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revision 1.1461 by jmc, Wed Jun 22 02:31:29 2011 UTC revision 1.1664 by jmc, Mon Jun 4 21:05:46 2012 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    checkpoint63n (2012/06/04)
8    o model/src:
9      - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
10        between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
11      - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
12        similar to calc_r_star.F); update results of experiment internal_wave and
13        tutorial_global_oce_in_p (affected @ truncation level).
14    o pkg/shelfice:
15      - add parameterisation of advective-diffusive flux into the ice shelf
16        according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
17      - simply eps3/3a computation
18    o eesupp:
19     - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
20       between tiles, just fill-in edges assuming locally periodic subdomain) and
21       add corresponding exchange subroutines (EXCH0);
22     - new CG-solver version (_EX0) for disconnected-tiles special case.
23    o model/src (CG-solvers):
24     - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
25       (similar final residual output and max-Iter number as with standard version);
26     - allows to store and use lowest-residual solution (standard & _SR versions);
27     - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
28     - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
29    o eesup/src:
30     - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
31       ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
32    o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
33    
34    checkpoint63m (2012/04/27)
35    o pkg/shelfice:
36     - account for partical cells in surface level below ice-shelf for hydrostatic
37       pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
38    o ad test experiments:
39     - update and rename to "ad_optfile.local" local AD-optfile specific to a
40       particular adjoint verification experiment (in verification/*/code_ad/)
41    o pkg/seaice & pkg/exf:
42     - Part two of ECCO-CLIVAR code merges.
43       Completes merge of seaice area relax. code.
44       Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
45       to be set in EXF_OPTIONS.h since this pkg controls its I/O
46       (and avoids second CPP option in SEAICE_OPTIONS.h)
47     - change default value of costIceStart & costIceEnd to a valid date.
48     - add snowPrecip to HSNOW in seaice_growth
49    o pkg/ptracers:
50     - move ptracers summary and setup check into separated S/R ; add a check for
51       valid PTRACERS_Iter0 value (error+stop or just warning).
52    o pkg/cal (+ pkg/ecco):
53     - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
54       as input; and for AD, unless both are not differentiable (e.g., k index)).
55    o model/src:
56     - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
57       is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
58       temporary set to usingZCoords value (to be changed to F when using shelfice).
59     - hydrostatic pressure: implement partial cell near the surface also for
60       Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
61       usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
62    o pkg/ctrl/ctrl_init.F:
63     - add a formal parameter to s/r ctrl_init_rec to print
64       xx_$(ctrl_valiable)_file for easier debugging
65     - move call of cal_* routines into the if-block where they are really
66       needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
67       to specify a startdate
68    o pkg/seaice:
69     - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
70       global_ocean.cs32x15/code versions).
71     - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
72       verification experiment global_ocean.cs32x15.seaice and update results.
73    o pkg/exf:
74     - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
75       (according to useExfYearlyFields).
76    o pkg/cal:
77     - move calendar setting & summary (previously in cal_readparams.F) into new
78       S/R CAL_INIT_FIXED to be called later in the initialisation process, once
79       length of the simulation is set (after SET_PARMS call); This is an attempt
80       to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
81     - For safety: keep a record of pkg/cal parameter settings status
82               to allow to STOP if one pkg/cal S/R is called too early.
83     - add a stop in all basic pkg/cal subroutines if called before setting is done.
84     - modify cal_getdate.F: stop when nothing was returned;
85       if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
86       this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
87    
88    checkpoint63l (2012/04/04)
89    o pkg/bbl:
90      - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
91        update global_with_exf output.yearly.txt file.
92    o pkg/cal:
93      - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
94      - remove 2 unsused and very short (1 line only) functions ;
95      - remove unsused subroutines from AD-Diff list.
96    o model/src:
97      - start to implement clean wait to stop in initialization S/R (config_check.F,
98         packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
99    o folowing PRINT_MESSAGE changes:
100      - remove reminder multiple print to the same file (STDOUT) when multi-threads.
101    o pkg/bbl:
102      - modification so it can work with z*
103      - replace deltaT with dTtracerLev(k) for asynchronous time stepping
104      - global_with_exf/input.yearly verification; changes output.yearly.txt
105    o eesupp/src:
106      - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
107        writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
108      - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
109        # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
110      - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
111      - when using MPI, always set usingMPI=T ; set default accordingly and stop
112        if not consistent.
113      - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
114        argument is zero (in case called within single-thread section).
115    o pkg/fizhi:
116        clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
117        in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
118    o pkg/exch2:
119      - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
120        activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
121      - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
122        but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
123        with bad ones coming from a not-yet-updated halo.
124        This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
125    o pkg/frazil:
126        move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
127        http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
128    o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
129    o verification/lab_sea
130      * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
131      * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
132      * nTimeSteps 3 -> 4
133      * changed reference output accordingly
134    o pkg/ctrl:
135      * fix ctrl_get_gen for xx_sst, xx_sss
136    o pkg/fizhi:
137      - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
138        update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
139      - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
140        fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
141        clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
142    o pkg/gmredi:
143      - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
144    o pkg/fizhi:
145      - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
146        (old)aces open64 tuv test.
147    o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
148    o pkg/mom_vecinv:
149      - fix 1 loop range in mom_vecinv.F to be like all the other loops which
150        set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
151        with non-lin free-surf).
152    o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
153      in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
154      some compilers (gfortran 4.6.0 on MacOS)
155    o momentum:
156      - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
157        & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
158        fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
159    
160    checkpoint63k (2012/03/17)
161    o model/src:
162       - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
163         flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
164       - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
165         (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
166    o model/src: solve_*diagonal.F
167       - replace division with multiplication by inverse (similar to original version)
168         update output of AD exp. global_ocean.90x40x15.
169       - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
170         to enable the use of the vectorized & differentiable solve_tridiagonal.F
171       - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
172         vertical advection (to get solve_tridiagonal tested in AD mode).
173    o pkg/seaice: ECCO-CLIVAR merge:
174      1. seaice AREA relaxation
175         * CPP option: SEAICE_ALLOW_AREA_RELAXATION
176         * runtime flag: SEAICE_tauAreaObsRelax
177      2. modified global mean cost imbalance code: CPP option
178          ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
179    o another iteration on solve_*diagonal.F
180       Make choices independent of AUTODIFF
181       Default will be the adjoinable vectorized version.
182       Alternative choices are:
183       * non-adjoinable original version with low memory footprint:
184         #define SOLVE_DIAGONAL_LOWMEMORY
185       * still adjoinable but does not vectorize (k as inner-most loop):
186         #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
187    o testreport
188     - add option to use a home made wrapper around "make"
189     - remove MITGCM_IEEE env. variable (no longer active)
190    o pkg/shelfice
191     - improve computation of friction velocity for velocity dependent
192       exchange coefficients: include velocities into SHELFICEBoundaryLayer
193       block to average velocities vertically
194     - add TAF store directives for SHI_ALLOW_GAMMAFRICT
195    o Modify diagonal solvers, now three versions (upon request):
196      #ifndef SOLVE_DIAGONAL_AUTODIFF
197        1. default version (dating back a while ago)
198      #else /* def SOLVE_DIAGONAL_AUTODIFF */
199      # ifdef SOLVE_DIAGONAL_KINNER
200        2. adjoinable version with k-innermost loop (G. Forget)
201      # else
202        3. adjoinable vectorized version of 2.
203      # endif
204      #endif /* SOLVE_DIAGONAL_AUTODIFF */
205      All flags are currently set within routines, but could/should be moved to CPP-options.
206      Array bounds for 1. are as before, for 2.,3. cover the entire domain
207      (could be changed for 1. too).
208    o verification/lab_sea (fwd):
209      - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
210        use 7 categories (except hb87), new solve4temp params (except salt_plume),
211        constant salinity (=4) or variable salinity (salt_plume) done through
212        SItracer.
213    o pkg/seaice:
214      - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
215      - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
216         SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
217        from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
218        SEAICE_freeze got retired) but already better than previously with
219        SEAICE_freeze=123456.7 deg.C;
220      - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
221        (safer multi-threaded setting); always set SEAICEuseEVP;
222      - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
223        SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
224        stop if multiple specifications for the same coeff; make sure default
225        SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
226    o pkg/obcs:
227      - allow to switch to upwind 1rst order advection scheme for the advective
228        flux computation at the open-boundary; disabled for adjoint built.
229    o pkg/ptracers:
230      - rename PTRACERS_RESTART.h -> PTRACERS_START.h
231      - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
232      - add parameter to decide when to start a tracer; use internal flag to
233        know which tracer to step-forward; switch this internal flag at the top
234        of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
235        for adjoint built.
236    o pkg/seaice:
237      - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
238      - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
239      - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
240    o pkg/ecco:
241      - fix writing of output file DiagnosCost_ClimSalt/Theta
242        and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
243    o pkg/seaice:
244      - add missing initialisation of COR_ICE array in dynsolver.F
245      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
246        compiled either way, and is tested in all exps (multidim was only tested
247        in lab_sea ad before).
248      - cosmetic change to prepare for future addition of ITD. no change to results.
249        no defaults change.
250      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
251      - by lack of adequate verification experiments, I further used custom versions
252        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
253        should be correct.
254      - avoid recomputations in ad.
255    o array initialisation in adjoint mode:
256      1) pkg/mom_common/mom_calc_ke.F:
257        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
258        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
259        part this initialisation is gone, resulting in Floating Point Exception
260        (caught by open64 compiler with debug option).
261      2) model/src/convective_weights.F
262        set output convectCount over the full array range (instead of doing
263        an update): this fix a similar issue when called within recomputation (adjoint)
264        which could by-pass the initialisation (normally done in the caller S/R).
265    o pkg/seaice:
266      - final version of turbulent flux params, as agreed at MIT ice meet:
267           SEAICE_mcPheePiston (default is ~ 0.000875)
268           SEAICE_mcPheeTaper (default is 0.)
269           SEAICE_frazilFrac (defualt is 1.)
270           SEAICE_mcPheeStepFunc (default is false)
271      - changes results at trunction error level
272      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
273    o added pkg/frazil:
274      - see frazil_description.tex for details
275      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
276    o pkg/shelfice/shelfice_thermodynamics.F
277      - fix exponents for velocity dependent exchange coefficients: change
278        from 2/3(=0) to 0.66666666666666667
279      - move computation of velocity dependent exchange coefficients into
280        separate loop, so that it applies to both thermodynamics
281      - move some divisions by constants out of loops
282    
283    checkpoint63j (2012/02/16)
284    o pkg/seaice:
285      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
286      - SItracer:  added run time params, and allow coupling to ocn salinity.
287    o pkg/seaice: remove (almost) all divisions by constants within loops
288      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
289      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
290      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
291      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
292    o pkg/seaice :
293      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
294        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
295      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
296      - add permanent SItflux diag that corresponds to TFLUX but includes
297        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
298      - allow activation/testing of a fix for suspected missing term in
299        ocn-ice heat budget (to be confirmed). To test this, you want to
300        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
301        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
302      - no change in results, fwd or ad.
303    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
304      - switch to variable freezing point.
305           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
306      - bug fix : the sublimation term that was missing is now activated.
307           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
308      - bug fix : flooding sign term for SIsal0.NE.0.
309           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
310    o pkg/seaice:
311      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
312        is now the default, and the old default constant freezing point is recovered
313        with SEAICE_tempFrz0    = -1.96,
314             SEAICE_dTempFrz_dS = 0.,
315      - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
316      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
317      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
318        activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
319      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
320        was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
321      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
322        seaice_growth r149 for legacy branch (no results change).
323      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
324        from I. Fenty).
325      - results did not change except for global_ocean.cs32x15, mostly due to the
326        switch to variable freezing point (see above item for detail).
327    o pkg/thsice:
328      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
329        seawater freezing in thsice_calc_thickn (not used).
330    o pkg/seaice: turbulent flux term specification via run time params.
331      - replace CPP switches with run time switches to facilitate testing
332      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
333                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
334      - added runtime parameter : SEAICEturbFluxFormula
335      - move Mcphee constants to SEAICE_PARAMS.h
336      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
337                 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
338                 remove seaice_summary call (moved to seaice_init_fixed)
339      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
340        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
341      - seaice_summary.F : add missing report of read turbulent flux term set up
342                           and SITRACER.
343      - seaice_check.F : check range; inform and stop if retired CPPs are used
344                         (incl. SEAICE_AGE).
345      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
346             CPP switch, same computation as before for the different options.
347      - change results at the truncation level.
348    o pkg/seaice:
349      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
350        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
351        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
352      - update verification/*/input*/data.seaice:
353        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
354        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
355        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
356        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
357    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
358      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
359        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
360        difference in results only due to machine truncation.
361      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
362        MaykutPolySatVap; keep MIN_LWDOWN.
363      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
364      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
365        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
366    o pkg/salt_plume:
367      - isolate saltPlumeFlux array exch into a specific S/R called from
368        do_oceanic_phys.F
369      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
370    o verification:
371      - move untested set-up to MITgcm_contrib/verification_other.
372    o pkg/seaice:
373      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
374    o pkg/seaice:
375      - seaice_solve4temp.F (keeping results unchanged):
376        * add 2 future run-time params to select which saturation vapor pressure
377          formula is used and how post-iteration fluxes are set.
378          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
379        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
380          the linearized expression to stay consistent with tsurf finding.
381      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
382        can be < 0.
383    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
384      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
385        conductive heat flux F_c , and add it explicitly when updating tsurf as
386        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
387        so that now F_ia has a consistent meaning through the entire routine.
388        This causes differences at truncation level: update output of fwd exp.
389        global_ocean.cs32x15.seaice.
390    o pkg/seaice:
391      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
392        of arrays, sign/direction of fluxes; no effect on results.
393      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
394        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
395        note: this should have been done before changing celsius2K default.
396      - to keep results unchanged, add back old value of celsius2K in verification
397        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
398      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
399        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
400        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
401        freezing temp is consistent with value in seaice_growth.F ; this causes
402        differences at machine truncation level: update lab_sea AD output (3/4).
403    o pkg/seaice:
404      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
405        and climsst/sss even when using seaice (to prevent calculation that might
406        use SST on land); does not affect any verification exp.
407      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
408        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
409    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
410      over land (non-legacy code)
411    o vectorize salt_plume package:
412      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
413      - this code computes plumebk everywhere (also over land), thus requires
414        code to avoid divisions by zero and catch the case of kLev=Nr.
415      - efficiency of salt_plume_frac is still sub-optimal
416    o tools (genmake2):
417      - fix makefile NAME specification (option: -makefile NAME) by adding
418        "-f $MAKEFILE" in few places where it was missing including makedepend
419        command (contribution from Paul).
420    
421    checkpoint63i (2012/01/24)
422    o model/src:
423      - add factorized versions of some EOS code to find_rho.F,
424        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
425    o model/src:
426      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
427      - change default celsius2K from 273.16 to 273.15
428      - to keep results unchanged, add back old value of celsius2K in verification
429        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
430         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
431    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
432      to make TAF generate vectorizable code
433    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
434       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
435       have flags that do this more efficiently.
436    o pkg/diagnostics/diagstats_calc.F
437      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
438    o pkg/obcs (with exch2):
439      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
440        and remove code (in obcs_readparms.F) which was based on EXCH of indices
441        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
442    o pkg/exf and seaice exp:
443      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
444        so that switching off area & heff advection flags does not affect results.
445      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
446      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
447        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
448        results of verification experiments: 1D_ocean_ice_column(fwd),
449        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
450        and offline_exf_seaice (all 4).
451    o pkg/seaice:
452      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
453        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
454      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
455        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
456        not multi-dim advection;
457      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
458        SHORTWAVE_HEATING #undef.
459    o optim: make Makefile more robust (?)
460    o pkg/obcs:
461      * fix treatment of obcs_read_pickup for TAF
462    o pkg/shelfice:
463      * add missing initialisation of num_shifwflx
464      * new adjoint verification exp. for isomip
465      * change Prandtl and Schmidt numbers from generic formulations
466        (in terms of model diffus. and visc.) to separate runtime
467        parameters, with Holland and Jenkins (1999) default values.
468    o pkg/exf (interpolation):
469      - extended input field (2 rows) near the N & S poles:
470        * fill in with the symetric value (when even Nb of data in longitude)
471        * add average value at the poles only for scalar quantities ; for vector
472          component interpolation, skip the averaging and keep duplicated values,
473          unless the 2 components have same location (uvInterp=T) in which case
474          interpolate the 2 components together using S/R EXF_INTERP_UV.
475      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
476        together: this allows to account properly for local orientation when
477        averaging at N & S pole.
478      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
479        exf-interpolation near N & S poles. Undef by default.
480      - add debug check/print on 1rst iter if debugLevel >=2.
481    o pkg/exf:
482      - change masking flags definition (no longer "parameter"), put them in
483        common block and set them in S/R EXF_INIT_FIXED.
484      - change recognized masking flag from s,u,v to c,w,s since the mask
485        to use (maskC,W,S) depends on position on model grid and has little to
486        do with scalar/vector difference; fix masking if using P-coordinates.
487      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
488        and update results of exp. global_with_exf (x2).
489      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
490    o pkg/obcs
491      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
492    o pkg/exf (interpolation):
493      - assume periodicity in X only if input field cover full longitude range.
494      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
495        and should vectorise).
496      - fix input lat of the 2 added row (in case we provide N.pole data).
497    
498    checkpoint63h (2011/12/30)
499    o pkg/seaice:
500      - change declaration of UVM from _RL to _RS in order to get B-grid
501        uIce,vIce monitor when _RS = real*4
502    o pkg/offline:
503      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
504      - compute vertical velocity if not read from file (switch on exactConserv
505        & staggerTimeStep);
506      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
507    o verification:
508      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
509        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
510        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
511      - update output of exp. global_ocean.cs32x15.viscA4 after changing
512        grid-file angles (used here for coriolis-3d);
513      - remove (or gzip) few files not needed to run fizhi-cs experiments.
514    o pkg/exf (vector interpolation):
515      - rotate vector component toward local grid-axis orientation using grid-angles
516        (stored in GRID.h) instead of locally computed rotation angle; keep old code
517        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
518    o pkg/seaice:
519      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
520        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
521    o pkg/PKG_OPTIONS.h files:
522      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
523        outside of the #ifdef ALLOW_THISPKG / #endif block.
524      - update verification/*/code/PKG_OPTIONS.h files.
525    o add a verification experiment (offline_exf_seaice/input.seaice) that test
526      the B-grid LSOR solver
527    o pkg/seaice: sort out emissivity and long wave radiation step 2:
528      - add emissivity for snow and ice as new run-time parameters
529        (unfortunately) that default to the corresponding exf values; this
530        changes results in most verification experiments so that for backward
531        compatibility these parameter have to be set explicitly to inconsistent
532        values (ugly);
533      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
534        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
535        until we agree how to handle this bug properly
536    o pkg/exf (interpolation):
537      - add a set of run-time param ({inputfield}_interpMethod), one for
538        each interpolated input field, to select the interpolation method
539        with a value of zero switching off the interpolation;
540      - print interpolation parameters to standard output;
541      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
542        (to use instead runoff_interpMethod=0 in data.exf).
543      - simplify default setting of interpolation parameters (for all fields,
544        set position to match model grid cell-center position, leading to trivial
545        interpolation in case of regular Lat-Lon grid) and fix for the case of
546        non-uniform delY.
547    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
548       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
549       this factor is absolutely required, because the lw exitance (= out-going
550       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
551       where the reflectivity rho = 1-emissivity for conservation reasons. Once
552       this is established, we can remove the CPP-Flag (if we want to).
553    o pkg/seaice:
554      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
555        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
556      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
557        what the name implies (and not emissivity*BoltzmannConstant), this means
558        the old default value of 5.5e-8 now means
559        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
560        S/R exf_readparms
561      - FV-discretization of the B-grid LSOR solver, turn on with
562        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
563        of the calling routine dynsolver, so that B and C-grid code look a
564        little more alike.
565      - fix index bugs in ostres.F (B-grid code)
566    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
567    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
568      default for SEAICE_emissivity, if useEXF; requires setting a wrong
569      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
570      backward compatiblity
571    o model/src: use sigmaR in calc_ivdc
572    
573    checkpoint63g (2011/12/16)
574    o pkg/seaice/seaice_growth.F:
575      fix heat conservation of the coupled ocean-seaice system.
576      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
577      solid vs liquid water treatment is resolved via QNET.
578    o pkg/seaice/seaice_growth.F:
579      add missing term for sublimation in saltFlux, which was breaking conservation.
580    o pkg/seaice/seaice_model.F:
581      Remove this patholigical case treatment in evolution branch,
582      where it is un-necessary and breaks conservation.
583      Update global_ocean.cs32x15/results accordingly for
584      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
585    o model/src:
586      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
587      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
588    o pkg/obcs:
589      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
590      tendency for temperature and salinity that is then applied to update
591      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
592      horizontal advection and diffusion contributions on the boundary (in
593      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
594      removing the mask in S/R timestep_tracer. The advantage of this approach is
595      that the updated tracer values include contributions from the surface
596      forcing and vertical diffusion.
597      This modification changes exp4.stevens because of vertical diffusion.
598    o model/src:
599      change non-curvilinear grid setting to also work with exch2 + blank tiles:
600      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
601        face dimensions.
602      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
603        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
604        and INI_SPHERICAL_POLAR_GRID.
605      change test-experiment global_ocean.90x40x15:
606      - split the domain in many more tiles (9x4 tiles of 10x10 each);
607      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
608      - update results of both test (std & dwnslp).
609    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
610       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
611    o model/src:
612      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
613        and fix initialisation when using sigma-coords.
614    o model/src:
615     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
616       to their current value at the beginning of forward_step.F": add a new run-time
617       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
618     - set doResetHFactors=T in the following test exp:
619        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
620        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
621        and tutorial_global_oce_in_p (nonLinFS in p)
622    o pkg/ecco
623      - added IES cost term
624    o verification/advect_xz
625      - scale down the depth by 1/100 (from 200 km to just 2.km)
626      - add secondary test using divergent flow, r-star and implicit vertical advection.
627      - add note (check_conserve_TS.txt) and matlab script to check global
628        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
629    o pkg/rbcs:
630      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
631    o pkg/obcs (Stevens BCs):
632      - fix various problems in the phase speed computations of the Stevens
633        boundary conditions:
634        - sign error for western and southern boundaries,
635        - time tendencies were underestimated by factor of dTracerLev and some just
636          zero (for multidim advection schemes) -> now estimate time tendencies
637          from difference between previous (n) time level and the one before (n-1);
638          this requires storing a field per tracer per boundary, also in the pickup
639          files.
640        - replace deltaTmom in cflMer/Zon computation with dTracerLev
641        - set default phase velocity to cflMer/Zon
642      - update verification experiment exp4.stevens
643    o pkg/generic_advdiff (implicit_r):
644      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
645        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
646      - fix implicit vertical diffusion or advection with NonLin FreeSurf
647        (was using current recip_hFacC instead of future recip_hFacC): set future
648        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
649        solver S/R ;
650      - fill diagnostics of vertical advective fluxes (computed from tendency)
651        when using implicit vert. advection;
652      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
653         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
654         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
655         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
656    o pkg/diagnostics:
657      - add diags for T & S tendency which goes through Adams-Bashforth.
658    
659    checkpoint63f (2011/11/30)
660    o pkg/obcs/obcs_calc_stevens.F:
661      - join some loops to reduce number of if-statements
662      - fix a bug in code for northern and southern boundaries.
663    o pkg/seaice/seaice_init_varia.F
664      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
665        caused zero ice-velocities for the B-grid code
666    o pkg/seaice/seaice_init_fixed.F
667      - fix a bug in the initialisation of the second metric terms
668        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
669      - this affects all seaice configurations with useCurviLinearGrid = .true.
670        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
671        = .true. (default)
672      - the only verification experiment affected is global_ocean.cs32x15:
673        icedyn, seaice, and seaice_dynmix (AD)
674    o pkg/thsice/thsice_diagnostics_state.F
675      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
676        not contain garbage that can lead to surprises in diagstats_calc.F
677    o model/src:
678      - move bi,bj loops inside INTEGR_CONTINUITY ;
679      - call INTEGR_CONTINUITY directly from forward_step.F
680        (previously called from momentum_correction_step.F)
681      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
682        forward_step.F and pkg/ecco/the_main_loop.F
683    o model/src/do_oceanic_phys.F:
684      - reset addMass to zero only if useICEFRONT ;
685      - separated k-loop for rhoInSitu calculation ;
686      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
687        and at constant T,S (= WdRHOdP);
688      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
689        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
690        transport of locally-referenced potential density);
691        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
692    o gluemnc:
693      - replace ncrcat with ncks when adding variables to *.glob.nc
694      - change the way variables without record dimensions are handled so that
695        files that have variables with and without record variables can be glued:
696        add a record dimension with a new unique name to be able to differentiate
697        between variable with and without a-prior record dimensions. Remove
698        this record dimension before adding the variable to the *.glob.nc file.
699        This procedure automatically works also for grid.*.nc files that do not
700        have any record dimension.
701    o verification/cpl_aim+ocn:
702      - generate new reference output on baudelaire (gfortran, mpich2) (previously
703        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
704    o pkg/obcs/obcs_calc_stevens.F:
705      - add code for northern and southern boundaries.
706      - reorder some loops to save some operations and so that drFBar can be scalar
707    o model/src:
708      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
709        truncation) and add diagnostics for Adams-Bashforth tendency increment.
710      - update test-exp. AD output:
711        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
712      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
713        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
714        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
715        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
716        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
717        tutorial_plume_on_slope.
718    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
719      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
720      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
721      does not even come with an F77 compiler anymore, this should not be
722      a limitation
723    
724    checkpoint63e (2011/11/06)
725    o pkg/seaice adjoint of LSR:
726      - substantially rework STORE dirs.
727      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
728        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
729        and only perform SOLV_MAX_FIXED adjoint iters.
730        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
731        always goes to same record, meaning that the last forward field will be
732        the one used in the adjoint - an approximation.
733      - now produces non-zero LSR-related gradients, and acceptable gradients for
734        An's zonal (x-z) test case (to be checked in)
735      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
736        (but these are screwed up by the thermodynamics in the first place);
737        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
738        output_adm.txt also reflects changes to seaice_lsr
739      - global_ocean.cs32x15:
740        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
741          (output_adm.seaice.txt was updated)
742        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
743          (output_adm.seaice_dynmix.txt)
744    o test-exp. exp4+stevens:
745      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
746    o pkg/seaice (lsr solver):
747      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
748        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
749      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
750      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
751        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
752      - compute (with new S/R) and print initial (+ free-driff sol. if available)
753        and final residual of linearised system.
754    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
755      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
756    o pkg/obcs: Stevens BCs (still only for east and west)
757      - fix Stevens BCs by using intermediate velocities of previous
758        time step as "baroclinic" contribution rather velocity of one grid cell
759        inside the boundaries; more consistent but makes the entire treatment
760        more complicated, requires new pickup files and two new S/Rs:
761        obcs_copy_uv_n and obcs_save_uv_n
762        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
763        (undefined by default)
764      - silently move computation of some grid factors into separate loops to
765        save some recomputations
766      - add a hack for non-linear free surface
767      - add a verification experiment to exp4 that tests this code
768    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
769    
770    checkpoint63d (2011/10/25)
771    o pkg/obcs + seaice-dynamics:
772      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
773        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
774        values (consistent with an implicit method).
775      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
776        return to older implementation (same results as before); note that none of
777        the "experimental" OBCS_SEAICE options are implemented in the new version.
778      - switch test exp. seaice_obcs to use new version (update output).
779    o pkg/seaice:
780      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
781      - add parenthesis in Water-Ice drag calculations (evp & lsr);
782      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
783        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
784      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
785        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
786    o pkg/layers:
787      - Include potential density as new coordinate (Thanks to David Munday)
788    o pkg/dic:
789      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
790        carbonate computation/output to CALC_PCO2_APPROX
791    o pkg/generic_advdiff
792      - make TAF generate code that vectorizes:
793        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
794    o model/src:
795      - improve vectorization also for adjoint code of
796        solve_tridiagonal and solve_pentadiagonal. As this requires up to
797        5 new 3D-fields, this code is only turned on for the combination of
798        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
799        for singular matrix check (only for TARGET_NEC_SX).
800      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
801        ALLOW_AUTODIFF. This flag now needs to be set outside of
802        solve_tri/pentadiagonal.F
803    o pkg/exf:
804      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
805        optional namelist EXF_NML_OBCS).
806      - add many debug-print (to trace down where pkg/cal error msg comes from)
807    o pkg/mom_vecinv/mom_vi_hdissip.F
808      - rearrange loops so that vectorization is improved and in particular
809        the adjoint routine vectorizes. The code is a little longer now, but I
810        think easier to read.
811        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
812    o pkg/seaice:
813      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
814    o pkg/exch2:
815      - alternative code (without tile x tile matrix) for cumulated (global) sum;
816        used as default; keep using matrix version in adjustment.cs-32x32x1.
817    o tools/build_options:
818      - after merging some MPI and/or multi-threads specific optfiles so that
819        the modified default optfile support both built (using genmake2 -mpi
820        for the MPI built, using genmake2 -omp for OpenMP built),
821        move now obsolete optfiles to tools/build_options/unsupported/
822       (add copy of email sent to support list in doc/optfiles_changes.txt)
823    
824    checkpoint63c (2011/09/28)
825    o pkg/ebm:
826      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
827        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
828    o pkg/seaice (SItracer pickup)
829    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
830      To be done:
831      - thorough testing of missing fields in S/R seaice_read_pickup
832      - thorough matching between generic tracers and specific fields used
833        (e.g. volume-weighted age, area-weighted age, salinity, ...)
834    o pkg/grdchk:
835      - all procs calculate and print finite-difference gradient (for testreport)
836      - change description output used by testreport;
837      - AD testing: also compare and report Finite-difference gradient;
838        => update all output_adm*.txt
839    o test exp. global_ocean_ebm:
840      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
841        and turn on exactConserve; update (fwd) output.
842    o pkg/seaice (LSR):
843      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
844      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
845        * identical results with non-CS topology (but save up to half of EXCH calls)
846        * no much changes in cs-32 verification tests since no ice at face edges
847         (differences due to convergence criteria, since nb of iterations changed)
848        * expect some differences on lat-lon-cap grid.
849        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
850    o pkg/exch2:
851      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
852        many tiles); until alternative coding is added, just add a stop.
853    o pkg/kpp:
854      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
855        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
856    o optfiles:
857      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
858        into corresponding standard one, which now support different build:
859        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
860      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
861    o pkg/obcs (seaice):
862      - add missing EXCH for uIce,vIce after applying OBCS;
863      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
864        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
865        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
866      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
867      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
868        and eedata.mth for MPI and mutlti-threaded testing.
869    o pkg/flt:
870      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
871      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
872      - fix pickup and trajectories + profiles output with multi-threads;
873      - add parameter to select group of fields to write along trajectory and
874        profile (default unchanged);
875      - only call PORT_RAND* function when flt_noise <> 0;
876      - add multi-threaded test for verification exp. flt_example.
877    o eesupp/src:
878      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
879      - USE_OMP_THREADING: check that number of threads (from eedata) matches
880        actual number (from env.var. setting).
881    o pkg/ebm:
882      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
883      - add multi-threaded test for verification exp. global_ocean_ebm
884    
885    checkpoint63b (2011/08/29)
886    o pkg/ebm:
887      - fix sign of runoff;
888      - update directly forcing fields (Qnet,EmPmR) to use standard
889        external_forcing_surf.F (remove ebm_forcing_surf.F);
890      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
891      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
892        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
893      - update global_ocean_ebm parameters file data and update output (fwd+ad).
894    o verification/matrix_example:
895      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
896        MPI and mutlti-threaded testing.
897    o pkg/matrix:
898      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
899      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
900      - fix for multi-threaded (remove DATA statement);
901      - use standard DIFFERENT_MULTIPLE function;
902      - add MATRIX_OPTIONS.h
903    o verification/matrix_example:
904       To allow to split the domain in several tiles, change the domain size
905        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
906        Western side) of land points.
907    o (*_)write_pickup:
908      - fix few bugs in mypackage_read/write_pickup.F
909      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
910        array of length 1 (was caught by compiler syntax-check).
911    o pkg/diagnostics (velocity potential solver):
912      - fix initialisation of main diagonal matrix (for overlap values)
913    o tools/build_options:
914      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
915        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
916      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
917        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
918        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
919        and use "-devel" testreport option for standard testing on baudelaire.
920    o pkg/grdchk:
921      - Assume that all gradient-check position are within the same tile
922        corresponding to global indices (iGloTile,jGloTile) and that
923        positions (i,j indices or nbeg) are local to this tile;
924      - set tile local-indices and proc. number according to tile global-indices;
925      - remove grdchkwhichproc from namelist (retired param);
926      - send adjoint gradient to all procs so that all procs print it to STDOUT;
927      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
928    o adding package bbl (Bottom Boundary Layer)
929      description in MITgcm/pkg/bbl/bbl_description.tex
930      example/test experiment in MITgcm_contrib/bbl
931    o adjoint verifications
932      - changed 5 experiments to multi-tiles
933        * global_ocean.90x40x15
934        * obcs_ctrl
935        * offline_exf_seaice
936        * tutorial_dic_adjoffline
937        * tutorial_tracer_adjsens
938        changed reference output for those that crossed tile boundaries
939        (changed choices of gradient check positions)
940      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
941      - temporary bug fix in grdchk_loc.F for obcs
942    o genmake2 & testreport
943      - add target "obj" (just for OBJFILES files) to Makefile;
944      - add option to specify FEXTRAFLAGS on command line.
945    o pkg/mypackage:
946      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
947    
948    checkpoint63a (2011/08/02)
949    o pkg/diagnostics (velocity potential):
950      - fix velocity-potential calculation when using OBCS: balance net inflow
951        at each level (new S/R OBCS_DIAG_BALANCE).
952      - fix some of the problems with OBCS in stream-function calculation.
953    o pkg/exf/exf_readparms.F
954      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
955        EXF_NML_OBCS) more consistent, so that you need not have these lists
956        in data.exf when they are not used.
957    o optim/optim_readdata.F:
958      - add some output about obcs variables that might help debugging
959      - add a check about nvarlength
960    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
961    o pkg/diagnostics (velocity potential):
962      - fix mask for OBCS (still problems in stream-function with OBCS);
963      - add specific parameter (default = main code CG2D params) for solver;
964      - in case of poor convergence, use solution corresponding to lowest residual.
965    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
966      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
967      and should be avoided where possible.
968    o model/src (rStar):
969      - include r* effect on reference-state (PhiRef) in totPhiHyd
970        (so that it's really the potential anomaly at the cell center);
971        affect solution only if z* with full pressure in EOS.
972      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
973        update output (because of z* in totPhiHyd and viscA4 changes);
974      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
975        @ constant r) until interpolation at constant r is implemented.
976    o pkg/diagnostics
977      - fix RCENTER diagnostics in case cell center is not at interface middle
978    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
979      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
980      that THETA and SALT are "conservative temperature" and "absolute
981      salinity"
982    o pkg/ctrl
983      - fix computation of endrec in s/r ctrl_init_rec
984      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
985    o pkg/seaice/seaice_growth.F
986      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
987        remove then obsolete STORE directives
988      - fix STORE directives for tice and tices, so that only the
989        appropriate part of the fields are stored (and not the entire
990        field); update global_ocean.cs32x15.seaice AD output.
991      - cosmetic changes: adjust CPP flags and indentation for better
992        legibilty
993    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
994      Chris Wilson)
995    o pkg/gmredi:
996       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
997       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
998    
999    checkpoint63  (2011/07/11)
1000    o pkg/exch2:
1001     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
1002     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
1003       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
1004       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
1005    o pkg/diagnostics:
1006     - deal with pairs of post-processed diags which are computed together; in
1007       particular, re-order list of diags within 1 file to save 2nd computation.
1008     - add S/R to compute velocity stream-function (called after velocity-potential
1009       calculation) from divergence free transport -> new diagnostics "PsiVEL".
1010     - add parameter to select grid-point location where PsiVEL == 0.
1011    o eesupp/src:
1012       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
1013       (specific S/R needed with exch2 topology - for now, just print an error msg)
1014    o pkg/shelfice
1015     - Implement friction velocity-dependent transfer coefficients following
1016       Holland and Jenkins, JPO, 1999
1017       Original code by M. Losch with small modifs.
1018       Enable with CPP option SHI_ALLOW_GAMMAFRICT
1019       and runtime flag SHELFICEuseGammaFrict
1020    o verification lab_sea & global_ocean.cs32x15:
1021     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
1022       does not miss some dependencies (but is slower) and also works with many files
1023       (default makedepend limitation for AD built).
1024     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
1025    o pkg/diagnostics:
1026     - add run-time parameter "useMissingValue" (def=False) to fill land-point
1027        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
1028       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
1029     - Extend the use of "missing_value" setting from data.diagnostics for the case
1030       of counter-diagnostics (where fraction-weight is zero). This applies both to
1031       MNC and MDS output files.
1032    o pkg/seaice/seaice_growth.F:
1033      - add 'a priori' cap of latent heat flux based on actual mass considerations
1034        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
1035        non-legacy seaice_solve4temp.
1036      - add diagnostic of the residual sublimation freshwater flux (the freshwater
1037        flux taken from the ocean if the total actual latent heat fluxes exceed
1038        the maximum)
1039      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
1040       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
1041      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
1042       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
1043      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
1044      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
1045    o verification 1D_ocean_ice_column:
1046       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
1047       update results
1048  o pkg/diagnostics:  o pkg/diagnostics:
1049   - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')   - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
1050     which are not filled-up but computed from other diags ; In this case, the mate     which are not filled-up but computed from other diags ; In this case, the mate
1051     diag points to the primary (filled-up) diag to used for post processing.     diag points to the primary (filled-up) diag to used for post processing.
1052   - Update Velocity-potential computation using post-processed diag framework.   - Update Velocity-potential computation using post-processed diag framework.
1053     ==> Change the ordering of fields and time-periods in MDS output file
1054       when using periodic averaging: now writes one time record with the full set
1055       of fields for this time period, then the next time reccord (it used to be
1056       one field with the full set of time records then the next field).
1057         Note: this is now similar to NetCDF (MNC) output file. <==
1058    
1059  checkpoint62z (2011/06/21)  checkpoint62z (2011/06/21)
1060  o adjoint monitor:  o adjoint monitor:
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