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revision 1.1575 by jmc, Tue Jan 17 17:14:06 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:  o pkg/exf and seaice exp:
515    - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)    - 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.      so that switching off area & heff advection flags does not affect results.
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