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revision 1.1531 by jmc, Wed Nov 9 13:38:04 2011 UTC revision 1.1687 by gforget, Wed Jul 11 21:51:27 2012 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o verification/global_ocean.cs32x15/input.seaice :
8     - add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget.
9     - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces).
10     - update results (output.seaice.txt) accordingly.
11    o verification/lab_sea/input/data.seaice :
12     - remove SEAICEheatConsFix, which is now be tested
13       in global_ocean.cs32x15. The presently coded fix
14       is only consistent with real fresh water + nlfs.
15     - update results (output.txt) accordingly.
16    o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd).
17    o AD_CONFIG.h file:
18     - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;
19     - remove #include "AD_CONFIG.h" from all included OPTIONS files and
20       add it explicitly in each fortran src file where it is needed.
21       motivation: header file AD_CONFIG.h is generated/modified after "make depend"
22       thus introducing potentially wrong dependency; therefore, better to include
23       it only where it's really needed, and after any other included OPTIONS file
24       (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN
25       or ALLOW_TANGENTLINEAR_RUN).
26    
27    checkpoint63p (2012/07/06)
28    o pkg/autodiff:
29      - rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ;
30      - create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters
31        which are now read from new parameter file "data.autodiff" (inAdExact
32        previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg)
33      - add file "data.autodiff" in all verification/*/input_ad/ directories.
34      - add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward
35        mode (used in global_ocean.cs32x15.seaice_dynmix test exp.)
36    o verification/tutorial_tracer_adjsens/
37      - add extra sub-verification which uses "SOM" advection scheme
38        (2nd Order-Moment Advection Scheme, Prather Limiter) with
39          #define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h
40        and in data:
41          multiDimAdvection=.TRUE.,
42          tempAdvScheme=81,
43          saltAdvScheme=81,
44    o model/src:
45      - introduce ALLOW_BALANCE_RELAX which allow the removal
46       of the global mean of relaxation terms by setting
47       balanceThetaClimRelax and balanceSaltClimRelax
48      - disable balanceEmPmR and balanceQnet in the case when useSeaice.
49       This case is now treated appropriately in seaice_growth.F
50    o pkg/seaice:
51      - do balanceEmPmR and balanceQnet based on the net fluxes
52        (SItflux) that enter the ocean+ice system rather than QNET
53        and EMPMR. Works best in real fresh water.
54      - SIatmFW, SIatmQnet, and SItflux computations had to be moved
55        out of the diagnotics bloc, and stored in global arrays.
56    
57    checkpoint63o (2012/06/29)
58    o vertical mixing schemes:
59      - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging)
60      - replace computation of density (in Function STATE1, opps_calc.F) by a call
61        to S/R FIND_RHO_SCALAR
62      - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC
63        and use it for N^2 calculation in ggl90_calc.F (save 2 density computations);
64        affects output (vermix.ggl90) at truncation level.
65    o testreport:
66      - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles
67        (nSx,nSy) for the number of threads (from eedata.mth)
68    o model/src:
69      - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part)
70        related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary).
71    o verification/tutorial_tracer_adjsens/
72      - compile with ALLOW_CG2D_NSA
73      - run with nonlinFreeSurf=3
74      - update reference output_adm.txt
75    o tools/genmake2:
76      - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
77        refine usePROFILES switching off (only when NetCDF is not available).
78    o verification (atmospheric set-up):
79      - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
80    o pkg/profiles : refine profiles and files handling.
81    o model/src and pkg/ecco : introduce run-time switch usePROFILES.
82    o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
83      - changes to use model/src/the_main_loop.F rather than the ecco version
84        in ecco type adjoint runs.
85    o model/src:
86      - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
87      - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
88      - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
89    o model/src:
90      - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
91        update output of test experiment bottom_ctrl_5x5.
92    o pkg/generic_advdiff:
93      - implement vertical bi-harmonic diffusion (for now, only for T & S and
94        only explicitly).
95    o verification/bottom_ctrl_5x5/
96      update reference output (results changed quite some time ago,
97      not sure when; but new reference results look ok in terms of grdchk)
98    o verification/1D_ocean_ice_column/
99      For verification purposes, the exact adjoint rather than an approx.
100      should be used (e.g., to comare against F.D. or TLM).
101      removed autodiff_inadmode*_ad.F routines in code_ad/
102      Update results/ accordingly.
103    o pkg/cal:
104      - change cal_getdate.F so that output date is function of input time only
105        (less ambiguous, not mixed up with input iteration number).
106      - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
107    o pkg/diagnostics:
108      - implement calendarDumps also for stats-diags
109      - implement calendarDumps also for snap-shot output (negative freq)
110      - for now, ignores calendarDumps if non-zero phase-lag.
111    
112    checkpoint63n (2012/06/04)
113    o model/src:
114      - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
115        between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
116      - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
117        similar to calc_r_star.F); update results of experiment internal_wave and
118        tutorial_global_oce_in_p (affected @ truncation level).
119    o pkg/shelfice:
120      - add parameterisation of advective-diffusive flux into the ice shelf
121        according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
122      - simply eps3/3a computation
123    o eesupp:
124     - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
125       between tiles, just fill-in edges assuming locally periodic subdomain) and
126       add corresponding exchange subroutines (EXCH0);
127     - new CG-solver version (_EX0) for disconnected-tiles special case.
128    o model/src (CG-solvers):
129     - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
130       (similar final residual output and max-Iter number as with standard version);
131     - allows to store and use lowest-residual solution (standard & _SR versions);
132     - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
133     - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
134    o eesup/src:
135     - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
136       ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
137    o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
138    
139    checkpoint63m (2012/04/27)
140    o pkg/shelfice:
141     - account for partical cells in surface level below ice-shelf for hydrostatic
142       pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
143    o ad test experiments:
144     - update and rename to "ad_optfile.local" local AD-optfile specific to a
145       particular adjoint verification experiment (in verification/*/code_ad/)
146    o pkg/seaice & pkg/exf:
147     - Part two of ECCO-CLIVAR code merges.
148       Completes merge of seaice area relax. code.
149       Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
150       to be set in EXF_OPTIONS.h since this pkg controls its I/O
151       (and avoids second CPP option in SEAICE_OPTIONS.h)
152     - change default value of costIceStart & costIceEnd to a valid date.
153     - add snowPrecip to HSNOW in seaice_growth
154    o pkg/ptracers:
155     - move ptracers summary and setup check into separated S/R ; add a check for
156       valid PTRACERS_Iter0 value (error+stop or just warning).
157    o pkg/cal (+ pkg/ecco):
158     - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
159       as input; and for AD, unless both are not differentiable (e.g., k index)).
160    o model/src:
161     - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
162       is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
163       temporary set to usingZCoords value (to be changed to F when using shelfice).
164     - hydrostatic pressure: implement partial cell near the surface also for
165       Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
166       usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
167    o pkg/ctrl/ctrl_init.F:
168     - add a formal parameter to s/r ctrl_init_rec to print
169       xx_$(ctrl_valiable)_file for easier debugging
170     - move call of cal_* routines into the if-block where they are really
171       needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
172       to specify a startdate
173    o pkg/seaice:
174     - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
175       global_ocean.cs32x15/code versions).
176     - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
177       verification experiment global_ocean.cs32x15.seaice and update results.
178    o pkg/exf:
179     - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
180       (according to useExfYearlyFields).
181    o pkg/cal:
182     - move calendar setting & summary (previously in cal_readparams.F) into new
183       S/R CAL_INIT_FIXED to be called later in the initialisation process, once
184       length of the simulation is set (after SET_PARMS call); This is an attempt
185       to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
186     - For safety: keep a record of pkg/cal parameter settings status
187               to allow to STOP if one pkg/cal S/R is called too early.
188     - add a stop in all basic pkg/cal subroutines if called before setting is done.
189     - modify cal_getdate.F: stop when nothing was returned;
190       if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
191       this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
192    
193    checkpoint63l (2012/04/04)
194    o pkg/bbl:
195      - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
196        update global_with_exf output.yearly.txt file.
197    o pkg/cal:
198      - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
199      - remove 2 unsused and very short (1 line only) functions ;
200      - remove unsused subroutines from AD-Diff list.
201    o model/src:
202      - start to implement clean wait to stop in initialization S/R (config_check.F,
203         packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
204    o folowing PRINT_MESSAGE changes:
205      - remove reminder multiple print to the same file (STDOUT) when multi-threads.
206    o pkg/bbl:
207      - modification so it can work with z*
208      - replace deltaT with dTtracerLev(k) for asynchronous time stepping
209      - global_with_exf/input.yearly verification; changes output.yearly.txt
210    o eesupp/src:
211      - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
212        writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
213      - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
214        # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
215      - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
216      - when using MPI, always set usingMPI=T ; set default accordingly and stop
217        if not consistent.
218      - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
219        argument is zero (in case called within single-thread section).
220    o pkg/fizhi:
221        clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
222        in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
223    o pkg/exch2:
224      - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
225        activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
226      - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
227        but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
228        with bad ones coming from a not-yet-updated halo.
229        This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
230    o pkg/frazil:
231        move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
232        http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
233    o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
234    o verification/lab_sea
235      * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
236      * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
237      * nTimeSteps 3 -> 4
238      * changed reference output accordingly
239    o pkg/ctrl:
240      * fix ctrl_get_gen for xx_sst, xx_sss
241    o pkg/fizhi:
242      - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
243        update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
244      - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
245        fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
246        clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
247    o pkg/gmredi:
248      - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
249    o pkg/fizhi:
250      - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
251        (old)aces open64 tuv test.
252    o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
253    o pkg/mom_vecinv:
254      - fix 1 loop range in mom_vecinv.F to be like all the other loops which
255        set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
256        with non-lin free-surf).
257    o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
258      in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
259      some compilers (gfortran 4.6.0 on MacOS)
260    o momentum:
261      - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
262        & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
263        fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
264    
265    checkpoint63k (2012/03/17)
266    o model/src:
267       - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
268         flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
269       - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
270         (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
271    o model/src: solve_*diagonal.F
272       - replace division with multiplication by inverse (similar to original version)
273         update output of AD exp. global_ocean.90x40x15.
274       - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
275         to enable the use of the vectorized & differentiable solve_tridiagonal.F
276       - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
277         vertical advection (to get solve_tridiagonal tested in AD mode).
278    o pkg/seaice: ECCO-CLIVAR merge:
279      1. seaice AREA relaxation
280         * CPP option: SEAICE_ALLOW_AREA_RELAXATION
281         * runtime flag: SEAICE_tauAreaObsRelax
282      2. modified global mean cost imbalance code: CPP option
283          ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
284    o another iteration on solve_*diagonal.F
285       Make choices independent of AUTODIFF
286       Default will be the adjoinable vectorized version.
287       Alternative choices are:
288       * non-adjoinable original version with low memory footprint:
289         #define SOLVE_DIAGONAL_LOWMEMORY
290       * still adjoinable but does not vectorize (k as inner-most loop):
291         #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
292    o testreport
293     - add option to use a home made wrapper around "make"
294     - remove MITGCM_IEEE env. variable (no longer active)
295    o pkg/shelfice
296     - improve computation of friction velocity for velocity dependent
297       exchange coefficients: include velocities into SHELFICEBoundaryLayer
298       block to average velocities vertically
299     - add TAF store directives for SHI_ALLOW_GAMMAFRICT
300    o Modify diagonal solvers, now three versions (upon request):
301      #ifndef SOLVE_DIAGONAL_AUTODIFF
302        1. default version (dating back a while ago)
303      #else /* def SOLVE_DIAGONAL_AUTODIFF */
304      # ifdef SOLVE_DIAGONAL_KINNER
305        2. adjoinable version with k-innermost loop (G. Forget)
306      # else
307        3. adjoinable vectorized version of 2.
308      # endif
309      #endif /* SOLVE_DIAGONAL_AUTODIFF */
310      All flags are currently set within routines, but could/should be moved to CPP-options.
311      Array bounds for 1. are as before, for 2.,3. cover the entire domain
312      (could be changed for 1. too).
313    o verification/lab_sea (fwd):
314      - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
315        use 7 categories (except hb87), new solve4temp params (except salt_plume),
316        constant salinity (=4) or variable salinity (salt_plume) done through
317        SItracer.
318    o pkg/seaice:
319      - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
320      - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
321         SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
322        from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
323        SEAICE_freeze got retired) but already better than previously with
324        SEAICE_freeze=123456.7 deg.C;
325      - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
326        (safer multi-threaded setting); always set SEAICEuseEVP;
327      - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
328        SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
329        stop if multiple specifications for the same coeff; make sure default
330        SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
331    o pkg/obcs:
332      - allow to switch to upwind 1rst order advection scheme for the advective
333        flux computation at the open-boundary; disabled for adjoint built.
334    o pkg/ptracers:
335      - rename PTRACERS_RESTART.h -> PTRACERS_START.h
336      - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
337      - add parameter to decide when to start a tracer; use internal flag to
338        know which tracer to step-forward; switch this internal flag at the top
339        of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
340        for adjoint built.
341    o pkg/seaice:
342      - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
343      - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
344      - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
345    o pkg/ecco:
346      - fix writing of output file DiagnosCost_ClimSalt/Theta
347        and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
348    o pkg/seaice:
349      - add missing initialisation of COR_ICE array in dynsolver.F
350      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
351        compiled either way, and is tested in all exps (multidim was only tested
352        in lab_sea ad before).
353      - cosmetic change to prepare for future addition of ITD. no change to results.
354        no defaults change.
355      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
356      - by lack of adequate verification experiments, I further used custom versions
357        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
358        should be correct.
359      - avoid recomputations in ad.
360    o array initialisation in adjoint mode:
361      1) pkg/mom_common/mom_calc_ke.F:
362        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
363        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
364        part this initialisation is gone, resulting in Floating Point Exception
365        (caught by open64 compiler with debug option).
366      2) model/src/convective_weights.F
367        set output convectCount over the full array range (instead of doing
368        an update): this fix a similar issue when called within recomputation (adjoint)
369        which could by-pass the initialisation (normally done in the caller S/R).
370    o pkg/seaice:
371      - final version of turbulent flux params, as agreed at MIT ice meet:
372           SEAICE_mcPheePiston (default is ~ 0.000875)
373           SEAICE_mcPheeTaper (default is 0.)
374           SEAICE_frazilFrac (defualt is 1.)
375           SEAICE_mcPheeStepFunc (default is false)
376      - changes results at trunction error level
377      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
378    o added pkg/frazil:
379      - see frazil_description.tex for details
380      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
381    o pkg/shelfice/shelfice_thermodynamics.F
382      - fix exponents for velocity dependent exchange coefficients: change
383        from 2/3(=0) to 0.66666666666666667
384      - move computation of velocity dependent exchange coefficients into
385        separate loop, so that it applies to both thermodynamics
386      - move some divisions by constants out of loops
387    
388    checkpoint63j (2012/02/16)
389    o pkg/seaice:
390      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
391      - SItracer:  added run time params, and allow coupling to ocn salinity.
392    o pkg/seaice: remove (almost) all divisions by constants within loops
393      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
394      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
395      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
396      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
397    o pkg/seaice :
398      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
399        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
400      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
401      - add permanent SItflux diag that corresponds to TFLUX but includes
402        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
403      - allow activation/testing of a fix for suspected missing term in
404        ocn-ice heat budget (to be confirmed). To test this, you want to
405        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
406        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
407      - no change in results, fwd or ad.
408    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
409      - switch to variable freezing point.
410           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
411      - bug fix : the sublimation term that was missing is now activated.
412           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
413      - bug fix : flooding sign term for SIsal0.NE.0.
414           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
415    o pkg/seaice:
416      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
417        is now the default, and the old default constant freezing point is recovered
418        with SEAICE_tempFrz0    = -1.96,
419             SEAICE_dTempFrz_dS = 0.,
420      - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
421      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
422      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
423        activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
424      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
425        was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
426      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
427        seaice_growth r149 for legacy branch (no results change).
428      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
429        from I. Fenty).
430      - results did not change except for global_ocean.cs32x15, mostly due to the
431        switch to variable freezing point (see above item for detail).
432    o pkg/thsice:
433      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
434        seawater freezing in thsice_calc_thickn (not used).
435    o pkg/seaice: turbulent flux term specification via run time params.
436      - replace CPP switches with run time switches to facilitate testing
437      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
438                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
439      - added runtime parameter : SEAICEturbFluxFormula
440      - move Mcphee constants to SEAICE_PARAMS.h
441      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
442                 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
443                 remove seaice_summary call (moved to seaice_init_fixed)
444      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
445        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
446      - seaice_summary.F : add missing report of read turbulent flux term set up
447                           and SITRACER.
448      - seaice_check.F : check range; inform and stop if retired CPPs are used
449                         (incl. SEAICE_AGE).
450      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
451             CPP switch, same computation as before for the different options.
452      - change results at the truncation level.
453    o pkg/seaice:
454      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
455        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
456        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
457      - update verification/*/input*/data.seaice:
458        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
459        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
460        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
461        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
462    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
463      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
464        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
465        difference in results only due to machine truncation.
466      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
467        MaykutPolySatVap; keep MIN_LWDOWN.
468      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
469      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
470        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
471    o pkg/salt_plume:
472      - isolate saltPlumeFlux array exch into a specific S/R called from
473        do_oceanic_phys.F
474      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
475    o verification:
476      - move untested set-up to MITgcm_contrib/verification_other.
477    o pkg/seaice:
478      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
479    o pkg/seaice:
480      - seaice_solve4temp.F (keeping results unchanged):
481        * add 2 future run-time params to select which saturation vapor pressure
482          formula is used and how post-iteration fluxes are set.
483          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
484        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
485          the linearized expression to stay consistent with tsurf finding.
486      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
487        can be < 0.
488    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
489      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
490        conductive heat flux F_c , and add it explicitly when updating tsurf as
491        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
492        so that now F_ia has a consistent meaning through the entire routine.
493        This causes differences at truncation level: update output of fwd exp.
494        global_ocean.cs32x15.seaice.
495    o pkg/seaice:
496      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
497        of arrays, sign/direction of fluxes; no effect on results.
498      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
499        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
500        note: this should have been done before changing celsius2K default.
501      - to keep results unchanged, add back old value of celsius2K in verification
502        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
503      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
504        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
505        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
506        freezing temp is consistent with value in seaice_growth.F ; this causes
507        differences at machine truncation level: update lab_sea AD output (3/4).
508    o pkg/seaice:
509      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
510        and climsst/sss even when using seaice (to prevent calculation that might
511        use SST on land); does not affect any verification exp.
512      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
513        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
514    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
515      over land (non-legacy code)
516    o vectorize salt_plume package:
517      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
518      - this code computes plumebk everywhere (also over land), thus requires
519        code to avoid divisions by zero and catch the case of kLev=Nr.
520      - efficiency of salt_plume_frac is still sub-optimal
521    o tools (genmake2):
522      - fix makefile NAME specification (option: -makefile NAME) by adding
523        "-f $MAKEFILE" in few places where it was missing including makedepend
524        command (contribution from Paul).
525    
526    checkpoint63i (2012/01/24)
527    o model/src:
528      - add factorized versions of some EOS code to find_rho.F,
529        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
530    o model/src:
531      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
532      - change default celsius2K from 273.16 to 273.15
533      - to keep results unchanged, add back old value of celsius2K in verification
534        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
535         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
536    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
537      to make TAF generate vectorizable code
538    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
539       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
540       have flags that do this more efficiently.
541    o pkg/diagnostics/diagstats_calc.F
542      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
543    o pkg/obcs (with exch2):
544      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
545        and remove code (in obcs_readparms.F) which was based on EXCH of indices
546        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
547    o pkg/exf and seaice exp:
548      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
549        so that switching off area & heff advection flags does not affect results.
550      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
551      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
552        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
553        results of verification experiments: 1D_ocean_ice_column(fwd),
554        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
555        and offline_exf_seaice (all 4).
556    o pkg/seaice:
557      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
558        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
559      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
560        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
561        not multi-dim advection;
562      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
563        SHORTWAVE_HEATING #undef.
564    o optim: make Makefile more robust (?)
565    o pkg/obcs:
566      * fix treatment of obcs_read_pickup for TAF
567    o pkg/shelfice:
568      * add missing initialisation of num_shifwflx
569      * new adjoint verification exp. for isomip
570      * change Prandtl and Schmidt numbers from generic formulations
571        (in terms of model diffus. and visc.) to separate runtime
572        parameters, with Holland and Jenkins (1999) default values.
573    o pkg/exf (interpolation):
574      - extended input field (2 rows) near the N & S poles:
575        * fill in with the symetric value (when even Nb of data in longitude)
576        * add average value at the poles only for scalar quantities ; for vector
577          component interpolation, skip the averaging and keep duplicated values,
578          unless the 2 components have same location (uvInterp=T) in which case
579          interpolate the 2 components together using S/R EXF_INTERP_UV.
580      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
581        together: this allows to account properly for local orientation when
582        averaging at N & S pole.
583      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
584        exf-interpolation near N & S poles. Undef by default.
585      - add debug check/print on 1rst iter if debugLevel >=2.
586    o pkg/exf:
587      - change masking flags definition (no longer "parameter"), put them in
588        common block and set them in S/R EXF_INIT_FIXED.
589      - change recognized masking flag from s,u,v to c,w,s since the mask
590        to use (maskC,W,S) depends on position on model grid and has little to
591        do with scalar/vector difference; fix masking if using P-coordinates.
592      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
593        and update results of exp. global_with_exf (x2).
594      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
595    o pkg/obcs
596      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
597    o pkg/exf (interpolation):
598      - assume periodicity in X only if input field cover full longitude range.
599      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
600        and should vectorise).
601      - fix input lat of the 2 added row (in case we provide N.pole data).
602    
603    checkpoint63h (2011/12/30)
604    o pkg/seaice:
605      - change declaration of UVM from _RL to _RS in order to get B-grid
606        uIce,vIce monitor when _RS = real*4
607    o pkg/offline:
608      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
609      - compute vertical velocity if not read from file (switch on exactConserv
610        & staggerTimeStep);
611      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
612    o verification:
613      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
614        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
615        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
616      - update output of exp. global_ocean.cs32x15.viscA4 after changing
617        grid-file angles (used here for coriolis-3d);
618      - remove (or gzip) few files not needed to run fizhi-cs experiments.
619    o pkg/exf (vector interpolation):
620      - rotate vector component toward local grid-axis orientation using grid-angles
621        (stored in GRID.h) instead of locally computed rotation angle; keep old code
622        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
623    o pkg/seaice:
624      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
625        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
626    o pkg/PKG_OPTIONS.h files:
627      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
628        outside of the #ifdef ALLOW_THISPKG / #endif block.
629      - update verification/*/code/PKG_OPTIONS.h files.
630    o add a verification experiment (offline_exf_seaice/input.seaice) that test
631      the B-grid LSOR solver
632    o pkg/seaice: sort out emissivity and long wave radiation step 2:
633      - add emissivity for snow and ice as new run-time parameters
634        (unfortunately) that default to the corresponding exf values; this
635        changes results in most verification experiments so that for backward
636        compatibility these parameter have to be set explicitly to inconsistent
637        values (ugly);
638      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
639        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
640        until we agree how to handle this bug properly
641    o pkg/exf (interpolation):
642      - add a set of run-time param ({inputfield}_interpMethod), one for
643        each interpolated input field, to select the interpolation method
644        with a value of zero switching off the interpolation;
645      - print interpolation parameters to standard output;
646      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
647        (to use instead runoff_interpMethod=0 in data.exf).
648      - simplify default setting of interpolation parameters (for all fields,
649        set position to match model grid cell-center position, leading to trivial
650        interpolation in case of regular Lat-Lon grid) and fix for the case of
651        non-uniform delY.
652    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
653       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
654       this factor is absolutely required, because the lw exitance (= out-going
655       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
656       where the reflectivity rho = 1-emissivity for conservation reasons. Once
657       this is established, we can remove the CPP-Flag (if we want to).
658    o pkg/seaice:
659      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
660        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
661      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
662        what the name implies (and not emissivity*BoltzmannConstant), this means
663        the old default value of 5.5e-8 now means
664        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
665        S/R exf_readparms
666      - FV-discretization of the B-grid LSOR solver, turn on with
667        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
668        of the calling routine dynsolver, so that B and C-grid code look a
669        little more alike.
670      - fix index bugs in ostres.F (B-grid code)
671    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
672    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
673      default for SEAICE_emissivity, if useEXF; requires setting a wrong
674      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
675      backward compatiblity
676    o model/src: use sigmaR in calc_ivdc
677    
678    checkpoint63g (2011/12/16)
679    o pkg/seaice/seaice_growth.F:
680      fix heat conservation of the coupled ocean-seaice system.
681      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
682      solid vs liquid water treatment is resolved via QNET.
683    o pkg/seaice/seaice_growth.F:
684      add missing term for sublimation in saltFlux, which was breaking conservation.
685    o pkg/seaice/seaice_model.F:
686      Remove this patholigical case treatment in evolution branch,
687      where it is un-necessary and breaks conservation.
688      Update global_ocean.cs32x15/results accordingly for
689      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
690    o model/src:
691      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
692      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
693    o pkg/obcs:
694      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
695      tendency for temperature and salinity that is then applied to update
696      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
697      horizontal advection and diffusion contributions on the boundary (in
698      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
699      removing the mask in S/R timestep_tracer. The advantage of this approach is
700      that the updated tracer values include contributions from the surface
701      forcing and vertical diffusion.
702      This modification changes exp4.stevens because of vertical diffusion.
703    o model/src:
704      change non-curvilinear grid setting to also work with exch2 + blank tiles:
705      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
706        face dimensions.
707      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
708        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
709        and INI_SPHERICAL_POLAR_GRID.
710      change test-experiment global_ocean.90x40x15:
711      - split the domain in many more tiles (9x4 tiles of 10x10 each);
712      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
713      - update results of both test (std & dwnslp).
714    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
715       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
716    o model/src:
717      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
718        and fix initialisation when using sigma-coords.
719    o model/src:
720     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
721       to their current value at the beginning of forward_step.F": add a new run-time
722       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
723     - set doResetHFactors=T in the following test exp:
724        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
725        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
726        and tutorial_global_oce_in_p (nonLinFS in p)
727    o pkg/ecco
728      - added IES cost term
729    o verification/advect_xz
730      - scale down the depth by 1/100 (from 200 km to just 2.km)
731      - add secondary test using divergent flow, r-star and implicit vertical advection.
732      - add note (check_conserve_TS.txt) and matlab script to check global
733        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
734    o pkg/rbcs:
735      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
736    o pkg/obcs (Stevens BCs):
737      - fix various problems in the phase speed computations of the Stevens
738        boundary conditions:
739        - sign error for western and southern boundaries,
740        - time tendencies were underestimated by factor of dTracerLev and some just
741          zero (for multidim advection schemes) -> now estimate time tendencies
742          from difference between previous (n) time level and the one before (n-1);
743          this requires storing a field per tracer per boundary, also in the pickup
744          files.
745        - replace deltaTmom in cflMer/Zon computation with dTracerLev
746        - set default phase velocity to cflMer/Zon
747      - update verification experiment exp4.stevens
748    o pkg/generic_advdiff (implicit_r):
749      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
750        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
751      - fix implicit vertical diffusion or advection with NonLin FreeSurf
752        (was using current recip_hFacC instead of future recip_hFacC): set future
753        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
754        solver S/R ;
755      - fill diagnostics of vertical advective fluxes (computed from tendency)
756        when using implicit vert. advection;
757      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
758         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
759         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
760         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
761    o pkg/diagnostics:
762      - add diags for T & S tendency which goes through Adams-Bashforth.
763    
764    checkpoint63f (2011/11/30)
765    o pkg/obcs/obcs_calc_stevens.F:
766      - join some loops to reduce number of if-statements
767      - fix a bug in code for northern and southern boundaries.
768    o pkg/seaice/seaice_init_varia.F
769      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
770        caused zero ice-velocities for the B-grid code
771    o pkg/seaice/seaice_init_fixed.F
772      - fix a bug in the initialisation of the second metric terms
773        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
774      - this affects all seaice configurations with useCurviLinearGrid = .true.
775        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
776        = .true. (default)
777      - the only verification experiment affected is global_ocean.cs32x15:
778        icedyn, seaice, and seaice_dynmix (AD)
779    o pkg/thsice/thsice_diagnostics_state.F
780      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
781        not contain garbage that can lead to surprises in diagstats_calc.F
782    o model/src:
783      - move bi,bj loops inside INTEGR_CONTINUITY ;
784      - call INTEGR_CONTINUITY directly from forward_step.F
785        (previously called from momentum_correction_step.F)
786      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
787        forward_step.F and pkg/ecco/the_main_loop.F
788    o model/src/do_oceanic_phys.F:
789      - reset addMass to zero only if useICEFRONT ;
790      - separated k-loop for rhoInSitu calculation ;
791      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
792        and at constant T,S (= WdRHOdP);
793      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
794        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
795        transport of locally-referenced potential density);
796        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
797    o gluemnc:
798      - replace ncrcat with ncks when adding variables to *.glob.nc
799      - change the way variables without record dimensions are handled so that
800        files that have variables with and without record variables can be glued:
801        add a record dimension with a new unique name to be able to differentiate
802        between variable with and without a-prior record dimensions. Remove
803        this record dimension before adding the variable to the *.glob.nc file.
804        This procedure automatically works also for grid.*.nc files that do not
805        have any record dimension.
806  o verification/cpl_aim+ocn:  o verification/cpl_aim+ocn:
807    - generate new reference output on baudelaire (gfortran, mpich2) (previously    - generate new reference output on baudelaire (gfortran, mpich2) (previously
808      from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.      from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
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