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revision 1.1442 by gforget, Wed May 25 23:56:29 2011 UTC revision 1.1673 by jmc, Fri Jun 22 18:31:45 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 verification (atmospheric set-up):
8      - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
9    o pkg/profiles : refine profiles and files handling.
10    o model/src and pkg/ecco : introduce run-time switch usePROFILES.
11    o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
12      - changes to use model/src/the_main_loop.F rather than the ecco version
13        in ecco type adjoint runs.
14    o model/src:
15      - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
16      - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
17      - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
18    o model/src:
19      - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
20        update output of test experiment bottom_ctrl_5x5.
21    o pkg/generic_advdiff:
22      - implement vertical bi-harmonic diffusion (for now, only for T & S and
23        only explicitly).
24    o verification/bottom_ctrl_5x5/
25      update reference output (results changed quite some time ago,
26      not sure when; but new reference results look ok in terms of grdchk)
27    o verification/1D_ocean_ice_column/
28      For verification purposes, the exact adjoint rather than an approx.
29      should be used (e.g., to comare against F.D. or TLM).
30      removed autodiff_inadmode*_ad.F routines in code_ad/
31      Update results/ accordingly.
32    o pkg/cal:
33      - change cal_getdate.F so that output date is function of input time only
34        (less ambiguous, not mixed up with input iteration number).
35      - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
36    o pkg/diagnostics:
37      - implement calendarDumps also for stats-diags
38      - implement calendarDumps also for snap-shot output (negative freq)
39      - for now, ignores calendarDumps if non-zero phase-lag.
40    
41    checkpoint63n (2012/06/04)
42    o model/src:
43      - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
44        between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
45      - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
46        similar to calc_r_star.F); update results of experiment internal_wave and
47        tutorial_global_oce_in_p (affected @ truncation level).
48    o pkg/shelfice:
49      - add parameterisation of advective-diffusive flux into the ice shelf
50        according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
51      - simply eps3/3a computation
52    o eesupp:
53     - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
54       between tiles, just fill-in edges assuming locally periodic subdomain) and
55       add corresponding exchange subroutines (EXCH0);
56     - new CG-solver version (_EX0) for disconnected-tiles special case.
57    o model/src (CG-solvers):
58     - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
59       (similar final residual output and max-Iter number as with standard version);
60     - allows to store and use lowest-residual solution (standard & _SR versions);
61     - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
62     - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
63    o eesup/src:
64     - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
65       ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
66    o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
67    
68    checkpoint63m (2012/04/27)
69    o pkg/shelfice:
70     - account for partical cells in surface level below ice-shelf for hydrostatic
71       pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
72    o ad test experiments:
73     - update and rename to "ad_optfile.local" local AD-optfile specific to a
74       particular adjoint verification experiment (in verification/*/code_ad/)
75    o pkg/seaice & pkg/exf:
76     - Part two of ECCO-CLIVAR code merges.
77       Completes merge of seaice area relax. code.
78       Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
79       to be set in EXF_OPTIONS.h since this pkg controls its I/O
80       (and avoids second CPP option in SEAICE_OPTIONS.h)
81     - change default value of costIceStart & costIceEnd to a valid date.
82     - add snowPrecip to HSNOW in seaice_growth
83    o pkg/ptracers:
84     - move ptracers summary and setup check into separated S/R ; add a check for
85       valid PTRACERS_Iter0 value (error+stop or just warning).
86    o pkg/cal (+ pkg/ecco):
87     - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
88       as input; and for AD, unless both are not differentiable (e.g., k index)).
89    o model/src:
90     - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
91       is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
92       temporary set to usingZCoords value (to be changed to F when using shelfice).
93     - hydrostatic pressure: implement partial cell near the surface also for
94       Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
95       usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
96    o pkg/ctrl/ctrl_init.F:
97     - add a formal parameter to s/r ctrl_init_rec to print
98       xx_$(ctrl_valiable)_file for easier debugging
99     - move call of cal_* routines into the if-block where they are really
100       needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
101       to specify a startdate
102    o pkg/seaice:
103     - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
104       global_ocean.cs32x15/code versions).
105     - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
106       verification experiment global_ocean.cs32x15.seaice and update results.
107    o pkg/exf:
108     - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
109       (according to useExfYearlyFields).
110    o pkg/cal:
111     - move calendar setting & summary (previously in cal_readparams.F) into new
112       S/R CAL_INIT_FIXED to be called later in the initialisation process, once
113       length of the simulation is set (after SET_PARMS call); This is an attempt
114       to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
115     - For safety: keep a record of pkg/cal parameter settings status
116               to allow to STOP if one pkg/cal S/R is called too early.
117     - add a stop in all basic pkg/cal subroutines if called before setting is done.
118     - modify cal_getdate.F: stop when nothing was returned;
119       if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
120       this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
121    
122    checkpoint63l (2012/04/04)
123    o pkg/bbl:
124      - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
125        update global_with_exf output.yearly.txt file.
126    o pkg/cal:
127      - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
128      - remove 2 unsused and very short (1 line only) functions ;
129      - remove unsused subroutines from AD-Diff list.
130    o model/src:
131      - start to implement clean wait to stop in initialization S/R (config_check.F,
132         packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
133    o folowing PRINT_MESSAGE changes:
134      - remove reminder multiple print to the same file (STDOUT) when multi-threads.
135    o pkg/bbl:
136      - modification so it can work with z*
137      - replace deltaT with dTtracerLev(k) for asynchronous time stepping
138      - global_with_exf/input.yearly verification; changes output.yearly.txt
139    o eesupp/src:
140      - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
141        writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
142      - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
143        # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
144      - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
145      - when using MPI, always set usingMPI=T ; set default accordingly and stop
146        if not consistent.
147      - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
148        argument is zero (in case called within single-thread section).
149    o pkg/fizhi:
150        clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
151        in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
152    o pkg/exch2:
153      - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
154        activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
155      - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
156        but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
157        with bad ones coming from a not-yet-updated halo.
158        This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
159    o pkg/frazil:
160        move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
161        http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
162    o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
163    o verification/lab_sea
164      * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
165      * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
166      * nTimeSteps 3 -> 4
167      * changed reference output accordingly
168    o pkg/ctrl:
169      * fix ctrl_get_gen for xx_sst, xx_sss
170    o pkg/fizhi:
171      - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
172        update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
173      - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
174        fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
175        clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
176    o pkg/gmredi:
177      - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
178    o pkg/fizhi:
179      - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
180        (old)aces open64 tuv test.
181    o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
182    o pkg/mom_vecinv:
183      - fix 1 loop range in mom_vecinv.F to be like all the other loops which
184        set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
185        with non-lin free-surf).
186    o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
187      in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
188      some compilers (gfortran 4.6.0 on MacOS)
189    o momentum:
190      - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
191        & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
192        fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
193    
194    checkpoint63k (2012/03/17)
195    o model/src:
196       - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
197         flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
198       - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
199         (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
200    o model/src: solve_*diagonal.F
201       - replace division with multiplication by inverse (similar to original version)
202         update output of AD exp. global_ocean.90x40x15.
203       - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
204         to enable the use of the vectorized & differentiable solve_tridiagonal.F
205       - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
206         vertical advection (to get solve_tridiagonal tested in AD mode).
207    o pkg/seaice: ECCO-CLIVAR merge:
208      1. seaice AREA relaxation
209         * CPP option: SEAICE_ALLOW_AREA_RELAXATION
210         * runtime flag: SEAICE_tauAreaObsRelax
211      2. modified global mean cost imbalance code: CPP option
212          ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
213    o another iteration on solve_*diagonal.F
214       Make choices independent of AUTODIFF
215       Default will be the adjoinable vectorized version.
216       Alternative choices are:
217       * non-adjoinable original version with low memory footprint:
218         #define SOLVE_DIAGONAL_LOWMEMORY
219       * still adjoinable but does not vectorize (k as inner-most loop):
220         #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
221    o testreport
222     - add option to use a home made wrapper around "make"
223     - remove MITGCM_IEEE env. variable (no longer active)
224    o pkg/shelfice
225     - improve computation of friction velocity for velocity dependent
226       exchange coefficients: include velocities into SHELFICEBoundaryLayer
227       block to average velocities vertically
228     - add TAF store directives for SHI_ALLOW_GAMMAFRICT
229    o Modify diagonal solvers, now three versions (upon request):
230      #ifndef SOLVE_DIAGONAL_AUTODIFF
231        1. default version (dating back a while ago)
232      #else /* def SOLVE_DIAGONAL_AUTODIFF */
233      # ifdef SOLVE_DIAGONAL_KINNER
234        2. adjoinable version with k-innermost loop (G. Forget)
235      # else
236        3. adjoinable vectorized version of 2.
237      # endif
238      #endif /* SOLVE_DIAGONAL_AUTODIFF */
239      All flags are currently set within routines, but could/should be moved to CPP-options.
240      Array bounds for 1. are as before, for 2.,3. cover the entire domain
241      (could be changed for 1. too).
242    o verification/lab_sea (fwd):
243      - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
244        use 7 categories (except hb87), new solve4temp params (except salt_plume),
245        constant salinity (=4) or variable salinity (salt_plume) done through
246        SItracer.
247    o pkg/seaice:
248      - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
249      - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
250         SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
251        from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
252        SEAICE_freeze got retired) but already better than previously with
253        SEAICE_freeze=123456.7 deg.C;
254      - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
255        (safer multi-threaded setting); always set SEAICEuseEVP;
256      - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
257        SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
258        stop if multiple specifications for the same coeff; make sure default
259        SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
260    o pkg/obcs:
261      - allow to switch to upwind 1rst order advection scheme for the advective
262        flux computation at the open-boundary; disabled for adjoint built.
263    o pkg/ptracers:
264      - rename PTRACERS_RESTART.h -> PTRACERS_START.h
265      - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
266      - add parameter to decide when to start a tracer; use internal flag to
267        know which tracer to step-forward; switch this internal flag at the top
268        of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
269        for adjoint built.
270    o pkg/seaice:
271      - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
272      - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
273      - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
274    o pkg/ecco:
275      - fix writing of output file DiagnosCost_ClimSalt/Theta
276        and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
277    o pkg/seaice:
278      - add missing initialisation of COR_ICE array in dynsolver.F
279      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
280        compiled either way, and is tested in all exps (multidim was only tested
281        in lab_sea ad before).
282      - cosmetic change to prepare for future addition of ITD. no change to results.
283        no defaults change.
284      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
285      - by lack of adequate verification experiments, I further used custom versions
286        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
287        should be correct.
288      - avoid recomputations in ad.
289    o array initialisation in adjoint mode:
290      1) pkg/mom_common/mom_calc_ke.F:
291        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
292        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
293        part this initialisation is gone, resulting in Floating Point Exception
294        (caught by open64 compiler with debug option).
295      2) model/src/convective_weights.F
296        set output convectCount over the full array range (instead of doing
297        an update): this fix a similar issue when called within recomputation (adjoint)
298        which could by-pass the initialisation (normally done in the caller S/R).
299    o pkg/seaice:
300      - final version of turbulent flux params, as agreed at MIT ice meet:
301           SEAICE_mcPheePiston (default is ~ 0.000875)
302           SEAICE_mcPheeTaper (default is 0.)
303           SEAICE_frazilFrac (defualt is 1.)
304           SEAICE_mcPheeStepFunc (default is false)
305      - changes results at trunction error level
306      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
307    o added pkg/frazil:
308      - see frazil_description.tex for details
309      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
310    o pkg/shelfice/shelfice_thermodynamics.F
311      - fix exponents for velocity dependent exchange coefficients: change
312        from 2/3(=0) to 0.66666666666666667
313      - move computation of velocity dependent exchange coefficients into
314        separate loop, so that it applies to both thermodynamics
315      - move some divisions by constants out of loops
316    
317    checkpoint63j (2012/02/16)
318    o pkg/seaice:
319      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
320      - SItracer:  added run time params, and allow coupling to ocn salinity.
321    o pkg/seaice: remove (almost) all divisions by constants within loops
322      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
323      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
324      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
325      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
326    o pkg/seaice :
327      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
328        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
329      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
330      - add permanent SItflux diag that corresponds to TFLUX but includes
331        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
332      - allow activation/testing of a fix for suspected missing term in
333        ocn-ice heat budget (to be confirmed). To test this, you want to
334        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
335        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
336      - no change in results, fwd or ad.
337    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
338      - switch to variable freezing point.
339           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
340      - bug fix : the sublimation term that was missing is now activated.
341           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
342      - bug fix : flooding sign term for SIsal0.NE.0.
343           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
344    o pkg/seaice:
345      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
346        is now the default, and the old default constant freezing point is recovered
347        with SEAICE_tempFrz0    = -1.96,
348             SEAICE_dTempFrz_dS = 0.,
349      - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
350      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
351      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
352        activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
353      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
354        was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
355      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
356        seaice_growth r149 for legacy branch (no results change).
357      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
358        from I. Fenty).
359      - results did not change except for global_ocean.cs32x15, mostly due to the
360        switch to variable freezing point (see above item for detail).
361    o pkg/thsice:
362      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
363        seawater freezing in thsice_calc_thickn (not used).
364    o pkg/seaice: turbulent flux term specification via run time params.
365      - replace CPP switches with run time switches to facilitate testing
366      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
367                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
368      - added runtime parameter : SEAICEturbFluxFormula
369      - move Mcphee constants to SEAICE_PARAMS.h
370      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
371                 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
372                 remove seaice_summary call (moved to seaice_init_fixed)
373      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
374        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
375      - seaice_summary.F : add missing report of read turbulent flux term set up
376                           and SITRACER.
377      - seaice_check.F : check range; inform and stop if retired CPPs are used
378                         (incl. SEAICE_AGE).
379      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
380             CPP switch, same computation as before for the different options.
381      - change results at the truncation level.
382    o pkg/seaice:
383      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
384        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
385        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
386      - update verification/*/input*/data.seaice:
387        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
388        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
389        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
390        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
391    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
392      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
393        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
394        difference in results only due to machine truncation.
395      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
396        MaykutPolySatVap; keep MIN_LWDOWN.
397      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
398      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
399        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
400    o pkg/salt_plume:
401      - isolate saltPlumeFlux array exch into a specific S/R called from
402        do_oceanic_phys.F
403      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
404    o verification:
405      - move untested set-up to MITgcm_contrib/verification_other.
406    o pkg/seaice:
407      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
408    o pkg/seaice:
409      - seaice_solve4temp.F (keeping results unchanged):
410        * add 2 future run-time params to select which saturation vapor pressure
411          formula is used and how post-iteration fluxes are set.
412          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
413        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
414          the linearized expression to stay consistent with tsurf finding.
415      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
416        can be < 0.
417    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
418      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
419        conductive heat flux F_c , and add it explicitly when updating tsurf as
420        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
421        so that now F_ia has a consistent meaning through the entire routine.
422        This causes differences at truncation level: update output of fwd exp.
423        global_ocean.cs32x15.seaice.
424    o pkg/seaice:
425      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
426        of arrays, sign/direction of fluxes; no effect on results.
427      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
428        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
429        note: this should have been done before changing celsius2K default.
430      - to keep results unchanged, add back old value of celsius2K in verification
431        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
432      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
433        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
434        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
435        freezing temp is consistent with value in seaice_growth.F ; this causes
436        differences at machine truncation level: update lab_sea AD output (3/4).
437    o pkg/seaice:
438      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
439        and climsst/sss even when using seaice (to prevent calculation that might
440        use SST on land); does not affect any verification exp.
441      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
442        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
443    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
444      over land (non-legacy code)
445    o vectorize salt_plume package:
446      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
447      - this code computes plumebk everywhere (also over land), thus requires
448        code to avoid divisions by zero and catch the case of kLev=Nr.
449      - efficiency of salt_plume_frac is still sub-optimal
450    o tools (genmake2):
451      - fix makefile NAME specification (option: -makefile NAME) by adding
452        "-f $MAKEFILE" in few places where it was missing including makedepend
453        command (contribution from Paul).
454    
455    checkpoint63i (2012/01/24)
456    o model/src:
457      - add factorized versions of some EOS code to find_rho.F,
458        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
459    o model/src:
460      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
461      - change default celsius2K from 273.16 to 273.15
462      - to keep results unchanged, add back old value of celsius2K in verification
463        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
464         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
465    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
466      to make TAF generate vectorizable code
467    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
468       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
469       have flags that do this more efficiently.
470    o pkg/diagnostics/diagstats_calc.F
471      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
472    o pkg/obcs (with exch2):
473      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
474        and remove code (in obcs_readparms.F) which was based on EXCH of indices
475        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
476    o pkg/exf and seaice exp:
477      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
478        so that switching off area & heff advection flags does not affect results.
479      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
480      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
481        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
482        results of verification experiments: 1D_ocean_ice_column(fwd),
483        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
484        and offline_exf_seaice (all 4).
485    o pkg/seaice:
486      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
487        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
488      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
489        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
490        not multi-dim advection;
491      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
492        SHORTWAVE_HEATING #undef.
493    o optim: make Makefile more robust (?)
494    o pkg/obcs:
495      * fix treatment of obcs_read_pickup for TAF
496    o pkg/shelfice:
497      * add missing initialisation of num_shifwflx
498      * new adjoint verification exp. for isomip
499      * change Prandtl and Schmidt numbers from generic formulations
500        (in terms of model diffus. and visc.) to separate runtime
501        parameters, with Holland and Jenkins (1999) default values.
502    o pkg/exf (interpolation):
503      - extended input field (2 rows) near the N & S poles:
504        * fill in with the symetric value (when even Nb of data in longitude)
505        * add average value at the poles only for scalar quantities ; for vector
506          component interpolation, skip the averaging and keep duplicated values,
507          unless the 2 components have same location (uvInterp=T) in which case
508          interpolate the 2 components together using S/R EXF_INTERP_UV.
509      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
510        together: this allows to account properly for local orientation when
511        averaging at N & S pole.
512      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
513        exf-interpolation near N & S poles. Undef by default.
514      - add debug check/print on 1rst iter if debugLevel >=2.
515    o pkg/exf:
516      - change masking flags definition (no longer "parameter"), put them in
517        common block and set them in S/R EXF_INIT_FIXED.
518      - change recognized masking flag from s,u,v to c,w,s since the mask
519        to use (maskC,W,S) depends on position on model grid and has little to
520        do with scalar/vector difference; fix masking if using P-coordinates.
521      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
522        and update results of exp. global_with_exf (x2).
523      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
524    o pkg/obcs
525      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
526    o pkg/exf (interpolation):
527      - assume periodicity in X only if input field cover full longitude range.
528      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
529        and should vectorise).
530      - fix input lat of the 2 added row (in case we provide N.pole data).
531    
532    checkpoint63h (2011/12/30)
533    o pkg/seaice:
534      - change declaration of UVM from _RL to _RS in order to get B-grid
535        uIce,vIce monitor when _RS = real*4
536    o pkg/offline:
537      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
538      - compute vertical velocity if not read from file (switch on exactConserv
539        & staggerTimeStep);
540      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
541    o verification:
542      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
543        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
544        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
545      - update output of exp. global_ocean.cs32x15.viscA4 after changing
546        grid-file angles (used here for coriolis-3d);
547      - remove (or gzip) few files not needed to run fizhi-cs experiments.
548    o pkg/exf (vector interpolation):
549      - rotate vector component toward local grid-axis orientation using grid-angles
550        (stored in GRID.h) instead of locally computed rotation angle; keep old code
551        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
552    o pkg/seaice:
553      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
554        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
555    o pkg/PKG_OPTIONS.h files:
556      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
557        outside of the #ifdef ALLOW_THISPKG / #endif block.
558      - update verification/*/code/PKG_OPTIONS.h files.
559    o add a verification experiment (offline_exf_seaice/input.seaice) that test
560      the B-grid LSOR solver
561    o pkg/seaice: sort out emissivity and long wave radiation step 2:
562      - add emissivity for snow and ice as new run-time parameters
563        (unfortunately) that default to the corresponding exf values; this
564        changes results in most verification experiments so that for backward
565        compatibility these parameter have to be set explicitly to inconsistent
566        values (ugly);
567      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
568        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
569        until we agree how to handle this bug properly
570    o pkg/exf (interpolation):
571      - add a set of run-time param ({inputfield}_interpMethod), one for
572        each interpolated input field, to select the interpolation method
573        with a value of zero switching off the interpolation;
574      - print interpolation parameters to standard output;
575      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
576        (to use instead runoff_interpMethod=0 in data.exf).
577      - simplify default setting of interpolation parameters (for all fields,
578        set position to match model grid cell-center position, leading to trivial
579        interpolation in case of regular Lat-Lon grid) and fix for the case of
580        non-uniform delY.
581    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
582       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
583       this factor is absolutely required, because the lw exitance (= out-going
584       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
585       where the reflectivity rho = 1-emissivity for conservation reasons. Once
586       this is established, we can remove the CPP-Flag (if we want to).
587    o pkg/seaice:
588      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
589        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
590      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
591        what the name implies (and not emissivity*BoltzmannConstant), this means
592        the old default value of 5.5e-8 now means
593        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
594        S/R exf_readparms
595      - FV-discretization of the B-grid LSOR solver, turn on with
596        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
597        of the calling routine dynsolver, so that B and C-grid code look a
598        little more alike.
599      - fix index bugs in ostres.F (B-grid code)
600    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
601    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
602      default for SEAICE_emissivity, if useEXF; requires setting a wrong
603      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
604      backward compatiblity
605    o model/src: use sigmaR in calc_ivdc
606    
607    checkpoint63g (2011/12/16)
608    o pkg/seaice/seaice_growth.F:
609      fix heat conservation of the coupled ocean-seaice system.
610      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
611      solid vs liquid water treatment is resolved via QNET.
612    o pkg/seaice/seaice_growth.F:
613      add missing term for sublimation in saltFlux, which was breaking conservation.
614    o pkg/seaice/seaice_model.F:
615      Remove this patholigical case treatment in evolution branch,
616      where it is un-necessary and breaks conservation.
617      Update global_ocean.cs32x15/results accordingly for
618      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
619    o model/src:
620      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
621      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
622    o pkg/obcs:
623      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
624      tendency for temperature and salinity that is then applied to update
625      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
626      horizontal advection and diffusion contributions on the boundary (in
627      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
628      removing the mask in S/R timestep_tracer. The advantage of this approach is
629      that the updated tracer values include contributions from the surface
630      forcing and vertical diffusion.
631      This modification changes exp4.stevens because of vertical diffusion.
632    o model/src:
633      change non-curvilinear grid setting to also work with exch2 + blank tiles:
634      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
635        face dimensions.
636      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
637        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
638        and INI_SPHERICAL_POLAR_GRID.
639      change test-experiment global_ocean.90x40x15:
640      - split the domain in many more tiles (9x4 tiles of 10x10 each);
641      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
642      - update results of both test (std & dwnslp).
643    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
644       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
645    o model/src:
646      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
647        and fix initialisation when using sigma-coords.
648    o model/src:
649     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
650       to their current value at the beginning of forward_step.F": add a new run-time
651       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
652     - set doResetHFactors=T in the following test exp:
653        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
654        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
655        and tutorial_global_oce_in_p (nonLinFS in p)
656    o pkg/ecco
657      - added IES cost term
658    o verification/advect_xz
659      - scale down the depth by 1/100 (from 200 km to just 2.km)
660      - add secondary test using divergent flow, r-star and implicit vertical advection.
661      - add note (check_conserve_TS.txt) and matlab script to check global
662        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
663    o pkg/rbcs:
664      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
665    o pkg/obcs (Stevens BCs):
666      - fix various problems in the phase speed computations of the Stevens
667        boundary conditions:
668        - sign error for western and southern boundaries,
669        - time tendencies were underestimated by factor of dTracerLev and some just
670          zero (for multidim advection schemes) -> now estimate time tendencies
671          from difference between previous (n) time level and the one before (n-1);
672          this requires storing a field per tracer per boundary, also in the pickup
673          files.
674        - replace deltaTmom in cflMer/Zon computation with dTracerLev
675        - set default phase velocity to cflMer/Zon
676      - update verification experiment exp4.stevens
677    o pkg/generic_advdiff (implicit_r):
678      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
679        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
680      - fix implicit vertical diffusion or advection with NonLin FreeSurf
681        (was using current recip_hFacC instead of future recip_hFacC): set future
682        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
683        solver S/R ;
684      - fill diagnostics of vertical advective fluxes (computed from tendency)
685        when using implicit vert. advection;
686      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
687         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
688         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
689         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
690    o pkg/diagnostics:
691      - add diags for T & S tendency which goes through Adams-Bashforth.
692    
693    checkpoint63f (2011/11/30)
694    o pkg/obcs/obcs_calc_stevens.F:
695      - join some loops to reduce number of if-statements
696      - fix a bug in code for northern and southern boundaries.
697    o pkg/seaice/seaice_init_varia.F
698      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
699        caused zero ice-velocities for the B-grid code
700    o pkg/seaice/seaice_init_fixed.F
701      - fix a bug in the initialisation of the second metric terms
702        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
703      - this affects all seaice configurations with useCurviLinearGrid = .true.
704        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
705        = .true. (default)
706      - the only verification experiment affected is global_ocean.cs32x15:
707        icedyn, seaice, and seaice_dynmix (AD)
708    o pkg/thsice/thsice_diagnostics_state.F
709      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
710        not contain garbage that can lead to surprises in diagstats_calc.F
711    o model/src:
712      - move bi,bj loops inside INTEGR_CONTINUITY ;
713      - call INTEGR_CONTINUITY directly from forward_step.F
714        (previously called from momentum_correction_step.F)
715      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
716        forward_step.F and pkg/ecco/the_main_loop.F
717    o model/src/do_oceanic_phys.F:
718      - reset addMass to zero only if useICEFRONT ;
719      - separated k-loop for rhoInSitu calculation ;
720      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
721        and at constant T,S (= WdRHOdP);
722      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
723        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
724        transport of locally-referenced potential density);
725        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
726    o gluemnc:
727      - replace ncrcat with ncks when adding variables to *.glob.nc
728      - change the way variables without record dimensions are handled so that
729        files that have variables with and without record variables can be glued:
730        add a record dimension with a new unique name to be able to differentiate
731        between variable with and without a-prior record dimensions. Remove
732        this record dimension before adding the variable to the *.glob.nc file.
733        This procedure automatically works also for grid.*.nc files that do not
734        have any record dimension.
735    o verification/cpl_aim+ocn:
736      - generate new reference output on baudelaire (gfortran, mpich2) (previously
737        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
738    o pkg/obcs/obcs_calc_stevens.F:
739      - add code for northern and southern boundaries.
740      - reorder some loops to save some operations and so that drFBar can be scalar
741    o model/src:
742      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
743        truncation) and add diagnostics for Adams-Bashforth tendency increment.
744      - update test-exp. AD output:
745        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
746      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
747        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
748        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
749        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
750        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
751        tutorial_plume_on_slope.
752    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
753      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
754      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
755      does not even come with an F77 compiler anymore, this should not be
756      a limitation
757    
758    checkpoint63e (2011/11/06)
759    o pkg/seaice adjoint of LSR:
760      - substantially rework STORE dirs.
761      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
762        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
763        and only perform SOLV_MAX_FIXED adjoint iters.
764        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
765        always goes to same record, meaning that the last forward field will be
766        the one used in the adjoint - an approximation.
767      - now produces non-zero LSR-related gradients, and acceptable gradients for
768        An's zonal (x-z) test case (to be checked in)
769      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
770        (but these are screwed up by the thermodynamics in the first place);
771        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
772        output_adm.txt also reflects changes to seaice_lsr
773      - global_ocean.cs32x15:
774        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
775          (output_adm.seaice.txt was updated)
776        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
777          (output_adm.seaice_dynmix.txt)
778    o test-exp. exp4+stevens:
779      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
780    o pkg/seaice (lsr solver):
781      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
782        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
783      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
784      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
785        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
786      - compute (with new S/R) and print initial (+ free-driff sol. if available)
787        and final residual of linearised system.
788    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
789      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
790    o pkg/obcs: Stevens BCs (still only for east and west)
791      - fix Stevens BCs by using intermediate velocities of previous
792        time step as "baroclinic" contribution rather velocity of one grid cell
793        inside the boundaries; more consistent but makes the entire treatment
794        more complicated, requires new pickup files and two new S/Rs:
795        obcs_copy_uv_n and obcs_save_uv_n
796        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
797        (undefined by default)
798      - silently move computation of some grid factors into separate loops to
799        save some recomputations
800      - add a hack for non-linear free surface
801      - add a verification experiment to exp4 that tests this code
802    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
803    
804    checkpoint63d (2011/10/25)
805    o pkg/obcs + seaice-dynamics:
806      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
807        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
808        values (consistent with an implicit method).
809      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
810        return to older implementation (same results as before); note that none of
811        the "experimental" OBCS_SEAICE options are implemented in the new version.
812      - switch test exp. seaice_obcs to use new version (update output).
813    o pkg/seaice:
814      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
815      - add parenthesis in Water-Ice drag calculations (evp & lsr);
816      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
817        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
818      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
819        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
820    o pkg/layers:
821      - Include potential density as new coordinate (Thanks to David Munday)
822    o pkg/dic:
823      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
824        carbonate computation/output to CALC_PCO2_APPROX
825    o pkg/generic_advdiff
826      - make TAF generate code that vectorizes:
827        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
828    o model/src:
829      - improve vectorization also for adjoint code of
830        solve_tridiagonal and solve_pentadiagonal. As this requires up to
831        5 new 3D-fields, this code is only turned on for the combination of
832        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
833        for singular matrix check (only for TARGET_NEC_SX).
834      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
835        ALLOW_AUTODIFF. This flag now needs to be set outside of
836        solve_tri/pentadiagonal.F
837    o pkg/exf:
838      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
839        optional namelist EXF_NML_OBCS).
840      - add many debug-print (to trace down where pkg/cal error msg comes from)
841    o pkg/mom_vecinv/mom_vi_hdissip.F
842      - rearrange loops so that vectorization is improved and in particular
843        the adjoint routine vectorizes. The code is a little longer now, but I
844        think easier to read.
845        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
846    o pkg/seaice:
847      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
848    o pkg/exch2:
849      - alternative code (without tile x tile matrix) for cumulated (global) sum;
850        used as default; keep using matrix version in adjustment.cs-32x32x1.
851    o tools/build_options:
852      - after merging some MPI and/or multi-threads specific optfiles so that
853        the modified default optfile support both built (using genmake2 -mpi
854        for the MPI built, using genmake2 -omp for OpenMP built),
855        move now obsolete optfiles to tools/build_options/unsupported/
856       (add copy of email sent to support list in doc/optfiles_changes.txt)
857    
858    checkpoint63c (2011/09/28)
859    o pkg/ebm:
860      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
861        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
862    o pkg/seaice (SItracer pickup)
863    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
864      To be done:
865      - thorough testing of missing fields in S/R seaice_read_pickup
866      - thorough matching between generic tracers and specific fields used
867        (e.g. volume-weighted age, area-weighted age, salinity, ...)
868    o pkg/grdchk:
869      - all procs calculate and print finite-difference gradient (for testreport)
870      - change description output used by testreport;
871      - AD testing: also compare and report Finite-difference gradient;
872        => update all output_adm*.txt
873    o test exp. global_ocean_ebm:
874      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
875        and turn on exactConserve; update (fwd) output.
876    o pkg/seaice (LSR):
877      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
878      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
879        * identical results with non-CS topology (but save up to half of EXCH calls)
880        * no much changes in cs-32 verification tests since no ice at face edges
881         (differences due to convergence criteria, since nb of iterations changed)
882        * expect some differences on lat-lon-cap grid.
883        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
884    o pkg/exch2:
885      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
886        many tiles); until alternative coding is added, just add a stop.
887    o pkg/kpp:
888      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
889        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
890    o optfiles:
891      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
892        into corresponding standard one, which now support different build:
893        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
894      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
895    o pkg/obcs (seaice):
896      - add missing EXCH for uIce,vIce after applying OBCS;
897      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
898        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
899        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
900      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
901      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
902        and eedata.mth for MPI and mutlti-threaded testing.
903    o pkg/flt:
904      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
905      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
906      - fix pickup and trajectories + profiles output with multi-threads;
907      - add parameter to select group of fields to write along trajectory and
908        profile (default unchanged);
909      - only call PORT_RAND* function when flt_noise <> 0;
910      - add multi-threaded test for verification exp. flt_example.
911    o eesupp/src:
912      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
913      - USE_OMP_THREADING: check that number of threads (from eedata) matches
914        actual number (from env.var. setting).
915    o pkg/ebm:
916      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
917      - add multi-threaded test for verification exp. global_ocean_ebm
918    
919    checkpoint63b (2011/08/29)
920    o pkg/ebm:
921      - fix sign of runoff;
922      - update directly forcing fields (Qnet,EmPmR) to use standard
923        external_forcing_surf.F (remove ebm_forcing_surf.F);
924      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
925      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
926        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
927      - update global_ocean_ebm parameters file data and update output (fwd+ad).
928    o verification/matrix_example:
929      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
930        MPI and mutlti-threaded testing.
931    o pkg/matrix:
932      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
933      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
934      - fix for multi-threaded (remove DATA statement);
935      - use standard DIFFERENT_MULTIPLE function;
936      - add MATRIX_OPTIONS.h
937    o verification/matrix_example:
938       To allow to split the domain in several tiles, change the domain size
939        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
940        Western side) of land points.
941    o (*_)write_pickup:
942      - fix few bugs in mypackage_read/write_pickup.F
943      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
944        array of length 1 (was caught by compiler syntax-check).
945    o pkg/diagnostics (velocity potential solver):
946      - fix initialisation of main diagonal matrix (for overlap values)
947    o tools/build_options:
948      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
949        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
950      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
951        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
952        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
953        and use "-devel" testreport option for standard testing on baudelaire.
954    o pkg/grdchk:
955      - Assume that all gradient-check position are within the same tile
956        corresponding to global indices (iGloTile,jGloTile) and that
957        positions (i,j indices or nbeg) are local to this tile;
958      - set tile local-indices and proc. number according to tile global-indices;
959      - remove grdchkwhichproc from namelist (retired param);
960      - send adjoint gradient to all procs so that all procs print it to STDOUT;
961      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
962    o adding package bbl (Bottom Boundary Layer)
963      description in MITgcm/pkg/bbl/bbl_description.tex
964      example/test experiment in MITgcm_contrib/bbl
965    o adjoint verifications
966      - changed 5 experiments to multi-tiles
967        * global_ocean.90x40x15
968        * obcs_ctrl
969        * offline_exf_seaice
970        * tutorial_dic_adjoffline
971        * tutorial_tracer_adjsens
972        changed reference output for those that crossed tile boundaries
973        (changed choices of gradient check positions)
974      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
975      - temporary bug fix in grdchk_loc.F for obcs
976    o genmake2 & testreport
977      - add target "obj" (just for OBJFILES files) to Makefile;
978      - add option to specify FEXTRAFLAGS on command line.
979    o pkg/mypackage:
980      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
981    
982    checkpoint63a (2011/08/02)
983    o pkg/diagnostics (velocity potential):
984      - fix velocity-potential calculation when using OBCS: balance net inflow
985        at each level (new S/R OBCS_DIAG_BALANCE).
986      - fix some of the problems with OBCS in stream-function calculation.
987    o pkg/exf/exf_readparms.F
988      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
989        EXF_NML_OBCS) more consistent, so that you need not have these lists
990        in data.exf when they are not used.
991    o optim/optim_readdata.F:
992      - add some output about obcs variables that might help debugging
993      - add a check about nvarlength
994    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
995    o pkg/diagnostics (velocity potential):
996      - fix mask for OBCS (still problems in stream-function with OBCS);
997      - add specific parameter (default = main code CG2D params) for solver;
998      - in case of poor convergence, use solution corresponding to lowest residual.
999    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
1000      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
1001      and should be avoided where possible.
1002    o model/src (rStar):
1003      - include r* effect on reference-state (PhiRef) in totPhiHyd
1004        (so that it's really the potential anomaly at the cell center);
1005        affect solution only if z* with full pressure in EOS.
1006      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
1007        update output (because of z* in totPhiHyd and viscA4 changes);
1008      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
1009        @ constant r) until interpolation at constant r is implemented.
1010    o pkg/diagnostics
1011      - fix RCENTER diagnostics in case cell center is not at interface middle
1012    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
1013      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
1014      that THETA and SALT are "conservative temperature" and "absolute
1015      salinity"
1016    o pkg/ctrl
1017      - fix computation of endrec in s/r ctrl_init_rec
1018      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
1019    o pkg/seaice/seaice_growth.F
1020      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
1021        remove then obsolete STORE directives
1022      - fix STORE directives for tice and tices, so that only the
1023        appropriate part of the fields are stored (and not the entire
1024        field); update global_ocean.cs32x15.seaice AD output.
1025      - cosmetic changes: adjust CPP flags and indentation for better
1026        legibilty
1027    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
1028      Chris Wilson)
1029    o pkg/gmredi:
1030       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
1031       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
1032    
1033    checkpoint63  (2011/07/11)
1034    o pkg/exch2:
1035     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
1036     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
1037       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
1038       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
1039    o pkg/diagnostics:
1040     - deal with pairs of post-processed diags which are computed together; in
1041       particular, re-order list of diags within 1 file to save 2nd computation.
1042     - add S/R to compute velocity stream-function (called after velocity-potential
1043       calculation) from divergence free transport -> new diagnostics "PsiVEL".
1044     - add parameter to select grid-point location where PsiVEL == 0.
1045    o eesupp/src:
1046       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
1047       (specific S/R needed with exch2 topology - for now, just print an error msg)
1048    o pkg/shelfice
1049     - Implement friction velocity-dependent transfer coefficients following
1050       Holland and Jenkins, JPO, 1999
1051       Original code by M. Losch with small modifs.
1052       Enable with CPP option SHI_ALLOW_GAMMAFRICT
1053       and runtime flag SHELFICEuseGammaFrict
1054    o verification lab_sea & global_ocean.cs32x15:
1055     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
1056       does not miss some dependencies (but is slower) and also works with many files
1057       (default makedepend limitation for AD built).
1058     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
1059    o pkg/diagnostics:
1060     - add run-time parameter "useMissingValue" (def=False) to fill land-point
1061        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
1062       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
1063     - Extend the use of "missing_value" setting from data.diagnostics for the case
1064       of counter-diagnostics (where fraction-weight is zero). This applies both to
1065       MNC and MDS output files.
1066    o pkg/seaice/seaice_growth.F:
1067      - add 'a priori' cap of latent heat flux based on actual mass considerations
1068        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
1069        non-legacy seaice_solve4temp.
1070      - add diagnostic of the residual sublimation freshwater flux (the freshwater
1071        flux taken from the ocean if the total actual latent heat fluxes exceed
1072        the maximum)
1073      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
1074       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
1075      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
1076       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
1077      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
1078      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
1079    o verification 1D_ocean_ice_column:
1080       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
1081       update results
1082    o pkg/diagnostics:
1083     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
1084       which are not filled-up but computed from other diags ; In this case, the mate
1085       diag points to the primary (filled-up) diag to used for post processing.
1086     - Update Velocity-potential computation using post-processed diag framework.
1087     ==> Change the ordering of fields and time-periods in MDS output file
1088       when using periodic averaging: now writes one time record with the full set
1089       of fields for this time period, then the next time reccord (it used to be
1090       one field with the full set of time records then the next field).
1091         Note: this is now similar to NetCDF (MNC) output file. <==
1092    
1093    checkpoint62z (2011/06/21)
1094    o adjoint monitor:
1095     - Add adjoint monitor output for packages exf, seaice
1096       and update relevant testreport output
1097    o pkg/seaice:
1098     - re-order diags inits so that they appear in order in available_diagnostics.log
1099     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
1100       area/heff/hsnow preceeding thermodynamic growth/melt.
1101     - modified diag: SIdA; output actual effect, as the description states.
1102     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
1103     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
1104       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
1105        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
1106     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
1107     - added diagnostics for seaice generic tracers (SItr*).
1108     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
1109     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
1110     I. Fenty: 18-Jun-2011:
1111     Minor changes to seaice package:
1112     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
1113        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
1114       - Differentiated "regularization variables" from "floor variables"
1115        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
1116        * hiceMin became SEAICE_hice_reg (old hiceMin)
1117          (with _reg meaning regularization variable)
1118       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
1119        so as to ensure energy conservation when going between phases
1120      - A22 was not used anywhere
1121     2) Changed regularization procedure for heffActual and hsnowActual to ensure
1122        well-boundedness and smooth adjoint in seaice_growth.F
1123     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
1124        because the old regularization always set heffActual >= 0.05 cm
1125     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
1126        on AREA when HEFF > 0.
1127      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
1128        requiring that DISABLE_AREA_FLOOR *not* be defined
1129     Affected verifications:
1130      - 1D_ocean_ice_column (output.txt output_adm.txt)
1131      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
1132    o pkg/diagnostics:
1133      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
1134      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
1135        (was _RL, now integer) with option = 0 to retrieve all levels.
1136      - add pieces of code to compute velocity potential at each level (new diagnostics
1137        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
1138        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
1139      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
1140        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
1141        and in diagnostics_fract_fill.F (do not need a valid pointer for the
1142        diagnostics counter-mate); check that definition of counter-diagnostic
1143        includes a valid counter-mate (in diagnostics_set_levels.F).
1144    o model/src (rStar):
1145      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
1146        affect solution only if z* with full pressure in EOS;
1147        update output of test-exp global_ocean.90x40x15.
1148    o pkg/seaice:
1149      - introduce siEps=1e-5 parameter
1150      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
1151      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
1152      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
1153        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
1154        as well as ice cover age and ridging index (attached to AREA).
1155        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
1156        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
1157        Up to SItrMaxNum=3 tracers can be used simultaneously.
1158    o pkg/salt_plume:
1159      -introduce SPsalFRAC run time parameter that sets the fraction of the
1160       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
1161       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
1162    o model debug options:
1163      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
1164        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
1165      - Refine debug-msg printing selection (3 new levels):
1166        debugMode  : controls printing of debug messages (sequence of S/R calls).
1167        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
1168         debLevZero =  0 ; /* level of disabled aux. msg printing */
1169         debLevA =  1 ; /* level of minimum  aux. msg printing */
1170         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
1171         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
1172         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
1173         debLevE =  5 ; /* level of extensive debug printing */
1174        New debugLevel default: with default debugMode value (=F),
1175          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
1176          and if debugMode=T, default debugLevel = 4 (debLevD).
1177        Relation with previous settings:
1178         debLevB (=2) corresponds to former debLevA (=1)
1179         debLevD (=4) corresponds to former debLevB (=2)
1180        Note:
1181         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
1182         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
1183            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
1184      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
1185        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
1186    o pkg/obcs:
1187      - change OBCSfixTopo default from True to False (should not change the results);
1188        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
1189    o pkg/thsice:
1190      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
1191        2nd layer seaice sublimation (unlikely to happen)
1192      - use Interior mask for OBCS in thsice_advection.F (similar to what is
1193        done in gad_advection & seaice_advection).
1194    o adjoint:
1195      bug fix spotted by Gael Forget:
1196      seaice_advection and thsice_advection still had
1197      legacy CPP options to avoid CS corner updates for adjoint
1198    o pkg/seaice:
1199      => Change some of the defaults (2011/05/29):
1200         - change SEAICEuseFluxForm default (from False to True)
1201         - change DIFF1 default (from 0.004 m/s to 0. m/s)
1202         And print warnings if DIFF1 is not set in data.seaice and centered
1203          avection scheme is used without any diffusion.
1204      also:
1205      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
1206      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
1207      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
1208        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
1209        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
1210      update results of test exp.:
1211         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
1212             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
1213             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
1214         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
1215         seaice_obcs: output (SEAICEuseFluxForm=T)
1216      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
1217          for standard fwd & AD lab_sea tests (to keep the same output).
1218    o pkg/seaice/seaice_growth.F:
1219      - use Ian Fenty's capping formulas for actual ice
1220      thickness thoughout EVOLUTION branch.
1221      - put treatment pathological case #2) in CPP brackets
1222      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
1223      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
1224    o pkg/seaice:
1225      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
1226      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
1227      also pass fac as a param, which can be 1. (to update the tendency
1228      field) or the time step (to update the field itself).
1229      - seaice_advdiff.F: for multidim, call seaice_diffusion with
1230      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
1231      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
1232      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
1233      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
1234    o pkg/seaice:
1235      diffusion with centered advection scheme (diffus.F & advect.F):
1236      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
1237        to just compute the laplacian of input-field.
1238      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
1239      - fix flux-form version in diffus.F to conserve tracer.
1240      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
1241       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
1242    
1243    checkpoint62y (2011/05/26)
1244  o pkg/seaice:  o pkg/seaice:
1245   - seaice_growth.F : in EVOLUTION branch, always include   - seaice_growth.F : in EVOLUTION branch, always include
1246     a_QSWbyATM_cover in qnet (as it should be).     a_QSWbyATM_cover in qnet (as it should be).
1247   - verification/global_ocean.cs32x15 : update results accordingly   - verification/global_ocean.cs32x15 : update results accordingly
1248     (output.seaice.txt output_adm.seaice.txt).     (output.seaice.txt output_adm.seaice.txt).
1249  o pkg/seaice + obcs:  o pkg/seaice + obcs:
1250   - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:   - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
1251     equivalent of assuming no tracer gradient outside the OB region.     equivalent of assuming no tracer gradient outside the OB region.
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