCO-CLIVAR merge:
228      1. seaice AREA relaxation
229         * CPP option: SEAICE_ALLOW_AREA_RELAXATION
230         * runtime flag: SEAICE_tauAreaObsRelax
231      2. modified global mean cost imbalance code: CPP option
232          ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
233    o another iteration on solve_*diagonal.F
234       Make choices independent of AUTODIFF
235       Default will be the adjoinable vectorized version.
236       Alternative choices are:
237       * non-adjoinable original version with low memory footprint:
238         #define SOLVE_DIAGONAL_LOWMEMORY
239       * still adjoinable but does not vectorize (k as inner-most loop):
240         #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
241    o testreport
242     - add option to use a home made wrapper around "make"
243     - remove MITGCM_IEEE env. variable (no longer active)
244    o pkg/shelfice
245     - improve computation of friction velocity for velocity dependent
246       exchange coefficients: include velocities into SHELFICEBoundaryLayer
247       block to average velocities vertically
248     - add TAF store directives for SHI_ALLOW_GAMMAFRICT
249    o Modify diagonal solvers, now three versions (upon request):
250      #ifndef SOLVE_DIAGONAL_AUTODIFF
251        1. default version (dating back a while ago)
252      #else /* def SOLVE_DIAGONAL_AUTODIFF */
253      # ifdef SOLVE_DIAGONAL_KINNER
254        2. adjoinable version with k-innermost loop (G. Forget)
255      # else
256        3. adjoinable vectorized version of 2.
257      # endif
258      #endif /* SOLVE_DIAGONAL_AUTODIFF */
259      All flags are currently set within routines, but could/should be moved to CPP-options.
260      Array bounds for 1. are as before, for 2.,3. cover the entire domain
261      (could be changed for 1. too).
262    o verification/lab_sea (fwd):
263      - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
264        use 7 categories (except hb87), new solve4temp params (except salt_plume),
265        constant salinity (=4) or variable salinity (salt_plume) done through
266        SItracer.
267    o pkg/seaice:
268      - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
269      - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
270         SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
271        from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
272        SEAICE_freeze got retired) but already better than previously with
273        SEAICE_freeze=123456.7 deg.C;
274      - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
275        (safer multi-threaded setting); always set SEAICEuseEVP;
276      - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
277        SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
278        stop if multiple specifications for the same coeff; make sure default
279        SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
280    o pkg/obcs:
281      - allow to switch to upwind 1rst order advection scheme for the advective
282        flux computation at the open-boundary; disabled for adjoint built.
283    o pkg/ptracers:
284      - rename PTRACERS_RESTART.h -> PTRACERS_START.h
285      - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
286      - add parameter to decide when to start a tracer; use internal flag to
287        know which tracer to step-forward; switch this internal flag at the top
288        of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
289        for adjoint built.
290    o pkg/seaice:
291      - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
292      - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
293      - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
294    o pkg/ecco:
295      - fix writing of output file DiagnosCost_ClimSalt/Theta
296        and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
297    o pkg/seaice:
298      - add missing initialisation of COR_ICE array in dynsolver.F
299      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
300        compiled either way, and is tested in all exps (multidim was only tested
301        in lab_sea ad before).
302      - cosmetic change to prepare for future addition of ITD. no change to results.
303        no defaults change.
304      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
305      - by lack of adequate verification experiments, I further used custom versions
306        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
307        should be correct.
308      - avoid recomputations in ad.
309    o array initialisation in adjoint mode:
310      1) pkg/mom_common/mom_calc_ke.F:
311        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
312        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
313        part this initialisation is gone, resulting in Floating Point Exception
314        (caught by open64 compiler with debug option).
315      2) model/src/convective_weights.F
316        set output convectCount over the full array range (instead of doing
317        an update): this fix a similar issue when called within recomputation (adjoint)
318        which could by-pass the initialisation (normally done in the caller S/R).
319    o pkg/seaice:
320      - final version of turbulent flux params, as agreed at MIT ice meet:
321           SEAICE_mcPheePiston (default is ~ 0.000875)
322           SEAICE_mcPheeTaper (default is 0.)
323           SEAICE_frazilFrac (defualt is 1.)
324           SEAICE_mcPheeStepFunc (default is false)
325      - changes results at trunction error level
326      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
327    o added pkg/frazil:
328      - see frazil_description.tex for details
329      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
330    o pkg/shelfice/shelfice_thermodynamics.F
331      - fix exponents for velocity dependent exchange coefficients: change
332        from 2/3(=0) to 0.66666666666666667
333      - move computation of velocity dependent exchange coefficients into
334        separate loop, so that it applies to both thermodynamics
335      - move some divisions by constants out of loops
336    
337    checkpoint63j (2012/02/16)
338    o pkg/seaice:
339      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
340      - SItracer:  added run time params, and allow coupling to ocn salinity.
341    o pkg/seaice: remove (almost) all divisions by constants within loops
342      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
343      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
344      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
345      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
346    o pkg/seaice :
347      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
348        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
349      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
350      - add permanent SItflux diag that corresponds to TFLUX but includes
351        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
352      - allow activation/testing of a fix for suspected missing term in
353        ocn-ice heat budget (to be confirmed). To test this, you want to
354        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
355        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
356      - no change in results, fwd or ad.
357    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
358      - switch to variable freezing point.
359           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
360      - bug fix : the sublimation term that was missing is now activated.
361           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
362      - bug fix : flooding sign term for SIsal0.NE.0.
363           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
364    o pkg/seaice:
365      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
366        is now the default, and the old default constant freezing point is recovered
367        with SEAICE_tempFrz0    = -1.96,
368             SEAICE_dTempFrz_dS = 0.,
369      - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
370      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
371      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
372        activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
373      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
374        was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
375      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
376        seaice_growth r149 for legacy branch (no results change).
377      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
378        from I. Fenty).
379      - results did not change except for global_ocean.cs32x15, mostly due to the
380        switch to variable freezing point (see above item for detail).
381    o pkg/thsice:
382      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
383        seawater freezing in thsice_calc_thickn (not used).
384    o pkg/seaice: turbulent flux term specification via run time params.
385      - replace CPP switches with run time switches to facilitate testing
386      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
387                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
388      - added runtime parameter : SEAICEturbFluxFormula
389      - move Mcphee constants to SEAICE_PARAMS.h
390      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
391                 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
392                 remove seaice_summary call (moved to seaice_init_fixed)
393      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
394        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
395      - seaice_summary.F : add missing report of read turbulent flux term set up
396                           and SITRACER.
397      - seaice_check.F : check range; inform and stop if retired CPPs are used
398                         (incl. SEAICE_AGE).
399      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
400             CPP switch, same computation as before for the different options.
401      - change results at the truncation level.
402    o pkg/seaice:
403      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
404        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
405        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
406      - update verification/*/input*/data.seaice:
407        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
408        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
409        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
410        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
411    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
412      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
413        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
414        difference in results only due to machine truncation.
415      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
416        MaykutPolySatVap; keep MIN_LWDOWN.
417      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
418      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
419        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
420    o pkg/salt_plume:
421      - isolate saltPlumeFlux array exch into a specific S/R called from
422        do_oceanic_phys.F
423      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
424    o verification:
425      - move untested set-up to MITgcm_contrib/verification_other.
426    o pkg/seaice:
427      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
428    o pkg/seaice:
429      - seaice_solve4temp.F (keeping results unchanged):
430        * add 2 future run-time params to select which saturation vapor pressure
431          formula is used and how post-iteration fluxes are set.
432          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
433        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
434          the linearized expression to stay consistent with tsurf finding.
435      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
436        can be < 0.
437    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
438      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
439        conductive heat flux F_c , and add it explicitly when updating tsurf as
440        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
441        so that now F_ia has a consistent meaning through the entire routine.
442        This causes differences at truncation level: update output of fwd exp.
443        global_ocean.cs32x15.seaice.
444    o pkg/seaice:
445      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
446        of arrays, sign/direction of fluxes; no effect on results.
447      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
448        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
449        note: this should have been done before changing celsius2K default.
450      - to keep results unchanged, add back old value of celsius2K in verification
451        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
452      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
453        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
454        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
455        freezing temp is consistent with value in seaice_growth.F ; this causes
456        differences at machine truncation level: update lab_sea AD output (3/4).
457    o pkg/seaice:
458      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
459        and climsst/sss even when using seaice (to prevent calculation that might
460        use SST on land); does not affect any verification exp.
461      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
462        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
463    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
464      over land (non-legacy code)
465    o vectorize salt_plume package:
466      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
467      - this code computes plumebk everywhere (also over land), thus requires
468        code to avoid divisions by zero and catch the case of kLev=Nr.
469      - efficiency of salt_plume_frac is still sub-optimal
470    o tools (genmake2):
471      - fix makefile NAME specification (option: -makefile NAME) by adding
472        "-f $MAKEFILE" in few places where it was missing including makedepend
473        command (contribution from Paul).
474    
475    checkpoint63i (2012/01/24)
476    o model/src:
477      - add factorized versions of some EOS code to find_rho.F,
478        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
479    o model/src:
480      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
481      - change default celsius2K from 273.16 to 273.15
482      - to keep results unchanged, add back old value of celsius2K in verification
483        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
484         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
485    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
486      to make TAF generate vectorizable code
487    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
488       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
489       have flags that do this more efficiently.
490    o pkg/diagnostics/diagstats_calc.F
491      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
492    o pkg/obcs (with exch2):
493      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
494        and remove code (in obcs_readparms.F) which was based on EXCH of indices
495        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
496    o pkg/exf and seaice exp:
497      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
498        so that switching off area & heff advection flags does not affect results.
499      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
500      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
501        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
502        results of verification experiments: 1D_ocean_ice_column(fwd),
503        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
504        and offline_exf_seaice (all 4).
505    o pkg/seaice:
506      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
507        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
508      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
509        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
510        not multi-dim advection;
511      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
512        SHORTWAVE_HEATING #undef.
513    o optim: make Makefile more robust (?)
514    o pkg/obcs:
515      * fix treatment of obcs_read_pickup for TAF
516    o pkg/shelfice:
517      * add missing initialisation of num_shifwflx
518      * new adjoint verification exp. for isomip
519      * change Prandtl and Schmidt numbers from generic formulations
520        (in terms of model diffus. and visc.) to separate runtime
521        parameters, with Holland and Jenkins (1999) default values.
522    o pkg/exf (interpolation):
523      - extended input field (2 rows) near the N & S poles:
524        * fill in with the symetric value (when even Nb of data in longitude)
525        * add average value at the poles only for scalar quantities ; for vector
526          component interpolation, skip the averaging and keep duplicated values,
527          unless the 2 components have same location (uvInterp=T) in which case
528          interpolate the 2 components together using S/R EXF_INTERP_UV.
529      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
530        together: this allows to account properly for local orientation when
531        averaging at N & S pole.
532      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
533        exf-interpolation near N & S poles. Undef by default.
534      - add debug check/print on 1rst iter if debugLevel >=2.
535    o pkg/exf:
536      - change masking flags definition (no longer "parameter"), put them in
537        common block and set them in S/R EXF_INIT_FIXED.
538      - change recognized masking flag from s,u,v to c,w,s since the mask
539        to use (maskC,W,S) depends on position on model grid and has little to
540        do with scalar/vector difference; fix masking if using P-coordinates.
541      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
542        and update results of exp. global_with_exf (x2).
543      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
544    o pkg/obcs
545      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
546    o pkg/exf (interpolation):
547      - assume periodicity in X only if input field cover full longitude range.
548      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
549        and should vectorise).
550      - fix input lat of the 2 added row (in case we provide N.pole data).
551    
552    checkpoint63h (2011/12/30)
553    o pkg/seaice:
554      - change declaration of UVM from _RL to _RS in order to get B-grid
555        uIce,vIce monitor when _RS = real*4
556    o pkg/offline:
557      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
558      - compute vertical velocity if not read from file (switch on exactConserv
559        & staggerTimeStep);
560      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
561    o verification:
562      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
563        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
564        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
565      - update output of exp. global_ocean.cs32x15.viscA4 after changing
566        grid-file angles (used here for coriolis-3d);
567      - remove (or gzip) few files not needed to run fizhi-cs experiments.
568    o pkg/exf (vector interpolation):
569      - rotate vector component toward local grid-axis orientation using grid-angles
570        (stored in GRID.h) instead of locally computed rotation angle; keep old code
571        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
572    o pkg/seaice:
573      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
574        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
575    o pkg/PKG_OPTIONS.h files:
576      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
577        outside of the #ifdef ALLOW_THISPKG / #endif block.
578      - update verification/*/code/PKG_OPTIONS.h files.
579    o add a verification experiment (offline_exf_seaice/input.seaice) that test
580      the B-grid LSOR solver
581    o pkg/seaice: sort out emissivity and long wave radiation step 2:
582      - add emissivity for snow and ice as new run-time parameters
583        (unfortunately) that default to the corresponding exf values; this
584        changes results in most verification experiments so that for backward
585        compatibility these parameter have to be set explicitly to inconsistent
586        values (ugly);
587      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
588        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
589        until we agree how to handle this bug properly
590    o pkg/exf (interpolation):
591      - add a set of run-time param ({inputfield}_interpMethod), one for
592        each interpolated input field, to select the interpolation method
593        with a value of zero switching off the interpolation;
594      - print interpolation parameters to standard output;
595      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
596        (to use instead runoff_interpMethod=0 in data.exf).
597      - simplify default setting of interpolation parameters (for all fields,
598        set position to match model grid cell-center position, leading to trivial
599        interpolation in case of regular Lat-Lon grid) and fix for the case of
600        non-uniform delY.
601    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
602       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
603       this factor is absolutely required, because the lw exitance (= out-going
604       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
605       where the reflectivity rho = 1-emissivity for conservation reasons. Once
606       this is established, we can remove the CPP-Flag (if we want to).
607    o pkg/seaice:
608      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
609        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
610      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
611        what the name implies (and not emissivity*BoltzmannConstant), this means
612        the old default value of 5.5e-8 now means
613        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
614        S/R exf_readparms
615      - FV-discretization of the B-grid LSOR solver, turn on with
616        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
617        of the calling routine dynsolver, so that B and C-grid code look a
618        little more alike.
619      - fix index bugs in ostres.F (B-grid code)
620    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
621    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
622      default for SEAICE_emissivity, if useEXF; requires setting a wrong
623      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
624      backward compatiblity
625    o model/src: use sigmaR in calc_ivdc
626    
627    checkpoint63g (2011/12/16)
628    o pkg/seaice/seaice_growth.F:
629      fix heat conservation of the coupled ocean-seaice system.
630      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
631      solid vs liquid water treatment is resolved via QNET.
632    o pkg/seaice/seaice_growth.F:
633      add missing term for sublimation in saltFlux, which was breaking conservation.
634    o pkg/seaice/seaice_model.F:
635      Remove this patholigical case treatment in evolution branch,
636      where it is un-necessary and breaks conservation.
637      Update global_ocean.cs32x15/results accordingly for
638      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
639    o model/src:
640      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
641      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
642    o pkg/obcs:
643      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
644      tendency for temperature and salinity that is then applied to update
645      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
646      horizontal advection and diffusion contributions on the boundary (in
647      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
648      removing the mask in S/R timestep_tracer. The advantage of this approach is
649      that the updated tracer values include contributions from the surface
650      forcing and vertical diffusion.
651      This modification changes exp4.stevens because of vertical diffusion.
652    o model/src:
653      change non-curvilinear grid setting to also work with exch2 + blank tiles:
654      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
655        face dimensions.
656      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
657        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
658        and INI_SPHERICAL_POLAR_GRID.
659      change test-experiment global_ocean.90x40x15:
660      - split the domain in many more tiles (9x4 tiles of 10x10 each);
661      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
662      - update results of both test (std & dwnslp).
663    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
664       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
665    o model/src:
666      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
667        and fix initialisation when using sigma-coords.
668    o model/src:
669     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
670       to their current value at the beginning of forward_step.F": add a new run-time
671       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
672     - set doResetHFactors=T in the following test exp:
673        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
674        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
675        and tutorial_global_oce_in_p (nonLinFS in p)
676    o pkg/ecco
677      - added IES cost term
678    o verification/advect_xz
679      - scale down the depth by 1/100 (from 200 km to just 2.km)
680      - add secondary test using divergent flow, r-star and implicit vertical advection.
681      - add note (check_conserve_TS.txt) and matlab script to check global
682        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
683    o pkg/rbcs:
684      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
685    o pkg/obcs (Stevens BCs):
686      - fix various problems in the phase speed computations of the Stevens
687        boundary conditions:
688        - sign error for western and southern boundaries,
689        - time tendencies were underestimated by factor of dTracerLev and some just
690          zero (for multidim advection schemes) -> now estimate time tendencies
691          from difference between previous (n) time level and the one before (n-1);
692          this requires storing a field per tracer per boundary, also in the pickup
693          files.
694        - replace deltaTmom in cflMer/Zon computation with dTracerLev
695        - set default phase velocity to cflMer/Zon
696      - update verification experiment exp4.stevens
697    o pkg/generic_advdiff (implicit_r):
698      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
699        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
700      - fix implicit vertical diffusion or advection with NonLin FreeSurf
701        (was using current recip_hFacC instead of future recip_hFacC): set future
702        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
703        solver S/R ;
704      - fill diagnostics of vertical advective fluxes (computed from tendency)
705        when using implicit vert. advection;
706      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
707         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
708         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
709         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
710    o pkg/diagnostics:
711      - add diags for T & S tendency which goes through Adams-Bashforth.
712    
713    checkpoint63f (2011/11/30)
714    o pkg/obcs/obcs_calc_stevens.F:
715      - join some loops to reduce number of if-statements
716      - fix a bug in code for northern and southern boundaries.
717    o pkg/seaice/seaice_init_varia.F
718      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
719        caused zero ice-velocities for the B-grid code
720    o pkg/seaice/seaice_init_fixed.F
721      - fix a bug in the initialisation of the second metric terms
722        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
723      - this affects all seaice configurations with useCurviLinearGrid = .true.
724        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
725        = .true. (default)
726      - the only verification experiment affected is global_ocean.cs32x15:
727        icedyn, seaice, and seaice_dynmix (AD)
728    o pkg/thsice/thsice_diagnostics_state.F
729      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
730        not contain garbage that can lead to surprises in diagstats_calc.F
731    o model/src:
732      - move bi,bj loops inside INTEGR_CONTINUITY ;
733      - call INTEGR_CONTINUITY directly from forward_step.F
734        (previously called from momentum_correction_step.F)
735      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
736        forward_step.F and pkg/ecco/the_main_loop.F
737    o model/src/do_oceanic_phys.F:
738      - reset addMass to zero only if useICEFRONT ;
739      - separated k-loop for rhoInSitu calculation ;
740      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
741        and at constant T,S (= WdRHOdP);
742      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
743        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
744        transport of locally-referenced potential density);
745        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
746    o gluemnc:
747      - replace ncrcat with ncks when adding variables to *.glob.nc
748      - change the way variables without record dimensions are handled so that
749        files that have variables with and without record variables can be glued:
750        add a record dimension with a new unique name to be able to differentiate
751        between variable with and without a-prior record dimensions. Remove
752        this record dimension before adding the variable to the *.glob.nc file.
753        This procedure automatically works also for grid.*.nc files that do not
754        have any record dimension.
755    o verification/cpl_aim+ocn:
756      - generate new reference output on baudelaire (gfortran, mpich2) (previously
757        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
758    o pkg/obcs/obcs_calc_stevens.F:
759      - add code for northern and southern boundaries.
760      - reorder some loops to save some operations and so that drFBar can be scalar
761    o model/src:
762      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
763        truncation) and add diagnostics for Adams-Bashforth tendency increment.
764      - update test-exp. AD output:
765        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
766      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
767        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
768        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
769        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
770        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
771        tutorial_plume_on_slope.
772    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
773      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
774      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
775      does not even come with an F77 compiler anymore, this should not be
776      a limitation
777    
778    checkpoint63e (2011/11/06)
779    o pkg/seaice adjoint of LSR:
780      - substantially rework STORE dirs.
781      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
782        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
783        and only perform SOLV_MAX_FIXED adjoint iters.
784        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
785        always goes to same record, meaning that the last forward field will be
786        the one used in the adjoint - an approximation.
787      - now produces non-zero LSR-related gradients, and acceptable gradients for
788        An's zonal (x-z) test case (to be checked in)
789      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
790        (but these are screwed up by the thermodynamics in the first place);
791        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
792        output_adm.txt also reflects changes to seaice_lsr
793      - global_ocean.cs32x15:
794        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
795          (output_adm.seaice.txt was updated)
796        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
797          (output_adm.seaice_dynmix.txt)
798    o test-exp. exp4+stevens:
799      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
800    o pkg/seaice (lsr solver):
801      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
802        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
803      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
804      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
805        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
806      - compute (with new S/R) and print initial (+ free-driff sol. if available)
807        and final residual of linearised system.
808    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
809      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
810    o pkg/obcs: Stevens BCs (still only for east and west)
811      - fix Stevens BCs by using intermediate velocities of previous
812        time step as "baroclinic" contribution rather velocity of one grid cell
813        inside the boundaries; more consistent but makes the entire treatment
814        more complicated, requires new pickup files and two new S/Rs:
815        obcs_copy_uv_n and obcs_save_uv_n
816        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
817        (undefined by default)
818      - silently move computation of some grid factors into separate loops to
819        save some recomputations
820      - add a hack for non-linear free surface
821      - add a verification experiment to exp4 that tests this code
822    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
823    
824    checkpoint63d (2011/10/25)
825    o pkg/obcs + seaice-dynamics:
826      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
827        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
828        values (consistent with an implicit method).
829      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
830        return to older implementation (same results as before); note that none of
831        the "experimental" OBCS_SEAICE options are implemented in the new version.
832      - switch test exp. seaice_obcs to use new version (update output).
833    o pkg/seaice:
834      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
835      - add parenthesis in Water-Ice drag calculations (evp & lsr);
836      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
837        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
838      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
839        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
840    o pkg/layers:
841      - Include potential density as new coordinate (Thanks to David Munday)
842    o pkg/dic:
843      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
844        carbonate computation/output to CALC_PCO2_APPROX
845    o pkg/generic_advdiff
846      - make TAF generate code that vectorizes:
847        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
848    o model/src:
849      - improve vectorization also for adjoint code of
850        solve_tridiagonal and solve_pentadiagonal. As this requires up to
851        5 new 3D-fields, this code is only turned on for the combination of
852        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
853        for singular matrix check (only for TARGET_NEC_SX).
854      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
855        ALLOW_AUTODIFF. This flag now needs to be set outside of
856        solve_tri/pentadiagonal.F
857    o pkg/exf:
858      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
859        optional namelist EXF_NML_OBCS).
860      - add many debug-print (to trace down where pkg/cal error msg comes from)
861    o pkg/mom_vecinv/mom_vi_hdissip.F
862      - rearrange loops so that vectorization is improved and in particular
863        the adjoint routine vectorizes. The code is a little longer now, but I
864        think easier to read.
865        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
866    o pkg/seaice:
867      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
868    o pkg/exch2:
869      - alternative code (without tile x tile matrix) for cumulated (global) sum;
870        used as default; keep using matrix version in adjustment.cs-32x32x1.
871    o tools/build_options:
872      - after merging some MPI and/or multi-threads specific optfiles so that
873        the modified default optfile support both built (using genmake2 -mpi
874        for the MPI built, using genmake2 -omp for OpenMP built),
875        move now obsolete optfiles to tools/build_options/unsupported/
876       (add copy of email sent to support list in doc/optfiles_changes.txt)
877    
878    checkpoint63c (2011/09/28)
879    o pkg/ebm:
880      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
881        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
882    o pkg/seaice (SItracer pickup)
883    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
884      To be done:
885      - thorough testing of missing fields in S/R seaice_read_pickup
886      - thorough matching between generic tracers and specific fields used
887        (e.g. volume-weighted age, area-weighted age, salinity, ...)
888    o pkg/grdchk:
889      - all procs calculate and print finite-difference gradient (for testreport)
890      - change description output used by testreport;
891      - AD testing: also compare and report Finite-difference gradient;
892        => update all output_adm*.txt
893    o test exp. global_ocean_ebm:
894      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
895        and turn on exactConserve; update (fwd) output.
896    o pkg/seaice (LSR):
897      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
898      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
899        * identical results with non-CS topology (but save up to half of EXCH calls)
900        * no much changes in cs-32 verification tests since no ice at face edges
901         (differences due to convergence criteria, since nb of iterations changed)
902        * expect some differences on lat-lon-cap grid.
903        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
904    o pkg/exch2:
905      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
906        many tiles); until alternative coding is added, just add a stop.
907    o pkg/kpp:
908      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
909        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
910    o optfiles:
911      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
912        into corresponding standard one, which now support different build:
913        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
914      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
915    o pkg/obcs (seaice):
916      - add missing EXCH for uIce,vIce after applying OBCS;
917      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
918        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
919        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
920      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
921      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
922        and eedata.mth for MPI and mutlti-threaded testing.
923    o pkg/flt:
924      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
925      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
926      - fix pickup and trajectories + profiles output with multi-threads;
927      - add parameter to select group of fields to write along trajectory and
928        profile (default unchanged);
929      - only call PORT_RAND* function when flt_noise <> 0;
930      - add multi-threaded test for verification exp. flt_example.
931    o eesupp/src:
932      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
933      - USE_OMP_THREADING: check that number of threads (from eedata) matches
934        actual number (from env.var. setting).
935    o pkg/ebm:
936      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
937      - add multi-threaded test for verification exp. global_ocean_ebm
938    
939    checkpoint63b (2011/08/29)
940    o pkg/ebm:
941      - fix sign of runoff;
942      - update directly forcing fields (Qnet,EmPmR) to use standard
943        external_forcing_surf.F (remove ebm_forcing_surf.F);
944      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
945      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
946        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
947      - update global_ocean_ebm parameters file data and update output (fwd+ad).
948    o verification/matrix_example:
949      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
950        MPI and mutlti-threaded testing.
951    o pkg/matrix:
952      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
953      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
954      - fix for multi-threaded (remove DATA statement);
955      - use standard DIFFERENT_MULTIPLE function;
956      - add MATRIX_OPTIONS.h
957    o verification/matrix_example:
958       To allow to split the domain in several tiles, change the domain size
959        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
960        Western side) of land points.
961    o (*_)write_pickup:
962      - fix few bugs in mypackage_read/write_pickup.F
963      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
964        array of length 1 (was caught by compiler syntax-check).
965    o pkg/diagnostics (velocity potential solver):
966      - fix initialisation of main diagonal matrix (for overlap values)
967    o tools/build_options:
968      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
969        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
970      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
971        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
972        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
973        and use "-devel" testreport option for standard testing on baudelaire.
974    o pkg/grdchk:
975      - Assume that all gradient-check position are within the same tile
976        corresponding to global indices (iGloTile,jGloTile) and that
977        positions (i,j indices or nbeg) are local to this tile;
978      - set tile local-indices and proc. number according to tile global-indices;
979      - remove grdchkwhichproc from namelist (retired param);
980      - send adjoint gradient to all procs so that all procs print it to STDOUT;
981      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
982    o adding package bbl (Bottom Boundary Layer)
983      description in MITgcm/pkg/bbl/bbl_description.tex
984      example/test experiment in MITgcm_contrib/bbl
985    o adjoint verifications
986      - changed 5 experiments to multi-tiles
987        * global_ocean.90x40x15
988        * obcs_ctrl
989        * offline_exf_seaice
990        * tutorial_dic_adjoffline
991        * tutorial_tracer_adjsens
992        changed reference output for those that crossed tile boundaries
993        (changed choices of gradient check positions)
994      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
995      - temporary bug fix in grdchk_loc.F for obcs
996    o genmake2 & testreport
997      - add target "obj" (just for OBJFILES files) to Makefile;
998      - add option to specify FEXTRAFLAGS on command line.
999    o pkg/mypackage:
1000      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
1001    
1002    checkpoint63a (2011/08/02)
1003    o pkg/diagnostics (velocity potential):
1004      - fix velocity-potential calculation when using OBCS: balance net inflow
1005        at each level (new S/R OBCS_DIAG_BALANCE).
1006      - fix some of the problems with OBCS in stream-function calculation.
1007    o pkg/exf/exf_readparms.F
1008      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
1009        EXF_NML_OBCS) more consistent, so that you need not have these lists
1010        in data.exf when they are not used.
1011    o optim/optim_readdata.F:
1012      - add some output about obcs variables that might help debugging
1013      - add a check about nvarlength
1014    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
1015    o pkg/diagnostics (velocity potential):
1016      - fix mask for OBCS (still problems in stream-function with OBCS);
1017      - add specific parameter (default = main code CG2D params) for solver;
1018      - in case of poor convergence, use solution corresponding to lowest residual.
1019    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
1020      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
1021      and should be avoided where possible.
1022    o model/src (rStar):
1023      - include r* effect on reference-state (PhiRef) in totPhiHyd
1024        (so that it's really the potential anomaly at the cell center);
1025        affect solution only if z* with full pressure in EOS.
1026      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
1027        update output (because of z* in totPhiHyd and viscA4 changes);
1028      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
1029        @ constant r) until interpolation at constant r is implemented.
1030    o pkg/diagnostics
1031      - fix RCENTER diagnostics in case cell center is not at interface middle
1032    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
1033      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
1034      that THETA and SALT are "conservative temperature" and "absolute
1035      salinity"
1036    o pkg/ctrl
1037      - fix computation of endrec in s/r ctrl_init_rec
1038      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
1039    o pkg/seaice/seaice_growth.F
1040      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
1041        remove then obsolete STORE directives
1042      - fix STORE directives for tice and tices, so that only the
1043        appropriate part of the fields are stored (and not the entire
1044        field); update global_ocean.cs32x15.seaice AD output.
1045      - cosmetic changes: adjust CPP flags and indentation for better
1046        legibilty
1047    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
1048      Chris Wilson)
1049    o pkg/gmredi:
1050       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
1051       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
1052    
1053    checkpoint63  (2011/07/11)
1054    o pkg/exch2:
1055     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
1056     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
1057       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
1058       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
1059    o pkg/diagnostics:
1060     - deal with pairs of post-processed diags which are computed together; in
1061       particular, re-order list of diags within 1 file to save 2nd computation.
1062     - add S/R to compute velocity stream-function (called after velocity-potential
1063       calculation) from divergence free transport -> new diagnostics "PsiVEL".
1064     - add parameter to select grid-point location where PsiVEL == 0.
1065    o eesupp/src:
1066       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
1067       (specific S/R needed with exch2 topology - for now, just print an error msg)
1068    o pkg/shelfice
1069     - Implement friction velocity-dependent transfer coefficients following
1070       Holland and Jenkins, JPO, 1999
1071       Original code by M. Losch with small modifs.
1072       Enable with CPP option SHI_ALLOW_GAMMAFRICT
1073       and runtime flag SHELFICEuseGammaFrict
1074    o verification lab_sea & global_ocean.cs32x15:
1075     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
1076       does not miss some dependencies (but is slower) and also works with many files
1077       (default makedepend limitation for AD built).
1078     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
1079    o pkg/diagnostics:
1080     - add run-time parameter "useMissingValue" (def=False) to fill land-point
1081        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
1082       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
1083     - Extend the use of "missing_value" setting from data.diagnostics for the case
1084       of counter-diagnostics (where fraction-weight is zero). This applies both to
1085       MNC and MDS output files.
1086    o pkg/seaice/seaice_growth.F:
1087      - add 'a priori' cap of latent heat flux based on actual mass considerations
1088        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
1089        non-legacy seaice_solve4temp.
1090      - add diagnostic of the residual sublimation freshwater flux (the freshwater
1091        flux taken from the ocean if the total actual latent heat fluxes exceed
1092        the maximum)
1093      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
1094       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
1095      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
1096       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
1097      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
1098      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
1099    o verification 1D_ocean_ice_column:
1100       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
1101       update results
1102    o pkg/diagnostics:
1103     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
1104       which are not filled-up but computed from other diags ; In this case, the mate
1105       diag points to the primary (filled-up) diag to used for post processing.
1106     - Update Velocity-potential computation using post-processed diag framework.
1107     ==> Change the ordering of fields and time-periods in MDS output file
1108       when using periodic averaging: now writes one time record with the full set
1109       of fields for this time period, then the next time reccord (it used to be
1110       one field with the full set of time records then the next field).
1111         Note: this is now similar to NetCDF (MNC) output file. <==
1112    
1113    checkpoint62z (2011/06/21)
1114    o adjoint monitor:
1115     - Add adjoint monitor output for packages exf, seaice
1116       and update relevant testreport output
1117    o pkg/seaice:
1118     - re-order diags inits so that they appear in order in available_diagnostics.log
1119     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
1120       area/heff/hsnow preceeding thermodynamic growth/melt.
1121     - modified diag: SIdA; output actual effect, as the description states.
1122     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
1123     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
1124       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
1125        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
1126     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
1127     - added diagnostics for seaice generic tracers (SItr*).
1128     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
1129     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
1130     I. Fenty: 18-Jun-2011:
1131     Minor changes to seaice package:
1132     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
1133        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
1134       - Differentiated "regularization variables" from "floor variables"
1135        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
1136        * hiceMin became SEAICE_hice_reg (old hiceMin)
1137          (with _reg meaning regularization variable)
1138       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
1139        so as to ensure energy conservation when going between phases
1140      - A22 was not used anywhere
1141     2) Changed regularization procedure for heffActual and hsnowActual to ensure
1142        well-boundedness and smooth adjoint in seaice_growth.F
1143     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
1144        because the old regularization always set heffActual >= 0.05 cm
1145     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
1146        on AREA when HEFF > 0.
1147      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
1148        requiring that DISABLE_AREA_FLOOR *not* be defined
1149     Affected verifications:
1150      - 1D_ocean_ice_column (output.txt output_adm.txt)
1151      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
1152    o pkg/diagnostics:
1153      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
1154      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
1155        (was _RL, now integer) with option = 0 to retrieve all levels.
1156      - add pieces of code to compute velocity potential at each level (new diagnostics
1157        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
1158        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
1159      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
1160        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
1161        and in diagnostics_fract_fill.F (do not need a valid pointer for the
1162        diagnostics counter-mate); check that definition of counter-diagnostic
1163        includes a valid counter-mate (in diagnostics_set_levels.F).
1164    o model/src (rStar):
1165      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
1166        affect solution only if z* with full pressure in EOS;
1167        update output of test-exp global_ocean.90x40x15.
1168    o pkg/seaice:
1169      - introduce siEps=1e-5 parameter
1170      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
1171      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
1172      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
1173        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
1174        as well as ice cover age and ridging index (attached to AREA).
1175        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
1176        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
1177        Up to SItrMaxNum=3 tracers can be used simultaneously.
1178    o pkg/salt_plume:
1179      -introduce SPsalFRAC run time parameter that sets the fraction of the
1180       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
1181       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
1182    o model debug options:
1183      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
1184        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
1185      - Refine debug-msg printing selection (3 new levels):
1186        debugMode  : controls printing of debug messages (sequence of S/R calls).
1187        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
1188         debLevZero =  0 ; /* level of disabled aux. msg printing */
1189         debLevA =  1 ; /* level of minimum  aux. msg printing */
1190         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
1191         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
1192         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
1193         debLevE =  5 ; /* level of extensive debug printing */
1194        New debugLevel default: with default debugMode value (=F),
1195          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
1196          and if debugMode=T, default debugLevel = 4 (debLevD).
1197        Relation with previous settings:
1198         debLevB (=2) corresponds to former debLevA (=1)
1199         debLevD (=4) corresponds to former debLevB (=2)
1200        Note:
1201         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
1202         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
1203            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
1204      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
1205        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
1206    o pkg/obcs:
1207      - change OBCSfixTopo default from True to False (should not change the results);
1208        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
1209    o pkg/thsice:
1210      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
1211        2nd layer seaice sublimation (unlikely to happen)
1212      - use Interior mask for OBCS in thsice_advection.F (similar to what is
1213        done in gad_advection & seaice_advection).
1214    o adjoint:
1215      bug fix spotted by Gael Forget:
1216      seaice_advection and thsice_advection still had
1217      legacy CPP options to avoid CS corner updates for adjoint
1218    o pkg/seaice:
1219      => Change some of the defaults (2011/05/29):
1220         - change SEAICEuseFluxForm default (from False to True)
1221         - change DIFF1 default (from 0.004 m/s to 0. m/s)
1222         And print warnings if DIFF1 is not set in data.seaice and centered
1223          avection scheme is used without any diffusion.
1224      also:
1225      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
1226      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
1227      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
1228        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
1229        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
1230      update results of test exp.:
1231         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
1232             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
1233             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
1234         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
1235         seaice_obcs: output (SEAICEuseFluxForm=T)
1236      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
1237          for standard fwd & AD lab_sea tests (to keep the same output).
1238  o pkg/seaice/seaice_growth.F:  o pkg/seaice/seaice_growth.F:
1239    - use Ian Fenty's capping formulas for actual ice    - use Ian Fenty's capping formulas for actual ice
1240    thickness thoughout EVOLUTION branch.    thickness thoughout EVOLUTION branch.
1241    - put treatment pathological case #2) in CPP brackets    - put treatment pathological case #2) in CPP brackets
1242    (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).    (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
1243    - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
1244  o pkg/seaice:  o pkg/seaice:
1245    - seaice_diffusion.F : remove the min(DX,DY) factor permanently;    - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
1246    pass the Laplacian diffusivity (in m/s2) diffKh as a parameter;    pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
1247    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
1248    field) or the time step (to update the field itself).    field) or the time step (to update the field itself).
1249    - seaice_advdiff.F: for multidim, call seaice_diffusion with    - seaice_advdiff.F: for multidim, call seaice_diffusion with
1250    e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call    e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
1251    seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.    seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
1252    - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :    - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
1253    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.  
1254  o pkg/seaice:  o pkg/seaice:
1255    diffusion with centered advection scheme (diffus.F & advect.F):    diffusion with centered advection scheme (diffus.F & advect.F):
1256    - 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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