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revision 1.1478 by mlosch, Thu Jul 21 13:45:55 2011 UTC revision 1.1702 by jmc, Thu Aug 2 22:48:11 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      re-write active I/O high-level (control) S/R:
9      - rename  S/R ACTIVE_READ/WRITE_RL to ACTIVE_READ/WRITE_3D_RL
10      - add 1 more argument (useCurrentDir) to replace the "_LOC" 2nd set of S/R.
11      - use standard pkg/mdsio I/O routines (MDS_READ/WRITE_SEC_XZ/YZ  and
12        MDS_READ/WRITE_FIELD); change loops to multi-threads.
13      - update and merge active_file_control_slice.flow into active_file_control.flow
14      - update the calls in lower level S/R (active_file.F, active_file_g.F and
15        active_file_ad.F) keeping the argument list and function unchanged.
16    o autodiff and RS=real*4:
17      - call the right type (_RS instead of _RL) of S/R in few output S/R (pkg/exf
18        ad-monitor and snapshots); disable arrType='RS' in mdsio_gl*.F ;
19      - change argument type of 3-D mask argument to _RS to match type in the call
20        (in seaice_cost*.F, ctrl_*_gen.F and *ctrl_bound.F); to be continued.
21    o pkg/thsice:
22      - re-anable balanceEmPmR when useSEAICE=T with useThSIce=T.
23      - option to correct ocean fresh-water flux for imbalance of Atmos+Land
24        fresh-water flux: uniform correction or proportional to local precip.
25    o pkg/ctrl:
26      - new header file CTRL_SIZE.h for parameters maxCtrlArr2D, maxCtrlArr3D
27      - redefine CPP option ALLOW_BOTTOMDRAG_CONTROL to
28                            ALLOW_BOTTOMDRAG_CONTROL_NONGENERIC
29      - verification/hs94.1x64x5/ tests ALLOW_GENARR{2D,3D}_CONTROL
30    
31    checkpoint63q (2012/07/30)
32    o pkg/autodiff:
33      note about monitor and snap-shot of ad-variables:
34      a) need to apply ADEXCH before monitor or output of ad-vars to include
35       overlap contributions (was done for adjDump but missing for monitor).
36      b) since ADEXCH implies adding overlap values to interior array, machine
37       truncation error is expected when adding an ADEXCH call in the middle of
38       the time-stepping (although mathematically identical).
39      modifs:
40      - fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars
41        declaration (adEddyPsiX,adEddyPsiY in adcommon.h).
42      - add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how  to
43        apply ADEXCH before monitor or snap-shot of ad-variables:
44           =0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy.
45      - implement new method (copy+adexch) for snap-shot and monitor of main model
46        ad-vars (initially not used by default -> output unchanged).
47      - change default (set to 2) to use new method and update few output_adm.txt
48        with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo
49        and both tutorial_tracer_adjsens tests).
50      - switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice)
51        and turn off momDissip_In_AB in the 2 other (needed for stable AB-3).
52    o pkg/ctrl:
53      enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of
54      generic control variables via
55      #define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL
56      Only required customization should be S/R ctrl_map_ini_genarr.F
57      (routine in repository contains example)
58    o pkg/exf:
59      - fix and refine checking of surface-relaxation setting when using EXF
60    o verification (adjoint exp):
61      - reduce length of simulation by half for experiment global_ocean.cs32x15
62        (std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output.
63    o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag)
64      - replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers
65        of KE that can occur with aggressive optimization
66      + put quadratic bottom drag calculation in separated loops (only done if
67        using bottomDragQuadratic)
68    o model/src: CG2D_NSA
69      - clean-up:  stop if cg2dNormaliseRHS=T and AUTODIFF
70         and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE.
71      - in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens),
72         change cg2d residual target to be expressed in Wunits (=> do not normalise
73         RHS ; this fix global_max Pb with TAF); update output.
74    o verification/tutorial_tracer_adjsens:
75       improve parameter consistency (and get rid of warnings):
76       - use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf);
77       - switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical)
78       - use staggerTimeStep (for stability) in som81; use default rotation period.
79    o pkg/exch2:
80      - with empty facet: fix compact-format (W2_mapIO=1) definition (was previously
81        reset to 0 = 1 long line in X)
82    o pkg/mdsio:
83      - fix reading of dimensions from meta file for large-size domain
84    o model/src:
85      - fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long);
86      - to refine CS-grid check, add logical flag "hasWetCSCorners": true if using
87        Cubed-Sphere Exch with CS-corners inside the domain;
88        make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate
89        globalArea and to set hasWetCSCorners.
90      - add warning if usingCurvilinearGrid and momAdvection in flux-form (missing
91        metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form.
92      - re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if
93        useCDscheme and useCubedSphereExchange).
94    o pkg/seaice/seaice_growth.F :
95      - compute the SEAICE_DISABLE_HEATCONSFIX term accordingly
96        for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0)
97        when the previous code was not correct.
98      - in all cases diagnoze the boundary condition mismatch to SIaaflux
99      - in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add
100        that term to QNET (essentially to set the melt/freeze water to 0degC).
101        when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed.
102    o verification/global_ocean.cs32x15/input.seaice :
103      - add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget.
104      - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces).
105      - update results (output.seaice.txt) accordingly.
106    o verification/lab_sea/input/data.seaice :
107      - remove SEAICEheatConsFix, which is now be tested
108        in global_ocean.cs32x15. The presently coded fix
109        is only consistent with real fresh water + nlfs.
110      - update results (output.txt) accordingly.
111    o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd).
112    o AD_CONFIG.h file:
113      - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;
114      - remove #include "AD_CONFIG.h" from all included OPTIONS files and
115        add it explicitly in each fortran src file where it is needed.
116        motivation: header file AD_CONFIG.h is generated/modified after "make depend"
117        thus introducing potentially wrong dependency; therefore, better to include
118        it only where it's really needed, and after any other included OPTIONS file
119        (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN
120        or ALLOW_TANGENTLINEAR_RUN).
121    
122    checkpoint63p (2012/07/06)
123    o pkg/autodiff:
124      - rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ;
125      - create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters
126        which are now read from new parameter file "data.autodiff" (inAdExact
127        previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg)
128      - add file "data.autodiff" in all verification/*/input_ad/ directories.
129      - add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward
130        mode (used in global_ocean.cs32x15.seaice_dynmix test exp.)
131    o verification/tutorial_tracer_adjsens/
132      - add extra sub-verification which uses "SOM" advection scheme
133        (2nd Order-Moment Advection Scheme, Prather Limiter) with
134          #define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h
135        and in data:
136          multiDimAdvection=.TRUE.,
137          tempAdvScheme=81,
138          saltAdvScheme=81,
139    o model/src:
140      - introduce ALLOW_BALANCE_RELAX which allow the removal
141       of the global mean of relaxation terms by setting
142       balanceThetaClimRelax and balanceSaltClimRelax
143      - disable balanceEmPmR and balanceQnet in the case when useSeaice.
144       This case is now treated appropriately in seaice_growth.F
145    o pkg/seaice:
146      - do balanceEmPmR and balanceQnet based on the net fluxes
147        (SItflux) that enter the ocean+ice system rather than QNET
148        and EMPMR. Works best in real fresh water.
149      - SIatmFW, SIatmQnet, and SItflux computations had to be moved
150        out of the diagnotics bloc, and stored in global arrays.
151    
152    checkpoint63o (2012/06/29)
153    o vertical mixing schemes:
154      - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging)
155      - replace computation of density (in Function STATE1, opps_calc.F) by a call
156        to S/R FIND_RHO_SCALAR
157      - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC
158        and use it for N^2 calculation in ggl90_calc.F (save 2 density computations);
159        affects output (vermix.ggl90) at truncation level.
160    o testreport:
161      - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles
162        (nSx,nSy) for the number of threads (from eedata.mth)
163    o model/src:
164      - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part)
165        related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary).
166    o verification/tutorial_tracer_adjsens/
167      - compile with ALLOW_CG2D_NSA
168      - run with nonlinFreeSurf=3
169      - update reference output_adm.txt
170    o tools/genmake2:
171      - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
172        refine usePROFILES switching off (only when NetCDF is not available).
173    o verification (atmospheric set-up):
174      - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
175    o pkg/profiles : refine profiles and files handling.
176    o model/src and pkg/ecco : introduce run-time switch usePROFILES.
177    o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
178      - changes to use model/src/the_main_loop.F rather than the ecco version
179        in ecco type adjoint runs.
180    o model/src:
181      - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
182      - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
183      - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
184    o model/src:
185      - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
186        update output of test experiment bottom_ctrl_5x5.
187    o pkg/generic_advdiff:
188      - implement vertical bi-harmonic diffusion (for now, only for T & S and
189        only explicitly).
190    o verification/bottom_ctrl_5x5/
191      update reference output (results changed quite some time ago,
192      not sure when; but new reference results look ok in terms of grdchk)
193    o verification/1D_ocean_ice_column/
194      For verification purposes, the exact adjoint rather than an approx.
195      should be used (e.g., to comare against F.D. or TLM).
196      removed autodiff_inadmode*_ad.F routines in code_ad/
197      Update results/ accordingly.
198    o pkg/cal:
199      - change cal_getdate.F so that output date is function of input time only
200        (less ambiguous, not mixed up with input iteration number).
201      - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
202    o pkg/diagnostics:
203      - implement calendarDumps also for stats-diags
204      - implement calendarDumps also for snap-shot output (negative freq)
205      - for now, ignores calendarDumps if non-zero phase-lag.
206    
207    checkpoint63n (2012/06/04)
208    o model/src:
209      - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
210        between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
211      - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
212        similar to calc_r_star.F); update results of experiment internal_wave and
213        tutorial_global_oce_in_p (affected @ truncation level).
214    o pkg/shelfice:
215      - add parameterisation of advective-diffusive flux into the ice shelf
216        according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
217      - simply eps3/3a computation
218    o eesupp:
219     - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
220       between tiles, just fill-in edges assuming locally periodic subdomain) and
221       add corresponding exchange subroutines (EXCH0);
222     - new CG-solver version (_EX0) for disconnected-tiles special case.
223    o model/src (CG-solvers):
224     - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
225       (similar final residual output and max-Iter number as with standard version);
226     - allows to store and use lowest-residual solution (standard & _SR versions);
227     - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
228     - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
229    o eesup/src:
230     - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
231       ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
232    o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
233    
234    checkpoint63m (2012/04/27)
235    o pkg/shelfice:
236     - account for partical cells in surface level below ice-shelf for hydrostatic
237       pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
238    o ad test experiments:
239     - update and rename to "ad_optfile.local" local AD-optfile specific to a
240       particular adjoint verification experiment (in verification/*/code_ad/)
241    o pkg/seaice & pkg/exf:
242     - Part two of ECCO-CLIVAR code merges.
243       Completes merge of seaice area relax. code.
244       Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
245       to be set in EXF_OPTIONS.h since this pkg controls its I/O
246       (and avoids second CPP option in SEAICE_OPTIONS.h)
247     - change default value of costIceStart & costIceEnd to a valid date.
248     - add snowPrecip to HSNOW in seaice_growth
249    o pkg/ptracers:
250     - move ptracers summary and setup check into separated S/R ; add a check for
251       valid PTRACERS_Iter0 value (error+stop or just warning).
252    o pkg/cal (+ pkg/ecco):
253     - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
254       as input; and for AD, unless both are not differentiable (e.g., k index)).
255    o model/src:
256     - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
257       is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
258       temporary set to usingZCoords value (to be changed to F when using shelfice).
259     - hydrostatic pressure: implement partial cell near the surface also for
260       Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
261       usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
262    o pkg/ctrl/ctrl_init.F:
263     - add a formal parameter to s/r ctrl_init_rec to print
264       xx_$(ctrl_valiable)_file for easier debugging
265     - move call of cal_* routines into the if-block where they are really
266       needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
267       to specify a startdate
268    o pkg/seaice:
269     - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
270       global_ocean.cs32x15/code versions).
271     - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
272       verification experiment global_ocean.cs32x15.seaice and update results.
273    o pkg/exf:
274     - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
275       (according to useExfYearlyFields).
276    o pkg/cal:
277     - move calendar setting & summary (previously in cal_readparams.F) into new
278       S/R CAL_INIT_FIXED to be called later in the initialisation process, once
279       length of the simulation is set (after SET_PARMS call); This is an attempt
280       to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
281     - For safety: keep a record of pkg/cal parameter settings status
282               to allow to STOP if one pkg/cal S/R is called too early.
283     - add a stop in all basic pkg/cal subroutines if called before setting is done.
284     - modify cal_getdate.F: stop when nothing was returned;
285       if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
286       this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
287    
288    checkpoint63l (2012/04/04)
289    o pkg/bbl:
290      - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
291        update global_with_exf output.yearly.txt file.
292    o pkg/cal:
293      - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
294      - remove 2 unsused and very short (1 line only) functions ;
295      - remove unsused subroutines from AD-Diff list.
296    o model/src:
297      - start to implement clean wait to stop in initialization S/R (config_check.F,
298         packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
299    o folowing PRINT_MESSAGE changes:
300      - remove reminder multiple print to the same file (STDOUT) when multi-threads.
301    o pkg/bbl:
302      - modification so it can work with z*
303      - replace deltaT with dTtracerLev(k) for asynchronous time stepping
304      - global_with_exf/input.yearly verification; changes output.yearly.txt
305    o eesupp/src:
306      - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
307        writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
308      - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
309        # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
310      - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
311      - when using MPI, always set usingMPI=T ; set default accordingly and stop
312        if not consistent.
313      - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
314        argument is zero (in case called within single-thread section).
315    o pkg/fizhi:
316        clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
317        in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
318    o pkg/exch2:
319      - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
320        activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
321      - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
322        but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
323        with bad ones coming from a not-yet-updated halo.
324        This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
325    o pkg/frazil:
326        move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
327        http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
328    o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
329    o verification/lab_sea
330      * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
331      * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
332      * nTimeSteps 3 -> 4
333      * changed reference output accordingly
334    o pkg/ctrl:
335      * fix ctrl_get_gen for xx_sst, xx_sss
336    o pkg/fizhi:
337      - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
338        update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
339      - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
340        fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
341        clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
342    o pkg/gmredi:
343      - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
344    o pkg/fizhi:
345      - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
346        (old)aces open64 tuv test.
347    o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
348    o pkg/mom_vecinv:
349      - fix 1 loop range in mom_vecinv.F to be like all the other loops which
350        set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
351        with non-lin free-surf).
352    o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
353      in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
354      some compilers (gfortran 4.6.0 on MacOS)
355    o momentum:
356      - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
357        & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
358        fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
359    
360    checkpoint63k (2012/03/17)
361    o model/src:
362       - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
363         flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
364       - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
365         (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
366    o model/src: solve_*diagonal.F
367       - replace division with multiplication by inverse (similar to original version)
368         update output of AD exp. global_ocean.90x40x15.
369       - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
370         to enable the use of the vectorized & differentiable solve_tridiagonal.F
371       - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
372         vertical advection (to get solve_tridiagonal tested in AD mode).
373    o pkg/seaice: ECCO-CLIVAR merge:
374      1. seaice AREA relaxation
375         * CPP option: SEAICE_ALLOW_AREA_RELAXATION
376         * runtime flag: SEAICE_tauAreaObsRelax
377      2. modified global mean cost imbalance code: CPP option
378          ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
379    o another iteration on solve_*diagonal.F
380       Make choices independent of AUTODIFF
381       Default will be the adjoinable vectorized version.
382       Alternative choices are:
383       * non-adjoinable original version with low memory footprint:
384         #define SOLVE_DIAGONAL_LOWMEMORY
385       * still adjoinable but does not vectorize (k as inner-most loop):
386         #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
387    o testreport
388     - add option to use a home made wrapper around "make"
389     - remove MITGCM_IEEE env. variable (no longer active)
390    o pkg/shelfice
391     - improve computation of friction velocity for velocity dependent
392       exchange coefficients: include velocities into SHELFICEBoundaryLayer
393       block to average velocities vertically
394     - add TAF store directives for SHI_ALLOW_GAMMAFRICT
395    o Modify diagonal solvers, now three versions (upon request):
396      #ifndef SOLVE_DIAGONAL_AUTODIFF
397        1. default version (dating back a while ago)
398      #else /* def SOLVE_DIAGONAL_AUTODIFF */
399      # ifdef SOLVE_DIAGONAL_KINNER
400        2. adjoinable version with k-innermost loop (G. Forget)
401      # else
402        3. adjoinable vectorized version of 2.
403      # endif
404      #endif /* SOLVE_DIAGONAL_AUTODIFF */
405      All flags are currently set within routines, but could/should be moved to CPP-options.
406      Array bounds for 1. are as before, for 2.,3. cover the entire domain
407      (could be changed for 1. too).
408    o verification/lab_sea (fwd):
409      - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
410        use 7 categories (except hb87), new solve4temp params (except salt_plume),
411        constant salinity (=4) or variable salinity (salt_plume) done through
412        SItracer.
413    o pkg/seaice:
414      - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
415      - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
416         SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
417        from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
418        SEAICE_freeze got retired) but already better than previously with
419        SEAICE_freeze=123456.7 deg.C;
420      - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
421        (safer multi-threaded setting); always set SEAICEuseEVP;
422      - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
423        SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
424        stop if multiple specifications for the same coeff; make sure default
425        SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
426    o pkg/obcs:
427      - allow to switch to upwind 1rst order advection scheme for the advective
428        flux computation at the open-boundary; disabled for adjoint built.
429    o pkg/ptracers:
430      - rename PTRACERS_RESTART.h -> PTRACERS_START.h
431      - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
432      - add parameter to decide when to start a tracer; use internal flag to
433        know which tracer to step-forward; switch this internal flag at the top
434        of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
435        for adjoint built.
436    o pkg/seaice:
437      - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
438      - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
439      - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
440    o pkg/ecco:
441      - fix writing of output file DiagnosCost_ClimSalt/Theta
442        and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
443    o pkg/seaice:
444      - add missing initialisation of COR_ICE array in dynsolver.F
445      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
446        compiled either way, and is tested in all exps (multidim was only tested
447        in lab_sea ad before).
448      - cosmetic change to prepare for future addition of ITD. no change to results.
449        no defaults change.
450      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
451      - by lack of adequate verification experiments, I further used custom versions
452        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
453        should be correct.
454      - avoid recomputations in ad.
455    o array initialisation in adjoint mode:
456      1) pkg/mom_common/mom_calc_ke.F:
457        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
458        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
459        part this initialisation is gone, resulting in Floating Point Exception
460        (caught by open64 compiler with debug option).
461      2) model/src/convective_weights.F
462        set output convectCount over the full array range (instead of doing
463        an update): this fix a similar issue when called within recomputation (adjoint)
464        which could by-pass the initialisation (normally done in the caller S/R).
465    o pkg/seaice:
466      - final version of turbulent flux params, as agreed at MIT ice meet:
467           SEAICE_mcPheePiston (default is ~ 0.000875)
468           SEAICE_mcPheeTaper (default is 0.)
469           SEAICE_frazilFrac (defualt is 1.)
470           SEAICE_mcPheeStepFunc (default is false)
471      - changes results at trunction error level
472      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
473    o added pkg/frazil:
474      - see frazil_description.tex for details
475      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
476    o pkg/shelfice/shelfice_thermodynamics.F
477      - fix exponents for velocity dependent exchange coefficients: change
478        from 2/3(=0) to 0.66666666666666667
479      - move computation of velocity dependent exchange coefficients into
480        separate loop, so that it applies to both thermodynamics
481      - move some divisions by constants out of loops
482    
483    checkpoint63j (2012/02/16)
484    o pkg/seaice:
485      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
486      - SItracer:  added run time params, and allow coupling to ocn salinity.
487    o pkg/seaice: remove (almost) all divisions by constants within loops
488      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
489      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
490      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
491      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
492    o pkg/seaice :
493      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
494        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
495      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
496      - add permanent SItflux diag that corresponds to TFLUX but includes
497        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
498      - allow activation/testing of a fix for suspected missing term in
499        ocn-ice heat budget (to be confirmed). To test this, you want to
500        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
501        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
502      - no change in results, fwd or ad.
503    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
504      - switch to variable freezing point.
505           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
506      - bug fix : the sublimation term that was missing is now activated.
507           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
508      - bug fix : flooding sign term for SIsal0.NE.0.
509           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
510    o pkg/seaice:
511      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
512        is now the default, and the old default constant freezing point is recovered
513        with SEAICE_tempFrz0    = -1.96,
514             SEAICE_dTempFrz_dS = 0.,
515      - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
516      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
517      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
518        activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
519      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
520        was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
521      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
522        seaice_growth r149 for legacy branch (no results change).
523      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
524        from I. Fenty).
525      - results did not change except for global_ocean.cs32x15, mostly due to the
526        switch to variable freezing point (see above item for detail).
527    o pkg/thsice:
528      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
529        seawater freezing in thsice_calc_thickn (not used).
530    o pkg/seaice: turbulent flux term specification via run time params.
531      - replace CPP switches with run time switches to facilitate testing
532      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
533                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
534      - added runtime parameter : SEAICEturbFluxFormula
535      - move Mcphee constants to SEAICE_PARAMS.h
536      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
537                 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
538                 remove seaice_summary call (moved to seaice_init_fixed)
539      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
540        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
541      - seaice_summary.F : add missing report of read turbulent flux term set up
542                           and SITRACER.
543      - seaice_check.F : check range; inform and stop if retired CPPs are used
544                         (incl. SEAICE_AGE).
545      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
546             CPP switch, same computation as before for the different options.
547      - change results at the truncation level.
548    o pkg/seaice:
549      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
550        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
551        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
552      - update verification/*/input*/data.seaice:
553        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
554        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
555        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
556        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
557    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
558      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
559        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
560        difference in results only due to machine truncation.
561      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
562        MaykutPolySatVap; keep MIN_LWDOWN.
563      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
564      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
565        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
566    o pkg/salt_plume:
567      - isolate saltPlumeFlux array exch into a specific S/R called from
568        do_oceanic_phys.F
569      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
570    o verification:
571      - move untested set-up to MITgcm_contrib/verification_other.
572    o pkg/seaice:
573      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
574    o pkg/seaice:
575      - seaice_solve4temp.F (keeping results unchanged):
576        * add 2 future run-time params to select which saturation vapor pressure
577          formula is used and how post-iteration fluxes are set.
578          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
579        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
580          the linearized expression to stay consistent with tsurf finding.
581      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
582        can be < 0.
583    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
584      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
585        conductive heat flux F_c , and add it explicitly when updating tsurf as
586        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
587        so that now F_ia has a consistent meaning through the entire routine.
588        This causes differences at truncation level: update output of fwd exp.
589        global_ocean.cs32x15.seaice.
590    o pkg/seaice:
591      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
592        of arrays, sign/direction of fluxes; no effect on results.
593      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
594        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
595        note: this should have been done before changing celsius2K default.
596      - to keep results unchanged, add back old value of celsius2K in verification
597        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
598      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
599        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
600        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
601        freezing temp is consistent with value in seaice_growth.F ; this causes
602        differences at machine truncation level: update lab_sea AD output (3/4).
603    o pkg/seaice:
604      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
605        and climsst/sss even when using seaice (to prevent calculation that might
606        use SST on land); does not affect any verification exp.
607      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
608        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
609    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
610      over land (non-legacy code)
611    o vectorize salt_plume package:
612      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
613      - this code computes plumebk everywhere (also over land), thus requires
614        code to avoid divisions by zero and catch the case of kLev=Nr.
615      - efficiency of salt_plume_frac is still sub-optimal
616    o tools (genmake2):
617      - fix makefile NAME specification (option: -makefile NAME) by adding
618        "-f $MAKEFILE" in few places where it was missing including makedepend
619        command (contribution from Paul).
620    
621    checkpoint63i (2012/01/24)
622    o model/src:
623      - add factorized versions of some EOS code to find_rho.F,
624        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
625    o model/src:
626      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
627      - change default celsius2K from 273.16 to 273.15
628      - to keep results unchanged, add back old value of celsius2K in verification
629        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
630         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
631    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
632      to make TAF generate vectorizable code
633    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
634       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
635       have flags that do this more efficiently.
636    o pkg/diagnostics/diagstats_calc.F
637      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
638    o pkg/obcs (with exch2):
639      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
640        and remove code (in obcs_readparms.F) which was based on EXCH of indices
641        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
642    o pkg/exf and seaice exp:
643      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
644        so that switching off area & heff advection flags does not affect results.
645      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
646      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
647        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
648        results of verification experiments: 1D_ocean_ice_column(fwd),
649        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
650        and offline_exf_seaice (all 4).
651    o pkg/seaice:
652      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
653        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
654      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
655        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
656        not multi-dim advection;
657      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
658        SHORTWAVE_HEATING #undef.
659    o optim: make Makefile more robust (?)
660    o pkg/obcs:
661      * fix treatment of obcs_read_pickup for TAF
662    o pkg/shelfice:
663      * add missing initialisation of num_shifwflx
664      * new adjoint verification exp. for isomip
665      * change Prandtl and Schmidt numbers from generic formulations
666        (in terms of model diffus. and visc.) to separate runtime
667        parameters, with Holland and Jenkins (1999) default values.
668    o pkg/exf (interpolation):
669      - extended input field (2 rows) near the N & S poles:
670        * fill in with the symetric value (when even Nb of data in longitude)
671        * add average value at the poles only for scalar quantities ; for vector
672          component interpolation, skip the averaging and keep duplicated values,
673          unless the 2 components have same location (uvInterp=T) in which case
674          interpolate the 2 components together using S/R EXF_INTERP_UV.
675      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
676        together: this allows to account properly for local orientation when
677        averaging at N & S pole.
678      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
679        exf-interpolation near N & S poles. Undef by default.
680      - add debug check/print on 1rst iter if debugLevel >=2.
681    o pkg/exf:
682      - change masking flags definition (no longer "parameter"), put them in
683        common block and set them in S/R EXF_INIT_FIXED.
684      - change recognized masking flag from s,u,v to c,w,s since the mask
685        to use (maskC,W,S) depends on position on model grid and has little to
686        do with scalar/vector difference; fix masking if using P-coordinates.
687      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
688        and update results of exp. global_with_exf (x2).
689      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
690    o pkg/obcs
691      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
692    o pkg/exf (interpolation):
693      - assume periodicity in X only if input field cover full longitude range.
694      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
695        and should vectorise).
696      - fix input lat of the 2 added row (in case we provide N.pole data).
697    
698    checkpoint63h (2011/12/30)
699    o pkg/seaice:
700      - change declaration of UVM from _RL to _RS in order to get B-grid
701        uIce,vIce monitor when _RS = real*4
702    o pkg/offline:
703      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
704      - compute vertical velocity if not read from file (switch on exactConserv
705        & staggerTimeStep);
706      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
707    o verification:
708      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
709        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
710        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
711      - update output of exp. global_ocean.cs32x15.viscA4 after changing
712        grid-file angles (used here for coriolis-3d);
713      - remove (or gzip) few files not needed to run fizhi-cs experiments.
714    o pkg/exf (vector interpolation):
715      - rotate vector component toward local grid-axis orientation using grid-angles
716        (stored in GRID.h) instead of locally computed rotation angle; keep old code
717        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
718    o pkg/seaice:
719      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
720        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
721    o pkg/PKG_OPTIONS.h files:
722      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
723        outside of the #ifdef ALLOW_THISPKG / #endif block.
724      - update verification/*/code/PKG_OPTIONS.h files.
725    o add a verification experiment (offline_exf_seaice/input.seaice) that test
726      the B-grid LSOR solver
727    o pkg/seaice: sort out emissivity and long wave radiation step 2:
728      - add emissivity for snow and ice as new run-time parameters
729        (unfortunately) that default to the corresponding exf values; this
730        changes results in most verification experiments so that for backward
731        compatibility these parameter have to be set explicitly to inconsistent
732        values (ugly);
733      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
734        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
735        until we agree how to handle this bug properly
736    o pkg/exf (interpolation):
737      - add a set of run-time param ({inputfield}_interpMethod), one for
738        each interpolated input field, to select the interpolation method
739        with a value of zero switching off the interpolation;
740      - print interpolation parameters to standard output;
741      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
742        (to use instead runoff_interpMethod=0 in data.exf).
743      - simplify default setting of interpolation parameters (for all fields,
744        set position to match model grid cell-center position, leading to trivial
745        interpolation in case of regular Lat-Lon grid) and fix for the case of
746        non-uniform delY.
747    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
748       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
749       this factor is absolutely required, because the lw exitance (= out-going
750       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
751       where the reflectivity rho = 1-emissivity for conservation reasons. Once
752       this is established, we can remove the CPP-Flag (if we want to).
753    o pkg/seaice:
754      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
755        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
756      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
757        what the name implies (and not emissivity*BoltzmannConstant), this means
758        the old default value of 5.5e-8 now means
759        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
760        S/R exf_readparms
761      - FV-discretization of the B-grid LSOR solver, turn on with
762        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
763        of the calling routine dynsolver, so that B and C-grid code look a
764        little more alike.
765      - fix index bugs in ostres.F (B-grid code)
766    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
767    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
768      default for SEAICE_emissivity, if useEXF; requires setting a wrong
769      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
770      backward compatiblity
771    o model/src: use sigmaR in calc_ivdc
772    
773    checkpoint63g (2011/12/16)
774    o pkg/seaice/seaice_growth.F:
775      fix heat conservation of the coupled ocean-seaice system.
776      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
777      solid vs liquid water treatment is resolved via QNET.
778    o pkg/seaice/seaice_growth.F:
779      add missing term for sublimation in saltFlux, which was breaking conservation.
780    o pkg/seaice/seaice_model.F:
781      Remove this patholigical case treatment in evolution branch,
782      where it is un-necessary and breaks conservation.
783      Update global_ocean.cs32x15/results accordingly for
784      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
785    o model/src:
786      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
787      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
788    o pkg/obcs:
789      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
790      tendency for temperature and salinity that is then applied to update
791      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
792      horizontal advection and diffusion contributions on the boundary (in
793      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
794      removing the mask in S/R timestep_tracer. The advantage of this approach is
795      that the updated tracer values include contributions from the surface
796      forcing and vertical diffusion.
797      This modification changes exp4.stevens because of vertical diffusion.
798    o model/src:
799      change non-curvilinear grid setting to also work with exch2 + blank tiles:
800      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
801        face dimensions.
802      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
803        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
804        and INI_SPHERICAL_POLAR_GRID.
805      change test-experiment global_ocean.90x40x15:
806      - split the domain in many more tiles (9x4 tiles of 10x10 each);
807      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
808      - update results of both test (std & dwnslp).
809    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
810       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
811    o model/src:
812      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
813        and fix initialisation when using sigma-coords.
814    o model/src:
815     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
816       to their current value at the beginning of forward_step.F": add a new run-time
817       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
818     - set doResetHFactors=T in the following test exp:
819        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
820        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
821        and tutorial_global_oce_in_p (nonLinFS in p)
822    o pkg/ecco
823      - added IES cost term
824    o verification/advect_xz
825      - scale down the depth by 1/100 (from 200 km to just 2.km)
826      - add secondary test using divergent flow, r-star and implicit vertical advection.
827      - add note (check_conserve_TS.txt) and matlab script to check global
828        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
829    o pkg/rbcs:
830      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
831    o pkg/obcs (Stevens BCs):
832      - fix various problems in the phase speed computations of the Stevens
833        boundary conditions:
834        - sign error for western and southern boundaries,
835        - time tendencies were underestimated by factor of dTracerLev and some just
836          zero (for multidim advection schemes) -> now estimate time tendencies
837          from difference between previous (n) time level and the one before (n-1);
838          this requires storing a field per tracer per boundary, also in the pickup
839          files.
840        - replace deltaTmom in cflMer/Zon computation with dTracerLev
841        - set default phase velocity to cflMer/Zon
842      - update verification experiment exp4.stevens
843    o pkg/generic_advdiff (implicit_r):
844      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
845        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
846      - fix implicit vertical diffusion or advection with NonLin FreeSurf
847        (was using current recip_hFacC instead of future recip_hFacC): set future
848        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
849        solver S/R ;
850      - fill diagnostics of vertical advective fluxes (computed from tendency)
851        when using implicit vert. advection;
852      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
853         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
854         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
855         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
856    o pkg/diagnostics:
857      - add diags for T & S tendency which goes through Adams-Bashforth.
858    
859    checkpoint63f (2011/11/30)
860    o pkg/obcs/obcs_calc_stevens.F:
861      - join some loops to reduce number of if-statements
862      - fix a bug in code for northern and southern boundaries.
863    o pkg/seaice/seaice_init_varia.F
864      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
865        caused zero ice-velocities for the B-grid code
866    o pkg/seaice/seaice_init_fixed.F
867      - fix a bug in the initialisation of the second metric terms
868        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
869      - this affects all seaice configurations with useCurviLinearGrid = .true.
870        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
871        = .true. (default)
872      - the only verification experiment affected is global_ocean.cs32x15:
873        icedyn, seaice, and seaice_dynmix (AD)
874    o pkg/thsice/thsice_diagnostics_state.F
875      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
876        not contain garbage that can lead to surprises in diagstats_calc.F
877    o model/src:
878      - move bi,bj loops inside INTEGR_CONTINUITY ;
879      - call INTEGR_CONTINUITY directly from forward_step.F
880        (previously called from momentum_correction_step.F)
881      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
882        forward_step.F and pkg/ecco/the_main_loop.F
883    o model/src/do_oceanic_phys.F:
884      - reset addMass to zero only if useICEFRONT ;
885      - separated k-loop for rhoInSitu calculation ;
886      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
887        and at constant T,S (= WdRHOdP);
888      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
889        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
890        transport of locally-referenced potential density);
891        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
892    o gluemnc:
893      - replace ncrcat with ncks when adding variables to *.glob.nc
894      - change the way variables without record dimensions are handled so that
895        files that have variables with and without record variables can be glued:
896        add a record dimension with a new unique name to be able to differentiate
897        between variable with and without a-prior record dimensions. Remove
898        this record dimension before adding the variable to the *.glob.nc file.
899        This procedure automatically works also for grid.*.nc files that do not
900        have any record dimension.
901    o verification/cpl_aim+ocn:
902      - generate new reference output on baudelaire (gfortran, mpich2) (previously
903        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
904    o pkg/obcs/obcs_calc_stevens.F:
905      - add code for northern and southern boundaries.
906      - reorder some loops to save some operations and so that drFBar can be scalar
907    o model/src:
908      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
909        truncation) and add diagnostics for Adams-Bashforth tendency increment.
910      - update test-exp. AD output:
911        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
912      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
913        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
914        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
915        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
916        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
917        tutorial_plume_on_slope.
918    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
919      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
920      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
921      does not even come with an F77 compiler anymore, this should not be
922      a limitation
923    
924    checkpoint63e (2011/11/06)
925    o pkg/seaice adjoint of LSR:
926      - substantially rework STORE dirs.
927      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
928        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
929        and only perform SOLV_MAX_FIXED adjoint iters.
930        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
931        always goes to same record, meaning that the last forward field will be
932        the one used in the adjoint - an approximation.
933      - now produces non-zero LSR-related gradients, and acceptable gradients for
934        An's zonal (x-z) test case (to be checked in)
935      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
936        (but these are screwed up by the thermodynamics in the first place);
937        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
938        output_adm.txt also reflects changes to seaice_lsr
939      - global_ocean.cs32x15:
940        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
941          (output_adm.seaice.txt was updated)
942        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
943          (output_adm.seaice_dynmix.txt)
944    o test-exp. exp4+stevens:
945      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
946    o pkg/seaice (lsr solver):
947      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
948        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
949      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
950      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
951        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
952      - compute (with new S/R) and print initial (+ free-driff sol. if available)
953        and final residual of linearised system.
954    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
955      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
956    o pkg/obcs: Stevens BCs (still only for east and west)
957      - fix Stevens BCs by using intermediate velocities of previous
958        time step as "baroclinic" contribution rather velocity of one grid cell
959        inside the boundaries; more consistent but makes the entire treatment
960        more complicated, requires new pickup files and two new S/Rs:
961        obcs_copy_uv_n and obcs_save_uv_n
962        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
963        (undefined by default)
964      - silently move computation of some grid factors into separate loops to
965        save some recomputations
966      - add a hack for non-linear free surface
967      - add a verification experiment to exp4 that tests this code
968    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
969    
970    checkpoint63d (2011/10/25)
971    o pkg/obcs + seaice-dynamics:
972      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
973        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
974        values (consistent with an implicit method).
975      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
976        return to older implementation (same results as before); note that none of
977        the "experimental" OBCS_SEAICE options are implemented in the new version.
978      - switch test exp. seaice_obcs to use new version (update output).
979    o pkg/seaice:
980      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
981      - add parenthesis in Water-Ice drag calculations (evp & lsr);
982      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
983        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
984      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
985        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
986    o pkg/layers:
987      - Include potential density as new coordinate (Thanks to David Munday)
988    o pkg/dic:
989      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
990        carbonate computation/output to CALC_PCO2_APPROX
991    o pkg/generic_advdiff
992      - make TAF generate code that vectorizes:
993        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
994    o model/src:
995      - improve vectorization also for adjoint code of
996        solve_tridiagonal and solve_pentadiagonal. As this requires up to
997        5 new 3D-fields, this code is only turned on for the combination of
998        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
999        for singular matrix check (only for TARGET_NEC_SX).
1000      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
1001        ALLOW_AUTODIFF. This flag now needs to be set outside of
1002        solve_tri/pentadiagonal.F
1003    o pkg/exf:
1004      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
1005        optional namelist EXF_NML_OBCS).
1006      - add many debug-print (to trace down where pkg/cal error msg comes from)
1007    o pkg/mom_vecinv/mom_vi_hdissip.F
1008      - rearrange loops so that vectorization is improved and in particular
1009        the adjoint routine vectorizes. The code is a little longer now, but I
1010        think easier to read.
1011        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
1012    o pkg/seaice:
1013      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
1014    o pkg/exch2:
1015      - alternative code (without tile x tile matrix) for cumulated (global) sum;
1016        used as default; keep using matrix version in adjustment.cs-32x32x1.
1017    o tools/build_options:
1018      - after merging some MPI and/or multi-threads specific optfiles so that
1019        the modified default optfile support both built (using genmake2 -mpi
1020        for the MPI built, using genmake2 -omp for OpenMP built),
1021        move now obsolete optfiles to tools/build_options/unsupported/
1022       (add copy of email sent to support list in doc/optfiles_changes.txt)
1023    
1024    checkpoint63c (2011/09/28)
1025    o pkg/ebm:
1026      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
1027        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
1028    o pkg/seaice (SItracer pickup)
1029    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
1030      To be done:
1031      - thorough testing of missing fields in S/R seaice_read_pickup
1032      - thorough matching between generic tracers and specific fields used
1033        (e.g. volume-weighted age, area-weighted age, salinity, ...)
1034    o pkg/grdchk:
1035      - all procs calculate and print finite-difference gradient (for testreport)
1036      - change description output used by testreport;
1037      - AD testing: also compare and report Finite-difference gradient;
1038        => update all output_adm*.txt
1039    o test exp. global_ocean_ebm:
1040      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
1041        and turn on exactConserve; update (fwd) output.
1042    o pkg/seaice (LSR):
1043      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
1044      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
1045        * identical results with non-CS topology (but save up to half of EXCH calls)
1046        * no much changes in cs-32 verification tests since no ice at face edges
1047         (differences due to convergence criteria, since nb of iterations changed)
1048        * expect some differences on lat-lon-cap grid.
1049        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
1050    o pkg/exch2:
1051      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
1052        many tiles); until alternative coding is added, just add a stop.
1053    o pkg/kpp:
1054      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
1055        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
1056    o optfiles:
1057      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
1058        into corresponding standard one, which now support different build:
1059        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
1060      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
1061    o pkg/obcs (seaice):
1062      - add missing EXCH for uIce,vIce after applying OBCS;
1063      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
1064        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
1065        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
1066      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
1067      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
1068        and eedata.mth for MPI and mutlti-threaded testing.
1069    o pkg/flt:
1070      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
1071      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
1072      - fix pickup and trajectories + profiles output with multi-threads;
1073      - add parameter to select group of fields to write along trajectory and
1074        profile (default unchanged);
1075      - only call PORT_RAND* function when flt_noise <> 0;
1076      - add multi-threaded test for verification exp. flt_example.
1077    o eesupp/src:
1078      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
1079      - USE_OMP_THREADING: check that number of threads (from eedata) matches
1080        actual number (from env.var. setting).
1081    o pkg/ebm:
1082      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
1083      - add multi-threaded test for verification exp. global_ocean_ebm
1084    
1085    checkpoint63b (2011/08/29)
1086    o pkg/ebm:
1087      - fix sign of runoff;
1088      - update directly forcing fields (Qnet,EmPmR) to use standard
1089        external_forcing_surf.F (remove ebm_forcing_surf.F);
1090      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
1091      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
1092        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
1093      - update global_ocean_ebm parameters file data and update output (fwd+ad).
1094    o verification/matrix_example:
1095      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
1096        MPI and mutlti-threaded testing.
1097    o pkg/matrix:
1098      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
1099      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
1100      - fix for multi-threaded (remove DATA statement);
1101      - use standard DIFFERENT_MULTIPLE function;
1102      - add MATRIX_OPTIONS.h
1103    o verification/matrix_example:
1104       To allow to split the domain in several tiles, change the domain size
1105        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
1106        Western side) of land points.
1107    o (*_)write_pickup:
1108      - fix few bugs in mypackage_read/write_pickup.F
1109      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
1110        array of length 1 (was caught by compiler syntax-check).
1111    o pkg/diagnostics (velocity potential solver):
1112      - fix initialisation of main diagonal matrix (for overlap values)
1113    o tools/build_options:
1114      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
1115        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
1116      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
1117        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
1118        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
1119        and use "-devel" testreport option for standard testing on baudelaire.
1120    o pkg/grdchk:
1121      - Assume that all gradient-check position are within the same tile
1122        corresponding to global indices (iGloTile,jGloTile) and that
1123        positions (i,j indices or nbeg) are local to this tile;
1124      - set tile local-indices and proc. number according to tile global-indices;
1125      - remove grdchkwhichproc from namelist (retired param);
1126      - send adjoint gradient to all procs so that all procs print it to STDOUT;
1127      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
1128    o adding package bbl (Bottom Boundary Layer)
1129      description in MITgcm/pkg/bbl/bbl_description.tex
1130      example/test experiment in MITgcm_contrib/bbl
1131    o adjoint verifications
1132      - changed 5 experiments to multi-tiles
1133        * global_ocean.90x40x15
1134        * obcs_ctrl
1135        * offline_exf_seaice
1136        * tutorial_dic_adjoffline
1137        * tutorial_tracer_adjsens
1138        changed reference output for those that crossed tile boundaries
1139        (changed choices of gradient check positions)
1140      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
1141      - temporary bug fix in grdchk_loc.F for obcs
1142    o genmake2 & testreport
1143      - add target "obj" (just for OBJFILES files) to Makefile;
1144      - add option to specify FEXTRAFLAGS on command line.
1145    o pkg/mypackage:
1146      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
1147    
1148    checkpoint63a (2011/08/02)
1149    o pkg/diagnostics (velocity potential):
1150      - fix velocity-potential calculation when using OBCS: balance net inflow
1151        at each level (new S/R OBCS_DIAG_BALANCE).
1152      - fix some of the problems with OBCS in stream-function calculation.
1153    o pkg/exf/exf_readparms.F
1154      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
1155        EXF_NML_OBCS) more consistent, so that you need not have these lists
1156        in data.exf when they are not used.
1157    o optim/optim_readdata.F:
1158      - add some output about obcs variables that might help debugging
1159      - add a check about nvarlength
1160    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
1161    o pkg/diagnostics (velocity potential):
1162      - fix mask for OBCS (still problems in stream-function with OBCS);
1163      - add specific parameter (default = main code CG2D params) for solver;
1164      - in case of poor convergence, use solution corresponding to lowest residual.
1165  o pkg/seaice/seaice_growth.F: small changes that permit vectorizable  o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
1166    adjoint code. In general statements like tmpscal=fld(i,j) are problematic    adjoint code. In general statements like tmpscal=fld(i,j) are problematic
1167    and should be avoided where possible.    and should be avoided where possible.
# Line 38  o pkg/gmredi: Line 1196  o pkg/gmredi:
1196     Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),     Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
1197     and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)     and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
1198    
1199  checkpoint63 (2011/07/11)  checkpoint63  (2011/07/11)
1200  o pkg/exch2:  o pkg/exch2:
1201   - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h   - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
1202   - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the   - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
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