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revision 1.1562 by jmc, Sun Dec 25 22:29:37 2011 UTC revision 1.1664 by jmc, Mon Jun 4 21:05:46 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 pkg/exf (vertor interpolation):  checkpoint63n (2012/06/04)
8    o model/src:
9      - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
10        between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
11      - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
12        similar to calc_r_star.F); update results of experiment internal_wave and
13        tutorial_global_oce_in_p (affected @ truncation level).
14    o pkg/shelfice:
15      - add parameterisation of advective-diffusive flux into the ice shelf
16        according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
17      - simply eps3/3a computation
18    o eesupp:
19     - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
20       between tiles, just fill-in edges assuming locally periodic subdomain) and
21       add corresponding exchange subroutines (EXCH0);
22     - new CG-solver version (_EX0) for disconnected-tiles special case.
23    o model/src (CG-solvers):
24     - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
25       (similar final residual output and max-Iter number as with standard version);
26     - allows to store and use lowest-residual solution (standard & _SR versions);
27     - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
28     - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
29    o eesup/src:
30     - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
31       ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
32    o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
33    
34    checkpoint63m (2012/04/27)
35    o pkg/shelfice:
36     - account for partical cells in surface level below ice-shelf for hydrostatic
37       pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
38    o ad test experiments:
39     - update and rename to "ad_optfile.local" local AD-optfile specific to a
40       particular adjoint verification experiment (in verification/*/code_ad/)
41    o pkg/seaice & pkg/exf:
42     - Part two of ECCO-CLIVAR code merges.
43       Completes merge of seaice area relax. code.
44       Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
45       to be set in EXF_OPTIONS.h since this pkg controls its I/O
46       (and avoids second CPP option in SEAICE_OPTIONS.h)
47     - change default value of costIceStart & costIceEnd to a valid date.
48     - add snowPrecip to HSNOW in seaice_growth
49    o pkg/ptracers:
50     - move ptracers summary and setup check into separated S/R ; add a check for
51       valid PTRACERS_Iter0 value (error+stop or just warning).
52    o pkg/cal (+ pkg/ecco):
53     - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
54       as input; and for AD, unless both are not differentiable (e.g., k index)).
55    o model/src:
56     - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
57       is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
58       temporary set to usingZCoords value (to be changed to F when using shelfice).
59     - hydrostatic pressure: implement partial cell near the surface also for
60       Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
61       usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
62    o pkg/ctrl/ctrl_init.F:
63     - add a formal parameter to s/r ctrl_init_rec to print
64       xx_$(ctrl_valiable)_file for easier debugging
65     - move call of cal_* routines into the if-block where they are really
66       needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
67       to specify a startdate
68    o pkg/seaice:
69     - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
70       global_ocean.cs32x15/code versions).
71     - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
72       verification experiment global_ocean.cs32x15.seaice and update results.
73    o pkg/exf:
74     - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
75       (according to useExfYearlyFields).
76    o pkg/cal:
77     - move calendar setting & summary (previously in cal_readparams.F) into new
78       S/R CAL_INIT_FIXED to be called later in the initialisation process, once
79       length of the simulation is set (after SET_PARMS call); This is an attempt
80       to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
81     - For safety: keep a record of pkg/cal parameter settings status
82               to allow to STOP if one pkg/cal S/R is called too early.
83     - add a stop in all basic pkg/cal subroutines if called before setting is done.
84     - modify cal_getdate.F: stop when nothing was returned;
85       if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
86       this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
87    
88    checkpoint63l (2012/04/04)
89    o pkg/bbl:
90      - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
91        update global_with_exf output.yearly.txt file.
92    o pkg/cal:
93      - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
94      - remove 2 unsused and very short (1 line only) functions ;
95      - remove unsused subroutines from AD-Diff list.
96    o model/src:
97      - start to implement clean wait to stop in initialization S/R (config_check.F,
98         packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
99    o folowing PRINT_MESSAGE changes:
100      - remove reminder multiple print to the same file (STDOUT) when multi-threads.
101    o pkg/bbl:
102      - modification so it can work with z*
103      - replace deltaT with dTtracerLev(k) for asynchronous time stepping
104      - global_with_exf/input.yearly verification; changes output.yearly.txt
105    o eesupp/src:
106      - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
107        writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
108      - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
109        # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
110      - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
111      - when using MPI, always set usingMPI=T ; set default accordingly and stop
112        if not consistent.
113      - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
114        argument is zero (in case called within single-thread section).
115    o pkg/fizhi:
116        clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
117        in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
118    o pkg/exch2:
119      - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
120        activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
121      - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
122        but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
123        with bad ones coming from a not-yet-updated halo.
124        This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
125    o pkg/frazil:
126        move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
127        http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
128    o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
129    o verification/lab_sea
130      * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
131      * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
132      * nTimeSteps 3 -> 4
133      * changed reference output accordingly
134    o pkg/ctrl:
135      * fix ctrl_get_gen for xx_sst, xx_sss
136    o pkg/fizhi:
137      - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
138        update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
139      - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
140        fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
141        clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
142    o pkg/gmredi:
143      - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
144    o pkg/fizhi:
145      - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
146        (old)aces open64 tuv test.
147    o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
148    o pkg/mom_vecinv:
149      - fix 1 loop range in mom_vecinv.F to be like all the other loops which
150        set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
151        with non-lin free-surf).
152    o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
153      in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
154      some compilers (gfortran 4.6.0 on MacOS)
155    o momentum:
156      - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
157        & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
158        fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
159    
160    checkpoint63k (2012/03/17)
161    o model/src:
162       - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
163         flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
164       - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
165         (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
166    o model/src: solve_*diagonal.F
167       - replace division with multiplication by inverse (similar to original version)
168         update output of AD exp. global_ocean.90x40x15.
169       - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
170         to enable the use of the vectorized & differentiable solve_tridiagonal.F
171       - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
172         vertical advection (to get solve_tridiagonal tested in AD mode).
173    o pkg/seaice: ECCO-CLIVAR merge:
174      1. seaice AREA relaxation
175         * CPP option: SEAICE_ALLOW_AREA_RELAXATION
176         * runtime flag: SEAICE_tauAreaObsRelax
177      2. modified global mean cost imbalance code: CPP option
178          ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
179    o another iteration on solve_*diagonal.F
180       Make choices independent of AUTODIFF
181       Default will be the adjoinable vectorized version.
182       Alternative choices are:
183       * non-adjoinable original version with low memory footprint:
184         #define SOLVE_DIAGONAL_LOWMEMORY
185       * still adjoinable but does not vectorize (k as inner-most loop):
186         #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
187    o testreport
188     - add option to use a home made wrapper around "make"
189     - remove MITGCM_IEEE env. variable (no longer active)
190    o pkg/shelfice
191     - improve computation of friction velocity for velocity dependent
192       exchange coefficients: include velocities into SHELFICEBoundaryLayer
193       block to average velocities vertically
194     - add TAF store directives for SHI_ALLOW_GAMMAFRICT
195    o Modify diagonal solvers, now three versions (upon request):
196      #ifndef SOLVE_DIAGONAL_AUTODIFF
197        1. default version (dating back a while ago)
198      #else /* def SOLVE_DIAGONAL_AUTODIFF */
199      # ifdef SOLVE_DIAGONAL_KINNER
200        2. adjoinable version with k-innermost loop (G. Forget)
201      # else
202        3. adjoinable vectorized version of 2.
203      # endif
204      #endif /* SOLVE_DIAGONAL_AUTODIFF */
205      All flags are currently set within routines, but could/should be moved to CPP-options.
206      Array bounds for 1. are as before, for 2.,3. cover the entire domain
207      (could be changed for 1. too).
208    o verification/lab_sea (fwd):
209      - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
210        use 7 categories (except hb87), new solve4temp params (except salt_plume),
211        constant salinity (=4) or variable salinity (salt_plume) done through
212        SItracer.
213    o pkg/seaice:
214      - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
215      - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
216         SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
217        from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
218        SEAICE_freeze got retired) but already better than previously with
219        SEAICE_freeze=123456.7 deg.C;
220      - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
221        (safer multi-threaded setting); always set SEAICEuseEVP;
222      - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
223        SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
224        stop if multiple specifications for the same coeff; make sure default
225        SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
226    o pkg/obcs:
227      - allow to switch to upwind 1rst order advection scheme for the advective
228        flux computation at the open-boundary; disabled for adjoint built.
229    o pkg/ptracers:
230      - rename PTRACERS_RESTART.h -> PTRACERS_START.h
231      - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
232      - add parameter to decide when to start a tracer; use internal flag to
233        know which tracer to step-forward; switch this internal flag at the top
234        of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
235        for adjoint built.
236    o pkg/seaice:
237      - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
238      - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
239      - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
240    o pkg/ecco:
241      - fix writing of output file DiagnosCost_ClimSalt/Theta
242        and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
243    o pkg/seaice:
244      - add missing initialisation of COR_ICE array in dynsolver.F
245      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
246        compiled either way, and is tested in all exps (multidim was only tested
247        in lab_sea ad before).
248      - cosmetic change to prepare for future addition of ITD. no change to results.
249        no defaults change.
250      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
251      - by lack of adequate verification experiments, I further used custom versions
252        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
253        should be correct.
254      - avoid recomputations in ad.
255    o array initialisation in adjoint mode:
256      1) pkg/mom_common/mom_calc_ke.F:
257        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
258        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
259        part this initialisation is gone, resulting in Floating Point Exception
260        (caught by open64 compiler with debug option).
261      2) model/src/convective_weights.F
262        set output convectCount over the full array range (instead of doing
263        an update): this fix a similar issue when called within recomputation (adjoint)
264        which could by-pass the initialisation (normally done in the caller S/R).
265    o pkg/seaice:
266      - final version of turbulent flux params, as agreed at MIT ice meet:
267           SEAICE_mcPheePiston (default is ~ 0.000875)
268           SEAICE_mcPheeTaper (default is 0.)
269           SEAICE_frazilFrac (defualt is 1.)
270           SEAICE_mcPheeStepFunc (default is false)
271      - changes results at trunction error level
272      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
273    o added pkg/frazil:
274      - see frazil_description.tex for details
275      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
276    o pkg/shelfice/shelfice_thermodynamics.F
277      - fix exponents for velocity dependent exchange coefficients: change
278        from 2/3(=0) to 0.66666666666666667
279      - move computation of velocity dependent exchange coefficients into
280        separate loop, so that it applies to both thermodynamics
281      - move some divisions by constants out of loops
282    
283    checkpoint63j (2012/02/16)
284    o pkg/seaice:
285      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
286      - SItracer:  added run time params, and allow coupling to ocn salinity.
287    o pkg/seaice: remove (almost) all divisions by constants within loops
288      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
289      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
290      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
291      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
292    o pkg/seaice :
293      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
294        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
295      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
296      - add permanent SItflux diag that corresponds to TFLUX but includes
297        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
298      - allow activation/testing of a fix for suspected missing term in
299        ocn-ice heat budget (to be confirmed). To test this, you want to
300        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
301        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
302      - no change in results, fwd or ad.
303    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
304      - switch to variable freezing point.
305           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
306      - bug fix : the sublimation term that was missing is now activated.
307           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
308      - bug fix : flooding sign term for SIsal0.NE.0.
309           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
310    o pkg/seaice:
311      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
312        is now the default, and the old default constant freezing point is recovered
313        with SEAICE_tempFrz0    = -1.96,
314             SEAICE_dTempFrz_dS = 0.,
315      - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
316      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
317      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
318        activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
319      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
320        was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
321      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
322        seaice_growth r149 for legacy branch (no results change).
323      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
324        from I. Fenty).
325      - results did not change except for global_ocean.cs32x15, mostly due to the
326        switch to variable freezing point (see above item for detail).
327    o pkg/thsice:
328      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
329        seawater freezing in thsice_calc_thickn (not used).
330    o pkg/seaice: turbulent flux term specification via run time params.
331      - replace CPP switches with run time switches to facilitate testing
332      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
333                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
334      - added runtime parameter : SEAICEturbFluxFormula
335      - move Mcphee constants to SEAICE_PARAMS.h
336      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
337                 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
338                 remove seaice_summary call (moved to seaice_init_fixed)
339      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
340        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
341      - seaice_summary.F : add missing report of read turbulent flux term set up
342                           and SITRACER.
343      - seaice_check.F : check range; inform and stop if retired CPPs are used
344                         (incl. SEAICE_AGE).
345      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
346             CPP switch, same computation as before for the different options.
347      - change results at the truncation level.
348    o pkg/seaice:
349      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
350        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
351        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
352      - update verification/*/input*/data.seaice:
353        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
354        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
355        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
356        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
357    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
358      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
359        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
360        difference in results only due to machine truncation.
361      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
362        MaykutPolySatVap; keep MIN_LWDOWN.
363      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
364      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
365        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
366    o pkg/salt_plume:
367      - isolate saltPlumeFlux array exch into a specific S/R called from
368        do_oceanic_phys.F
369      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
370    o verification:
371      - move untested set-up to MITgcm_contrib/verification_other.
372    o pkg/seaice:
373      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
374    o pkg/seaice:
375      - seaice_solve4temp.F (keeping results unchanged):
376        * add 2 future run-time params to select which saturation vapor pressure
377          formula is used and how post-iteration fluxes are set.
378          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
379        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
380          the linearized expression to stay consistent with tsurf finding.
381      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
382        can be < 0.
383    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
384      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
385        conductive heat flux F_c , and add it explicitly when updating tsurf as
386        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
387        so that now F_ia has a consistent meaning through the entire routine.
388        This causes differences at truncation level: update output of fwd exp.
389        global_ocean.cs32x15.seaice.
390    o pkg/seaice:
391      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
392        of arrays, sign/direction of fluxes; no effect on results.
393      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
394        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
395        note: this should have been done before changing celsius2K default.
396      - to keep results unchanged, add back old value of celsius2K in verification
397        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
398      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
399        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
400        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
401        freezing temp is consistent with value in seaice_growth.F ; this causes
402        differences at machine truncation level: update lab_sea AD output (3/4).
403    o pkg/seaice:
404      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
405        and climsst/sss even when using seaice (to prevent calculation that might
406        use SST on land); does not affect any verification exp.
407      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
408        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
409    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
410      over land (non-legacy code)
411    o vectorize salt_plume package:
412      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
413      - this code computes plumebk everywhere (also over land), thus requires
414        code to avoid divisions by zero and catch the case of kLev=Nr.
415      - efficiency of salt_plume_frac is still sub-optimal
416    o tools (genmake2):
417      - fix makefile NAME specification (option: -makefile NAME) by adding
418        "-f $MAKEFILE" in few places where it was missing including makedepend
419        command (contribution from Paul).
420    
421    checkpoint63i (2012/01/24)
422    o model/src:
423      - add factorized versions of some EOS code to find_rho.F,
424        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
425    o model/src:
426      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
427      - change default celsius2K from 273.16 to 273.15
428      - to keep results unchanged, add back old value of celsius2K in verification
429        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
430         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
431    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
432      to make TAF generate vectorizable code
433    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
434       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
435       have flags that do this more efficiently.
436    o pkg/diagnostics/diagstats_calc.F
437      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
438    o pkg/obcs (with exch2):
439      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
440        and remove code (in obcs_readparms.F) which was based on EXCH of indices
441        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
442    o pkg/exf and seaice exp:
443      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
444        so that switching off area & heff advection flags does not affect results.
445      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
446      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
447        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
448        results of verification experiments: 1D_ocean_ice_column(fwd),
449        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
450        and offline_exf_seaice (all 4).
451    o pkg/seaice:
452      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
453        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
454      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
455        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
456        not multi-dim advection;
457      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
458        SHORTWAVE_HEATING #undef.
459    o optim: make Makefile more robust (?)
460    o pkg/obcs:
461      * fix treatment of obcs_read_pickup for TAF
462    o pkg/shelfice:
463      * add missing initialisation of num_shifwflx
464      * new adjoint verification exp. for isomip
465      * change Prandtl and Schmidt numbers from generic formulations
466        (in terms of model diffus. and visc.) to separate runtime
467        parameters, with Holland and Jenkins (1999) default values.
468    o pkg/exf (interpolation):
469      - extended input field (2 rows) near the N & S poles:
470        * fill in with the symetric value (when even Nb of data in longitude)
471        * add average value at the poles only for scalar quantities ; for vector
472          component interpolation, skip the averaging and keep duplicated values,
473          unless the 2 components have same location (uvInterp=T) in which case
474          interpolate the 2 components together using S/R EXF_INTERP_UV.
475      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
476        together: this allows to account properly for local orientation when
477        averaging at N & S pole.
478      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
479        exf-interpolation near N & S poles. Undef by default.
480      - add debug check/print on 1rst iter if debugLevel >=2.
481    o pkg/exf:
482      - change masking flags definition (no longer "parameter"), put them in
483        common block and set them in S/R EXF_INIT_FIXED.
484      - change recognized masking flag from s,u,v to c,w,s since the mask
485        to use (maskC,W,S) depends on position on model grid and has little to
486        do with scalar/vector difference; fix masking if using P-coordinates.
487      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
488        and update results of exp. global_with_exf (x2).
489      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
490    o pkg/obcs
491      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
492    o pkg/exf (interpolation):
493      - assume periodicity in X only if input field cover full longitude range.
494      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
495        and should vectorise).
496      - fix input lat of the 2 added row (in case we provide N.pole data).
497    
498    checkpoint63h (2011/12/30)
499    o pkg/seaice:
500      - change declaration of UVM from _RL to _RS in order to get B-grid
501        uIce,vIce monitor when _RS = real*4
502    o pkg/offline:
503      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
504      - compute vertical velocity if not read from file (switch on exactConserv
505        & staggerTimeStep);
506      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
507    o verification:
508      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
509        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
510        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
511      - update output of exp. global_ocean.cs32x15.viscA4 after changing
512        grid-file angles (used here for coriolis-3d);
513      - remove (or gzip) few files not needed to run fizhi-cs experiments.
514    o pkg/exf (vector interpolation):
515    - rotate vector component toward local grid-axis orientation using grid-angles    - rotate vector component toward local grid-axis orientation using grid-angles
516      (stored in GRID.h) instead of locally computed rotation angle; keep old code      (stored in GRID.h) instead of locally computed rotation angle; keep old code
517      available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).      available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
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