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revision 1.1572 by heimbach, Fri Jan 6 14:06:18 2012 UTC revision 1.1682 by jmc, Thu Jul 5 19:38:02 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/autodiff:
8      - rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ;
9      - create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters
10        which are now read from new parameter file "data.autodiff" (inAdExact
11        previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg)
12      - add file "data.autodiff" in all verification/*/input_ad/ directories.
13      - add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward
14        mode (used in global_ocean.cs32x15.seaice_dynmix test exp.)
15    o verification/tutorial_tracer_adjsens/
16      - add extra sub-verification which uses "SOM" advection scheme
17        (2nd Order-Moment Advection Scheme, Prather Limiter) with
18          #define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h
19        and in data:
20          multiDimAdvection=.TRUE.,
21          tempAdvScheme=81,
22          saltAdvScheme=81,
23    
24    checkpoint63o (2012/06/29)
25    o vertical mixing schemes:
26      - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging)
27      - replace computation of density (in Function STATE1, opps_calc.F) by a call
28        to S/R FIND_RHO_SCALAR
29      - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC
30        and use it for N^2 calculation in ggl90_calc.F (save 2 density computations);
31        affects output (vermix.ggl90) at truncation level.
32    o testreport:
33      - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles
34        (nSx,nSy) for the number of threads (from eedata.mth)
35    o model/src:
36      - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part)
37        related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary).
38    o verification/tutorial_tracer_adjsens/
39      - compile with ALLOW_CG2D_NSA
40      - run with nonlinFreeSurf=3
41      - update reference output_adm.txt
42    o tools/genmake2:
43      - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
44        refine usePROFILES switching off (only when NetCDF is not available).
45    o verification (atmospheric set-up):
46      - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
47    o pkg/profiles : refine profiles and files handling.
48    o model/src and pkg/ecco : introduce run-time switch usePROFILES.
49    o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
50      - changes to use model/src/the_main_loop.F rather than the ecco version
51        in ecco type adjoint runs.
52    o model/src:
53      - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
54      - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
55      - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
56    o model/src:
57      - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
58        update output of test experiment bottom_ctrl_5x5.
59    o pkg/generic_advdiff:
60      - implement vertical bi-harmonic diffusion (for now, only for T & S and
61        only explicitly).
62    o verification/bottom_ctrl_5x5/
63      update reference output (results changed quite some time ago,
64      not sure when; but new reference results look ok in terms of grdchk)
65    o verification/1D_ocean_ice_column/
66      For verification purposes, the exact adjoint rather than an approx.
67      should be used (e.g., to comare against F.D. or TLM).
68      removed autodiff_inadmode*_ad.F routines in code_ad/
69      Update results/ accordingly.
70    o pkg/cal:
71      - change cal_getdate.F so that output date is function of input time only
72        (less ambiguous, not mixed up with input iteration number).
73      - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
74    o pkg/diagnostics:
75      - implement calendarDumps also for stats-diags
76      - implement calendarDumps also for snap-shot output (negative freq)
77      - for now, ignores calendarDumps if non-zero phase-lag.
78    
79    checkpoint63n (2012/06/04)
80    o model/src:
81      - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
82        between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
83      - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
84        similar to calc_r_star.F); update results of experiment internal_wave and
85        tutorial_global_oce_in_p (affected @ truncation level).
86    o pkg/shelfice:
87      - add parameterisation of advective-diffusive flux into the ice shelf
88        according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
89      - simply eps3/3a computation
90    o eesupp:
91     - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
92       between tiles, just fill-in edges assuming locally periodic subdomain) and
93       add corresponding exchange subroutines (EXCH0);
94     - new CG-solver version (_EX0) for disconnected-tiles special case.
95    o model/src (CG-solvers):
96     - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
97       (similar final residual output and max-Iter number as with standard version);
98     - allows to store and use lowest-residual solution (standard & _SR versions);
99     - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
100     - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
101    o eesup/src:
102     - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
103       ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
104    o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
105    
106    checkpoint63m (2012/04/27)
107    o pkg/shelfice:
108     - account for partical cells in surface level below ice-shelf for hydrostatic
109       pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
110    o ad test experiments:
111     - update and rename to "ad_optfile.local" local AD-optfile specific to a
112       particular adjoint verification experiment (in verification/*/code_ad/)
113    o pkg/seaice & pkg/exf:
114     - Part two of ECCO-CLIVAR code merges.
115       Completes merge of seaice area relax. code.
116       Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
117       to be set in EXF_OPTIONS.h since this pkg controls its I/O
118       (and avoids second CPP option in SEAICE_OPTIONS.h)
119     - change default value of costIceStart & costIceEnd to a valid date.
120     - add snowPrecip to HSNOW in seaice_growth
121    o pkg/ptracers:
122     - move ptracers summary and setup check into separated S/R ; add a check for
123       valid PTRACERS_Iter0 value (error+stop or just warning).
124    o pkg/cal (+ pkg/ecco):
125     - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
126       as input; and for AD, unless both are not differentiable (e.g., k index)).
127    o model/src:
128     - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
129       is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
130       temporary set to usingZCoords value (to be changed to F when using shelfice).
131     - hydrostatic pressure: implement partial cell near the surface also for
132       Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
133       usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
134    o pkg/ctrl/ctrl_init.F:
135     - add a formal parameter to s/r ctrl_init_rec to print
136       xx_$(ctrl_valiable)_file for easier debugging
137     - move call of cal_* routines into the if-block where they are really
138       needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
139       to specify a startdate
140    o pkg/seaice:
141     - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
142       global_ocean.cs32x15/code versions).
143     - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
144       verification experiment global_ocean.cs32x15.seaice and update results.
145    o pkg/exf:
146     - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
147       (according to useExfYearlyFields).
148    o pkg/cal:
149     - move calendar setting & summary (previously in cal_readparams.F) into new
150       S/R CAL_INIT_FIXED to be called later in the initialisation process, once
151       length of the simulation is set (after SET_PARMS call); This is an attempt
152       to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
153     - For safety: keep a record of pkg/cal parameter settings status
154               to allow to STOP if one pkg/cal S/R is called too early.
155     - add a stop in all basic pkg/cal subroutines if called before setting is done.
156     - modify cal_getdate.F: stop when nothing was returned;
157       if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
158       this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
159    
160    checkpoint63l (2012/04/04)
161    o pkg/bbl:
162      - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
163        update global_with_exf output.yearly.txt file.
164    o pkg/cal:
165      - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
166      - remove 2 unsused and very short (1 line only) functions ;
167      - remove unsused subroutines from AD-Diff list.
168    o model/src:
169      - start to implement clean wait to stop in initialization S/R (config_check.F,
170         packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
171    o folowing PRINT_MESSAGE changes:
172      - remove reminder multiple print to the same file (STDOUT) when multi-threads.
173    o pkg/bbl:
174      - modification so it can work with z*
175      - replace deltaT with dTtracerLev(k) for asynchronous time stepping
176      - global_with_exf/input.yearly verification; changes output.yearly.txt
177    o eesupp/src:
178      - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
179        writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
180      - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
181        # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
182      - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
183      - when using MPI, always set usingMPI=T ; set default accordingly and stop
184        if not consistent.
185      - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
186        argument is zero (in case called within single-thread section).
187    o pkg/fizhi:
188        clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
189        in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
190    o pkg/exch2:
191      - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
192        activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
193      - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
194        but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
195        with bad ones coming from a not-yet-updated halo.
196        This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
197    o pkg/frazil:
198        move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
199        http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
200    o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
201    o verification/lab_sea
202      * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
203      * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
204      * nTimeSteps 3 -> 4
205      * changed reference output accordingly
206    o pkg/ctrl:
207      * fix ctrl_get_gen for xx_sst, xx_sss
208    o pkg/fizhi:
209      - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
210        update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
211      - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
212        fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
213        clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
214    o pkg/gmredi:
215      - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
216    o pkg/fizhi:
217      - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
218        (old)aces open64 tuv test.
219    o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
220    o pkg/mom_vecinv:
221      - fix 1 loop range in mom_vecinv.F to be like all the other loops which
222        set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
223        with non-lin free-surf).
224    o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
225      in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
226      some compilers (gfortran 4.6.0 on MacOS)
227    o momentum:
228      - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
229        & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
230        fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
231    
232    checkpoint63k (2012/03/17)
233    o model/src:
234       - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
235         flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
236       - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
237         (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
238    o model/src: solve_*diagonal.F
239       - replace division with multiplication by inverse (similar to original version)
240         update output of AD exp. global_ocean.90x40x15.
241       - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
242         to enable the use of the vectorized & differentiable solve_tridiagonal.F
243       - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
244         vertical advection (to get solve_tridiagonal tested in AD mode).
245    o pkg/seaice: ECCO-CLIVAR merge:
246      1. seaice AREA relaxation
247         * CPP option: SEAICE_ALLOW_AREA_RELAXATION
248         * runtime flag: SEAICE_tauAreaObsRelax
249      2. modified global mean cost imbalance code: CPP option
250          ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
251    o another iteration on solve_*diagonal.F
252       Make choices independent of AUTODIFF
253       Default will be the adjoinable vectorized version.
254       Alternative choices are:
255       * non-adjoinable original version with low memory footprint:
256         #define SOLVE_DIAGONAL_LOWMEMORY
257       * still adjoinable but does not vectorize (k as inner-most loop):
258         #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
259    o testreport
260     - add option to use a home made wrapper around "make"
261     - remove MITGCM_IEEE env. variable (no longer active)
262    o pkg/shelfice
263     - improve computation of friction velocity for velocity dependent
264       exchange coefficients: include velocities into SHELFICEBoundaryLayer
265       block to average velocities vertically
266     - add TAF store directives for SHI_ALLOW_GAMMAFRICT
267    o Modify diagonal solvers, now three versions (upon request):
268      #ifndef SOLVE_DIAGONAL_AUTODIFF
269        1. default version (dating back a while ago)
270      #else /* def SOLVE_DIAGONAL_AUTODIFF */
271      # ifdef SOLVE_DIAGONAL_KINNER
272        2. adjoinable version with k-innermost loop (G. Forget)
273      # else
274        3. adjoinable vectorized version of 2.
275      # endif
276      #endif /* SOLVE_DIAGONAL_AUTODIFF */
277      All flags are currently set within routines, but could/should be moved to CPP-options.
278      Array bounds for 1. are as before, for 2.,3. cover the entire domain
279      (could be changed for 1. too).
280    o verification/lab_sea (fwd):
281      - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
282        use 7 categories (except hb87), new solve4temp params (except salt_plume),
283        constant salinity (=4) or variable salinity (salt_plume) done through
284        SItracer.
285    o pkg/seaice:
286      - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
287      - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
288         SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
289        from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
290        SEAICE_freeze got retired) but already better than previously with
291        SEAICE_freeze=123456.7 deg.C;
292      - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
293        (safer multi-threaded setting); always set SEAICEuseEVP;
294      - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
295        SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
296        stop if multiple specifications for the same coeff; make sure default
297        SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
298    o pkg/obcs:
299      - allow to switch to upwind 1rst order advection scheme for the advective
300        flux computation at the open-boundary; disabled for adjoint built.
301    o pkg/ptracers:
302      - rename PTRACERS_RESTART.h -> PTRACERS_START.h
303      - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
304      - add parameter to decide when to start a tracer; use internal flag to
305        know which tracer to step-forward; switch this internal flag at the top
306        of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
307        for adjoint built.
308    o pkg/seaice:
309      - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
310      - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
311      - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
312    o pkg/ecco:
313      - fix writing of output file DiagnosCost_ClimSalt/Theta
314        and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
315    o pkg/seaice:
316      - add missing initialisation of COR_ICE array in dynsolver.F
317      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
318        compiled either way, and is tested in all exps (multidim was only tested
319        in lab_sea ad before).
320      - cosmetic change to prepare for future addition of ITD. no change to results.
321        no defaults change.
322      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
323      - by lack of adequate verification experiments, I further used custom versions
324        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
325        should be correct.
326      - avoid recomputations in ad.
327    o array initialisation in adjoint mode:
328      1) pkg/mom_common/mom_calc_ke.F:
329        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
330        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
331        part this initialisation is gone, resulting in Floating Point Exception
332        (caught by open64 compiler with debug option).
333      2) model/src/convective_weights.F
334        set output convectCount over the full array range (instead of doing
335        an update): this fix a similar issue when called within recomputation (adjoint)
336        which could by-pass the initialisation (normally done in the caller S/R).
337    o pkg/seaice:
338      - final version of turbulent flux params, as agreed at MIT ice meet:
339           SEAICE_mcPheePiston (default is ~ 0.000875)
340           SEAICE_mcPheeTaper (default is 0.)
341           SEAICE_frazilFrac (defualt is 1.)
342           SEAICE_mcPheeStepFunc (default is false)
343      - changes results at trunction error level
344      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
345    o added pkg/frazil:
346      - see frazil_description.tex for details
347      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
348    o pkg/shelfice/shelfice_thermodynamics.F
349      - fix exponents for velocity dependent exchange coefficients: change
350        from 2/3(=0) to 0.66666666666666667
351      - move computation of velocity dependent exchange coefficients into
352        separate loop, so that it applies to both thermodynamics
353      - move some divisions by constants out of loops
354    
355    checkpoint63j (2012/02/16)
356    o pkg/seaice:
357      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
358      - SItracer:  added run time params, and allow coupling to ocn salinity.
359    o pkg/seaice: remove (almost) all divisions by constants within loops
360      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
361      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
362      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
363      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
364    o pkg/seaice :
365      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
366        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
367      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
368      - add permanent SItflux diag that corresponds to TFLUX but includes
369        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
370      - allow activation/testing of a fix for suspected missing term in
371        ocn-ice heat budget (to be confirmed). To test this, you want to
372        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
373        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
374      - no change in results, fwd or ad.
375    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
376      - switch to variable freezing point.
377           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
378      - bug fix : the sublimation term that was missing is now activated.
379           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
380      - bug fix : flooding sign term for SIsal0.NE.0.
381           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
382    o pkg/seaice:
383      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
384        is now the default, and the old default constant freezing point is recovered
385        with SEAICE_tempFrz0    = -1.96,
386             SEAICE_dTempFrz_dS = 0.,
387      - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
388      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
389      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
390        activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
391      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
392        was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
393      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
394        seaice_growth r149 for legacy branch (no results change).
395      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
396        from I. Fenty).
397      - results did not change except for global_ocean.cs32x15, mostly due to the
398        switch to variable freezing point (see above item for detail).
399    o pkg/thsice:
400      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
401        seawater freezing in thsice_calc_thickn (not used).
402    o pkg/seaice: turbulent flux term specification via run time params.
403      - replace CPP switches with run time switches to facilitate testing
404      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
405                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
406      - added runtime parameter : SEAICEturbFluxFormula
407      - move Mcphee constants to SEAICE_PARAMS.h
408      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
409                 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
410                 remove seaice_summary call (moved to seaice_init_fixed)
411      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
412        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
413      - seaice_summary.F : add missing report of read turbulent flux term set up
414                           and SITRACER.
415      - seaice_check.F : check range; inform and stop if retired CPPs are used
416                         (incl. SEAICE_AGE).
417      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
418             CPP switch, same computation as before for the different options.
419      - change results at the truncation level.
420    o pkg/seaice:
421      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
422        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
423        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
424      - update verification/*/input*/data.seaice:
425        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
426        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
427        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
428        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
429    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
430      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
431        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
432        difference in results only due to machine truncation.
433      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
434        MaykutPolySatVap; keep MIN_LWDOWN.
435      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
436      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
437        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
438    o pkg/salt_plume:
439      - isolate saltPlumeFlux array exch into a specific S/R called from
440        do_oceanic_phys.F
441      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
442    o verification:
443      - move untested set-up to MITgcm_contrib/verification_other.
444    o pkg/seaice:
445      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
446    o pkg/seaice:
447      - seaice_solve4temp.F (keeping results unchanged):
448        * add 2 future run-time params to select which saturation vapor pressure
449          formula is used and how post-iteration fluxes are set.
450          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
451        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
452          the linearized expression to stay consistent with tsurf finding.
453      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
454        can be < 0.
455    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
456      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
457        conductive heat flux F_c , and add it explicitly when updating tsurf as
458        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
459        so that now F_ia has a consistent meaning through the entire routine.
460        This causes differences at truncation level: update output of fwd exp.
461        global_ocean.cs32x15.seaice.
462    o pkg/seaice:
463      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
464        of arrays, sign/direction of fluxes; no effect on results.
465      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
466        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
467        note: this should have been done before changing celsius2K default.
468      - to keep results unchanged, add back old value of celsius2K in verification
469        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
470      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
471        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
472        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
473        freezing temp is consistent with value in seaice_growth.F ; this causes
474        differences at machine truncation level: update lab_sea AD output (3/4).
475    o pkg/seaice:
476      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
477        and climsst/sss even when using seaice (to prevent calculation that might
478        use SST on land); does not affect any verification exp.
479      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
480        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
481    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
482      over land (non-legacy code)
483    o vectorize salt_plume package:
484      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
485      - this code computes plumebk everywhere (also over land), thus requires
486        code to avoid divisions by zero and catch the case of kLev=Nr.
487      - efficiency of salt_plume_frac is still sub-optimal
488    o tools (genmake2):
489      - fix makefile NAME specification (option: -makefile NAME) by adding
490        "-f $MAKEFILE" in few places where it was missing including makedepend
491        command (contribution from Paul).
492    
493    checkpoint63i (2012/01/24)
494    o model/src:
495      - add factorized versions of some EOS code to find_rho.F,
496        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
497    o model/src:
498      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
499      - change default celsius2K from 273.16 to 273.15
500      - to keep results unchanged, add back old value of celsius2K in verification
501        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
502         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
503    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
504      to make TAF generate vectorizable code
505    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
506       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
507       have flags that do this more efficiently.
508    o pkg/diagnostics/diagstats_calc.F
509      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
510    o pkg/obcs (with exch2):
511      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
512        and remove code (in obcs_readparms.F) which was based on EXCH of indices
513        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
514    o pkg/exf and seaice exp:
515      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
516        so that switching off area & heff advection flags does not affect results.
517      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
518      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
519        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
520        results of verification experiments: 1D_ocean_ice_column(fwd),
521        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
522        and offline_exf_seaice (all 4).
523    o pkg/seaice:
524      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
525        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
526      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
527        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
528        not multi-dim advection;
529      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
530        SHORTWAVE_HEATING #undef.
531  o optim: make Makefile more robust (?)  o optim: make Makefile more robust (?)
532  o pkg/obcs:  o pkg/obcs:
533    * fix treatment of obcs_read_pickup for TAF    * fix treatment of obcs_read_pickup for TAF
534  o pkg/shelfice:  o pkg/shelfice:
535    * add missing initialisation of num_shifwflx    * add missing initialisation of num_shifwflx
536    * new adjoint verification exp. for isomip    * new adjoint verification exp. for isomip
537    * change Prandtl and Schmidt numbers from generic formulations    * change Prandtl and Schmidt numbers from generic formulations
538      (in terms of model diffus. and visc.) to separate runtime      (in terms of model diffus. and visc.) to separate runtime
539      parameters, with Holland and Jenkins (1999) default values.      parameters, with Holland and Jenkins (1999) default values.
540  o pkg/exf (interpolation):  o pkg/exf (interpolation):
541    - extended input field (2 rows) near the N & S poles:    - extended input field (2 rows) near the N & S poles:
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