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revision 1.1533 by jmc, Thu Nov 10 21:04:47 2011 UTC revision 1.1701 by jmc, Wed Aug 1 18:24:45 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/thsice:
8      - re-anable balanceEmPmR when useSEAICE=T with useThSIce=T.
9      - option to correct ocean fresh-water flux for imbalance of Atmos+Land
10        fresh-water flux: uniform correction or proportional to local precip.
11    o pkg/ctrl:
12      - new header file CTRL_SIZE.h for parameters maxCtrlArr2D, maxCtrlArr3D
13      - redefine CPP option ALLOW_BOTTOMDRAG_CONTROL to
14                            ALLOW_BOTTOMDRAG_CONTROL_NONGENERIC
15      - verification/hs94.1x64x5/ tests ALLOW_GENARR{2D,3D}_CONTROL
16    
17    checkpoint63q (2012/07/30)
18    o pkg/autodiff:
19      note about monitor and snap-shot of ad-variables:
20      a) need to apply ADEXCH before monitor or output of ad-vars to include
21       overlap contributions (was done for adjDump but missing for monitor).
22      b) since ADEXCH implies adding overlap values to interior array, machine
23       truncation error is expected when adding an ADEXCH call in the middle of
24       the time-stepping (although mathematically identical).
25      modifs:
26      - fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars
27        declaration (adEddyPsiX,adEddyPsiY in adcommon.h).
28      - add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how  to
29        apply ADEXCH before monitor or snap-shot of ad-variables:
30           =0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy.
31      - implement new method (copy+adexch) for snap-shot and monitor of main model
32        ad-vars (initially not used by default -> output unchanged).
33      - change default (set to 2) to use new method and update few output_adm.txt
34        with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo
35        and both tutorial_tracer_adjsens tests).
36      - switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice)
37        and turn off momDissip_In_AB in the 2 other (needed for stable AB-3).
38    o pkg/ctrl:
39      enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of
40      generic control variables via
41      #define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL
42      Only required customization should be S/R ctrl_map_ini_genarr.F
43      (routine in repository contains example)
44    o pkg/exf:
45      - fix and refine checking of surface-relaxation setting when using EXF
46    o verification (adjoint exp):
47      - reduce length of simulation by half for experiment global_ocean.cs32x15
48        (std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output.
49    o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag)
50      - replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers
51        of KE that can occur with aggressive optimization
52      + put quadratic bottom drag calculation in separated loops (only done if
53        using bottomDragQuadratic)
54    o model/src: CG2D_NSA
55      - clean-up:  stop if cg2dNormaliseRHS=T and AUTODIFF
56         and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE.
57      - in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens),
58         change cg2d residual target to be expressed in Wunits (=> do not normalise
59         RHS ; this fix global_max Pb with TAF); update output.
60    o verification/tutorial_tracer_adjsens:
61       improve parameter consistency (and get rid of warnings):
62       - use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf);
63       - switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical)
64       - use staggerTimeStep (for stability) in som81; use default rotation period.
65    o pkg/exch2:
66      - with empty facet: fix compact-format (W2_mapIO=1) definition (was previously
67        reset to 0 = 1 long line in X)
68    o pkg/mdsio:
69      - fix reading of dimensions from meta file for large-size domain
70    o model/src:
71      - fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long);
72      - to refine CS-grid check, add logical flag "hasWetCSCorners": true if using
73        Cubed-Sphere Exch with CS-corners inside the domain;
74        make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate
75        globalArea and to set hasWetCSCorners.
76      - add warning if usingCurvilinearGrid and momAdvection in flux-form (missing
77        metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form.
78      - re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if
79        useCDscheme and useCubedSphereExchange).
80    o pkg/seaice/seaice_growth.F :
81      - compute the SEAICE_DISABLE_HEATCONSFIX term accordingly
82        for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0)
83        when the previous code was not correct.
84      - in all cases diagnoze the boundary condition mismatch to SIaaflux
85      - in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add
86        that term to QNET (essentially to set the melt/freeze water to 0degC).
87        when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed.
88    o verification/global_ocean.cs32x15/input.seaice :
89      - add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget.
90      - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces).
91      - update results (output.seaice.txt) accordingly.
92    o verification/lab_sea/input/data.seaice :
93      - remove SEAICEheatConsFix, which is now be tested
94        in global_ocean.cs32x15. The presently coded fix
95        is only consistent with real fresh water + nlfs.
96      - update results (output.txt) accordingly.
97    o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd).
98    o AD_CONFIG.h file:
99      - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;
100      - remove #include "AD_CONFIG.h" from all included OPTIONS files and
101        add it explicitly in each fortran src file where it is needed.
102        motivation: header file AD_CONFIG.h is generated/modified after "make depend"
103        thus introducing potentially wrong dependency; therefore, better to include
104        it only where it's really needed, and after any other included OPTIONS file
105        (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN
106        or ALLOW_TANGENTLINEAR_RUN).
107    
108    checkpoint63p (2012/07/06)
109    o pkg/autodiff:
110      - rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ;
111      - create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters
112        which are now read from new parameter file "data.autodiff" (inAdExact
113        previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg)
114      - add file "data.autodiff" in all verification/*/input_ad/ directories.
115      - add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward
116        mode (used in global_ocean.cs32x15.seaice_dynmix test exp.)
117    o verification/tutorial_tracer_adjsens/
118      - add extra sub-verification which uses "SOM" advection scheme
119        (2nd Order-Moment Advection Scheme, Prather Limiter) with
120          #define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h
121        and in data:
122          multiDimAdvection=.TRUE.,
123          tempAdvScheme=81,
124          saltAdvScheme=81,
125    o model/src:
126      - introduce ALLOW_BALANCE_RELAX which allow the removal
127       of the global mean of relaxation terms by setting
128       balanceThetaClimRelax and balanceSaltClimRelax
129      - disable balanceEmPmR and balanceQnet in the case when useSeaice.
130       This case is now treated appropriately in seaice_growth.F
131    o pkg/seaice:
132      - do balanceEmPmR and balanceQnet based on the net fluxes
133        (SItflux) that enter the ocean+ice system rather than QNET
134        and EMPMR. Works best in real fresh water.
135      - SIatmFW, SIatmQnet, and SItflux computations had to be moved
136        out of the diagnotics bloc, and stored in global arrays.
137    
138    checkpoint63o (2012/06/29)
139    o vertical mixing schemes:
140      - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging)
141      - replace computation of density (in Function STATE1, opps_calc.F) by a call
142        to S/R FIND_RHO_SCALAR
143      - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC
144        and use it for N^2 calculation in ggl90_calc.F (save 2 density computations);
145        affects output (vermix.ggl90) at truncation level.
146    o testreport:
147      - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles
148        (nSx,nSy) for the number of threads (from eedata.mth)
149    o model/src:
150      - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part)
151        related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary).
152    o verification/tutorial_tracer_adjsens/
153      - compile with ALLOW_CG2D_NSA
154      - run with nonlinFreeSurf=3
155      - update reference output_adm.txt
156    o tools/genmake2:
157      - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
158        refine usePROFILES switching off (only when NetCDF is not available).
159    o verification (atmospheric set-up):
160      - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
161    o pkg/profiles : refine profiles and files handling.
162    o model/src and pkg/ecco : introduce run-time switch usePROFILES.
163    o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
164      - changes to use model/src/the_main_loop.F rather than the ecco version
165        in ecco type adjoint runs.
166    o model/src:
167      - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
168      - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
169      - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
170    o model/src:
171      - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
172        update output of test experiment bottom_ctrl_5x5.
173    o pkg/generic_advdiff:
174      - implement vertical bi-harmonic diffusion (for now, only for T & S and
175        only explicitly).
176    o verification/bottom_ctrl_5x5/
177      update reference output (results changed quite some time ago,
178      not sure when; but new reference results look ok in terms of grdchk)
179    o verification/1D_ocean_ice_column/
180      For verification purposes, the exact adjoint rather than an approx.
181      should be used (e.g., to comare against F.D. or TLM).
182      removed autodiff_inadmode*_ad.F routines in code_ad/
183      Update results/ accordingly.
184    o pkg/cal:
185      - change cal_getdate.F so that output date is function of input time only
186        (less ambiguous, not mixed up with input iteration number).
187      - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
188    o pkg/diagnostics:
189      - implement calendarDumps also for stats-diags
190      - implement calendarDumps also for snap-shot output (negative freq)
191      - for now, ignores calendarDumps if non-zero phase-lag.
192    
193    checkpoint63n (2012/06/04)
194    o model/src:
195      - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
196        between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
197      - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
198        similar to calc_r_star.F); update results of experiment internal_wave and
199        tutorial_global_oce_in_p (affected @ truncation level).
200    o pkg/shelfice:
201      - add parameterisation of advective-diffusive flux into the ice shelf
202        according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
203      - simply eps3/3a computation
204    o eesupp:
205     - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
206       between tiles, just fill-in edges assuming locally periodic subdomain) and
207       add corresponding exchange subroutines (EXCH0);
208     - new CG-solver version (_EX0) for disconnected-tiles special case.
209    o model/src (CG-solvers):
210     - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
211       (similar final residual output and max-Iter number as with standard version);
212     - allows to store and use lowest-residual solution (standard & _SR versions);
213     - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
214     - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
215    o eesup/src:
216     - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
217       ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
218    o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
219    
220    checkpoint63m (2012/04/27)
221    o pkg/shelfice:
222     - account for partical cells in surface level below ice-shelf for hydrostatic
223       pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
224    o ad test experiments:
225     - update and rename to "ad_optfile.local" local AD-optfile specific to a
226       particular adjoint verification experiment (in verification/*/code_ad/)
227    o pkg/seaice & pkg/exf:
228     - Part two of ECCO-CLIVAR code merges.
229       Completes merge of seaice area relax. code.
230       Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
231       to be set in EXF_OPTIONS.h since this pkg controls its I/O
232       (and avoids second CPP option in SEAICE_OPTIONS.h)
233     - change default value of costIceStart & costIceEnd to a valid date.
234     - add snowPrecip to HSNOW in seaice_growth
235    o pkg/ptracers:
236     - move ptracers summary and setup check into separated S/R ; add a check for
237       valid PTRACERS_Iter0 value (error+stop or just warning).
238    o pkg/cal (+ pkg/ecco):
239     - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
240       as input; and for AD, unless both are not differentiable (e.g., k index)).
241    o model/src:
242     - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
243       is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
244       temporary set to usingZCoords value (to be changed to F when using shelfice).
245     - hydrostatic pressure: implement partial cell near the surface also for
246       Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
247       usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
248    o pkg/ctrl/ctrl_init.F:
249     - add a formal parameter to s/r ctrl_init_rec to print
250       xx_$(ctrl_valiable)_file for easier debugging
251     - move call of cal_* routines into the if-block where they are really
252       needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
253       to specify a startdate
254    o pkg/seaice:
255     - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
256       global_ocean.cs32x15/code versions).
257     - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
258       verification experiment global_ocean.cs32x15.seaice and update results.
259    o pkg/exf:
260     - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
261       (according to useExfYearlyFields).
262    o pkg/cal:
263     - move calendar setting & summary (previously in cal_readparams.F) into new
264       S/R CAL_INIT_FIXED to be called later in the initialisation process, once
265       length of the simulation is set (after SET_PARMS call); This is an attempt
266       to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
267     - For safety: keep a record of pkg/cal parameter settings status
268               to allow to STOP if one pkg/cal S/R is called too early.
269     - add a stop in all basic pkg/cal subroutines if called before setting is done.
270     - modify cal_getdate.F: stop when nothing was returned;
271       if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
272       this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
273    
274    checkpoint63l (2012/04/04)
275    o pkg/bbl:
276      - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
277        update global_with_exf output.yearly.txt file.
278    o pkg/cal:
279      - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
280      - remove 2 unsused and very short (1 line only) functions ;
281      - remove unsused subroutines from AD-Diff list.
282    o model/src:
283      - start to implement clean wait to stop in initialization S/R (config_check.F,
284         packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
285    o folowing PRINT_MESSAGE changes:
286      - remove reminder multiple print to the same file (STDOUT) when multi-threads.
287    o pkg/bbl:
288      - modification so it can work with z*
289      - replace deltaT with dTtracerLev(k) for asynchronous time stepping
290      - global_with_exf/input.yearly verification; changes output.yearly.txt
291    o eesupp/src:
292      - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
293        writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
294      - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
295        # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
296      - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
297      - when using MPI, always set usingMPI=T ; set default accordingly and stop
298        if not consistent.
299      - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
300        argument is zero (in case called within single-thread section).
301    o pkg/fizhi:
302        clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
303        in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
304    o pkg/exch2:
305      - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
306        activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
307      - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
308        but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
309        with bad ones coming from a not-yet-updated halo.
310        This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
311    o pkg/frazil:
312        move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
313        http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
314    o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
315    o verification/lab_sea
316      * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
317      * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
318      * nTimeSteps 3 -> 4
319      * changed reference output accordingly
320    o pkg/ctrl:
321      * fix ctrl_get_gen for xx_sst, xx_sss
322    o pkg/fizhi:
323      - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
324        update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
325      - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
326        fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
327        clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
328    o pkg/gmredi:
329      - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
330    o pkg/fizhi:
331      - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
332        (old)aces open64 tuv test.
333    o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
334    o pkg/mom_vecinv:
335      - fix 1 loop range in mom_vecinv.F to be like all the other loops which
336        set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
337        with non-lin free-surf).
338    o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
339      in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
340      some compilers (gfortran 4.6.0 on MacOS)
341    o momentum:
342      - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
343        & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
344        fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
345    
346    checkpoint63k (2012/03/17)
347    o model/src:
348       - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
349         flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
350       - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
351         (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
352    o model/src: solve_*diagonal.F
353       - replace division with multiplication by inverse (similar to original version)
354         update output of AD exp. global_ocean.90x40x15.
355       - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
356         to enable the use of the vectorized & differentiable solve_tridiagonal.F
357       - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
358         vertical advection (to get solve_tridiagonal tested in AD mode).
359    o pkg/seaice: ECCO-CLIVAR merge:
360      1. seaice AREA relaxation
361         * CPP option: SEAICE_ALLOW_AREA_RELAXATION
362         * runtime flag: SEAICE_tauAreaObsRelax
363      2. modified global mean cost imbalance code: CPP option
364          ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
365    o another iteration on solve_*diagonal.F
366       Make choices independent of AUTODIFF
367       Default will be the adjoinable vectorized version.
368       Alternative choices are:
369       * non-adjoinable original version with low memory footprint:
370         #define SOLVE_DIAGONAL_LOWMEMORY
371       * still adjoinable but does not vectorize (k as inner-most loop):
372         #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
373    o testreport
374     - add option to use a home made wrapper around "make"
375     - remove MITGCM_IEEE env. variable (no longer active)
376    o pkg/shelfice
377     - improve computation of friction velocity for velocity dependent
378       exchange coefficients: include velocities into SHELFICEBoundaryLayer
379       block to average velocities vertically
380     - add TAF store directives for SHI_ALLOW_GAMMAFRICT
381    o Modify diagonal solvers, now three versions (upon request):
382      #ifndef SOLVE_DIAGONAL_AUTODIFF
383        1. default version (dating back a while ago)
384      #else /* def SOLVE_DIAGONAL_AUTODIFF */
385      # ifdef SOLVE_DIAGONAL_KINNER
386        2. adjoinable version with k-innermost loop (G. Forget)
387      # else
388        3. adjoinable vectorized version of 2.
389      # endif
390      #endif /* SOLVE_DIAGONAL_AUTODIFF */
391      All flags are currently set within routines, but could/should be moved to CPP-options.
392      Array bounds for 1. are as before, for 2.,3. cover the entire domain
393      (could be changed for 1. too).
394    o verification/lab_sea (fwd):
395      - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
396        use 7 categories (except hb87), new solve4temp params (except salt_plume),
397        constant salinity (=4) or variable salinity (salt_plume) done through
398        SItracer.
399    o pkg/seaice:
400      - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
401      - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
402         SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
403        from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
404        SEAICE_freeze got retired) but already better than previously with
405        SEAICE_freeze=123456.7 deg.C;
406      - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
407        (safer multi-threaded setting); always set SEAICEuseEVP;
408      - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
409        SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
410        stop if multiple specifications for the same coeff; make sure default
411        SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
412    o pkg/obcs:
413      - allow to switch to upwind 1rst order advection scheme for the advective
414        flux computation at the open-boundary; disabled for adjoint built.
415    o pkg/ptracers:
416      - rename PTRACERS_RESTART.h -> PTRACERS_START.h
417      - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
418      - add parameter to decide when to start a tracer; use internal flag to
419        know which tracer to step-forward; switch this internal flag at the top
420        of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
421        for adjoint built.
422    o pkg/seaice:
423      - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
424      - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
425      - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
426    o pkg/ecco:
427      - fix writing of output file DiagnosCost_ClimSalt/Theta
428        and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
429    o pkg/seaice:
430      - add missing initialisation of COR_ICE array in dynsolver.F
431      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
432        compiled either way, and is tested in all exps (multidim was only tested
433        in lab_sea ad before).
434      - cosmetic change to prepare for future addition of ITD. no change to results.
435        no defaults change.
436      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
437      - by lack of adequate verification experiments, I further used custom versions
438        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
439        should be correct.
440      - avoid recomputations in ad.
441    o array initialisation in adjoint mode:
442      1) pkg/mom_common/mom_calc_ke.F:
443        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
444        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
445        part this initialisation is gone, resulting in Floating Point Exception
446        (caught by open64 compiler with debug option).
447      2) model/src/convective_weights.F
448        set output convectCount over the full array range (instead of doing
449        an update): this fix a similar issue when called within recomputation (adjoint)
450        which could by-pass the initialisation (normally done in the caller S/R).
451    o pkg/seaice:
452      - final version of turbulent flux params, as agreed at MIT ice meet:
453           SEAICE_mcPheePiston (default is ~ 0.000875)
454           SEAICE_mcPheeTaper (default is 0.)
455           SEAICE_frazilFrac (defualt is 1.)
456           SEAICE_mcPheeStepFunc (default is false)
457      - changes results at trunction error level
458      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
459    o added pkg/frazil:
460      - see frazil_description.tex for details
461      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
462    o pkg/shelfice/shelfice_thermodynamics.F
463      - fix exponents for velocity dependent exchange coefficients: change
464        from 2/3(=0) to 0.66666666666666667
465      - move computation of velocity dependent exchange coefficients into
466        separate loop, so that it applies to both thermodynamics
467      - move some divisions by constants out of loops
468    
469    checkpoint63j (2012/02/16)
470    o pkg/seaice:
471      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
472      - SItracer:  added run time params, and allow coupling to ocn salinity.
473    o pkg/seaice: remove (almost) all divisions by constants within loops
474      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
475      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
476      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
477      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
478    o pkg/seaice :
479      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
480        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
481      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
482      - add permanent SItflux diag that corresponds to TFLUX but includes
483        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
484      - allow activation/testing of a fix for suspected missing term in
485        ocn-ice heat budget (to be confirmed). To test this, you want to
486        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
487        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
488      - no change in results, fwd or ad.
489    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
490      - switch to variable freezing point.
491           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
492      - bug fix : the sublimation term that was missing is now activated.
493           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
494      - bug fix : flooding sign term for SIsal0.NE.0.
495           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
496    o pkg/seaice:
497      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
498        is now the default, and the old default constant freezing point is recovered
499        with SEAICE_tempFrz0    = -1.96,
500             SEAICE_dTempFrz_dS = 0.,
501      - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
502      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
503      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
504        activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
505      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
506        was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
507      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
508        seaice_growth r149 for legacy branch (no results change).
509      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
510        from I. Fenty).
511      - results did not change except for global_ocean.cs32x15, mostly due to the
512        switch to variable freezing point (see above item for detail).
513    o pkg/thsice:
514      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
515        seawater freezing in thsice_calc_thickn (not used).
516    o pkg/seaice: turbulent flux term specification via run time params.
517      - replace CPP switches with run time switches to facilitate testing
518      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
519                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
520      - added runtime parameter : SEAICEturbFluxFormula
521      - move Mcphee constants to SEAICE_PARAMS.h
522      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
523                 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
524                 remove seaice_summary call (moved to seaice_init_fixed)
525      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
526        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
527      - seaice_summary.F : add missing report of read turbulent flux term set up
528                           and SITRACER.
529      - seaice_check.F : check range; inform and stop if retired CPPs are used
530                         (incl. SEAICE_AGE).
531      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
532             CPP switch, same computation as before for the different options.
533      - change results at the truncation level.
534    o pkg/seaice:
535      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
536        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
537        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
538      - update verification/*/input*/data.seaice:
539        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
540        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
541        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
542        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
543    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
544      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
545        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
546        difference in results only due to machine truncation.
547      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
548        MaykutPolySatVap; keep MIN_LWDOWN.
549      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
550      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
551        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
552    o pkg/salt_plume:
553      - isolate saltPlumeFlux array exch into a specific S/R called from
554        do_oceanic_phys.F
555      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
556    o verification:
557      - move untested set-up to MITgcm_contrib/verification_other.
558    o pkg/seaice:
559      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
560    o pkg/seaice:
561      - seaice_solve4temp.F (keeping results unchanged):
562        * add 2 future run-time params to select which saturation vapor pressure
563          formula is used and how post-iteration fluxes are set.
564          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
565        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
566          the linearized expression to stay consistent with tsurf finding.
567      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
568        can be < 0.
569    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
570      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
571        conductive heat flux F_c , and add it explicitly when updating tsurf as
572        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
573        so that now F_ia has a consistent meaning through the entire routine.
574        This causes differences at truncation level: update output of fwd exp.
575        global_ocean.cs32x15.seaice.
576    o pkg/seaice:
577      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
578        of arrays, sign/direction of fluxes; no effect on results.
579      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
580        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
581        note: this should have been done before changing celsius2K default.
582      - to keep results unchanged, add back old value of celsius2K in verification
583        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
584      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
585        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
586        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
587        freezing temp is consistent with value in seaice_growth.F ; this causes
588        differences at machine truncation level: update lab_sea AD output (3/4).
589    o pkg/seaice:
590      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
591        and climsst/sss even when using seaice (to prevent calculation that might
592        use SST on land); does not affect any verification exp.
593      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
594        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
595    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
596      over land (non-legacy code)
597    o vectorize salt_plume package:
598      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
599      - this code computes plumebk everywhere (also over land), thus requires
600        code to avoid divisions by zero and catch the case of kLev=Nr.
601      - efficiency of salt_plume_frac is still sub-optimal
602    o tools (genmake2):
603      - fix makefile NAME specification (option: -makefile NAME) by adding
604        "-f $MAKEFILE" in few places where it was missing including makedepend
605        command (contribution from Paul).
606    
607    checkpoint63i (2012/01/24)
608    o model/src:
609      - add factorized versions of some EOS code to find_rho.F,
610        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
611    o model/src:
612      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
613      - change default celsius2K from 273.16 to 273.15
614      - to keep results unchanged, add back old value of celsius2K in verification
615        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
616         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
617    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
618      to make TAF generate vectorizable code
619    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
620       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
621       have flags that do this more efficiently.
622    o pkg/diagnostics/diagstats_calc.F
623      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
624    o pkg/obcs (with exch2):
625      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
626        and remove code (in obcs_readparms.F) which was based on EXCH of indices
627        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
628    o pkg/exf and seaice exp:
629      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
630        so that switching off area & heff advection flags does not affect results.
631      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
632      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
633        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
634        results of verification experiments: 1D_ocean_ice_column(fwd),
635        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
636        and offline_exf_seaice (all 4).
637    o pkg/seaice:
638      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
639        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
640      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
641        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
642        not multi-dim advection;
643      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
644        SHORTWAVE_HEATING #undef.
645    o optim: make Makefile more robust (?)
646    o pkg/obcs:
647      * fix treatment of obcs_read_pickup for TAF
648    o pkg/shelfice:
649      * add missing initialisation of num_shifwflx
650      * new adjoint verification exp. for isomip
651      * change Prandtl and Schmidt numbers from generic formulations
652        (in terms of model diffus. and visc.) to separate runtime
653        parameters, with Holland and Jenkins (1999) default values.
654    o pkg/exf (interpolation):
655      - extended input field (2 rows) near the N & S poles:
656        * fill in with the symetric value (when even Nb of data in longitude)
657        * add average value at the poles only for scalar quantities ; for vector
658          component interpolation, skip the averaging and keep duplicated values,
659          unless the 2 components have same location (uvInterp=T) in which case
660          interpolate the 2 components together using S/R EXF_INTERP_UV.
661      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
662        together: this allows to account properly for local orientation when
663        averaging at N & S pole.
664      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
665        exf-interpolation near N & S poles. Undef by default.
666      - add debug check/print on 1rst iter if debugLevel >=2.
667    o pkg/exf:
668      - change masking flags definition (no longer "parameter"), put them in
669        common block and set them in S/R EXF_INIT_FIXED.
670      - change recognized masking flag from s,u,v to c,w,s since the mask
671        to use (maskC,W,S) depends on position on model grid and has little to
672        do with scalar/vector difference; fix masking if using P-coordinates.
673      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
674        and update results of exp. global_with_exf (x2).
675      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
676    o pkg/obcs
677      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
678    o pkg/exf (interpolation):
679      - assume periodicity in X only if input field cover full longitude range.
680      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
681        and should vectorise).
682      - fix input lat of the 2 added row (in case we provide N.pole data).
683    
684    checkpoint63h (2011/12/30)
685    o pkg/seaice:
686      - change declaration of UVM from _RL to _RS in order to get B-grid
687        uIce,vIce monitor when _RS = real*4
688    o pkg/offline:
689      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
690      - compute vertical velocity if not read from file (switch on exactConserv
691        & staggerTimeStep);
692      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
693    o verification:
694      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
695        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
696        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
697      - update output of exp. global_ocean.cs32x15.viscA4 after changing
698        grid-file angles (used here for coriolis-3d);
699      - remove (or gzip) few files not needed to run fizhi-cs experiments.
700    o pkg/exf (vector interpolation):
701      - rotate vector component toward local grid-axis orientation using grid-angles
702        (stored in GRID.h) instead of locally computed rotation angle; keep old code
703        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
704    o pkg/seaice:
705      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
706        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
707    o pkg/PKG_OPTIONS.h files:
708      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
709        outside of the #ifdef ALLOW_THISPKG / #endif block.
710      - update verification/*/code/PKG_OPTIONS.h files.
711    o add a verification experiment (offline_exf_seaice/input.seaice) that test
712      the B-grid LSOR solver
713    o pkg/seaice: sort out emissivity and long wave radiation step 2:
714      - add emissivity for snow and ice as new run-time parameters
715        (unfortunately) that default to the corresponding exf values; this
716        changes results in most verification experiments so that for backward
717        compatibility these parameter have to be set explicitly to inconsistent
718        values (ugly);
719      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
720        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
721        until we agree how to handle this bug properly
722    o pkg/exf (interpolation):
723      - add a set of run-time param ({inputfield}_interpMethod), one for
724        each interpolated input field, to select the interpolation method
725        with a value of zero switching off the interpolation;
726      - print interpolation parameters to standard output;
727      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
728        (to use instead runoff_interpMethod=0 in data.exf).
729      - simplify default setting of interpolation parameters (for all fields,
730        set position to match model grid cell-center position, leading to trivial
731        interpolation in case of regular Lat-Lon grid) and fix for the case of
732        non-uniform delY.
733    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
734       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
735       this factor is absolutely required, because the lw exitance (= out-going
736       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
737       where the reflectivity rho = 1-emissivity for conservation reasons. Once
738       this is established, we can remove the CPP-Flag (if we want to).
739    o pkg/seaice:
740      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
741        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
742      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
743        what the name implies (and not emissivity*BoltzmannConstant), this means
744        the old default value of 5.5e-8 now means
745        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
746        S/R exf_readparms
747      - FV-discretization of the B-grid LSOR solver, turn on with
748        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
749        of the calling routine dynsolver, so that B and C-grid code look a
750        little more alike.
751      - fix index bugs in ostres.F (B-grid code)
752    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
753    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
754      default for SEAICE_emissivity, if useEXF; requires setting a wrong
755      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
756      backward compatiblity
757    o model/src: use sigmaR in calc_ivdc
758    
759    checkpoint63g (2011/12/16)
760    o pkg/seaice/seaice_growth.F:
761      fix heat conservation of the coupled ocean-seaice system.
762      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
763      solid vs liquid water treatment is resolved via QNET.
764    o pkg/seaice/seaice_growth.F:
765      add missing term for sublimation in saltFlux, which was breaking conservation.
766    o pkg/seaice/seaice_model.F:
767      Remove this patholigical case treatment in evolution branch,
768      where it is un-necessary and breaks conservation.
769      Update global_ocean.cs32x15/results accordingly for
770      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
771    o model/src:
772      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
773      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
774    o pkg/obcs:
775      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
776      tendency for temperature and salinity that is then applied to update
777      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
778      horizontal advection and diffusion contributions on the boundary (in
779      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
780      removing the mask in S/R timestep_tracer. The advantage of this approach is
781      that the updated tracer values include contributions from the surface
782      forcing and vertical diffusion.
783      This modification changes exp4.stevens because of vertical diffusion.
784    o model/src:
785      change non-curvilinear grid setting to also work with exch2 + blank tiles:
786      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
787        face dimensions.
788      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
789        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
790        and INI_SPHERICAL_POLAR_GRID.
791      change test-experiment global_ocean.90x40x15:
792      - split the domain in many more tiles (9x4 tiles of 10x10 each);
793      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
794      - update results of both test (std & dwnslp).
795    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
796       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
797    o model/src:
798      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
799        and fix initialisation when using sigma-coords.
800    o model/src:
801     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
802       to their current value at the beginning of forward_step.F": add a new run-time
803       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
804     - set doResetHFactors=T in the following test exp:
805        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
806        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
807        and tutorial_global_oce_in_p (nonLinFS in p)
808    o pkg/ecco
809      - added IES cost term
810    o verification/advect_xz
811      - scale down the depth by 1/100 (from 200 km to just 2.km)
812      - add secondary test using divergent flow, r-star and implicit vertical advection.
813      - add note (check_conserve_TS.txt) and matlab script to check global
814        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
815    o pkg/rbcs:
816      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
817    o pkg/obcs (Stevens BCs):
818      - fix various problems in the phase speed computations of the Stevens
819        boundary conditions:
820        - sign error for western and southern boundaries,
821        - time tendencies were underestimated by factor of dTracerLev and some just
822          zero (for multidim advection schemes) -> now estimate time tendencies
823          from difference between previous (n) time level and the one before (n-1);
824          this requires storing a field per tracer per boundary, also in the pickup
825          files.
826        - replace deltaTmom in cflMer/Zon computation with dTracerLev
827        - set default phase velocity to cflMer/Zon
828      - update verification experiment exp4.stevens
829    o pkg/generic_advdiff (implicit_r):
830      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
831        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
832      - fix implicit vertical diffusion or advection with NonLin FreeSurf
833        (was using current recip_hFacC instead of future recip_hFacC): set future
834        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
835        solver S/R ;
836      - fill diagnostics of vertical advective fluxes (computed from tendency)
837        when using implicit vert. advection;
838      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
839         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
840         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
841         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
842    o pkg/diagnostics:
843      - add diags for T & S tendency which goes through Adams-Bashforth.
844    
845    checkpoint63f (2011/11/30)
846    o pkg/obcs/obcs_calc_stevens.F:
847      - join some loops to reduce number of if-statements
848      - fix a bug in code for northern and southern boundaries.
849    o pkg/seaice/seaice_init_varia.F
850      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
851        caused zero ice-velocities for the B-grid code
852    o pkg/seaice/seaice_init_fixed.F
853      - fix a bug in the initialisation of the second metric terms
854        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
855      - this affects all seaice configurations with useCurviLinearGrid = .true.
856        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
857        = .true. (default)
858      - the only verification experiment affected is global_ocean.cs32x15:
859        icedyn, seaice, and seaice_dynmix (AD)
860    o pkg/thsice/thsice_diagnostics_state.F
861      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
862        not contain garbage that can lead to surprises in diagstats_calc.F
863    o model/src:
864      - move bi,bj loops inside INTEGR_CONTINUITY ;
865      - call INTEGR_CONTINUITY directly from forward_step.F
866        (previously called from momentum_correction_step.F)
867      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
868        forward_step.F and pkg/ecco/the_main_loop.F
869  o model/src/do_oceanic_phys.F:  o model/src/do_oceanic_phys.F:
870    - reset addMass to zero only if useICEFRONT ;    - reset addMass to zero only if useICEFRONT ;
871    - separated k-loop for rhoInSitu calculation ;    - separated k-loop for rhoInSitu calculation ;
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