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revision 1.1557 by jmc, Wed Dec 21 17:31:53 2011 UTC revision 1.1669 by jmc, Fri Jun 15 13:40:36 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/generic_advdiff:
8      - implement vertical bi-harmonic diffusion (for now, only for T & S and
9        only explicitly).
10    o verification/bottom_ctrl_5x5/
11      update reference output (results changed quite some time ago,
12      not sure when; but new reference results look ok in terms of grdchk)
13    o verification/1D_ocean_ice_column/
14      For verification purposes, the exact adjoint rather than an approx.
15      should be used (e.g., to comare against F.D. or TLM).
16      removed autodiff_inadmode*_ad.F routines in code_ad/
17      Update results/ accordingly.
18    o pkg/cal:
19      - change cal_getdate.F so that output date is function of input time only
20        (less ambiguous, not mixed up with input iteration number).
21      - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
22    o pkg/diagnostics:
23      - implement calendarDumps also for stats-diags
24      - implement calendarDumps also for snap-shot output (negative freq)
25      - for now, ignores calendarDumps if non-zero phase-lag.
26    
27    checkpoint63n (2012/06/04)
28    o model/src:
29      - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
30        between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
31      - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
32        similar to calc_r_star.F); update results of experiment internal_wave and
33        tutorial_global_oce_in_p (affected @ truncation level).
34    o pkg/shelfice:
35      - add parameterisation of advective-diffusive flux into the ice shelf
36        according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
37      - simply eps3/3a computation
38    o eesupp:
39     - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
40       between tiles, just fill-in edges assuming locally periodic subdomain) and
41       add corresponding exchange subroutines (EXCH0);
42     - new CG-solver version (_EX0) for disconnected-tiles special case.
43    o model/src (CG-solvers):
44     - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
45       (similar final residual output and max-Iter number as with standard version);
46     - allows to store and use lowest-residual solution (standard & _SR versions);
47     - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
48     - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
49    o eesup/src:
50     - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
51       ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
52    o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
53    
54    checkpoint63m (2012/04/27)
55    o pkg/shelfice:
56     - account for partical cells in surface level below ice-shelf for hydrostatic
57       pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
58    o ad test experiments:
59     - update and rename to "ad_optfile.local" local AD-optfile specific to a
60       particular adjoint verification experiment (in verification/*/code_ad/)
61    o pkg/seaice & pkg/exf:
62     - Part two of ECCO-CLIVAR code merges.
63       Completes merge of seaice area relax. code.
64       Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
65       to be set in EXF_OPTIONS.h since this pkg controls its I/O
66       (and avoids second CPP option in SEAICE_OPTIONS.h)
67     - change default value of costIceStart & costIceEnd to a valid date.
68     - add snowPrecip to HSNOW in seaice_growth
69    o pkg/ptracers:
70     - move ptracers summary and setup check into separated S/R ; add a check for
71       valid PTRACERS_Iter0 value (error+stop or just warning).
72    o pkg/cal (+ pkg/ecco):
73     - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
74       as input; and for AD, unless both are not differentiable (e.g., k index)).
75    o model/src:
76     - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
77       is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
78       temporary set to usingZCoords value (to be changed to F when using shelfice).
79     - hydrostatic pressure: implement partial cell near the surface also for
80       Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
81       usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
82    o pkg/ctrl/ctrl_init.F:
83     - add a formal parameter to s/r ctrl_init_rec to print
84       xx_$(ctrl_valiable)_file for easier debugging
85     - move call of cal_* routines into the if-block where they are really
86       needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
87       to specify a startdate
88    o pkg/seaice:
89     - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
90       global_ocean.cs32x15/code versions).
91     - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
92       verification experiment global_ocean.cs32x15.seaice and update results.
93    o pkg/exf:
94     - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
95       (according to useExfYearlyFields).
96    o pkg/cal:
97     - move calendar setting & summary (previously in cal_readparams.F) into new
98       S/R CAL_INIT_FIXED to be called later in the initialisation process, once
99       length of the simulation is set (after SET_PARMS call); This is an attempt
100       to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
101     - For safety: keep a record of pkg/cal parameter settings status
102               to allow to STOP if one pkg/cal S/R is called too early.
103     - add a stop in all basic pkg/cal subroutines if called before setting is done.
104     - modify cal_getdate.F: stop when nothing was returned;
105       if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
106       this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
107    
108    checkpoint63l (2012/04/04)
109    o pkg/bbl:
110      - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
111        update global_with_exf output.yearly.txt file.
112    o pkg/cal:
113      - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
114      - remove 2 unsused and very short (1 line only) functions ;
115      - remove unsused subroutines from AD-Diff list.
116    o model/src:
117      - start to implement clean wait to stop in initialization S/R (config_check.F,
118         packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
119    o folowing PRINT_MESSAGE changes:
120      - remove reminder multiple print to the same file (STDOUT) when multi-threads.
121    o pkg/bbl:
122      - modification so it can work with z*
123      - replace deltaT with dTtracerLev(k) for asynchronous time stepping
124      - global_with_exf/input.yearly verification; changes output.yearly.txt
125    o eesupp/src:
126      - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
127        writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
128      - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
129        # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
130      - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
131      - when using MPI, always set usingMPI=T ; set default accordingly and stop
132        if not consistent.
133      - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
134        argument is zero (in case called within single-thread section).
135    o pkg/fizhi:
136        clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
137        in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
138    o pkg/exch2:
139      - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
140        activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
141      - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
142        but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
143        with bad ones coming from a not-yet-updated halo.
144        This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
145    o pkg/frazil:
146        move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
147        http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
148    o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
149    o verification/lab_sea
150      * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
151      * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
152      * nTimeSteps 3 -> 4
153      * changed reference output accordingly
154    o pkg/ctrl:
155      * fix ctrl_get_gen for xx_sst, xx_sss
156    o pkg/fizhi:
157      - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
158        update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
159      - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
160        fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
161        clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
162    o pkg/gmredi:
163      - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
164    o pkg/fizhi:
165      - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
166        (old)aces open64 tuv test.
167    o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
168    o pkg/mom_vecinv:
169      - fix 1 loop range in mom_vecinv.F to be like all the other loops which
170        set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
171        with non-lin free-surf).
172    o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
173      in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
174      some compilers (gfortran 4.6.0 on MacOS)
175    o momentum:
176      - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
177        & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
178        fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
179    
180    checkpoint63k (2012/03/17)
181    o model/src:
182       - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
183         flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
184       - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
185         (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
186    o model/src: solve_*diagonal.F
187       - replace division with multiplication by inverse (similar to original version)
188         update output of AD exp. global_ocean.90x40x15.
189       - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
190         to enable the use of the vectorized & differentiable solve_tridiagonal.F
191       - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
192         vertical advection (to get solve_tridiagonal tested in AD mode).
193    o pkg/seaice: ECCO-CLIVAR merge:
194      1. seaice AREA relaxation
195         * CPP option: SEAICE_ALLOW_AREA_RELAXATION
196         * runtime flag: SEAICE_tauAreaObsRelax
197      2. modified global mean cost imbalance code: CPP option
198          ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
199    o another iteration on solve_*diagonal.F
200       Make choices independent of AUTODIFF
201       Default will be the adjoinable vectorized version.
202       Alternative choices are:
203       * non-adjoinable original version with low memory footprint:
204         #define SOLVE_DIAGONAL_LOWMEMORY
205       * still adjoinable but does not vectorize (k as inner-most loop):
206         #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
207    o testreport
208     - add option to use a home made wrapper around "make"
209     - remove MITGCM_IEEE env. variable (no longer active)
210    o pkg/shelfice
211     - improve computation of friction velocity for velocity dependent
212       exchange coefficients: include velocities into SHELFICEBoundaryLayer
213       block to average velocities vertically
214     - add TAF store directives for SHI_ALLOW_GAMMAFRICT
215    o Modify diagonal solvers, now three versions (upon request):
216      #ifndef SOLVE_DIAGONAL_AUTODIFF
217        1. default version (dating back a while ago)
218      #else /* def SOLVE_DIAGONAL_AUTODIFF */
219      # ifdef SOLVE_DIAGONAL_KINNER
220        2. adjoinable version with k-innermost loop (G. Forget)
221      # else
222        3. adjoinable vectorized version of 2.
223      # endif
224      #endif /* SOLVE_DIAGONAL_AUTODIFF */
225      All flags are currently set within routines, but could/should be moved to CPP-options.
226      Array bounds for 1. are as before, for 2.,3. cover the entire domain
227      (could be changed for 1. too).
228    o verification/lab_sea (fwd):
229      - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
230        use 7 categories (except hb87), new solve4temp params (except salt_plume),
231        constant salinity (=4) or variable salinity (salt_plume) done through
232        SItracer.
233    o pkg/seaice:
234      - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
235      - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
236         SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
237        from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
238        SEAICE_freeze got retired) but already better than previously with
239        SEAICE_freeze=123456.7 deg.C;
240      - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
241        (safer multi-threaded setting); always set SEAICEuseEVP;
242      - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
243        SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
244        stop if multiple specifications for the same coeff; make sure default
245        SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
246    o pkg/obcs:
247      - allow to switch to upwind 1rst order advection scheme for the advective
248        flux computation at the open-boundary; disabled for adjoint built.
249    o pkg/ptracers:
250      - rename PTRACERS_RESTART.h -> PTRACERS_START.h
251      - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
252      - add parameter to decide when to start a tracer; use internal flag to
253        know which tracer to step-forward; switch this internal flag at the top
254        of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
255        for adjoint built.
256    o pkg/seaice:
257      - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
258      - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
259      - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
260    o pkg/ecco:
261      - fix writing of output file DiagnosCost_ClimSalt/Theta
262        and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
263    o pkg/seaice:
264      - add missing initialisation of COR_ICE array in dynsolver.F
265      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
266        compiled either way, and is tested in all exps (multidim was only tested
267        in lab_sea ad before).
268      - cosmetic change to prepare for future addition of ITD. no change to results.
269        no defaults change.
270      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
271      - by lack of adequate verification experiments, I further used custom versions
272        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
273        should be correct.
274      - avoid recomputations in ad.
275    o array initialisation in adjoint mode:
276      1) pkg/mom_common/mom_calc_ke.F:
277        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
278        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
279        part this initialisation is gone, resulting in Floating Point Exception
280        (caught by open64 compiler with debug option).
281      2) model/src/convective_weights.F
282        set output convectCount over the full array range (instead of doing
283        an update): this fix a similar issue when called within recomputation (adjoint)
284        which could by-pass the initialisation (normally done in the caller S/R).
285    o pkg/seaice:
286      - final version of turbulent flux params, as agreed at MIT ice meet:
287           SEAICE_mcPheePiston (default is ~ 0.000875)
288           SEAICE_mcPheeTaper (default is 0.)
289           SEAICE_frazilFrac (defualt is 1.)
290           SEAICE_mcPheeStepFunc (default is false)
291      - changes results at trunction error level
292      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
293    o added pkg/frazil:
294      - see frazil_description.tex for details
295      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
296    o pkg/shelfice/shelfice_thermodynamics.F
297      - fix exponents for velocity dependent exchange coefficients: change
298        from 2/3(=0) to 0.66666666666666667
299      - move computation of velocity dependent exchange coefficients into
300        separate loop, so that it applies to both thermodynamics
301      - move some divisions by constants out of loops
302    
303    checkpoint63j (2012/02/16)
304    o pkg/seaice:
305      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
306      - SItracer:  added run time params, and allow coupling to ocn salinity.
307    o pkg/seaice: remove (almost) all divisions by constants within loops
308      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
309      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
310      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
311      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
312    o pkg/seaice :
313      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
314        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
315      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
316      - add permanent SItflux diag that corresponds to TFLUX but includes
317        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
318      - allow activation/testing of a fix for suspected missing term in
319        ocn-ice heat budget (to be confirmed). To test this, you want to
320        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
321        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
322      - no change in results, fwd or ad.
323    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
324      - switch to variable freezing point.
325           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
326      - bug fix : the sublimation term that was missing is now activated.
327           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
328      - bug fix : flooding sign term for SIsal0.NE.0.
329           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
330    o pkg/seaice:
331      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
332        is now the default, and the old default constant freezing point is recovered
333        with SEAICE_tempFrz0    = -1.96,
334             SEAICE_dTempFrz_dS = 0.,
335      - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
336      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
337      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
338        activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
339      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
340        was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
341      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
342        seaice_growth r149 for legacy branch (no results change).
343      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
344        from I. Fenty).
345      - results did not change except for global_ocean.cs32x15, mostly due to the
346        switch to variable freezing point (see above item for detail).
347    o pkg/thsice:
348      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
349        seawater freezing in thsice_calc_thickn (not used).
350    o pkg/seaice: turbulent flux term specification via run time params.
351      - replace CPP switches with run time switches to facilitate testing
352      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
353                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
354      - added runtime parameter : SEAICEturbFluxFormula
355      - move Mcphee constants to SEAICE_PARAMS.h
356      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
357                 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
358                 remove seaice_summary call (moved to seaice_init_fixed)
359      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
360        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
361      - seaice_summary.F : add missing report of read turbulent flux term set up
362                           and SITRACER.
363      - seaice_check.F : check range; inform and stop if retired CPPs are used
364                         (incl. SEAICE_AGE).
365      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
366             CPP switch, same computation as before for the different options.
367      - change results at the truncation level.
368    o pkg/seaice:
369      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
370        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
371        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
372      - update verification/*/input*/data.seaice:
373        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
374        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
375        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
376        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
377    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
378      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
379        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
380        difference in results only due to machine truncation.
381      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
382        MaykutPolySatVap; keep MIN_LWDOWN.
383      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
384      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
385        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
386    o pkg/salt_plume:
387      - isolate saltPlumeFlux array exch into a specific S/R called from
388        do_oceanic_phys.F
389      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
390    o verification:
391      - move untested set-up to MITgcm_contrib/verification_other.
392    o pkg/seaice:
393      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
394    o pkg/seaice:
395      - seaice_solve4temp.F (keeping results unchanged):
396        * add 2 future run-time params to select which saturation vapor pressure
397          formula is used and how post-iteration fluxes are set.
398          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
399        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
400          the linearized expression to stay consistent with tsurf finding.
401      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
402        can be < 0.
403    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
404      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
405        conductive heat flux F_c , and add it explicitly when updating tsurf as
406        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
407        so that now F_ia has a consistent meaning through the entire routine.
408        This causes differences at truncation level: update output of fwd exp.
409        global_ocean.cs32x15.seaice.
410    o pkg/seaice:
411      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
412        of arrays, sign/direction of fluxes; no effect on results.
413      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
414        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
415        note: this should have been done before changing celsius2K default.
416      - to keep results unchanged, add back old value of celsius2K in verification
417        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
418      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
419        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
420        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
421        freezing temp is consistent with value in seaice_growth.F ; this causes
422        differences at machine truncation level: update lab_sea AD output (3/4).
423    o pkg/seaice:
424      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
425        and climsst/sss even when using seaice (to prevent calculation that might
426        use SST on land); does not affect any verification exp.
427      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
428        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
429    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
430      over land (non-legacy code)
431    o vectorize salt_plume package:
432      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
433      - this code computes plumebk everywhere (also over land), thus requires
434        code to avoid divisions by zero and catch the case of kLev=Nr.
435      - efficiency of salt_plume_frac is still sub-optimal
436    o tools (genmake2):
437      - fix makefile NAME specification (option: -makefile NAME) by adding
438        "-f $MAKEFILE" in few places where it was missing including makedepend
439        command (contribution from Paul).
440    
441    checkpoint63i (2012/01/24)
442    o model/src:
443      - add factorized versions of some EOS code to find_rho.F,
444        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
445    o model/src:
446      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
447      - change default celsius2K from 273.16 to 273.15
448      - to keep results unchanged, add back old value of celsius2K in verification
449        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
450         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
451    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
452      to make TAF generate vectorizable code
453    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
454       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
455       have flags that do this more efficiently.
456    o pkg/diagnostics/diagstats_calc.F
457      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
458    o pkg/obcs (with exch2):
459      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
460        and remove code (in obcs_readparms.F) which was based on EXCH of indices
461        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
462    o pkg/exf and seaice exp:
463      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
464        so that switching off area & heff advection flags does not affect results.
465      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
466      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
467        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
468        results of verification experiments: 1D_ocean_ice_column(fwd),
469        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
470        and offline_exf_seaice (all 4).
471    o pkg/seaice:
472      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
473        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
474      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
475        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
476        not multi-dim advection;
477      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
478        SHORTWAVE_HEATING #undef.
479    o optim: make Makefile more robust (?)
480    o pkg/obcs:
481      * fix treatment of obcs_read_pickup for TAF
482    o pkg/shelfice:
483      * add missing initialisation of num_shifwflx
484      * new adjoint verification exp. for isomip
485      * change Prandtl and Schmidt numbers from generic formulations
486        (in terms of model diffus. and visc.) to separate runtime
487        parameters, with Holland and Jenkins (1999) default values.
488    o pkg/exf (interpolation):
489      - extended input field (2 rows) near the N & S poles:
490        * fill in with the symetric value (when even Nb of data in longitude)
491        * add average value at the poles only for scalar quantities ; for vector
492          component interpolation, skip the averaging and keep duplicated values,
493          unless the 2 components have same location (uvInterp=T) in which case
494          interpolate the 2 components together using S/R EXF_INTERP_UV.
495      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
496        together: this allows to account properly for local orientation when
497        averaging at N & S pole.
498      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
499        exf-interpolation near N & S poles. Undef by default.
500      - add debug check/print on 1rst iter if debugLevel >=2.
501    o pkg/exf:
502      - change masking flags definition (no longer "parameter"), put them in
503        common block and set them in S/R EXF_INIT_FIXED.
504      - change recognized masking flag from s,u,v to c,w,s since the mask
505        to use (maskC,W,S) depends on position on model grid and has little to
506        do with scalar/vector difference; fix masking if using P-coordinates.
507      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
508        and update results of exp. global_with_exf (x2).
509      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
510    o pkg/obcs
511      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
512    o pkg/exf (interpolation):
513      - assume periodicity in X only if input field cover full longitude range.
514      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
515        and should vectorise).
516      - fix input lat of the 2 added row (in case we provide N.pole data).
517    
518    checkpoint63h (2011/12/30)
519    o pkg/seaice:
520      - change declaration of UVM from _RL to _RS in order to get B-grid
521        uIce,vIce monitor when _RS = real*4
522    o pkg/offline:
523      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
524      - compute vertical velocity if not read from file (switch on exactConserv
525        & staggerTimeStep);
526      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
527    o verification:
528      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
529        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
530        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
531      - update output of exp. global_ocean.cs32x15.viscA4 after changing
532        grid-file angles (used here for coriolis-3d);
533      - remove (or gzip) few files not needed to run fizhi-cs experiments.
534    o pkg/exf (vector interpolation):
535      - rotate vector component toward local grid-axis orientation using grid-angles
536        (stored in GRID.h) instead of locally computed rotation angle; keep old code
537        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
538    o pkg/seaice:
539      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
540        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
541    o pkg/PKG_OPTIONS.h files:
542      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
543        outside of the #ifdef ALLOW_THISPKG / #endif block.
544      - update verification/*/code/PKG_OPTIONS.h files.
545    o add a verification experiment (offline_exf_seaice/input.seaice) that test
546      the B-grid LSOR solver
547    o pkg/seaice: sort out emissivity and long wave radiation step 2:
548      - add emissivity for snow and ice as new run-time parameters
549        (unfortunately) that default to the corresponding exf values; this
550        changes results in most verification experiments so that for backward
551        compatibility these parameter have to be set explicitly to inconsistent
552        values (ugly);
553      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
554        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
555        until we agree how to handle this bug properly
556  o pkg/exf (interpolation):  o pkg/exf (interpolation):
557    - add a set of run-time param ({inputfield}_interpMethod), one for    - add a set of run-time param ({inputfield}_interpMethod), one for
558      each interpolated input field, to select the interpolation method      each interpolated input field, to select the interpolation method
# Line 11  o pkg/exf (interpolation): Line 560  o pkg/exf (interpolation):
560    - print interpolation parameters to standard output;    - print interpolation parameters to standard output;
561    - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined    - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
562      (to use instead runoff_interpMethod=0 in data.exf).      (to use instead runoff_interpMethod=0 in data.exf).
563      - simplify default setting of interpolation parameters (for all fields,
564        set position to match model grid cell-center position, leading to trivial
565        interpolation in case of regular Lat-Lon grid) and fix for the case of
566        non-uniform delY.
567  o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for  o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
568     within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.     within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
569     this factor is absolutely required, because the lw exitance (= out-going     this factor is absolutely required, because the lw exitance (= out-going
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