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revision 1.1491 by jmc, Fri Aug 12 22:22:50 2011 UTC revision 1.1670 by jmc, Fri Jun 15 22:01:45 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 model/src:
8      - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
9        update output of test experiment bottom_ctrl_5x5.
10    o pkg/generic_advdiff:
11      - implement vertical bi-harmonic diffusion (for now, only for T & S and
12        only explicitly).
13    o verification/bottom_ctrl_5x5/
14      update reference output (results changed quite some time ago,
15      not sure when; but new reference results look ok in terms of grdchk)
16    o verification/1D_ocean_ice_column/
17      For verification purposes, the exact adjoint rather than an approx.
18      should be used (e.g., to comare against F.D. or TLM).
19      removed autodiff_inadmode*_ad.F routines in code_ad/
20      Update results/ accordingly.
21    o pkg/cal:
22      - change cal_getdate.F so that output date is function of input time only
23        (less ambiguous, not mixed up with input iteration number).
24      - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
25    o pkg/diagnostics:
26      - implement calendarDumps also for stats-diags
27      - implement calendarDumps also for snap-shot output (negative freq)
28      - for now, ignores calendarDumps if non-zero phase-lag.
29    
30    checkpoint63n (2012/06/04)
31    o model/src:
32      - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
33        between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
34      - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
35        similar to calc_r_star.F); update results of experiment internal_wave and
36        tutorial_global_oce_in_p (affected @ truncation level).
37    o pkg/shelfice:
38      - add parameterisation of advective-diffusive flux into the ice shelf
39        according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
40      - simply eps3/3a computation
41    o eesupp:
42     - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
43       between tiles, just fill-in edges assuming locally periodic subdomain) and
44       add corresponding exchange subroutines (EXCH0);
45     - new CG-solver version (_EX0) for disconnected-tiles special case.
46    o model/src (CG-solvers):
47     - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
48       (similar final residual output and max-Iter number as with standard version);
49     - allows to store and use lowest-residual solution (standard & _SR versions);
50     - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
51     - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
52    o eesup/src:
53     - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
54       ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
55    o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
56    
57    checkpoint63m (2012/04/27)
58    o pkg/shelfice:
59     - account for partical cells in surface level below ice-shelf for hydrostatic
60       pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
61    o ad test experiments:
62     - update and rename to "ad_optfile.local" local AD-optfile specific to a
63       particular adjoint verification experiment (in verification/*/code_ad/)
64    o pkg/seaice & pkg/exf:
65     - Part two of ECCO-CLIVAR code merges.
66       Completes merge of seaice area relax. code.
67       Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
68       to be set in EXF_OPTIONS.h since this pkg controls its I/O
69       (and avoids second CPP option in SEAICE_OPTIONS.h)
70     - change default value of costIceStart & costIceEnd to a valid date.
71     - add snowPrecip to HSNOW in seaice_growth
72    o pkg/ptracers:
73     - move ptracers summary and setup check into separated S/R ; add a check for
74       valid PTRACERS_Iter0 value (error+stop or just warning).
75    o pkg/cal (+ pkg/ecco):
76     - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
77       as input; and for AD, unless both are not differentiable (e.g., k index)).
78    o model/src:
79     - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
80       is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
81       temporary set to usingZCoords value (to be changed to F when using shelfice).
82     - hydrostatic pressure: implement partial cell near the surface also for
83       Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
84       usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
85    o pkg/ctrl/ctrl_init.F:
86     - add a formal parameter to s/r ctrl_init_rec to print
87       xx_$(ctrl_valiable)_file for easier debugging
88     - move call of cal_* routines into the if-block where they are really
89       needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
90       to specify a startdate
91    o pkg/seaice:
92     - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
93       global_ocean.cs32x15/code versions).
94     - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
95       verification experiment global_ocean.cs32x15.seaice and update results.
96    o pkg/exf:
97     - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
98       (according to useExfYearlyFields).
99    o pkg/cal:
100     - move calendar setting & summary (previously in cal_readparams.F) into new
101       S/R CAL_INIT_FIXED to be called later in the initialisation process, once
102       length of the simulation is set (after SET_PARMS call); This is an attempt
103       to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
104     - For safety: keep a record of pkg/cal parameter settings status
105               to allow to STOP if one pkg/cal S/R is called too early.
106     - add a stop in all basic pkg/cal subroutines if called before setting is done.
107     - modify cal_getdate.F: stop when nothing was returned;
108       if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
109       this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
110    
111    checkpoint63l (2012/04/04)
112    o pkg/bbl:
113      - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
114        update global_with_exf output.yearly.txt file.
115    o pkg/cal:
116      - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
117      - remove 2 unsused and very short (1 line only) functions ;
118      - remove unsused subroutines from AD-Diff list.
119    o model/src:
120      - start to implement clean wait to stop in initialization S/R (config_check.F,
121         packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
122    o folowing PRINT_MESSAGE changes:
123      - remove reminder multiple print to the same file (STDOUT) when multi-threads.
124    o pkg/bbl:
125      - modification so it can work with z*
126      - replace deltaT with dTtracerLev(k) for asynchronous time stepping
127      - global_with_exf/input.yearly verification; changes output.yearly.txt
128    o eesupp/src:
129      - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
130        writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
131      - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
132        # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
133      - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
134      - when using MPI, always set usingMPI=T ; set default accordingly and stop
135        if not consistent.
136      - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
137        argument is zero (in case called within single-thread section).
138    o pkg/fizhi:
139        clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
140        in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
141    o pkg/exch2:
142      - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
143        activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
144      - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
145        but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
146        with bad ones coming from a not-yet-updated halo.
147        This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
148    o pkg/frazil:
149        move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
150        http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
151    o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
152    o verification/lab_sea
153      * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
154      * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
155      * nTimeSteps 3 -> 4
156      * changed reference output accordingly
157    o pkg/ctrl:
158      * fix ctrl_get_gen for xx_sst, xx_sss
159    o pkg/fizhi:
160      - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
161        update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
162      - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
163        fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
164        clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
165    o pkg/gmredi:
166      - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
167    o pkg/fizhi:
168      - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
169        (old)aces open64 tuv test.
170    o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
171    o pkg/mom_vecinv:
172      - fix 1 loop range in mom_vecinv.F to be like all the other loops which
173        set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
174        with non-lin free-surf).
175    o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
176      in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
177      some compilers (gfortran 4.6.0 on MacOS)
178    o momentum:
179      - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
180        & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
181        fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
182    
183    checkpoint63k (2012/03/17)
184    o model/src:
185       - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
186         flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
187       - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
188         (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
189    o model/src: solve_*diagonal.F
190       - replace division with multiplication by inverse (similar to original version)
191         update output of AD exp. global_ocean.90x40x15.
192       - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
193         to enable the use of the vectorized & differentiable solve_tridiagonal.F
194       - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
195         vertical advection (to get solve_tridiagonal tested in AD mode).
196    o pkg/seaice: ECCO-CLIVAR merge:
197      1. seaice AREA relaxation
198         * CPP option: SEAICE_ALLOW_AREA_RELAXATION
199         * runtime flag: SEAICE_tauAreaObsRelax
200      2. modified global mean cost imbalance code: CPP option
201          ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
202    o another iteration on solve_*diagonal.F
203       Make choices independent of AUTODIFF
204       Default will be the adjoinable vectorized version.
205       Alternative choices are:
206       * non-adjoinable original version with low memory footprint:
207         #define SOLVE_DIAGONAL_LOWMEMORY
208       * still adjoinable but does not vectorize (k as inner-most loop):
209         #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
210    o testreport
211     - add option to use a home made wrapper around "make"
212     - remove MITGCM_IEEE env. variable (no longer active)
213    o pkg/shelfice
214     - improve computation of friction velocity for velocity dependent
215       exchange coefficients: include velocities into SHELFICEBoundaryLayer
216       block to average velocities vertically
217     - add TAF store directives for SHI_ALLOW_GAMMAFRICT
218    o Modify diagonal solvers, now three versions (upon request):
219      #ifndef SOLVE_DIAGONAL_AUTODIFF
220        1. default version (dating back a while ago)
221      #else /* def SOLVE_DIAGONAL_AUTODIFF */
222      # ifdef SOLVE_DIAGONAL_KINNER
223        2. adjoinable version with k-innermost loop (G. Forget)
224      # else
225        3. adjoinable vectorized version of 2.
226      # endif
227      #endif /* SOLVE_DIAGONAL_AUTODIFF */
228      All flags are currently set within routines, but could/should be moved to CPP-options.
229      Array bounds for 1. are as before, for 2.,3. cover the entire domain
230      (could be changed for 1. too).
231    o verification/lab_sea (fwd):
232      - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
233        use 7 categories (except hb87), new solve4temp params (except salt_plume),
234        constant salinity (=4) or variable salinity (salt_plume) done through
235        SItracer.
236    o pkg/seaice:
237      - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
238      - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
239         SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
240        from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
241        SEAICE_freeze got retired) but already better than previously with
242        SEAICE_freeze=123456.7 deg.C;
243      - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
244        (safer multi-threaded setting); always set SEAICEuseEVP;
245      - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
246        SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
247        stop if multiple specifications for the same coeff; make sure default
248        SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
249    o pkg/obcs:
250      - allow to switch to upwind 1rst order advection scheme for the advective
251        flux computation at the open-boundary; disabled for adjoint built.
252    o pkg/ptracers:
253      - rename PTRACERS_RESTART.h -> PTRACERS_START.h
254      - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
255      - add parameter to decide when to start a tracer; use internal flag to
256        know which tracer to step-forward; switch this internal flag at the top
257        of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
258        for adjoint built.
259    o pkg/seaice:
260      - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
261      - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
262      - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
263    o pkg/ecco:
264      - fix writing of output file DiagnosCost_ClimSalt/Theta
265        and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
266    o pkg/seaice:
267      - add missing initialisation of COR_ICE array in dynsolver.F
268      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
269        compiled either way, and is tested in all exps (multidim was only tested
270        in lab_sea ad before).
271      - cosmetic change to prepare for future addition of ITD. no change to results.
272        no defaults change.
273      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
274      - by lack of adequate verification experiments, I further used custom versions
275        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
276        should be correct.
277      - avoid recomputations in ad.
278    o array initialisation in adjoint mode:
279      1) pkg/mom_common/mom_calc_ke.F:
280        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
281        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
282        part this initialisation is gone, resulting in Floating Point Exception
283        (caught by open64 compiler with debug option).
284      2) model/src/convective_weights.F
285        set output convectCount over the full array range (instead of doing
286        an update): this fix a similar issue when called within recomputation (adjoint)
287        which could by-pass the initialisation (normally done in the caller S/R).
288    o pkg/seaice:
289      - final version of turbulent flux params, as agreed at MIT ice meet:
290           SEAICE_mcPheePiston (default is ~ 0.000875)
291           SEAICE_mcPheeTaper (default is 0.)
292           SEAICE_frazilFrac (defualt is 1.)
293           SEAICE_mcPheeStepFunc (default is false)
294      - changes results at trunction error level
295      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
296    o added pkg/frazil:
297      - see frazil_description.tex for details
298      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
299    o pkg/shelfice/shelfice_thermodynamics.F
300      - fix exponents for velocity dependent exchange coefficients: change
301        from 2/3(=0) to 0.66666666666666667
302      - move computation of velocity dependent exchange coefficients into
303        separate loop, so that it applies to both thermodynamics
304      - move some divisions by constants out of loops
305    
306    checkpoint63j (2012/02/16)
307    o pkg/seaice:
308      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
309      - SItracer:  added run time params, and allow coupling to ocn salinity.
310    o pkg/seaice: remove (almost) all divisions by constants within loops
311      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
312      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
313      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
314      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
315    o pkg/seaice :
316      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
317        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
318      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
319      - add permanent SItflux diag that corresponds to TFLUX but includes
320        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
321      - allow activation/testing of a fix for suspected missing term in
322        ocn-ice heat budget (to be confirmed). To test this, you want to
323        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
324        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
325      - no change in results, fwd or ad.
326    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
327      - switch to variable freezing point.
328           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
329      - bug fix : the sublimation term that was missing is now activated.
330           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
331      - bug fix : flooding sign term for SIsal0.NE.0.
332           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
333    o pkg/seaice:
334      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
335        is now the default, and the old default constant freezing point is recovered
336        with SEAICE_tempFrz0    = -1.96,
337             SEAICE_dTempFrz_dS = 0.,
338      - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
339      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
340      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
341        activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
342      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
343        was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
344      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
345        seaice_growth r149 for legacy branch (no results change).
346      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
347        from I. Fenty).
348      - results did not change except for global_ocean.cs32x15, mostly due to the
349        switch to variable freezing point (see above item for detail).
350    o pkg/thsice:
351      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
352        seawater freezing in thsice_calc_thickn (not used).
353    o pkg/seaice: turbulent flux term specification via run time params.
354      - replace CPP switches with run time switches to facilitate testing
355      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
356                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
357      - added runtime parameter : SEAICEturbFluxFormula
358      - move Mcphee constants to SEAICE_PARAMS.h
359      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
360                 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
361                 remove seaice_summary call (moved to seaice_init_fixed)
362      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
363        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
364      - seaice_summary.F : add missing report of read turbulent flux term set up
365                           and SITRACER.
366      - seaice_check.F : check range; inform and stop if retired CPPs are used
367                         (incl. SEAICE_AGE).
368      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
369             CPP switch, same computation as before for the different options.
370      - change results at the truncation level.
371    o pkg/seaice:
372      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
373        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
374        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
375      - update verification/*/input*/data.seaice:
376        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
377        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
378        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
379        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
380    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
381      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
382        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
383        difference in results only due to machine truncation.
384      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
385        MaykutPolySatVap; keep MIN_LWDOWN.
386      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
387      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
388        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
389    o pkg/salt_plume:
390      - isolate saltPlumeFlux array exch into a specific S/R called from
391        do_oceanic_phys.F
392      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
393    o verification:
394      - move untested set-up to MITgcm_contrib/verification_other.
395    o pkg/seaice:
396      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
397    o pkg/seaice:
398      - seaice_solve4temp.F (keeping results unchanged):
399        * add 2 future run-time params to select which saturation vapor pressure
400          formula is used and how post-iteration fluxes are set.
401          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
402        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
403          the linearized expression to stay consistent with tsurf finding.
404      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
405        can be < 0.
406    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
407      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
408        conductive heat flux F_c , and add it explicitly when updating tsurf as
409        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
410        so that now F_ia has a consistent meaning through the entire routine.
411        This causes differences at truncation level: update output of fwd exp.
412        global_ocean.cs32x15.seaice.
413    o pkg/seaice:
414      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
415        of arrays, sign/direction of fluxes; no effect on results.
416      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
417        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
418        note: this should have been done before changing celsius2K default.
419      - to keep results unchanged, add back old value of celsius2K in verification
420        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
421      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
422        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
423        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
424        freezing temp is consistent with value in seaice_growth.F ; this causes
425        differences at machine truncation level: update lab_sea AD output (3/4).
426    o pkg/seaice:
427      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
428        and climsst/sss even when using seaice (to prevent calculation that might
429        use SST on land); does not affect any verification exp.
430      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
431        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
432    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
433      over land (non-legacy code)
434    o vectorize salt_plume package:
435      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
436      - this code computes plumebk everywhere (also over land), thus requires
437        code to avoid divisions by zero and catch the case of kLev=Nr.
438      - efficiency of salt_plume_frac is still sub-optimal
439    o tools (genmake2):
440      - fix makefile NAME specification (option: -makefile NAME) by adding
441        "-f $MAKEFILE" in few places where it was missing including makedepend
442        command (contribution from Paul).
443    
444    checkpoint63i (2012/01/24)
445    o model/src:
446      - add factorized versions of some EOS code to find_rho.F,
447        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
448    o model/src:
449      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
450      - change default celsius2K from 273.16 to 273.15
451      - to keep results unchanged, add back old value of celsius2K in verification
452        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
453         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
454    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
455      to make TAF generate vectorizable code
456    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
457       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
458       have flags that do this more efficiently.
459    o pkg/diagnostics/diagstats_calc.F
460      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
461    o pkg/obcs (with exch2):
462      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
463        and remove code (in obcs_readparms.F) which was based on EXCH of indices
464        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
465    o pkg/exf and seaice exp:
466      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
467        so that switching off area & heff advection flags does not affect results.
468      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
469      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
470        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
471        results of verification experiments: 1D_ocean_ice_column(fwd),
472        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
473        and offline_exf_seaice (all 4).
474    o pkg/seaice:
475      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
476        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
477      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
478        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
479        not multi-dim advection;
480      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
481        SHORTWAVE_HEATING #undef.
482    o optim: make Makefile more robust (?)
483    o pkg/obcs:
484      * fix treatment of obcs_read_pickup for TAF
485    o pkg/shelfice:
486      * add missing initialisation of num_shifwflx
487      * new adjoint verification exp. for isomip
488      * change Prandtl and Schmidt numbers from generic formulations
489        (in terms of model diffus. and visc.) to separate runtime
490        parameters, with Holland and Jenkins (1999) default values.
491    o pkg/exf (interpolation):
492      - extended input field (2 rows) near the N & S poles:
493        * fill in with the symetric value (when even Nb of data in longitude)
494        * add average value at the poles only for scalar quantities ; for vector
495          component interpolation, skip the averaging and keep duplicated values,
496          unless the 2 components have same location (uvInterp=T) in which case
497          interpolate the 2 components together using S/R EXF_INTERP_UV.
498      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
499        together: this allows to account properly for local orientation when
500        averaging at N & S pole.
501      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
502        exf-interpolation near N & S poles. Undef by default.
503      - add debug check/print on 1rst iter if debugLevel >=2.
504    o pkg/exf:
505      - change masking flags definition (no longer "parameter"), put them in
506        common block and set them in S/R EXF_INIT_FIXED.
507      - change recognized masking flag from s,u,v to c,w,s since the mask
508        to use (maskC,W,S) depends on position on model grid and has little to
509        do with scalar/vector difference; fix masking if using P-coordinates.
510      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
511        and update results of exp. global_with_exf (x2).
512      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
513    o pkg/obcs
514      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
515    o pkg/exf (interpolation):
516      - assume periodicity in X only if input field cover full longitude range.
517      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
518        and should vectorise).
519      - fix input lat of the 2 added row (in case we provide N.pole data).
520    
521    checkpoint63h (2011/12/30)
522    o pkg/seaice:
523      - change declaration of UVM from _RL to _RS in order to get B-grid
524        uIce,vIce monitor when _RS = real*4
525    o pkg/offline:
526      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
527      - compute vertical velocity if not read from file (switch on exactConserv
528        & staggerTimeStep);
529      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
530    o verification:
531      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
532        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
533        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
534      - update output of exp. global_ocean.cs32x15.viscA4 after changing
535        grid-file angles (used here for coriolis-3d);
536      - remove (or gzip) few files not needed to run fizhi-cs experiments.
537    o pkg/exf (vector interpolation):
538      - rotate vector component toward local grid-axis orientation using grid-angles
539        (stored in GRID.h) instead of locally computed rotation angle; keep old code
540        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
541    o pkg/seaice:
542      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
543        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
544    o pkg/PKG_OPTIONS.h files:
545      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
546        outside of the #ifdef ALLOW_THISPKG / #endif block.
547      - update verification/*/code/PKG_OPTIONS.h files.
548    o add a verification experiment (offline_exf_seaice/input.seaice) that test
549      the B-grid LSOR solver
550    o pkg/seaice: sort out emissivity and long wave radiation step 2:
551      - add emissivity for snow and ice as new run-time parameters
552        (unfortunately) that default to the corresponding exf values; this
553        changes results in most verification experiments so that for backward
554        compatibility these parameter have to be set explicitly to inconsistent
555        values (ugly);
556      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
557        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
558        until we agree how to handle this bug properly
559    o pkg/exf (interpolation):
560      - add a set of run-time param ({inputfield}_interpMethod), one for
561        each interpolated input field, to select the interpolation method
562        with a value of zero switching off the interpolation;
563      - print interpolation parameters to standard output;
564      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
565        (to use instead runoff_interpMethod=0 in data.exf).
566      - simplify default setting of interpolation parameters (for all fields,
567        set position to match model grid cell-center position, leading to trivial
568        interpolation in case of regular Lat-Lon grid) and fix for the case of
569        non-uniform delY.
570    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
571       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
572       this factor is absolutely required, because the lw exitance (= out-going
573       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
574       where the reflectivity rho = 1-emissivity for conservation reasons. Once
575       this is established, we can remove the CPP-Flag (if we want to).
576    o pkg/seaice:
577      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
578        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
579      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
580        what the name implies (and not emissivity*BoltzmannConstant), this means
581        the old default value of 5.5e-8 now means
582        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
583        S/R exf_readparms
584      - FV-discretization of the B-grid LSOR solver, turn on with
585        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
586        of the calling routine dynsolver, so that B and C-grid code look a
587        little more alike.
588      - fix index bugs in ostres.F (B-grid code)
589    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
590    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
591      default for SEAICE_emissivity, if useEXF; requires setting a wrong
592      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
593      backward compatiblity
594    o model/src: use sigmaR in calc_ivdc
595    
596    checkpoint63g (2011/12/16)
597    o pkg/seaice/seaice_growth.F:
598      fix heat conservation of the coupled ocean-seaice system.
599      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
600      solid vs liquid water treatment is resolved via QNET.
601    o pkg/seaice/seaice_growth.F:
602      add missing term for sublimation in saltFlux, which was breaking conservation.
603    o pkg/seaice/seaice_model.F:
604      Remove this patholigical case treatment in evolution branch,
605      where it is un-necessary and breaks conservation.
606      Update global_ocean.cs32x15/results accordingly for
607      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
608    o model/src:
609      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
610      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
611    o pkg/obcs:
612      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
613      tendency for temperature and salinity that is then applied to update
614      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
615      horizontal advection and diffusion contributions on the boundary (in
616      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
617      removing the mask in S/R timestep_tracer. The advantage of this approach is
618      that the updated tracer values include contributions from the surface
619      forcing and vertical diffusion.
620      This modification changes exp4.stevens because of vertical diffusion.
621    o model/src:
622      change non-curvilinear grid setting to also work with exch2 + blank tiles:
623      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
624        face dimensions.
625      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
626        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
627        and INI_SPHERICAL_POLAR_GRID.
628      change test-experiment global_ocean.90x40x15:
629      - split the domain in many more tiles (9x4 tiles of 10x10 each);
630      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
631      - update results of both test (std & dwnslp).
632    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
633       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
634    o model/src:
635      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
636        and fix initialisation when using sigma-coords.
637    o model/src:
638     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
639       to their current value at the beginning of forward_step.F": add a new run-time
640       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
641     - set doResetHFactors=T in the following test exp:
642        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
643        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
644        and tutorial_global_oce_in_p (nonLinFS in p)
645    o pkg/ecco
646      - added IES cost term
647    o verification/advect_xz
648      - scale down the depth by 1/100 (from 200 km to just 2.km)
649      - add secondary test using divergent flow, r-star and implicit vertical advection.
650      - add note (check_conserve_TS.txt) and matlab script to check global
651        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
652    o pkg/rbcs:
653      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
654    o pkg/obcs (Stevens BCs):
655      - fix various problems in the phase speed computations of the Stevens
656        boundary conditions:
657        - sign error for western and southern boundaries,
658        - time tendencies were underestimated by factor of dTracerLev and some just
659          zero (for multidim advection schemes) -> now estimate time tendencies
660          from difference between previous (n) time level and the one before (n-1);
661          this requires storing a field per tracer per boundary, also in the pickup
662          files.
663        - replace deltaTmom in cflMer/Zon computation with dTracerLev
664        - set default phase velocity to cflMer/Zon
665      - update verification experiment exp4.stevens
666    o pkg/generic_advdiff (implicit_r):
667      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
668        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
669      - fix implicit vertical diffusion or advection with NonLin FreeSurf
670        (was using current recip_hFacC instead of future recip_hFacC): set future
671        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
672        solver S/R ;
673      - fill diagnostics of vertical advective fluxes (computed from tendency)
674        when using implicit vert. advection;
675      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
676         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
677         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
678         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
679    o pkg/diagnostics:
680      - add diags for T & S tendency which goes through Adams-Bashforth.
681    
682    checkpoint63f (2011/11/30)
683    o pkg/obcs/obcs_calc_stevens.F:
684      - join some loops to reduce number of if-statements
685      - fix a bug in code for northern and southern boundaries.
686    o pkg/seaice/seaice_init_varia.F
687      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
688        caused zero ice-velocities for the B-grid code
689    o pkg/seaice/seaice_init_fixed.F
690      - fix a bug in the initialisation of the second metric terms
691        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
692      - this affects all seaice configurations with useCurviLinearGrid = .true.
693        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
694        = .true. (default)
695      - the only verification experiment affected is global_ocean.cs32x15:
696        icedyn, seaice, and seaice_dynmix (AD)
697    o pkg/thsice/thsice_diagnostics_state.F
698      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
699        not contain garbage that can lead to surprises in diagstats_calc.F
700    o model/src:
701      - move bi,bj loops inside INTEGR_CONTINUITY ;
702      - call INTEGR_CONTINUITY directly from forward_step.F
703        (previously called from momentum_correction_step.F)
704      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
705        forward_step.F and pkg/ecco/the_main_loop.F
706    o model/src/do_oceanic_phys.F:
707      - reset addMass to zero only if useICEFRONT ;
708      - separated k-loop for rhoInSitu calculation ;
709      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
710        and at constant T,S (= WdRHOdP);
711      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
712        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
713        transport of locally-referenced potential density);
714        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
715    o gluemnc:
716      - replace ncrcat with ncks when adding variables to *.glob.nc
717      - change the way variables without record dimensions are handled so that
718        files that have variables with and without record variables can be glued:
719        add a record dimension with a new unique name to be able to differentiate
720        between variable with and without a-prior record dimensions. Remove
721        this record dimension before adding the variable to the *.glob.nc file.
722        This procedure automatically works also for grid.*.nc files that do not
723        have any record dimension.
724    o verification/cpl_aim+ocn:
725      - generate new reference output on baudelaire (gfortran, mpich2) (previously
726        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
727    o pkg/obcs/obcs_calc_stevens.F:
728      - add code for northern and southern boundaries.
729      - reorder some loops to save some operations and so that drFBar can be scalar
730    o model/src:
731      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
732        truncation) and add diagnostics for Adams-Bashforth tendency increment.
733      - update test-exp. AD output:
734        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
735      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
736        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
737        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
738        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
739        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
740        tutorial_plume_on_slope.
741    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
742      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
743      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
744      does not even come with an F77 compiler anymore, this should not be
745      a limitation
746    
747    checkpoint63e (2011/11/06)
748    o pkg/seaice adjoint of LSR:
749      - substantially rework STORE dirs.
750      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
751        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
752        and only perform SOLV_MAX_FIXED adjoint iters.
753        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
754        always goes to same record, meaning that the last forward field will be
755        the one used in the adjoint - an approximation.
756      - now produces non-zero LSR-related gradients, and acceptable gradients for
757        An's zonal (x-z) test case (to be checked in)
758      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
759        (but these are screwed up by the thermodynamics in the first place);
760        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
761        output_adm.txt also reflects changes to seaice_lsr
762      - global_ocean.cs32x15:
763        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
764          (output_adm.seaice.txt was updated)
765        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
766          (output_adm.seaice_dynmix.txt)
767    o test-exp. exp4+stevens:
768      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
769    o pkg/seaice (lsr solver):
770      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
771        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
772      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
773      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
774        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
775      - compute (with new S/R) and print initial (+ free-driff sol. if available)
776        and final residual of linearised system.
777    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
778      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
779    o pkg/obcs: Stevens BCs (still only for east and west)
780      - fix Stevens BCs by using intermediate velocities of previous
781        time step as "baroclinic" contribution rather velocity of one grid cell
782        inside the boundaries; more consistent but makes the entire treatment
783        more complicated, requires new pickup files and two new S/Rs:
784        obcs_copy_uv_n and obcs_save_uv_n
785        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
786        (undefined by default)
787      - silently move computation of some grid factors into separate loops to
788        save some recomputations
789      - add a hack for non-linear free surface
790      - add a verification experiment to exp4 that tests this code
791    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
792    
793    checkpoint63d (2011/10/25)
794    o pkg/obcs + seaice-dynamics:
795      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
796        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
797        values (consistent with an implicit method).
798      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
799        return to older implementation (same results as before); note that none of
800        the "experimental" OBCS_SEAICE options are implemented in the new version.
801      - switch test exp. seaice_obcs to use new version (update output).
802    o pkg/seaice:
803      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
804      - add parenthesis in Water-Ice drag calculations (evp & lsr);
805      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
806        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
807      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
808        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
809    o pkg/layers:
810      - Include potential density as new coordinate (Thanks to David Munday)
811    o pkg/dic:
812      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
813        carbonate computation/output to CALC_PCO2_APPROX
814    o pkg/generic_advdiff
815      - make TAF generate code that vectorizes:
816        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
817    o model/src:
818      - improve vectorization also for adjoint code of
819        solve_tridiagonal and solve_pentadiagonal. As this requires up to
820        5 new 3D-fields, this code is only turned on for the combination of
821        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
822        for singular matrix check (only for TARGET_NEC_SX).
823      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
824        ALLOW_AUTODIFF. This flag now needs to be set outside of
825        solve_tri/pentadiagonal.F
826    o pkg/exf:
827      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
828        optional namelist EXF_NML_OBCS).
829      - add many debug-print (to trace down where pkg/cal error msg comes from)
830    o pkg/mom_vecinv/mom_vi_hdissip.F
831      - rearrange loops so that vectorization is improved and in particular
832        the adjoint routine vectorizes. The code is a little longer now, but I
833        think easier to read.
834        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
835    o pkg/seaice:
836      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
837    o pkg/exch2:
838      - alternative code (without tile x tile matrix) for cumulated (global) sum;
839        used as default; keep using matrix version in adjustment.cs-32x32x1.
840    o tools/build_options:
841      - after merging some MPI and/or multi-threads specific optfiles so that
842        the modified default optfile support both built (using genmake2 -mpi
843        for the MPI built, using genmake2 -omp for OpenMP built),
844        move now obsolete optfiles to tools/build_options/unsupported/
845       (add copy of email sent to support list in doc/optfiles_changes.txt)
846    
847    checkpoint63c (2011/09/28)
848    o pkg/ebm:
849      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
850        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
851    o pkg/seaice (SItracer pickup)
852    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
853      To be done:
854      - thorough testing of missing fields in S/R seaice_read_pickup
855      - thorough matching between generic tracers and specific fields used
856        (e.g. volume-weighted age, area-weighted age, salinity, ...)
857    o pkg/grdchk:
858      - all procs calculate and print finite-difference gradient (for testreport)
859      - change description output used by testreport;
860      - AD testing: also compare and report Finite-difference gradient;
861        => update all output_adm*.txt
862    o test exp. global_ocean_ebm:
863      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
864        and turn on exactConserve; update (fwd) output.
865    o pkg/seaice (LSR):
866      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
867      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
868        * identical results with non-CS topology (but save up to half of EXCH calls)
869        * no much changes in cs-32 verification tests since no ice at face edges
870         (differences due to convergence criteria, since nb of iterations changed)
871        * expect some differences on lat-lon-cap grid.
872        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
873    o pkg/exch2:
874      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
875        many tiles); until alternative coding is added, just add a stop.
876    o pkg/kpp:
877      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
878        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
879    o optfiles:
880      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
881        into corresponding standard one, which now support different build:
882        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
883      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
884    o pkg/obcs (seaice):
885      - add missing EXCH for uIce,vIce after applying OBCS;
886      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
887        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
888        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
889      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
890      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
891        and eedata.mth for MPI and mutlti-threaded testing.
892    o pkg/flt:
893      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
894      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
895      - fix pickup and trajectories + profiles output with multi-threads;
896      - add parameter to select group of fields to write along trajectory and
897        profile (default unchanged);
898      - only call PORT_RAND* function when flt_noise <> 0;
899      - add multi-threaded test for verification exp. flt_example.
900    o eesupp/src:
901      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
902      - USE_OMP_THREADING: check that number of threads (from eedata) matches
903        actual number (from env.var. setting).
904    o pkg/ebm:
905      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
906      - add multi-threaded test for verification exp. global_ocean_ebm
907    
908    checkpoint63b (2011/08/29)
909    o pkg/ebm:
910      - fix sign of runoff;
911      - update directly forcing fields (Qnet,EmPmR) to use standard
912        external_forcing_surf.F (remove ebm_forcing_surf.F);
913      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
914      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
915        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
916      - update global_ocean_ebm parameters file data and update output (fwd+ad).
917    o verification/matrix_example:
918      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
919        MPI and mutlti-threaded testing.
920    o pkg/matrix:
921      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
922      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
923      - fix for multi-threaded (remove DATA statement);
924      - use standard DIFFERENT_MULTIPLE function;
925      - add MATRIX_OPTIONS.h
926    o verification/matrix_example:
927       To allow to split the domain in several tiles, change the domain size
928        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
929        Western side) of land points.
930    o (*_)write_pickup:
931      - fix few bugs in mypackage_read/write_pickup.F
932      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
933        array of length 1 (was caught by compiler syntax-check).
934    o pkg/diagnostics (velocity potential solver):
935      - fix initialisation of main diagonal matrix (for overlap values)
936    o tools/build_options:
937      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
938        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
939      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
940        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
941        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
942        and use "-devel" testreport option for standard testing on baudelaire.
943  o pkg/grdchk:  o pkg/grdchk:
944    - Assume that all gradient-check position are within the same tile    - Assume that all gradient-check position are within the same tile
945      corresponding to global indices (iGloTile,jGloTile) and that      corresponding to global indices (iGloTile,jGloTile) and that
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